Starting phenix.real_space_refine
on Thu Jul  2 02:54:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9tqj_56152/07_2026/9tqj_56152.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9tqj_56152/07_2026/9tqj_56152.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9tqj_56152/07_2026/9tqj_56152.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9tqj_56152/07_2026/9tqj_56152.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9tqj_56152/07_2026/9tqj_56152.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9tqj_56152/07_2026/9tqj_56152.cif"
  }
  resolution = 3.5
  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
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       2      5.49       5
     S      20      5.16       5
     C    3813      2.51       5
     N    1014      2.21       5
     O    1167      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6016
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 354, 2746
          Classifications: {'peptide': 354}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 338}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 3242
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 420, 3242
          Classifications: {'peptide': 420}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 404}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'GDP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.16, per 1000 atoms: 0.19
  Number of scatterers: 6016
  At special positions: 0
  Unit cell: (74.49, 72.58, 106.005, 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      20     16.00
     P       2     15.00
     O    1167      8.00
     N    1014      7.00
     C    3813      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.40
  Conformation dependent library (CDL) restraints added in 226.3 milliseconds
  

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1424

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 4 sheets defined
      47.9% alpha, 15.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 28
    Processing helix  chain 'A' and resid 83 through 85
      No H-bonds generated for 'chain 'A' and resid 83 through 85'
    Processing helix  chain 'A' and resid 107 through 123
      removed outlier: 4.708A  pdb=" N   GLU A 111 " --> pdb=" O   ALA A 107 " (cutoff:3.500A)
      removed outlier: 4.787A  pdb=" N   GLN A 112 " --> pdb=" O   GLN A 108 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LYS A 123 " --> pdb=" O   ASN A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 156
      removed outlier: 3.570A  pdb=" N   THR A 146 " --> pdb=" O   SER A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 193
      removed outlier: 3.897A  pdb=" N   ARG A 191 " --> pdb=" O   TYR A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 211
    Processing helix  chain 'A' and resid 217 through 238
      removed outlier: 3.627A  pdb=" N   LEU A 221 " --> pdb=" O   THR A 217 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   GLY A 235 " --> pdb=" O   ASN A 231 " (cutoff:3.500A)
      removed outlier: 4.897A  pdb=" N   MET A 236 " --> pdb=" O   ILE A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 254
      removed outlier: 3.557A  pdb=" N   LEU A 249 " --> pdb=" O   ASP A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 288
      removed outlier: 3.750A  pdb=" N   PHE A 288 " --> pdb=" O   ALA A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 329
    Processing helix  chain 'A' and resid 366 through 374
      removed outlier: 3.727A  pdb=" N   PHE A 370 " --> pdb=" O   ILE A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 417
      removed outlier: 3.547A  pdb=" N   THR A 417 " --> pdb=" O   GLU A 413 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 30
    Processing helix  chain 'B' and resid 67 through 78
      removed outlier: 4.513A  pdb=" N   ILE B  71 " --> pdb=" O   GLU B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 108
      removed outlier: 5.146A  pdb=" N   ALA B 105 " --> pdb=" O   GLY B 101 " (cutoff:3.500A)
      removed outlier: 8.017A  pdb=" N   ASP B 106 " --> pdb=" O   TYR B 102 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   GLY B 107 " --> pdb=" O   ARG B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 125
      removed outlier: 3.551A  pdb=" N   VAL B 114 " --> pdb=" O   ASN B 110 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   GLU B 124 " --> pdb=" O   LYS B 120 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   THR B 125 " --> pdb=" O   ALA B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 157
    Processing helix  chain 'B' and resid 178 through 194
      removed outlier: 3.579A  pdb=" N   ASN B 182 " --> pdb=" O   THR B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 212
    Processing helix  chain 'B' and resid 219 through 240
      removed outlier: 3.550A  pdb=" N   LEU B 223 " --> pdb=" O   SER B 219 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   SER B 237 " --> pdb=" O   GLY B 233 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   LEU B 238 " --> pdb=" O   VAL B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 256
    Processing helix  chain 'B' and resid 282 through 291
      removed outlier: 3.793A  pdb=" N   PHE B 291 " --> pdb=" O   ILE B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 296
      removed outlier: 3.518A  pdb=" N   ALA B 296 " --> pdb=" O   PRO B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 320 through 332
      removed outlier: 3.634A  pdb=" N   VAL B 324 " --> pdb=" O   LYS B 320 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 386
      removed outlier: 3.544A  pdb=" N   ALA B 383 " --> pdb=" O   ALA B 379 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   MET B 384 " --> pdb=" O   GLN B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 391 through 396
