Starting phenix.real_space_refine
on Wed Mar  4 01:04:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f24_31427/03_2026/7f24_31427.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f24_31427/03_2026/7f24_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_31427/03_2026/7f24_31427.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f24_31427/03_2026/7f24_31427.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f24_31427/03_2026/7f24_31427.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f24_31427/03_2026/7f24_31427.cif"
  }
  resolution = 4.16
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ARG:plan': 1, 'TRP:plan': 1, 'GLU: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: 2.09, per 1000 atoms: 0.29
  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: 0.72
  Conformation dependent library (CDL) restraints added in 363.9 milliseconds
  

  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: 0.23
  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: 1.18

  Time building geometry restraints manager: 0.91 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:             0.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.900
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.780
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.006   0.001   ARG B 197 
 TYR   0.018   0.003   TYR F 218 
 PHE   0.040   0.003   PHE A 238 
 TRP   0.013   0.002   TRP F 318 
 HIS   0.015   0.003   HIS A 357 

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

*********************** 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  : 0.282 
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   34 LYS cc_start: 0.7824 (mttp) cc_final: 0.7482 (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: 0.8034 (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: 0.6657 (mmmt) cc_final: 0.6119 (tppt)
REVERT: B   85 TYR cc_start: 0.8582 (m-10) cc_final: 0.8371 (m-80)
REVERT: B  209 LYS cc_start: 0.7814 (mttp) cc_final: 0.7559 (mttp)
REVERT: B  295 ASN cc_start: 0.6510 (m110) cc_final: 0.6128 (t0)
REVERT: B  297 TRP cc_start: 0.6352 (m100) cc_final: 0.5749 (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: 0.8341 (tptt)
  outliers start: 3
  outliers final: 0
  residues processed: 214
  average time/residue: 0.0917
  time to fit residues: 25.9505
Evaluate side-chains
  161 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 159
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.2980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:   20.0000
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    8.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
A 213 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3860 r_free = 0.3860 target = 0.128337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.099004 restraints weight = 56549.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.101405 restraints weight = 43670.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.104561 restraints weight = 20245.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.104302 restraints weight = 15171.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.105624 restraints weight = 11149.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3482
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3482 r_free = 0.3482    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3481 r_free = 0.3481    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
r_final: 0.3481
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.2322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   7319  Z= 0.171
  Angle     :  0.666   7.596   9931  Z= 0.357
  Chirality :  0.046   0.227   1125
  Planarity :  0.005   0.051   1256
  Dihedral  :  9.552 157.465   1003
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 14.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  3.50 %
    Favored  : 96.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.53 (0.26), residues: 890
  helix:  0.12 (0.23), residues: 407
  sheet:  0.05 (0.42), residues: 134
  loop : -0.95 (0.31), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 214 
 TYR   0.015   0.002   TYR B  59 
 PHE   0.024   0.002   PHE F  61 
 TRP   0.014   0.002   TRP B 169 
 HIS   0.010   0.002   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 7318)
  covalent geometry    : angle       0.66574 ( 9929)
  SS BOND              : bond        0.00266 (    1)
  SS BOND              : angle       0.92982 (    2)
  hydrogen bonds       : bond        0.05063 (  388)
  hydrogen bonds       : angle       5.25714 ( 1131)

