Starting phenix.real_space_refine
on Sat Jul  4 19:44:59 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8adg_15362/07_2026/8adg_15362.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8adg_15362/07_2026/8adg_15362.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/8adg_15362/07_2026/8adg_15362.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8adg_15362/07_2026/8adg_15362.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8adg_15362/07_2026/8adg_15362.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8adg_15362/07_2026/8adg_15362.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8adg_15362/07_2026/8adg_15362.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8adg_15362/07_2026/8adg_15362.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.051
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
     S      32      5.16       5
     C    7440      2.51       5
     N    2019      2.21       5
     O    2317      1.98       5
     H   11383      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s

  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: 23191
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 12167
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 787, 12167
          Classifications: {'peptide': 787}
          Link IDs: {'PTRANS': 29, 'TRANS': 757}
    Chain: "B"
      Number of atoms: 5393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 361, 5393
          Classifications: {'peptide': 361}
          Link IDs: {'PTRANS': 11, 'TRANS': 349}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 845
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 6, 'TRANS': 51}
    Chain: "D"
      Number of atoms: 3348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 3348
          Classifications: {'peptide': 209}
          Link IDs: {'PTRANS': 12, 'TRANS': 196}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1292
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1292
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 5, 'TRANS': 78}
    Chain: "F"
      Number of atoms: 146
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 146
          Classifications: {'peptide': 7}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 6}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'UX8:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 3.73, per 1000 atoms: 0.16
  Number of scatterers: 23191
  At special positions: 0
  Unit cell: (97.75, 133.45, 125.8, 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      32     16.00
     O    2317      8.00
     N    2019      7.00
     C    7440      6.00
     H   11383      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 690 " - pdb=" SG  CYS A 700 " distance=2.04

  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: 3.56
  Conformation dependent library (CDL) restraints added in 683.1 milliseconds
  

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2756

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 17 sheets defined
      24.2% alpha, 30.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 46
    Processing helix  chain 'A' and resid 55 through 69
    Processing helix  chain 'A' and resid 106 through 118
    Processing helix  chain 'A' and resid 129 through 145
    Processing helix  chain 'A' and resid 189 through 194
    Processing helix  chain 'A' and resid 195 through 197
      No H-bonds generated for 'chain 'A' and resid 195 through 197'
    Processing helix  chain 'A' and resid 215 through 232
    Processing helix  chain 'A' and resid 280 through 286
      removed outlier: 4.019A  pdb=" N   GLN A 286 " --> pdb=" O   ALA A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 289
      No H-bonds generated for 'chain 'A' and resid 287 through 289'
    Processing helix  chain 'A' and resid 298 through 314
    Processing helix  chain 'A' and resid 361 through 367
      removed outlier: 3.795A  pdb=" N   LEU A 365 " --> pdb=" O   LYS A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 393
      removed outlier: 4.042A  pdb=" N   GLY A 393 " --> pdb=" O   LEU A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 452
    Processing helix  chain 'A' and resid 497 through 500
      removed outlier: 3.980A  pdb=" N   ASP A 500 " --> pdb=" O   ASP A 497 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 497 through 500'
    Processing helix  chain 'A' and resid 542 through 552
      removed outlier: 3.607A  pdb=" N   TYR A 550 " --> pdb=" O   TRP A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 691 through 695