    Processing helix  chain 'B' and resid 400 through 421
      removed outlier: 3.599A  pdb=" N   MET B 404 " --> pdb=" O   SER B 400 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88
      removed outlier: 8.065A  pdb=" N   VAL A  88 " --> pdb=" O   ALA A  60 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   LEU A  62 " --> pdb=" O   VAL A  88 " (cutoff:3.500A)
      removed outlier: 8.511A  pdb=" N   VAL A  61 " --> pdb=" O   VAL A   4 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   VAL A   6 " --> pdb=" O   VAL A  61 " (cutoff:3.500A)
      removed outlier: 7.457A  pdb=" N   VAL A  63 " --> pdb=" O   VAL A   6 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   ALA A   8 " --> pdb=" O   VAL A  63 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   GLU A   3 " --> pdb=" O   GLY A 128 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   PHE A 130 " --> pdb=" O   GLU A   3 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   VAL A   5 " --> pdb=" O   PHE A 130 " (cutoff:3.500A)
      removed outlier: 5.567A  pdb=" N   VAL A 132 " --> pdb=" O   VAL A   5 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   VAL A   7 " --> pdb=" O   VAL A 132 " (cutoff:3.500A)
      removed outlier: 5.953A  pdb=" N   HIS A 134 " --> pdb=" O   VAL A   7 " (cutoff:3.500A)
      removed outlier: 7.524A  pdb=" N   VAL A   9 " --> pdb=" O   HIS A 134 " (cutoff:3.500A)
      removed outlier: 8.130A  pdb=" N   LEU A 162 " --> pdb=" O   GLY A 128 " (cutoff:3.500A)
      removed outlier: 6.040A  pdb=" N   PHE A 130 " --> pdb=" O   LEU A 162 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   PHE A 164 " --> pdb=" O   PHE A 130 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   VAL A 132 " --> pdb=" O   PHE A 164 " (cutoff:3.500A)
      removed outlier: 7.618A  pdb=" N   ILE A 166 " --> pdb=" O   VAL A 132 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   HIS A 134 " --> pdb=" O   ILE A 166 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   CYS A 195 " --> pdb=" O   LEU A 161 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   THR A 264 " --> pdb=" O   ILE A 198 " (cutoff:3.500A)
      removed outlier: 7.530A  pdb=" N   ASP A 200 " --> pdb=" O   THR A 264 " (cutoff:3.500A)
      removed outlier: 11.389A  pdb=" N   THR A 266 " --> pdb=" O   ASP A 200 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   PHE A 261 " --> pdb=" O   HIS A 363 " (cutoff:3.500A)
      removed outlier: 4.561A  pdb=" N   HIS A 363 " --> pdb=" O   PHE A 261 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   ALA A 356 " --> pdb=" O   PHE A 311 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   PHE A 311 " --> pdb=" O   ALA A 356 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   ALA A 358 " --> pdb=" O   VAL A 309 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   VAL A 309 " --> pdb=" O   ALA A 358 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   VAL A 360 " --> pdb=" O   THR A 307 " (cutoff:3.500A)
      removed outlier: 4.736A  pdb=" N   THR A 307 " --> pdb=" O   VAL A 360 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   ASN A 362 " --> pdb=" O   ILE A 305 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 52
    Processing sheet with id=AA3, first strand: chain 'B' and resid 88 through 89
      removed outlier: 7.509A  pdb=" N   ILE B  88 " --> pdb=" O   ALA B  61 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   LEU B  63 " --> pdb=" O   ILE B  88 " (cutoff:3.500A)
      removed outlier: 8.383A  pdb=" N   ILE B  62 " --> pdb=" O   ILE B   5 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   SER B   7 " --> pdb=" O   ILE B  62 " (cutoff:3.500A)
      removed outlier: 7.220A  pdb=" N   VAL B  64 " --> pdb=" O   SER B   7 " (cutoff:3.500A)
      removed outlier: 5.608A  pdb=" N   HIS B   9 " --> pdb=" O   VAL B  64 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   ILE B   6 " --> pdb=" O   SER B 132 " (cutoff:3.500A)
      removed outlier: 7.811A  pdb=" N   SER B 134 " --> pdb=" O   ILE B   6 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   ILE B   8 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
      removed outlier: 8.837A  pdb=" N   SER B 136 " --> pdb=" O   ILE B   8 " (cutoff:3.500A)
      removed outlier: 8.474A  pdb=" N   VAL B  10 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   ILE B 162 " --> pdb=" O   GLU B 196 " (cutoff:3.500A)
      removed outlier: 8.248A  pdb=" N   ILE B 198 " --> pdb=" O   ILE B 162 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   THR B 164 " --> pdb=" O   ILE B 198 " (cutoff:3.500A)
      removed outlier: 7.725A  pdb=" N   LEU B 200 " --> pdb=" O   THR B 164 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   SER B 166 " --> pdb=" O   LEU B 200 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   THR B 197 " --> pdb=" O   LEU B 264 " (cutoff:3.500A)
      removed outlier: 7.733A  pdb=" N   SER B 266 " --> pdb=" O   THR B 197 " (cutoff:3.500A)
      removed outlier: 7.272A  pdb=" N   VAL B 199 " --> pdb=" O   SER B 266 " (cutoff:3.500A)
      removed outlier: 9.140A  pdb=" N   PHE B 268 " --> pdb=" O   VAL B 199 " (cutoff:3.500A)
      removed outlier: 12.437A  pdb=" N   ASP B 201 " --> pdb=" O   PHE B 268 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   PHE B 263 " --> pdb=" O   HIS B 367 " (cutoff:3.500A)
      removed outlier: 4.986A  pdb=" N   HIS B 367 " --> pdb=" O   PHE B 263 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 49 through 51

    286 hydrogen bonds defined for protein.
    849 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: 1.00