*********************** 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
  240 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 239
  time to evaluate  : 0.282 
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: 0.7704 (mttp) cc_final: 0.7319 (tttt)
REVERT: A  283 ARG cc_start: 0.7572 (mtp85) cc_final: 0.7095 (mmt-90)
REVERT: A  291 LEU cc_start: 0.9133 (mt) cc_final: 0.8537 (mt)
REVERT: A  343 ASP cc_start: 0.8051 (p0) cc_final: 0.7626 (m-30)
REVERT: A  386 MET cc_start: 0.7994 (tmm) cc_final: 0.7643 (tpp)
REVERT: F   70 ASP cc_start: 0.9013 (m-30) cc_final: 0.8675 (m-30)
REVERT: F  105 MET cc_start: 0.8674 (ttp) cc_final: 0.8384 (tmm)
REVERT: F  222 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.7597 (pm20)
REVERT: F  289 PHE cc_start: 0.7930 (m-80) cc_final: 0.7564 (m-80)
REVERT: F  321 TRP cc_start: 0.9118 (m-10) cc_final: 0.8793 (m-10)
REVERT: F  324 SER cc_start: 0.8715 (m) cc_final: 0.8122 (m)
REVERT: F  327 ASN cc_start: 0.8740 (m110) cc_final: 0.8063 (m110)
REVERT: F  337 PHE cc_start: 0.8059 (m-80) cc_final: 0.7791 (m-80)
REVERT: B   52 ARG cc_start: 0.7659 (mtt-85) cc_final: 0.7272 (mtm110)
REVERT: B   78 LYS cc_start: 0.6844 (mmmt) cc_final: 0.6600 (tppt)
REVERT: B   85 TYR cc_start: 0.8691 (m-10) cc_final: 0.8261 (m-80)
REVERT: B   91 HIS cc_start: 0.7964 (m90) cc_final: 0.7695 (m-70)
REVERT: B  110 ASN cc_start: 0.7846 (t0) cc_final: 0.7605 (t0)
REVERT: B  124 TYR cc_start: 0.8312 (m-10) cc_final: 0.8103 (m-10)
REVERT: B  142 HIS cc_start: 0.7437 (m-70) cc_final: 0.7225 (m-70)
REVERT: B  171 ILE cc_start: 0.8941 (pt) cc_final: 0.8729 (pt)
REVERT: B  172 GLU cc_start: 0.8546 (tp30) cc_final: 0.8011 (tm-30)
REVERT: B  228 ASP cc_start: 0.8081 (m-30) cc_final: 0.7565 (m-30)
REVERT: B  284 LEU cc_start: 0.8334 (tp) cc_final: 0.8130 (tp)
REVERT: B  297 TRP cc_start: 0.6286 (m100) cc_final: 0.5792 (m100)
REVERT: B  311 HIS cc_start: 0.6126 (m-70) cc_final: 0.5921 (m-70)
REVERT: B  313 ASN cc_start: 0.7244 (t0) cc_final: 0.6739 (m-40)
REVERT: B  335 PHE cc_start: 0.7151 (m-80) cc_final: 0.6547 (m-80)
REVERT: D   32 LYS cc_start: 0.8785 (tptp) cc_final: 0.8437 (tptt)
REVERT: D   61 PHE cc_start: 0.7832 (m-80) cc_final: 0.7627 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 239
  average time/residue: 0.0796
  time to fit residues: 25.7632
Evaluate side-chains
  189 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 188
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 59 optimal weight:    7.9990
   chunk 62 optimal weight:    9.9990
   chunk 0 optimal weight:    9.9990
   chunk 31 optimal weight:    1.9990
   chunk 67 optimal weight:    9.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
F 113 ASN
** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 156 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.130237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.099255 restraints weight = 67010.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.100914 restraints weight = 38483.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.103378 restraints weight = 19266.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.103513 restraints weight = 13961.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.104529 restraints weight = 11933.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3441
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3441 r_free = 0.3441    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 = 0.3441 r_free = 0.3441    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
r_final: 0.3441
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.3173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7319  Z= 0.138
  Angle     :  0.634  12.416   9931  Z= 0.330
  Chirality :  0.044   0.199   1125
  Planarity :  0.004   0.048   1256
  Dihedral  :  9.360 150.202   1003
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 13.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.85 %
    Favored  : 97.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.27), residues: 890
  helix:  0.99 (0.24), residues: 393
  sheet: -0.00 (0.40), residues: 145
  loop : -0.81 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 214 
 TYR   0.019   0.002   TYR A  37 
 PHE   0.023   0.002   PHE F 333 
 TRP   0.016   0.001   TRP B 169 
 HIS   0.013   0.002   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 7318)
  covalent geometry    : angle       0.63383 ( 9929)
  SS BOND              : bond        0.00683 (    1)
  SS BOND              : angle       0.72868 (    2)
  hydrogen bonds       : bond        0.04512 (  388)
  hydrogen bonds       : angle       4.94344 ( 1131)

*********************** 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
  225 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 225
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 LYS cc_start: 0.7475 (mttp) cc_final: 0.7186 (tttt)
REVERT: A  283 ARG cc_start: 0.7488 (mtp85) cc_final: 0.7189 (mmt-90)
REVERT: A  291 LEU cc_start: 0.9118 (mt) cc_final: 0.8609 (mt)
REVERT: A  343 ASP cc_start: 0.8100 (p0) cc_final: 0.7739 (m-30)
REVERT: F   61 PHE cc_start: 0.7603 (m-80) cc_final: 0.7389 (m-80)
REVERT: F  105 MET cc_start: 0.8773 (ttp) cc_final: 0.8513 (tmm)
REVERT: F  123 TRP cc_start: 0.6858 (m100) cc_final: 0.6584 (t60)
REVERT: F  324 SER cc_start: 0.8655 (m) cc_final: 0.8051 (m)
REVERT: F  327 ASN cc_start: 0.8796 (m110) cc_final: 0.8174 (m110)
REVERT: F  336 ASP cc_start: 0.8438 (p0) cc_final: 0.8192 (p0)
REVERT: B   45 MET cc_start: 0.6708 (mmt) cc_final: 0.6472 (mmt)
REVERT: B   52 ARG cc_start: 0.7548 (mtt-85) cc_final: 0.7188 (mtm110)
REVERT: B   75 GLN cc_start: 0.6980 (mm-40) cc_final: 0.6636 (mm-40)
REVERT: B   85 TYR cc_start: 0.8719 (m-10) cc_final: 0.8199 (m-80)
REVERT: B   91 HIS cc_start: 0.8028 (m90) cc_final: 0.7397 (m90)
REVERT: B   99 TRP cc_start: 0.7184 (m-90) cc_final: 0.6558 (m-90)
REVERT: B  171 ILE cc_start: 0.8965 (pt) cc_final: 0.8762 (pt)
REVERT: B  172 GLU cc_start: 0.8661 (tp30) cc_final: 0.7989 (tm-30)
REVERT: B  228 ASP cc_start: 0.7980 (m-30) cc_final: 0.7254 (m-30)
REVERT: B  297 TRP cc_start: 0.5534 (m100) cc_final: 0.5226 (m100)
REVERT: B  335 PHE cc_start: 0.7203 (m-80) cc_final: 0.6604 (m-80)
REVERT: D   32 LYS cc_start: 0.8704 (tptp) cc_final: 0.8387 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 225
  average time/residue: 0.0751
  time to fit residues: 23.3592
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  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 78 optimal weight:    9.9990
   chunk 66 optimal weight:   20.0000
   chunk 39 optimal weight:    0.6980
   chunk 8 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   overall best weight:    1.4986