      removed outlier: 3.616A  pdb=" N   GLY A 695 " --> pdb=" O   THR A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 729 through 731
      No H-bonds generated for 'chain 'A' and resid 729 through 731'
    Processing helix  chain 'C' and resid 31 through 39
      removed outlier: 4.039A  pdb=" N   VAL C  35 " --> pdb=" O   TYR C  31 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   SER C  36 " --> pdb=" O   LYS C  32 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLU C  39 " --> pdb=" O   VAL C  35 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 31 through 46
    Processing helix  chain 'D' and resid 47 through 62
      removed outlier: 4.080A  pdb=" N   ALA D  51 " --> pdb=" O   ASN D  47 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 67 through 82
    Processing helix  chain 'D' and resid 84 through 99
    Processing helix  chain 'D' and resid 102 through 104
      No H-bonds generated for 'chain 'D' and resid 102 through 104'
    Processing helix  chain 'D' and resid 105 through 121
    Processing helix  chain 'D' and resid 137 through 154
    Processing helix  chain 'D' and resid 159 through 189
      removed outlier: 3.502A  pdb=" N   GLU D 187 " --> pdb=" O   GLU D 183 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 190 through 205
      removed outlier: 3.669A  pdb=" N   VAL D 195 " --> pdb=" O   TRP D 191 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 208 through 225
      removed outlier: 3.659A  pdb=" N   ARG D 212 " --> pdb=" O   THR D 208 " (cutoff:3.500A)
      Proline residue:  D 216  - end of helix
    Processing helix  chain 'D' and resid 227 through 242
      removed outlier: 3.529A  pdb=" N   LYS D 233 " --> pdb=" O   ALA D 229 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 42 through 46
      removed outlier: 3.815A  pdb=" N   ILE E  46 " --> pdb=" O   VAL E  43 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 59
    Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32
      removed outlier: 7.357A  pdb=" N   HIS A  30 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 8.345A  pdb=" N   VAL A  88 " --> pdb=" O   HIS A  30 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   GLU A  32 " --> pdb=" O   VAL A  88 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   GLU A  90 " --> pdb=" O   GLU A  32 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ASP A  74 " --> pdb=" O   LYS A  89 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100
      removed outlier: 4.428A  pdb=" N   ILE A  94 " --> pdb=" O   VAL A 163 " (cutoff:3.500A)
      removed outlier: 7.923A  pdb=" N   LEU A 165 " --> pdb=" O   ILE A  94 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   SER A  96 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   LEU A 167 " --> pdb=" O   SER A  96 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   THR A  98 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.969A  pdb=" N   PHE A 169 " --> pdb=" O   THR A  98 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   SER A 100 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183
      removed outlier: 7.460A  pdb=" N   VAL A 256 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   ILE A 180 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 7.359A  pdb=" N   VAL A 258 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   ILE A 182 " --> pdb=" O   VAL A 258 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   ILE A 260 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   THR A 261 " --> pdb=" O   ILE A 240 " (cutoff:3.500A)
      removed outlier: 5.546A  pdb=" N   ILE A 240 " --> pdb=" O   THR A 261 " (cutoff:3.500A)
      removed outlier: 8.820A  pdb=" N   SER B 193 " --> pdb=" O   THR A 243 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   VAL A 245 " --> pdb=" O   SER B 193 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 270
      removed outlier: 6.251A  pdb=" N   LYS A 267 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 7.743A  pdb=" N   LEU A 337 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
      removed outlier: 8.451A  pdb=" N   SER A 269 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 12.623A  pdb=" N   VAL A 339 " --> pdb=" O   SER A 269 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   SER A 274 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