  Time building geometry restraints manager: 0.57 seconds

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

  Histogram of bond lengths:
        1.17 -     1.31: 1018
        1.31 -     1.44: 1590
        1.44 -     1.57: 3480
        1.57 -     1.70: 5
        1.70 -     1.83: 40
  Bond restraints: 6133
  Sorted by residual:
  bond pdb=" CG  GLN A  22 "
       pdb=" CD  GLN A  22 "
    ideal  model  delta    sigma   weight residual
    1.516  1.789 -0.273 2.50e-02 1.60e+03 1.19e+02
  bond pdb=" CB  GLN A  22 "
       pdb=" CG  GLN A  22 "
    ideal  model  delta    sigma   weight residual
    1.520  1.831 -0.311 3.00e-02 1.11e+03 1.07e+02
  bond pdb=" C   GLN A  22 "
       pdb=" N   LEU A  23 "
    ideal  model  delta    sigma   weight residual
    1.334  1.418 -0.084 1.27e-02 6.20e+03 4.37e+01
  bond pdb=" CA  GLN A  22 "
       pdb=" C   GLN A  22 "
    ideal  model  delta    sigma   weight residual
    1.524  1.607 -0.083 1.32e-02 5.74e+03 3.99e+01
  bond pdb=" CD  GLN A  22 "
       pdb=" NE2 GLN A  22 "
    ideal  model  delta    sigma   weight residual
    1.328  1.449 -0.121 2.10e-02 2.27e+03 3.31e+01
  ... (remaining 6128 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    11.84: 8305
       11.84 -    23.67: 4
       23.67 -    35.51: 4
       35.51 -    47.34: 0
       47.34 -    59.18: 1
  Bond angle restraints: 8314
  Sorted by residual:
  angle pdb=" CG  GLN A  22 "
        pdb=" CD  GLN A  22 "
        pdb=" OE1 GLN A  22 "
      ideal   model   delta    sigma   weight residual
     120.80  179.98  -59.18 2.00e+00 2.50e-01 8.76e+02
  angle pdb=" OE1 GLN A  22 "
        pdb=" CD  GLN A  22 "
        pdb=" NE2 GLN A  22 "
      ideal   model   delta    sigma   weight residual
     122.60   96.23   26.37 1.00e+00 1.00e+00 6.95e+02
  angle pdb=" CG  GLN A  22 "
        pdb=" CD  GLN A  22 "
        pdb=" NE2 GLN A  22 "
      ideal   model   delta    sigma   weight residual
     116.40   83.76   32.64 1.50e+00 4.44e-01 4.73e+02
  angle pdb=" N   GLN A  22 "
        pdb=" CA  GLN A  22 "
        pdb=" CB  GLN A  22 "
      ideal   model   delta    sigma   weight residual
     110.20  134.34  -24.14 1.49e+00 4.50e-01 2.62e+02
  angle pdb=" CA  GLN A  22 "
        pdb=" CB  GLN A  22 "
        pdb=" CG  GLN A  22 "
      ideal   model   delta    sigma   weight residual
     114.10   85.80   28.30 2.00e+00 2.50e-01 2.00e+02
  ... (remaining 8309 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.45: 3197
       16.45 -    32.89: 358
       32.89 -    49.33: 77
       49.33 -    65.78: 18
       65.78 -    82.22: 2
  Dihedral angle restraints: 3652
    sinusoidal: 1435
      harmonic: 2217
  Sorted by residual:
  dihedral pdb=" C   GLN A  22 "
           pdb=" N   GLN A  22 "
           pdb=" CA  GLN A  22 "
           pdb=" CB  GLN A  22 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -100.27  -22.33     0      2.50e+00 1.60e-01 7.98e+01
  dihedral pdb=" N   GLN A  22 "
           pdb=" C   GLN A  22 "
           pdb=" CA  GLN A  22 "
           pdb=" CB  GLN A  22 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  135.11  -12.31     0      2.50e+00 1.60e-01 2.43e+01
  dihedral pdb=" CA  TRP A  21 "
           pdb=" C   TRP A  21 "
           pdb=" N   GLN A  22 "
           pdb=" CA  GLN A  22 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.01  -21.99     0      5.00e+00 4.00e-02 1.93e+01
  ... (remaining 3649 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 638
       0.035 -    0.070: 212
       0.070 -    0.106: 68
       0.106 -    0.141: 29
       0.141 -    0.176: 4
  Chirality restraints: 951
  Sorted by residual:
  chirality pdb=" CA  MET A 149 "
            pdb=" N   MET A 149 "
            pdb=" C   MET A 149 "
            pdb=" CB  MET A 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.74e-01
  chirality pdb=" CA  ILE A 166 "
            pdb=" N   ILE A 166 "
            pdb=" C   ILE A 166 "
            pdb=" CB  ILE A 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.52e-01
  chirality pdb=" CA  ASN B  55 "
            pdb=" N   ASN B  55 "
            pdb=" C   ASN B  55 "
            pdb=" CB  ASN B  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.42e-01
  ... (remaining 948 not shown)