-------------------------------------------------------------------------------
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  75 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 = 0.3885 r_free = 0.3885 target = 0.130265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.100229 restraints weight = 45945.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.103774 restraints weight = 37848.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.105542 restraints weight = 16262.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.106379 restraints weight = 11244.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.108180 restraints weight = 9143.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3518
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3518 r_free = 0.3518    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3517 r_free = 0.3517    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
r_final: 0.3517
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.3606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7319  Z= 0.138
  Angle     :  0.605  11.715   9931  Z= 0.317
  Chirality :  0.045   0.212   1125
  Planarity :  0.004   0.049   1256
  Dihedral  :  9.179 148.714   1003
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  2.72 %
    Favored  : 97.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.28), residues: 890
  helix:  1.18 (0.25), residues: 398
  sheet: -0.15 (0.43), residues: 132
  loop : -0.84 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 232 
 TYR   0.023   0.002   TYR B  59 
 PHE   0.020   0.002   PHE F 289 
 TRP   0.023   0.002   TRP B 339 
 HIS   0.004   0.001   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 7318)
  covalent geometry    : angle       0.60466 ( 9929)
  SS BOND              : bond        0.00536 (    1)
  SS BOND              : angle       0.66069 (    2)
  hydrogen bonds       : bond        0.04278 (  388)
  hydrogen bonds       : angle       4.82884 ( 1131)

*********************** 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
  224 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 223
  time to evaluate  : 0.270 
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: 0.8396 (mtmt) cc_final: 0.7798 (mmtt)
REVERT: A   34 LYS cc_start: 0.7724 (mttp) cc_final: 0.7497 (tttt)
REVERT: A  277 TRP cc_start: 0.8799 (t-100) cc_final: 0.8286 (t-100)
REVERT: A  279 ASN cc_start: 0.8969 (t0) cc_final: 0.8763 (t0)
REVERT: A  283 ARG cc_start: 0.7616 (mtp85) cc_final: 0.7279 (mmt-90)
REVERT: A  291 LEU cc_start: 0.9089 (mt) cc_final: 0.8576 (mt)
REVERT: A  343 ASP cc_start: 0.8061 (p0) cc_final: 0.7703 (m-30)
REVERT: A  386 MET cc_start: 0.8078 (tmm) cc_final: 0.7187 (tmm)
REVERT: F   61 PHE cc_start: 0.7550 (m-80) cc_final: 0.7261 (m-80)
REVERT: F  105 MET cc_start: 0.9085 (ttp) cc_final: 0.8635 (tmm)
REVERT: F  123 TRP cc_start: 0.7113 (m100) cc_final: 0.6720 (t60)
REVERT: F  324 SER cc_start: 0.8754 (m) cc_final: 0.8409 (m)
REVERT: B   46 ARG cc_start: 0.7640 (mtm180) cc_final: 0.6912 (ttp-110)
REVERT: B   52 ARG cc_start: 0.7587 (mtt-85) cc_final: 0.7339 (mtm110)
REVERT: B   61 MET cc_start: 0.8695 (ppp) cc_final: 0.8474 (ppp)
REVERT: B   85 TYR cc_start: 0.8633 (m-10) cc_final: 0.8057 (m-80)
REVERT: B  172 GLU cc_start: 0.8450 (tp30) cc_final: 0.7890 (tm-30)
REVERT: B  220 GLN cc_start: 0.8009 (pp30) cc_final: 0.7697 (pp30)
REVERT: B  228 ASP cc_start: 0.8011 (m-30) cc_final: 0.7351 (m-30)
REVERT: B  284 LEU cc_start: 0.8104 (tp) cc_final: 0.7904 (tp)
REVERT: B  312 ASP cc_start: 0.5678 (m-30) cc_final: 0.4947 (t0)
REVERT: B  335 PHE cc_start: 0.6626 (m-80) cc_final: 0.6190 (m-80)
REVERT: D   32 LYS cc_start: 0.8713 (tptp) cc_final: 0.8434 (tptt)
  outliers start: 1
  outliers final: 0
  residues processed: 223
  average time/residue: 0.0769
  time to fit residues: 23.8534
Evaluate side-chains
  174 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 76 optimal weight:    5.9990
   chunk 85 optimal weight:   20.0000
   chunk 80 optimal weight:    8.9990
   chunk 52 optimal weight:   20.0000
   chunk 63 optimal weight:   10.0000
   chunk 84 optimal weight:    1.9990
   chunk 20 optimal weight:    0.3980
   chunk 59 optimal weight:    9.9990
   chunk 41 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.6788