      removed outlier: 8.075A  pdb=" N   ALA A 343 " --> pdb=" O   SER A 274 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   ASN A 276 " --> pdb=" O   ALA A 343 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 270
      removed outlier: 6.251A  pdb=" N   LYS A 267 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 7.743A  pdb=" N   LEU A 337 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
      removed outlier: 8.451A  pdb=" N   SER A 269 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 12.623A  pdb=" N   VAL A 339 " --> pdb=" O   SER A 269 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 355
      removed outlier: 4.715A  pdb=" N   VAL A 349 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
      removed outlier: 7.557A  pdb=" N   VAL A 414 " --> pdb=" O   VAL A 349 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   LYS A 351 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 7.988A  pdb=" N   TYR A 416 " --> pdb=" O   LYS A 351 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   ARG A 353 " --> pdb=" O   TYR A 416 " (cutoff:3.500A)
      removed outlier: 7.780A  pdb=" N   VAL A 418 " --> pdb=" O   ARG A 353 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   GLU A 355 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
      removed outlier: 7.716A  pdb=" N   GLU A 420 " --> pdb=" O   GLU A 355 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   THR A 397 " --> pdb=" O   LYS A 419 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 3 through 5
      removed outlier: 3.519A  pdb=" N   ALA A 770 " --> pdb=" O   GLN A 789 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   MET A 768 " --> pdb=" O   PHE A 791 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   THR A 735 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
      removed outlier: 5.159A  pdb=" N   TYR A 608 " --> pdb=" O   THR A 600 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   GLY A 590 " --> pdb=" O   TYR A 618 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   TYR A 574 " --> pdb=" O   GLY A 597 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 45 through 50
      removed outlier: 5.157A  pdb=" N   THR B  46 " --> pdb=" O   THR B 391 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   THR B 391 " --> pdb=" O   THR B  46 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   TRP B  48 " --> pdb=" O   SER B 389 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   LEU B 378 " --> pdb=" O   ILE B 390 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 67
      removed outlier: 6.610A  pdb=" N   VAL B  81 " --> pdb=" O   SER B  94 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   SER B  94 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   ALA B  83 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 111 through 117
      removed outlier: 6.245A  pdb=" N   GLY B 114 " --> pdb=" O   GLY B 125 " (cutoff:3.500A)
      removed outlier: 5.104A  pdb=" N   GLY B 125 " --> pdb=" O   GLY B 114 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   GLN B 130 " --> pdb=" O   SER B 126 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 158
      removed outlier: 3.765A  pdb=" N   TRP B 183 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 202
      removed outlier: 6.733A  pdb=" N   VAL B 216 " --> pdb=" O   GLN B 229 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   GLN B 229 " --> pdb=" O   VAL B 216 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   ALA B 218 " --> pdb=" O   ILE B 227 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 254
      removed outlier: 3.517A  pdb=" N   ALA B 269 " --> pdb=" O   TRP B 279 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   TRP B 279 " --> pdb=" O   ALA B 269 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   ASP B 271 " --> pdb=" O   ILE B 277 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   ILE B 277 " --> pdb=" O   ASP B 271 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 290 through 292
      removed outlier: 3.543A  pdb=" N   LEU B 298 " --> pdb=" O   MET B 306 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   TRP B 317 " --> pdb=" O   ALA B 307 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 333
      removed outlier: 3.807A  pdb=" N   ALA B 358 " --> pdb=" O   TRP B 348 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 32 through 35
      removed outlier: 4.036A  pdb=" N   MET E  64 " --> pdb=" O   PHE E  74 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 35

    525 hydrogen bonds defined for protein.