  Planarity restraints: 1068
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP A  21 "    0.017 2.00e-02 2.50e+03   3.15e-02 9.95e+00
        pdb=" C   TRP A  21 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   TRP A  21 "    0.020 2.00e-02 2.50e+03
        pdb=" N   GLN A  22 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 311 "    0.012 2.00e-02 2.50e+03   1.77e-02 5.50e+00
        pdb=" CG  PHE A 311 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 311 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 311 "    0.009 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 311 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 311 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 311 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 316 "   -0.025 5.00e-02 4.00e+02   3.73e-02 2.23e+00
        pdb=" N   PRO A 317 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 317 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 317 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1065 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.84: 1963
        2.84 -     3.36: 5543
        3.36 -     3.87: 9761
        3.87 -     4.39: 11059
        4.39 -     4.90: 19404
  Nonbonded interactions: 47730
  Sorted by model distance:
  nonbonded pdb=" O   LEU A  23 "
            pdb=" OE1 GLU A  27 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" N   GLN A  22 "
            pdb=" N   LEU A  23 "
     model   vdw
     2.517 2.560
  nonbonded pdb=" ND2 ASN B 224 "
            pdb=" O6  GDP B 501 "
     model   vdw
     2.532 3.120
  nonbonded pdb=" O   LEU A  23 "
            pdb=" N   GLN A  26 "
     model   vdw
     2.556 3.120
  nonbonded pdb=" O3' GDP B 501 "
            pdb=" O2' GDP B 501 "
     model   vdw
     2.560 2.432
  ... (remaining 47725 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.860
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6970
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      :  0.007   0.311   6135  Z= 0.297
  Angle     :  1.147  59.181   8314  Z= 0.677
  Chirality :  0.043   0.176    951
  Planarity :  0.004   0.037   1068
  Dihedral  : 14.491  82.224   2228
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 16.11 %
    Favored  : 83.59 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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:  0.70 (0.30), residues: 762
  helix:  1.37 (0.28), residues: 336
  sheet:  0.64 (0.49), residues: 120
  loop : -0.57 (0.34), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 325 
 TYR   0.017   0.001   TYR A 167 
 PHE   0.040   0.001   PHE A 311 
 TRP   0.012   0.001   TRP B  98 
 HIS   0.006   0.001   HIS A 363 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00658 /  0.30 ( 6133)
  covalent geometry    : angle       1.14720 /  0.68 ( 8314)
  hydrogen bonds       : bond        0.11168 /  8.16 (  286)
  hydrogen bonds       : angle       6.29751 /  4.35 (  849)
  Misc. bond           : bond        0.00419 /  0.20 (    2)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ASN cc_start: 0.5152 (t0) cc_final: 0.3894 (t0)
REVERT: A  353 MET cc_start: 0.5931 (tpp) cc_final: 0.5014 (mtt)
REVERT: B  120 LYS cc_start: 0.6999 (mtpt) cc_final: 0.6292 (tptt)
  outliers start: 2
  outliers final: 2
  residues processed: 76
  average time/residue: 0.0633
  time to fit residues: 6.7155
Evaluate side-chains
  78 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLN
Chi-restraints excluded: chain A residue  116 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    0.4980
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.8980
   overall best weight:    1.1982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  76 ASN
B 262 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.200265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.169429 restraints weight = 7054.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.169336 restraints weight = 6707.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.170106 restraints weight = 7140.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.170593 restraints weight = 5584.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.172226 restraints weight = 5030.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6889
moved from start:          0.0807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6135  Z= 0.121
  Angle     :  0.514   6.396   8314  Z= 0.266
  Chirality :  0.043   0.149    951
  Planarity :  0.003   0.035   1068
  Dihedral  :  5.371  55.405    837
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 13.07 %
    Favored  : 84.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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:  1.18 (0.30), residues: 762
  helix:  2.04 (0.28), residues: 333
  sheet:  0.77 (0.50), residues: 120
  loop : -0.60 (0.33), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 188 
 TYR   0.011   0.001   TYR B 102 
 PHE   0.019   0.001   PHE A 311 
 TRP   0.005   0.001   TRP B  98 
 HIS   0.004   0.001   HIS B 189 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.12 ( 6133)
  covalent geometry    : angle       0.51406 /  0.27 ( 8314)
  hydrogen bonds       : bond        0.03656 /  2.48 (  286)
  hydrogen bonds       : angle       4.68116 /  3.28 (  849)
  Misc. bond           : bond        0.00358 /  0.17 (    2)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 GLN cc_start: 0.6182 (tt0) cc_final: 0.4898 (mt0)
REVERT: A  149 MET cc_start: 0.6672 (OUTLIER) cc_final: 0.6398 (mtm)
REVERT: A  243 ASN cc_start: 0.4793 (t0) cc_final: 0.3994 (t0)
REVERT: A  353 MET cc_start: 0.5862 (tpp) cc_final: 0.5245 (mtt)
REVERT: B  120 LYS cc_start: 0.7203 (mtpt) cc_final: 0.6824 (mtpt)
REVERT: B  153 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7562 (mp)
REVERT: B  313 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.7094 (ptp)
REVERT: B  406 LYS cc_start: 0.6320 (mmtm) cc_final: 0.5901 (mmtp)
  outliers start: 18
  outliers final: 9
  residues processed: 98
  average time/residue: 0.0795
  time to fit residues: 10.5050
Evaluate side-chains
  89 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue  135 SER
Chi-restraints excluded: chain A residue  149 MET
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain B residue   45 SER
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  313 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 63 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9990
   chunk 30 optimal weight:    8.9990
   chunk 59 optimal weight:    0.0470
   chunk 25 optimal weight:    4.9990
   chunk 23 optimal weight:   10.0000
   chunk 58 optimal weight:    4.9990
   overall best weight:    2.0084

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 151 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.202007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.170385 restraints weight = 7008.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.170558 restraints weight = 7008.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.171408 restraints weight = 6894.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.171947 restraints weight = 5461.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.172741 restraints weight = 4790.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6997
moved from start:          0.1488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6135  Z= 0.155
  Angle     :  0.548   7.492   8314  Z= 0.287
  Chirality :  0.044   0.149    951
  Planarity :  0.004   0.035   1068
  Dihedral  :  4.972  36.840    830
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 14.29 %
    Favored  : 82.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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:  1.11 (0.30), residues: 762
  helix:  2.02 (0.28), residues: 333
  sheet:  0.75 (0.51), residues: 120
  loop : -0.71 (0.33), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 247 
 TYR   0.014   0.002   TYR B 102 
 PHE   0.013   0.002   PHE A  20 
 TRP   0.004   0.001   TRP B  22 
 HIS   0.005   0.001   HIS B 189 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00360 /  0.16 ( 6133)
  covalent geometry    : angle       0.54758 /  0.29 ( 8314)
  hydrogen bonds       : bond        0.04122 /  2.86 (  286)
  hydrogen bonds       : angle       4.71394 /  3.31 (  849)
  Misc. bond           : bond        0.00411 /  0.20 (    2)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 78
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 GLN cc_start: 0.6397 (tt0) cc_final: 0.4965 (mt0)
REVERT: A  198 ILE cc_start: 0.8550 (mm) cc_final: 0.8317 (mm)
REVERT: A  243 ASN cc_start: 0.4765 (t0) cc_final: 0.4074 (t0)
REVERT: A  353 MET cc_start: 0.6143 (tpp) cc_final: 0.5564 (mtt)
REVERT: B  120 LYS cc_start: 0.7189 (mtpt) cc_final: 0.6765 (mtpt)
REVERT: B  124 GLU cc_start: 0.7172 (tm-30) cc_final: 0.5967 (mt-10)
REVERT: B  153 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7666 (mp)
REVERT: B  313 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7023 (ptp)
REVERT: B  406 LYS cc_start: 0.6387 (mmtm) cc_final: 0.5917 (mmtp)
  outliers start: 22
  outliers final: 12
  residues processed: 93
  average time/residue: 0.0593
  time to fit residues: 7.7336
Evaluate side-chains
  85 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue  116 LYS
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain B residue   45 SER
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  313 MET
Chi-restraints excluded: chain B residue  416 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 18 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 40 optimal weight:    0.0370
   chunk 27 optimal weight:    2.9990
   chunk 14 optimal weight:    8.9990
   chunk 25 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9980
   chunk 5 optimal weight:    8.9990
   overall best weight:    1.0062