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 313 ASN ** 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 = 0.3873 r_free = 0.3873 target = 0.129675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.097332 restraints weight = 57891.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.099253 restraints weight = 36046.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.103264 restraints weight = 16224.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.103311 restraints weight = 10285.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.103907 restraints weight = 9400.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3444
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3444 r_free = 0.3444    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 = 0.3444 r_free = 0.3444    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
r_final: 0.3444
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.3846

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= 0.142
  Angle     :  0.606  11.570   9931  Z= 0.315
  Chirality :  0.044   0.215   1125
  Planarity :  0.004   0.050   1256
  Dihedral  :  9.140 147.841   1003
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 14.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.08 %
    Favored  : 97.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.31 (0.28), residues: 890
  helix:  1.20 (0.25), residues: 398
  sheet:  0.03 (0.43), residues: 127
  loop : -0.80 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 232 
 TYR   0.020   0.002   TYR B  59 
 PHE   0.018   0.002   PHE B 253 
 TRP   0.031   0.002   TRP B 297 
 HIS   0.007   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 7318)
  covalent geometry    : angle       0.60601 ( 9929)
  SS BOND              : bond        0.00544 (    1)
  SS BOND              : angle       0.61439 (    2)
  hydrogen bonds       : bond        0.04162 (  388)
  hydrogen bonds       : angle       4.81043 ( 1131)

*********************** 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
  213 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.277 
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: 0.8487 (mtmt) cc_final: 0.7931 (mmtt)
REVERT: A  277 TRP cc_start: 0.8732 (t-100) cc_final: 0.8307 (t-100)
REVERT: A  283 ARG cc_start: 0.7625 (mtp85) cc_final: 0.7352 (mmt-90)
REVERT: A  291 LEU cc_start: 0.9146 (mt) cc_final: 0.8828 (mt)
REVERT: A  343 ASP cc_start: 0.8085 (p0) cc_final: 0.7856 (m-30)
REVERT: F   61 PHE cc_start: 0.7656 (m-80) cc_final: 0.7366 (m-80)
REVERT: F  105 MET cc_start: 0.8725 (ttp) cc_final: 0.8369 (tmm)
REVERT: F  123 TRP cc_start: 0.6998 (m100) cc_final: 0.6727 (t60)
REVERT: F  285 TRP cc_start: 0.8606 (m100) cc_final: 0.8283 (m100)
REVERT: F  323 ASN cc_start: 0.9283 (t0) cc_final: 0.9067 (t0)
REVERT: F  324 SER cc_start: 0.8803 (m) cc_final: 0.8534 (m)
REVERT: B   46 ARG cc_start: 0.7560 (mtm180) cc_final: 0.6867 (ttp-110)
REVERT: B   52 ARG cc_start: 0.7658 (mtt-85) cc_final: 0.7337 (mtm110)
REVERT: B   61 MET cc_start: 0.8697 (ppp) cc_final: 0.8382 (ppp)
REVERT: B   85 TYR cc_start: 0.8624 (m-10) cc_final: 0.8097 (m-80)
REVERT: B  172 GLU cc_start: 0.8505 (tp30) cc_final: 0.7909 (tm-30)
REVERT: B  228 ASP cc_start: 0.8120 (m-30) cc_final: 0.7423 (m-30)
REVERT: B  331 SER cc_start: 0.8419 (t) cc_final: 0.7449 (t)
REVERT: B  335 PHE cc_start: 0.6767 (m-80) cc_final: 0.6407 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 213
  average time/residue: 0.0782
  time to fit residues: 22.6830
Evaluate side-chains
  165 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 86 optimal weight:    0.6980
   chunk 7 optimal weight:   10.0000
   chunk 66 optimal weight:   10.0000
   chunk 25 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 82 optimal weight:   20.0000
   chunk 69 optimal weight:    6.9990
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
A 218 ASN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 237 HIS
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  44 GLN
** B  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 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 = 0.3894 r_free = 0.3894 target = 0.130744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.099289 restraints weight = 61069.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.099197 restraints weight = 34596.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.102158 restraints weight = 19040.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.102177 restraints weight = 12263.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.104969 restraints weight = 10318.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3477
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3477 r_free = 0.3477    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3477 r_free = 0.3477    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
r_final: 0.3477
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.4170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7319  Z= 0.127
  Angle     :  0.589  11.551   9931  Z= 0.307
  Chirality :  0.043   0.192   1125
  Planarity :  0.004   0.050   1256
  Dihedral  :  9.080 146.901   1003
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.95 %
    Favored  : 97.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.28), residues: 890
  helix:  1.21 (0.25), residues: 398
  sheet: -0.04 (0.43), residues: 138
  loop : -0.73 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  42 
 TYR   0.018   0.002   TYR B  59 
 PHE   0.023   0.002   PHE B 292 
 TRP   0.037   0.002   TRP B  99 
 HIS   0.007   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 7318)
  covalent geometry    : angle       0.58947 ( 9929)
  SS BOND              : bond        0.00524 (    1)
  SS BOND              : angle       0.47990 (    2)
  hydrogen bonds       : bond        0.04008 (  388)
  hydrogen bonds       : angle       4.75319 ( 1131)