    1467 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: 5.26

  Time building geometry restraints manager: 2.93 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 11339
        1.03 -     1.23: 59
        1.23 -     1.42: 5210
        1.42 -     1.61: 6781
        1.61 -     1.81: 62
  Bond restraints: 23451
  Sorted by residual:
  bond pdb=" CG  PRO B  34 "
       pdb=" CD  PRO B  34 "
    ideal  model  delta    sigma   weight residual
    1.503  1.047  0.456 3.40e-02 8.65e+02 1.80e+02
  bond pdb=" C   UX8 F   3 "
       pdb=" O   UX8 F   3 "
    ideal  model  delta    sigma   weight residual
    1.231  1.395 -0.164 2.00e-02 2.50e+03 6.74e+01
  bond pdb=" CZ2 TRP F   1 "
       pdb=" HZ2 TRP F   1 "
    ideal  model  delta    sigma   weight residual
    0.930  1.090 -0.160 2.00e-02 2.50e+03 6.40e+01
  bond pdb=" CZ3 UX8 F   3 "
       pdb=" HZ3 UX8 F   3 "
    ideal  model  delta    sigma   weight residual
    0.930  1.080 -0.150 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" CD1 TRP F   7 "
       pdb=" HD1 TRP F   7 "
    ideal  model  delta    sigma   weight residual
    0.930  1.080 -0.150 2.00e-02 2.50e+03 5.65e+01
  ... (remaining 23446 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.92: 42151
        4.92 -     9.83: 11
        9.83 -    14.75: 5
       14.75 -    19.67: 3
       19.67 -    24.59: 1
  Bond angle restraints: 42171
  Sorted by residual:
  angle pdb=" N   PRO B  34 "
        pdb=" CD  PRO B  34 "
        pdb=" CG  PRO B  34 "
      ideal   model   delta    sigma   weight residual
     103.20   78.61   24.59 1.50e+00 4.44e-01 2.69e+02
  angle pdb=" CA  PRO B  34 "
        pdb=" CB  PRO B  34 "
        pdb=" CG  PRO B  34 "
      ideal   model   delta    sigma   weight residual
     104.50   87.73   16.77 1.90e+00 2.77e-01 7.79e+01
  angle pdb=" CA  PRO B  34 "
        pdb=" N   PRO B  34 "
        pdb=" CD  PRO B  34 "
      ideal   model   delta    sigma   weight residual
     112.00  100.72   11.28 1.40e+00 5.10e-01 6.49e+01
  angle pdb=" CA  LYS F   5 "
        pdb=" CB  LYS F   5 "
        pdb=" HB2 LYS F   5 "
      ideal   model   delta    sigma   weight residual
     109.00   90.49   18.51 3.00e+00 1.11e-01 3.81e+01
  angle pdb=" CG  LYS F   5 "
        pdb=" CB  LYS F   5 "
        pdb=" HB2 LYS F   5 "
      ideal   model   delta    sigma   weight residual
     108.00   90.51   17.49 3.00e+00 1.11e-01 3.40e+01
  ... (remaining 42166 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 10127
       17.96 -    35.91: 726
       35.91 -    53.87: 197
       53.87 -    71.82: 46
       71.82 -    89.78: 14
  Dihedral angle restraints: 11110
    sinusoidal: 5984
      harmonic: 5126
  Sorted by residual:
  dihedral pdb=" CD2 TRP F   1 "
           pdb=" CE2 TRP F   1 "
           pdb=" CZ2 TRP F   1 "
           pdb=" HZ2 TRP F   1 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -125.33  -54.67     0      5.00e+00 4.00e-02 1.20e+02
  dihedral pdb=" CB  CYS A 690 "
           pdb=" SG  CYS A 690 "
           pdb=" SG  CYS A 700 "
           pdb=" CB  CYS A 700 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -131.25   45.25     1      1.00e+01 1.00e-02 2.84e+01
  dihedral pdb=" CA  LEU A 699 "
           pdb=" C   LEU A 699 "
           pdb=" N   CYS A 700 "
           pdb=" CA  CYS A 700 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.12  -19.88     0      5.00e+00 4.00e-02 1.58e+01
  ... (remaining 11107 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 994
       0.029 -    0.058: 521
       0.058 -    0.087: 115
       0.087 -    0.116: 109
       0.116 -    0.145: 44
  Chirality restraints: 1783
  Sorted by residual:
  chirality pdb=" CA  ILE C  67 "
            pdb=" N   ILE C  67 "
            pdb=" C   ILE C  67 "
            pdb=" CB  ILE C  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.25e-01
  chirality pdb=" CA  ILE B 296 "
            pdb=" N   ILE B 296 "
            pdb=" C   ILE B 296 "
            pdb=" CB  ILE B 296 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.90e-01
  chirality pdb=" CA  ILE E 104 "
            pdb=" N   ILE E 104 "
            pdb=" C   ILE E 104 "
            pdb=" CB  ILE E 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.89e-01
  ... (remaining 1780 not shown)

  Planarity restraints: 3593
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP F   1 "   -0.129 2.00e-02 2.50e+03   1.84e-01 1.27e+03