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 151 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.200833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.169127 restraints weight = 7081.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.168848 restraints weight = 7093.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.169880 restraints weight = 6803.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.170310 restraints weight = 5525.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.170574 restraints weight = 5040.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6963
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6135  Z= 0.110
  Angle     :  0.497   6.646   8314  Z= 0.256
  Chirality :  0.042   0.143    951
  Planarity :  0.003   0.035   1068
  Dihedral  :  4.783  34.275    830
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 14.89 %
    Favored  : 82.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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:  1.29 (0.31), residues: 762
  helix:  2.22 (0.28), residues: 333
  sheet:  0.80 (0.50), residues: 122
  loop : -0.66 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  44 
 TYR   0.008   0.001   TYR B 102 
 PHE   0.012   0.001   PHE A 311 
 TRP   0.003   0.001   TRP B 229 
 HIS   0.004   0.001   HIS B 367 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00250 /  0.11 ( 6133)
  covalent geometry    : angle       0.49683 /  0.26 ( 8314)
  hydrogen bonds       : bond        0.03361 /  2.26 (  286)
  hydrogen bonds       : angle       4.48938 /  3.16 (  849)
  Misc. bond           : bond        0.00276 /  0.13 (    2)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 72
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 GLN cc_start: 0.6347 (tt0) cc_final: 0.4952 (mt0)
REVERT: A  152 ILE cc_start: 0.8171 (mt) cc_final: 0.7845 (mt)
REVERT: A  198 ILE cc_start: 0.8566 (mm) cc_final: 0.8283 (mm)
REVERT: A  243 ASN cc_start: 0.4576 (t0) cc_final: 0.3987 (t0)
REVERT: A  353 MET cc_start: 0.6090 (tpp) cc_final: 0.5617 (mtt)
REVERT: B   42 LYS cc_start: 0.6229 (mtmt) cc_final: 0.5951 (mtpt)
REVERT: B  120 LYS cc_start: 0.7145 (mtpt) cc_final: 0.6778 (mtpt)
REVERT: B  153 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7553 (mp)
REVERT: B  313 MET cc_start: 0.7434 (OUTLIER) cc_final: 0.7089 (ptp)
REVERT: B  406 LYS cc_start: 0.6383 (mmtm) cc_final: 0.5909 (mmtp)
  outliers start: 20
  outliers final: 13
  residues processed: 85
  average time/residue: 0.0671
  time to fit residues: 7.9236
Evaluate side-chains
  85 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue  116 LYS
Chi-restraints excluded: chain A residue  135 SER
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain B residue   45 SER
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  313 MET
Chi-restraints excluded: chain B residue  416 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 57 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 1 optimal weight:    6.9990
   chunk 14 optimal weight:    4.9990
   chunk 26 optimal weight:    0.0670
   chunk 11 optimal weight:    1.9990
   chunk 50 optimal weight:    0.4980
   chunk 18 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.8522

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.198688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.167055 restraints weight = 7221.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.166672 restraints weight = 7192.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.167316 restraints weight = 6893.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.167957 restraints weight = 5751.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.168715 restraints weight = 5250.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6953
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6135  Z= 0.101
  Angle     :  0.477   6.886   8314  Z= 0.245
  Chirality :  0.042   0.143    951
  Planarity :  0.003   0.035   1068
  Dihedral  :  4.615  32.271    830
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 14.74 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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:  1.39 (0.31), residues: 762
  helix:  2.33 (0.28), residues: 333
  sheet:  0.79 (0.50), residues: 122
  loop : -0.63 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 191 
 TYR   0.008   0.001   TYR B 102 
 PHE   0.010   0.001   PHE A 311 
 TRP   0.004   0.001   TRP A  21 
 HIS   0.003   0.001   HIS B 367 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00226 /  0.10 ( 6133)
  covalent geometry    : angle       0.47667 /  0.24 ( 8314)
  hydrogen bonds       : bond        0.03154 /  2.12 (  286)
  hydrogen bonds       : angle       4.31808 /  3.03 (  849)
  Misc. bond           : bond        0.00235 /  0.11 (    2)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 76
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 GLN cc_start: 0.6470 (tt0) cc_final: 0.5178 (mt0)
REVERT: A   27 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6696 (pm20)
REVERT: A  152 ILE cc_start: 0.8111 (mt) cc_final: 0.7824 (mt)
REVERT: A  243 ASN cc_start: 0.4646 (t0) cc_final: 0.4095 (t0)
REVERT: B  120 LYS cc_start: 0.7114 (mtpt) cc_final: 0.6458 (tptt)
REVERT: B  124 GLU cc_start: 0.6990 (tm-30) cc_final: 0.5989 (mt-10)
REVERT: B  153 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7461 (mp)
REVERT: B  313 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.7169 (ptp)
REVERT: B  387 ARG cc_start: 0.6866 (mtt90) cc_final: 0.6282 (mtp180)
REVERT: B  406 LYS cc_start: 0.6395 (mmtm) cc_final: 0.5889 (mmtp)
  outliers start: 25
  outliers final: 13
  residues processed: 95
  average time/residue: 0.0717
  time to fit residues: 9.3152
Evaluate side-chains
  89 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue  116 LYS
Chi-restraints excluded: chain A residue  149 MET
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  414 TYR
Chi-restraints excluded: chain B residue   45 SER
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  313 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 19 optimal weight:    5.9990
   chunk 66 optimal weight:    3.9990
   chunk 48 optimal weight:   10.0000
   chunk 4 optimal weight:    1.9990
   chunk 39 optimal weight:    9.9990
   chunk 13 optimal weight:    9.9990
   chunk 53 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   chunk 12 optimal weight:    6.9990
   overall best weight:    1.1384