*********************** 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
  212 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.264 
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: 0.8414 (mtmt) cc_final: 0.7877 (mmtt)
REVERT: A  277 TRP cc_start: 0.8695 (t-100) cc_final: 0.8139 (t-100)
REVERT: A  279 ASN cc_start: 0.8958 (t0) cc_final: 0.8753 (t0)
REVERT: A  283 ARG cc_start: 0.7667 (mtp85) cc_final: 0.7387 (mmt-90)
REVERT: A  291 LEU cc_start: 0.9140 (mt) cc_final: 0.8751 (mt)
REVERT: A  343 ASP cc_start: 0.8097 (p0) cc_final: 0.7705 (m-30)
REVERT: A  386 MET cc_start: 0.7965 (tmm) cc_final: 0.7765 (tpp)
REVERT: F   61 PHE cc_start: 0.7472 (m-80) cc_final: 0.7254 (m-80)
REVERT: F  105 MET cc_start: 0.8756 (ttp) cc_final: 0.8401 (tmm)
REVERT: F  204 TYR cc_start: 0.7921 (m-80) cc_final: 0.7686 (m-80)
REVERT: F  285 TRP cc_start: 0.8603 (m100) cc_final: 0.8056 (m100)
REVERT: F  323 ASN cc_start: 0.9195 (t0) cc_final: 0.8621 (t0)
REVERT: F  324 SER cc_start: 0.8877 (m) cc_final: 0.8584 (p)
REVERT: B   46 ARG cc_start: 0.7514 (mtm180) cc_final: 0.7113 (ttp-110)
REVERT: B   52 ARG cc_start: 0.7597 (mtt-85) cc_final: 0.7231 (mtm110)
REVERT: B   61 MET cc_start: 0.8779 (ppp) cc_final: 0.8403 (ppp)
REVERT: B   85 TYR cc_start: 0.8615 (m-10) cc_final: 0.8168 (m-80)
REVERT: B   91 HIS cc_start: 0.8247 (m90) cc_final: 0.7727 (m90)
REVERT: B  105 TYR cc_start: 0.7374 (t80) cc_final: 0.6952 (t80)
REVERT: B  110 ASN cc_start: 0.7493 (t0) cc_final: 0.6971 (t0)
REVERT: B  172 GLU cc_start: 0.8479 (tp30) cc_final: 0.7889 (tm-30)
REVERT: B  228 ASP cc_start: 0.8007 (m-30) cc_final: 0.7333 (m-30)
REVERT: B  284 LEU cc_start: 0.8425 (tp) cc_final: 0.8193 (tp)
REVERT: B  331 SER cc_start: 0.8201 (t) cc_final: 0.7177 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.0746
  time to fit residues: 21.8483
Evaluate side-chains
  172 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 50 optimal weight:    8.9990
   chunk 21 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   chunk 7 optimal weight:   10.0000
   chunk 33 optimal weight:    4.9990
   chunk 72 optimal weight:    6.9990
   chunk 15 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 237 HIS
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3902 r_free = 0.3902 target = 0.131095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.099651 restraints weight = 50353.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.103539 restraints weight = 29587.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.103850 restraints weight = 17855.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.105020 restraints weight = 11569.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.107909 restraints weight = 9179.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3523
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3523 r_free = 0.3523    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3522 r_free = 0.3522    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
r_final: 0.3522
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.4436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7319  Z= 0.120
  Angle     :  0.608  11.504   9931  Z= 0.312
  Chirality :  0.044   0.180   1125
  Planarity :  0.004   0.052   1256
  Dihedral  :  8.862 142.597   1003
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.28), residues: 890
  helix:  1.17 (0.25), residues: 408
  sheet: -0.01 (0.43), residues: 130
  loop : -0.71 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 232 
 TYR   0.020   0.002   TYR B  59 
 PHE   0.021   0.001   PHE A 340 
 TRP   0.043   0.002   TRP B  99 
 HIS   0.007   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7318)
  covalent geometry    : angle       0.60850 ( 9929)
  SS BOND              : bond        0.00418 (    1)
  SS BOND              : angle       0.44757 (    2)
  hydrogen bonds       : bond        0.03961 (  388)
  hydrogen bonds       : angle       4.73584 ( 1131)

*********************** 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
  221 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 0.205 
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: 0.8328 (mtmt) cc_final: 0.7803 (mmtt)
REVERT: A  277 TRP cc_start: 0.8699 (t-100) cc_final: 0.7976 (t-100)
REVERT: A  291 LEU cc_start: 0.9063 (mt) cc_final: 0.8862 (mt)
REVERT: A  343 ASP cc_start: 0.7823 (p0) cc_final: 0.7414 (m-30)
REVERT: A  386 MET cc_start: 0.8163 (tmm) cc_final: 0.7853 (tpp)
REVERT: F   61 PHE cc_start: 0.7409 (m-80) cc_final: 0.7195 (m-80)
REVERT: F  138 LYS cc_start: 0.8665 (tttt) cc_final: 0.8267 (tttt)
REVERT: F  324 SER cc_start: 0.8838 (m) cc_final: 0.8520 (p)
REVERT: B   61 MET cc_start: 0.8767 (ppp) cc_final: 0.8408 (ppp)
REVERT: B   85 TYR cc_start: 0.8506 (m-10) cc_final: 0.8002 (m-80)
REVERT: B  110 ASN cc_start: 0.7044 (t0) cc_final: 0.6750 (t0)
REVERT: B  171 ILE cc_start: 0.8923 (pt) cc_final: 0.8721 (pt)
REVERT: B  172 GLU cc_start: 0.8329 (tp30) cc_final: 0.7781 (tm-30)
REVERT: B  228 ASP cc_start: 0.7978 (m-30) cc_final: 0.7328 (m-30)
REVERT: B  263 THR cc_start: 0.8280 (m) cc_final: 0.7808 (m)
REVERT: B  331 SER cc_start: 0.8530 (t) cc_final: 0.7794 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 221
  average time/residue: 0.0695
  time to fit residues: 21.3483
Evaluate side-chains
  173 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 60 optimal weight:    0.9980
   chunk 8 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9980
   chunk 75 optimal weight:    0.1980
   chunk 49 optimal weight:    0.4980
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 3 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 14 optimal weight:   10.0000
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 237 HIS
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  54 HIS ** 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 = 0.3916 r_free = 0.3916 target = 0.132194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.101088 restraints weight = 47502.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.105968 restraints weight = 31946.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.106679 restraints weight = 16042.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.106968 restraints weight = 12324.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.109987 restraints weight = 9565.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3552
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3552 r_free = 0.3552    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3552 r_free = 0.3552    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
r_final: 0.3552
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.4633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7319  Z= 0.121
  Angle     :  0.595  10.886   9931  Z= 0.312
  Chirality :  0.044   0.191   1125
  Planarity :  0.004   0.052   1256
  Dihedral  :  8.856 143.234   1003
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 13.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.47 (0.28), residues: 890
  helix:  1.34 (0.25), residues: 406
  sheet: -0.15 (0.43), residues: 139
  loop : -0.66 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 232 
 TYR   0.030   0.002   TYR B  59 
 PHE   0.020   0.001   PHE A 340 
 TRP   0.023   0.002   TRP F 321 
 HIS   0.003   0.001   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 7318)
  covalent geometry    : angle       0.59515 ( 9929)
  SS BOND              : bond        0.00299 (    1)
  SS BOND              : angle       0.34107 (    2)
  hydrogen bonds       : bond        0.03989 (  388)
  hydrogen bonds       : angle       4.75087 ( 1131)

*********************** 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
  219 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 219
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.8304 (mtmt) cc_final: 0.7839 (mmtt)
REVERT: A   37 TYR cc_start: 0.8082 (t80) cc_final: 0.7781 (t80)
REVERT: A  277 TRP cc_start: 0.8658 (t-100) cc_final: 0.7954 (t-100)
REVERT: A  340 PHE cc_start: 0.8330 (t80) cc_final: 0.7666 (t80)
REVERT: A  343 ASP cc_start: 0.8015 (p0) cc_final: 0.7682 (m-30)
REVERT: A  386 MET cc_start: 0.8060 (tmm) cc_final: 0.7781 (tpp)
REVERT: F   61 PHE cc_start: 0.7483 (m-80) cc_final: 0.7190 (m-80)
REVERT: F  105 MET cc_start: 0.9022 (ttp) cc_final: 0.8639 (tmm)
REVERT: F  123 TRP cc_start: 0.6945 (m-10) cc_final: 0.6515 (t60)
REVERT: F  138 LYS cc_start: 0.8612 (tttt) cc_final: 0.8297 (tttt)
REVERT: B   61 MET cc_start: 0.8770 (ppp) cc_final: 0.8259 (ppp)
REVERT: B   85 TYR cc_start: 0.8546 (m-10) cc_final: 0.8112 (m-80)
REVERT: B   99 TRP cc_start: 0.6890 (m-90) cc_final: 0.6673 (m-90)
REVERT: B  105 TYR cc_start: 0.7277 (t80) cc_final: 0.6843 (t80)
REVERT: B  110 ASN cc_start: 0.7169 (t0) cc_final: 0.6833 (t0)
REVERT: B  156 GLN cc_start: 0.7595 (mm110) cc_final: 0.6888 (mm110)
REVERT: B  172 GLU cc_start: 0.8438 (tp30) cc_final: 0.7825 (tm-30)
REVERT: B  228 ASP cc_start: 0.8019 (m-30) cc_final: 0.7283 (m-30)
REVERT: B  331 SER cc_start: 0.8402 (t) cc_final: 0.7143 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 219
  average time/residue: 0.0667
  time to fit residues: 20.7142
Evaluate side-chains
  166 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 60 optimal weight:    0.7980
   chunk 2 optimal weight:    9.9990
   chunk 28 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0870
   chunk 9 optimal weight:    9.9990
   chunk 87 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 68 optimal weight:   30.0000
   overall best weight:    0.7360