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.200223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.168564 restraints weight = 7086.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.169358 restraints weight = 7100.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.169725 restraints weight = 6846.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.170270 restraints weight = 5589.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.171525 restraints weight = 4884.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6971
moved from start:          0.1883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6135  Z= 0.111
  Angle     :  0.489   7.474   8314  Z= 0.252
  Chirality :  0.042   0.153    951
  Planarity :  0.003   0.038   1068
  Dihedral  :  4.617  32.586    830
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 14.44 %
    Favored  : 81.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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:  1.37 (0.31), residues: 762
  helix:  2.36 (0.28), residues: 333
  sheet:  0.72 (0.50), residues: 122
  loop : -0.66 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 191 
 TYR   0.009   0.001   TYR B 102 
 PHE   0.013   0.001   PHE A 311 
 TRP   0.004   0.001   TRP A  21 
 HIS   0.003   0.001   HIS B 367 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00250 /  0.11 ( 6133)
  covalent geometry    : angle       0.48942 /  0.25 ( 8314)
  hydrogen bonds       : bond        0.03313 /  2.25 (  286)
  hydrogen bonds       : angle       4.36144 /  3.06 (  849)
  Misc. bond           : bond        0.00260 /  0.12 (    2)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 76
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 GLN cc_start: 0.6570 (tt0) cc_final: 0.5196 (mt0)
REVERT: A   27 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6750 (pm20)
REVERT: A  243 ASN cc_start: 0.4558 (t0) cc_final: 0.4056 (t0)
REVERT: A  353 MET cc_start: 0.5974 (tpp) cc_final: 0.5681 (mtt)
REVERT: B  120 LYS cc_start: 0.7149 (mtpt) cc_final: 0.6733 (mtpt)
REVERT: B  124 GLU cc_start: 0.6976 (tm-30) cc_final: 0.5942 (mt-10)
REVERT: B  147 SER cc_start: 0.8301 (m) cc_final: 0.8047 (p)
REVERT: B  153 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7562 (mp)
REVERT: B  313 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.7184 (ptp)
REVERT: B  387 ARG cc_start: 0.6760 (mtt90) cc_final: 0.6332 (mtp180)
REVERT: B  406 LYS cc_start: 0.6383 (mmtm) cc_final: 0.5877 (mmtp)
  outliers start: 24
  outliers final: 16
  residues processed: 95
  average time/residue: 0.0739
  time to fit residues: 9.5276
Evaluate side-chains
  92 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue  135 SER
Chi-restraints excluded: chain A residue  149 MET
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  414 TYR
Chi-restraints excluded: chain B residue   45 SER
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  313 MET
Chi-restraints excluded: chain B residue  416 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9990
   chunk 35 optimal weight:    8.9990
   chunk 38 optimal weight:    9.9990
   chunk 8 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0170
   chunk 74 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   overall best weight:    0.9222

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 292 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.197368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.162298 restraints weight = 7223.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.164692 restraints weight = 5543.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.166481 restraints weight = 4683.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.167466 restraints weight = 4184.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.168210 restraints weight = 3883.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6972
moved from start:          0.2027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6135  Z= 0.101
  Angle     :  0.476   7.310   8314  Z= 0.245
  Chirality :  0.042   0.149    951
  Planarity :  0.003   0.037   1068
  Dihedral  :  4.545  31.336    830
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 15.81 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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:  1.37 (0.31), residues: 762
  helix:  2.35 (0.28), residues: 337
  sheet:  0.72 (0.50), residues: 122
  loop : -0.70 (0.34), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  44 
 TYR   0.007   0.001   TYR A 199 
 PHE   0.012   0.001   PHE A 311 
 TRP   0.004   0.001   TRP B  98 
 HIS   0.003   0.001   HIS B 367 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00226 /  0.10 ( 6133)
  covalent geometry    : angle       0.47591 /  0.24 ( 8314)
  hydrogen bonds       : bond        0.03092 /  2.07 (  286)
  hydrogen bonds       : angle       4.31319 /  3.03 (  849)
  Misc. bond           : bond        0.00221 /  0.11 (    2)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 76
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 GLN cc_start: 0.6496 (tt0) cc_final: 0.5146 (mt0)
REVERT: A   27 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6546 (pm20)
REVERT: A   29 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7395 (mmmt)
REVERT: A  239 VAL cc_start: 0.6307 (t) cc_final: 0.6087 (p)
REVERT: A  243 ASN cc_start: 0.4645 (t0) cc_final: 0.4165 (t0)
REVERT: A  353 MET cc_start: 0.6132 (tpp) cc_final: 0.5769 (mtt)
REVERT: B  120 LYS cc_start: 0.7206 (mtpt) cc_final: 0.6576 (tptt)
REVERT: B  124 GLU cc_start: 0.6929 (tm-30) cc_final: 0.5945 (mt-10)
REVERT: B  147 SER cc_start: 0.8267 (m) cc_final: 0.8020 (p)
REVERT: B  153 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7541 (mp)
REVERT: B  313 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.7211 (ptp)
REVERT: B  387 ARG cc_start: 0.6805 (mtt90) cc_final: 0.6337 (mtp180)
REVERT: B  406 LYS cc_start: 0.6341 (mmtm) cc_final: 0.5826 (mmtp)
  outliers start: 21
  outliers final: 13
  residues processed: 93
  average time/residue: 0.0702
  time to fit residues: 8.9298
Evaluate side-chains
  91 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 74
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue  135 SER
Chi-restraints excluded: chain A residue  149 MET
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  414 TYR
Chi-restraints excluded: chain B residue   45 SER
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  313 MET
Chi-restraints excluded: chain B residue  416 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 30 optimal weight:   10.0000
   chunk 17 optimal weight:    7.9990
   chunk 66 optimal weight:    0.4980
   chunk 48 optimal weight:    7.9990
   chunk 55 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 34 optimal weight:    9.9990
   chunk 6 optimal weight:    9.9990
   overall best weight:    1.6986

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.197519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.168771 restraints weight = 7159.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.167622 restraints weight = 9192.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.169018 restraints weight = 8639.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.169088 restraints weight = 6664.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.169187 restraints weight = 6189.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7085
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6135  Z= 0.138
  Angle     :  0.525   8.545   8314  Z= 0.272
  Chirality :  0.043   0.147    951
  Planarity :  0.003   0.035   1068
  Dihedral  :  4.729  33.312    830
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 15.50 %
    Favored  : 80.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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:  1.18 (0.30), residues: 762
  helix:  2.24 (0.28), residues: 336
  sheet:  0.63 (0.50), residues: 116
  loop : -0.81 (0.33), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 247 
 TYR   0.011   0.001   TYR B 102 
 PHE   0.012   0.001   PHE A 311 
 TRP   0.005   0.001   TRP B  98 
 HIS   0.004   0.001   HIS B 189 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00322 /  0.14 ( 6133)
  covalent geometry    : angle       0.52473 /  0.27 ( 8314)
  hydrogen bonds       : bond        0.03730 /  2.53 (  286)
  hydrogen bonds       : angle       4.54370 /  3.20 (  849)
  Misc. bond           : bond        0.00327 /  0.16 (    2)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 79
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 GLN cc_start: 0.6744 (tt0) cc_final: 0.5497 (mt0)
REVERT: A   27 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6810 (pm20)
REVERT: A   32 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6643 (mt)
REVERT: A  198 ILE cc_start: 0.8544 (mm) cc_final: 0.8290 (mm)
REVERT: A  243 ASN cc_start: 0.4467 (t0) cc_final: 0.4156 (t0)
REVERT: B  120 LYS cc_start: 0.7277 (mtpt) cc_final: 0.6901 (mtpt)
REVERT: B  124 GLU cc_start: 0.6902 (tm-30) cc_final: 0.6042 (mt-10)
REVERT: B  153 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7720 (mp)
REVERT: B  313 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6972 (ptp)
REVERT: B  387 ARG cc_start: 0.6958 (mtt90) cc_final: 0.6674 (mtp180)
REVERT: B  406 LYS cc_start: 0.6342 (mmtm) cc_final: 0.5840 (mmtp)
  outliers start: 24
  outliers final: 18
  residues processed: 99
  average time/residue: 0.0604
  time to fit residues: 8.3621
Evaluate side-chains
  95 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 73
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue  135 SER
Chi-restraints excluded: chain A residue  149 MET
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  341 PHE
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  414 TYR
Chi-restraints excluded: chain B residue   45 SER
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  313 MET
Chi-restraints excluded: chain B residue  416 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 57 optimal weight:    0.8980
   chunk 59 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 26 optimal weight:    7.9990
   chunk 23 optimal weight:    7.9990
   chunk 34 optimal weight:    0.9980
   chunk 7 optimal weight:    5.9990
   chunk 52 optimal weight:    0.0970
   chunk 55 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 18 optimal weight:    6.9990
   overall best weight:    0.7178