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

Flipped N/Q/H residues before XYZ refinement:
A 218 ASN
** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 237 HIS
F 323 ASN
** B  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  59 ASN ** 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 = 0.3922 r_free = 0.3922 target = 0.132688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.102495 restraints weight = 56840.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.106022 restraints weight = 41939.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.107544 restraints weight = 19490.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.107975 restraints weight = 14287.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.109041 restraints weight = 11267.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3520
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3520 r_free = 0.3520    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3520 r_free = 0.3520    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
r_final: 0.3520
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.4823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7319  Z= 0.119
  Angle     :  0.612  10.759   9931  Z= 0.315
  Chirality :  0.044   0.171   1125
  Planarity :  0.004   0.053   1256
  Dihedral  :  8.762 142.498   1003
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 13.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.91 %
    Favored  : 98.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.51 (0.28), residues: 890
  helix:  1.43 (0.25), residues: 406
  sheet: -0.05 (0.44), residues: 123
  loop : -0.73 (0.33), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 232 
 TYR   0.021   0.001   TYR A  37 
 PHE   0.016   0.001   PHE A 212 
 TRP   0.019   0.002   TRP F 321 
 HIS   0.002   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 7318)
  covalent geometry    : angle       0.61228 ( 9929)
  SS BOND              : bond        0.00273 (    1)
  SS BOND              : angle       0.32068 (    2)
  hydrogen bonds       : bond        0.03847 (  388)
  hydrogen bonds       : angle       4.69403 ( 1131)

*********************** 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
  213 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.280 
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: 0.8262 (mtmt) cc_final: 0.7823 (mmtt)
REVERT: A   37 TYR cc_start: 0.8102 (t80) cc_final: 0.7859 (t80)
REVERT: A  277 TRP cc_start: 0.8670 (t-100) cc_final: 0.7977 (t-100)
REVERT: A  340 PHE cc_start: 0.8371 (t80) cc_final: 0.7970 (t80)
REVERT: A  364 THR cc_start: 0.8483 (p) cc_final: 0.7907 (t)
REVERT: A  386 MET cc_start: 0.8062 (tmm) cc_final: 0.7837 (tpp)
REVERT: F   61 PHE cc_start: 0.7318 (m-80) cc_final: 0.7107 (m-80)
REVERT: F   73 VAL cc_start: 0.9381 (t) cc_final: 0.9045 (t)
REVERT: F   78 MET cc_start: 0.8271 (mtt) cc_final: 0.8056 (mtm)
REVERT: F  123 TRP cc_start: 0.6896 (m-10) cc_final: 0.6482 (t60)
REVERT: F  138 LYS cc_start: 0.8594 (tttt) cc_final: 0.8363 (tttt)
REVERT: B   61 MET cc_start: 0.8718 (ppp) cc_final: 0.8322 (ppp)
REVERT: B   85 TYR cc_start: 0.8537 (m-10) cc_final: 0.7998 (m-80)
REVERT: B   91 HIS cc_start: 0.8328 (m90) cc_final: 0.7698 (m90)
REVERT: B  110 ASN cc_start: 0.7128 (t0) cc_final: 0.6791 (t0)
REVERT: B  156 GLN cc_start: 0.7659 (mm110) cc_final: 0.6945 (mm110)
REVERT: B  172 GLU cc_start: 0.8422 (tp30) cc_final: 0.7808 (tm-30)
REVERT: B  331 SER cc_start: 0.8327 (t) cc_final: 0.7313 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 213
  average time/residue: 0.0686
  time to fit residues: 20.7964
Evaluate side-chains
  165 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 79 optimal weight:   20.0000
   chunk 40 optimal weight:    0.6980
   chunk 22 optimal weight:    9.9990
   chunk 53 optimal weight:    0.0070
   chunk 85 optimal weight:    3.9990
   chunk 3 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   chunk 16 optimal weight:    7.9990
   chunk 34 optimal weight:    0.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    1.3002

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

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 237 HIS
F 323 ASN
** B  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  59 ASN ** 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 = 0.3898 r_free = 0.3898 target = 0.130552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.098536 restraints weight = 60526.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.100651 restraints weight = 34328.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.103136 restraints weight = 17331.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.103193 restraints weight = 12231.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.106508 restraints weight = 10117.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3508
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3508 r_free = 0.3508    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 = 0.3508 r_free = 0.3508    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
r_final: 0.3508
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.4950