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.195425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.163161 restraints weight = 7170.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.162555 restraints weight = 6629.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.163361 restraints weight = 6406.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.163637 restraints weight = 5552.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.163847 restraints weight = 5213.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7068
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6135  Z= 0.100
  Angle     :  0.492   8.031   8314  Z= 0.251
  Chirality :  0.042   0.167    951
  Planarity :  0.003   0.035   1068
  Dihedral  :  4.529  30.890    830
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 16.72 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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:  1.32 (0.30), residues: 762
  helix:  2.30 (0.28), residues: 339
  sheet:  0.67 (0.50), residues: 122
  loop : -0.71 (0.33), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 191 
 TYR   0.008   0.001   TYR A 199 
 PHE   0.014   0.001   PHE A 311 
 TRP   0.004   0.001   TRP A  21 
 HIS   0.004   0.001   HIS B 367 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00221 /  0.10 ( 6133)
  covalent geometry    : angle       0.49232 /  0.25 ( 8314)
  hydrogen bonds       : bond        0.03094 /  2.06 (  286)
  hydrogen bonds       : angle       4.41740 /  3.14 (  849)
  Misc. bond           : bond        0.00199 /  0.09 (    2)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 GLN cc_start: 0.6633 (tt0) cc_final: 0.5471 (mt0)
REVERT: A   27 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6851 (pm20)
REVERT: A  198 ILE cc_start: 0.8515 (mm) cc_final: 0.8254 (mm)
REVERT: A  243 ASN cc_start: 0.4524 (t0) cc_final: 0.4164 (t0)
REVERT: B   42 LYS cc_start: 0.6308 (mtmt) cc_final: 0.6073 (mtpt)
REVERT: B  120 LYS cc_start: 0.7258 (mtpt) cc_final: 0.6878 (mtpt)
REVERT: B  124 GLU cc_start: 0.6815 (tm-30) cc_final: 0.5978 (mt-10)
REVERT: B  387 ARG cc_start: 0.6956 (mtt90) cc_final: 0.6668 (mtp180)
REVERT: B  406 LYS cc_start: 0.6269 (mmtm) cc_final: 0.6068 (mmtm)
  outliers start: 15
  outliers final: 12
  residues processed: 88
  average time/residue: 0.0569
  time to fit residues: 6.9327
Evaluate side-chains
  85 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue  135 SER
Chi-restraints excluded: chain A residue  149 MET
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  414 TYR
Chi-restraints excluded: chain B residue   45 SER
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  416 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 30 optimal weight:    9.9990
   chunk 73 optimal weight:    0.6980
   chunk 50 optimal weight:    0.0010
   chunk 48 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 22 optimal weight:    8.9990
   chunk 28 optimal weight:    3.9990
   chunk 52 optimal weight:    0.2980
   chunk 8 optimal weight:    4.9990
   overall best weight:    0.9990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.202095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.174547 restraints weight = 7079.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.173262 restraints weight = 8881.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.174148 restraints weight = 8609.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.174335 restraints weight = 7188.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.174536 restraints weight = 6627.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7031
moved from start:          0.2341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6135  Z= 0.107
  Angle     :  0.492   8.031   8314  Z= 0.254
  Chirality :  0.042   0.151    951
  Planarity :  0.003   0.035   1068
  Dihedral  :  4.493  31.009    830
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 17.02 %
    Favored  : 80.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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:  1.30 (0.30), residues: 762
  helix:  2.32 (0.28), residues: 339
  sheet:  0.67 (0.50), residues: 122
  loop : -0.78 (0.33), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  44 
 TYR   0.008   0.001   TYR B 102 
 PHE   0.013   0.001   PHE A 311 
 TRP   0.004   0.001   TRP A  21 
 HIS   0.003   0.001   HIS B 367 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00240 /  0.11 ( 6133)
  covalent geometry    : angle       0.49232 /  0.25 ( 8314)
  hydrogen bonds       : bond        0.03170 /  2.11 (  286)
  hydrogen bonds       : angle       4.44762 /  3.19 (  849)
  Misc. bond           : bond        0.00231 /  0.11 (    2)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 GLN cc_start: 0.6689 (tt0) cc_final: 0.5583 (mt0)
REVERT: A   27 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6859 (pm20)
REVERT: A  198 ILE cc_start: 0.8519 (mm) cc_final: 0.8242 (mm)
REVERT: A  243 ASN cc_start: 0.4541 (t0) cc_final: 0.4208 (t0)
REVERT: B   42 LYS cc_start: 0.6323 (mtmt) cc_final: 0.6071 (mtpt)
REVERT: B  120 LYS cc_start: 0.7264 (mtpt) cc_final: 0.6886 (mtpt)
REVERT: B  124 GLU cc_start: 0.6802 (tm-30) cc_final: 0.6005 (mt-10)
REVERT: B  387 ARG cc_start: 0.6977 (mtt90) cc_final: 0.6708 (mtp180)
  outliers start: 15
  outliers final: 13
  residues processed: 88
  average time/residue: 0.0678
  time to fit residues: 8.2041
Evaluate side-chains
  87 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue  135 SER
Chi-restraints excluded: chain A residue  149 MET
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  414 TYR
Chi-restraints excluded: chain B residue   45 SER
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  416 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 64 optimal weight:    0.0070
   chunk 30 optimal weight:   10.0000
   chunk 76 optimal weight:    7.9990
   chunk 75 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 46 optimal weight:    0.0770
   chunk 59 optimal weight:    4.9990
   chunk 61 optimal weight:    4.9990
   chunk 63 optimal weight:    0.8980
   chunk 66 optimal weight:    0.0370
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.4036

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.210314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.181503 restraints weight = 6919.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.180824 restraints weight = 6827.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.181176 restraints weight = 6264.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.181713 restraints weight = 5817.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.181923 restraints weight = 5344.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7002
moved from start:          0.2403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6135  Z= 0.090
  Angle     :  0.470   6.556   8314  Z= 0.241
  Chirality :  0.042   0.151    951
  Planarity :  0.003   0.037   1068
  Dihedral  :  4.300  30.842    830
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 17.33 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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:  1.39 (0.31), residues: 762
  helix:  2.43 (0.28), residues: 338
  sheet:  0.69 (0.50), residues: 122
  loop : -0.76 (0.33), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  44 
 TYR   0.006   0.001   TYR A 199 
 PHE   0.013   0.001   PHE A 311 
 TRP   0.005   0.001   TRP B  98 
 HIS   0.004   0.001   HIS B 367 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00190 /  0.09 ( 6133)
  covalent geometry    : angle       0.47008 /  0.24 ( 8314)
  hydrogen bonds       : bond        0.02759 /  1.82 (  286)
  hydrogen bonds       : angle       4.31358 /  3.10 (  849)
  Misc. bond           : bond        0.00133 /  0.06 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 956.57 seconds
wall clock time: 17 minutes 16.57 seconds (1036.57 seconds total)