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= 0.133
  Angle     :  0.640  10.382   9931  Z= 0.336
  Chirality :  0.045   0.166   1125
  Planarity :  0.004   0.053   1256
  Dihedral  :  8.796 142.798   1003
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 13.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.78 %
    Favored  : 99.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.49 (0.28), residues: 890
  helix:  1.41 (0.25), residues: 402
  sheet: -0.20 (0.42), residues: 133
  loop : -0.67 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  52 
 TYR   0.022   0.002   TYR A  37 
 PHE   0.039   0.002   PHE A 340 
 TRP   0.042   0.002   TRP B  99 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 7318)
  covalent geometry    : angle       0.63962 ( 9929)
  SS BOND              : bond        0.00360 (    1)
  SS BOND              : angle       0.35201 (    2)
  hydrogen bonds       : bond        0.04040 (  388)
  hydrogen bonds       : angle       4.84923 ( 1131)

********************** 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
  202 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.8273 (mtmt) cc_final: 0.7818 (mmtt)
REVERT: A   37 TYR cc_start: 0.8137 (t80) cc_final: 0.7887 (t80)
REVERT: A  277 TRP cc_start: 0.8652 (t-100) cc_final: 0.7979 (t-100)
REVERT: A  364 THR cc_start: 0.8483 (p) cc_final: 0.7924 (t)
REVERT: A  386 MET cc_start: 0.8137 (tmm) cc_final: 0.7865 (tpp)
REVERT: F   61 PHE cc_start: 0.7394 (m-80) cc_final: 0.7150 (m-80)
REVERT: F   73 VAL cc_start: 0.9352 (t) cc_final: 0.9029 (t)
REVERT: F  105 MET cc_start: 0.8794 (ttp) cc_final: 0.8547 (tmm)
REVERT: F  123 TRP cc_start: 0.6931 (m-10) cc_final: 0.6567 (t60)
REVERT: F  138 LYS cc_start: 0.8599 (tttt) cc_final: 0.8362 (tttt)
REVERT: B   61 MET cc_start: 0.8745 (ppp) cc_final: 0.8244 (ppp)
REVERT: B   85 TYR cc_start: 0.8536 (m-10) cc_final: 0.8071 (m-80)
REVERT: B   91 HIS cc_start: 0.8384 (m90) cc_final: 0.7735 (m90)
REVERT: B  110 ASN cc_start: 0.7263 (t0) cc_final: 0.6909 (t0)
REVERT: B  124 TYR cc_start: 0.8491 (m-10) cc_final: 0.8258 (m-10)
REVERT: B  156 GLN cc_start: 0.7690 (mm110) cc_final: 0.6991 (mm110)
REVERT: B  171 ILE cc_start: 0.8889 (pt) cc_final: 0.8686 (pt)
REVERT: B  172 GLU cc_start: 0.8460 (tp30) cc_final: 0.7810 (tm-30)
REVERT: B  331 SER cc_start: 0.8418 (t) cc_final: 0.7239 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 202
  average time/residue: 0.0702
  time to fit residues: 19.9899
Evaluate side-chains
  164 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 33 optimal weight:    7.9990
   chunk 70 optimal weight:    0.0770
   chunk 63 optimal weight:    8.9990
   chunk 43 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0770
   chunk 60 optimal weight:    6.9990
   chunk 55 optimal weight:    8.9990
   chunk 64 optimal weight:    6.9990
   chunk 57 optimal weight:    8.9990
   chunk 86 optimal weight:    2.9990
   chunk 4 optimal weight:   20.0000
   overall best weight:    2.2300

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

Flipped N/Q/H residues before XYZ refinement:
A 218 ASN
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 377 ASN
F 237 HIS
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  44 HIS
** D  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.128828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.097663 restraints weight = 45837.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.103255 restraints weight = 29984.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.102911 restraints weight = 16007.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.103596 restraints weight = 11678.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.105560 restraints weight = 9290.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3495
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3495 r_free = 0.3495    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3495 r_free = 0.3495    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
r_final: 0.3495
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.4846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   7319  Z= 0.166
  Angle     :  0.665  10.202   9931  Z= 0.344
  Chirality :  0.046   0.178   1125
  Planarity :  0.004   0.054   1256
  Dihedral  :  8.887 144.560   1003
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 14.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.39 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.38 (0.28), residues: 890
  helix:  1.37 (0.25), residues: 400
  sheet: -0.31 (0.45), residues: 117
  loop : -0.74 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 232 
 TYR   0.024   0.002   TYR A  37 
 PHE   0.047   0.002   PHE A 340 
 TRP   0.044   0.003   TRP F 321 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 7318)
  covalent geometry    : angle       0.66479 ( 9929)
  SS BOND              : bond        0.00557 (    1)
  SS BOND              : angle       0.41770 (    2)
  hydrogen bonds       : bond        0.04246 (  388)
  hydrogen bonds       : angle       4.96814 ( 1131)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1385.68 seconds
wall clock time: 24 minutes 42.21 seconds (1482.21 seconds total)