        pdb=" CG  TRP F   1 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 TRP F   1 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 TRP F   1 "    0.014 2.00e-02 2.50e+03
        pdb=" NE1 TRP F   1 "    0.107 2.00e-02 2.50e+03
        pdb=" CE2 TRP F   1 "    0.108 2.00e-02 2.50e+03
        pdb=" CE3 TRP F   1 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP F   1 "    0.183 2.00e-02 2.50e+03
        pdb=" CZ3 TRP F   1 "    0.068 2.00e-02 2.50e+03
        pdb=" CH2 TRP F   1 "    0.159 2.00e-02 2.50e+03
        pdb=" HD1 TRP F   1 "   -0.004 2.00e-02 2.50e+03
        pdb=" HE1 TRP F   1 "    0.155 2.00e-02 2.50e+03
        pdb=" HE3 TRP F   1 "   -0.078 2.00e-02 2.50e+03
        pdb=" HZ2 TRP F   1 "   -0.608 2.00e-02 2.50e+03
        pdb=" HZ3 TRP F   1 "    0.055 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 546 "   -0.034 2.00e-02 2.50e+03   2.19e-02 1.92e+01
        pdb=" CG  TRP A 546 "    0.074 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 546 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 546 "    0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 546 "    0.010 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 546 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 546 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 546 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 546 "   -0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 546 "   -0.011 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 546 "   -0.013 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 546 "   -0.003 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 546 "    0.004 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 546 "    0.001 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 546 "    0.000 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 546 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B  33 "   -0.042 5.00e-02 4.00e+02   5.77e-02 5.33e+00
        pdb=" N   PRO B  34 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO B  34 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B  34 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 3590 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.15: 591
        2.15 -     2.76: 42757
        2.76 -     3.37: 61231
        3.37 -     3.99: 81598
        3.99 -     4.60: 128113
  Nonbonded interactions: 314290
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP C  38 "
            pdb=" H   GLU C  39 "
     model   vdw
     1.533 2.450
  nonbonded pdb=" OD1 ASN E  96 "
            pdb=" H   SER E  98 "
     model   vdw
     1.584 2.450
  nonbonded pdb=" HD1 HIS A 533 "
            pdb=" OD1 ASP A 568 "
     model   vdw
     1.614 2.450
  nonbonded pdb=" O   ARG A 661 "
            pdb=" HG  SER A 769 "
     model   vdw
     1.614 2.450
  nonbonded pdb="HE21 GLN B 319 "
            pdb=" O   GLY B 354 "
     model   vdw
     1.620 2.450
  ... (remaining 314285 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.930
  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:             0.160
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.060
  Process input model:                     21.570
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
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      :  0.006   0.456  12071  Z= 0.232
  Angle     :  0.622  24.587  16405  Z= 0.351
  Chirality :  0.044   0.145   1783
  Planarity :  0.004   0.058   2158
  Dihedral  : 14.028  89.781   4366
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.21), residues: 1487
  helix:  2.32 (0.29), residues: 326
  sheet:  0.30 (0.25), residues: 445
  loop : -0.98 (0.21), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 583 
 TYR   0.015   0.001   TYR A 794 
 PHE   0.015   0.001   PHE A 791 
 TRP   0.072   0.002   TRP A 546 
 HIS   0.014   0.001   HIS D 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00603 /  0.23 (12068)
  covalent geometry    : angle       0.62218 /  0.35 (16403)
  SS BOND              : bond        0.00403 /  0.21 (    1)
  SS BOND              : angle       1.81828 /  1.07 (    2)
  hydrogen bonds       : bond        0.08422 /  5.21 (  521)
  hydrogen bonds       : angle       4.92835 /  3.54 ( 1467)
  Misc. bond           : bond        0.00139 /  0.07 (    2)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.645 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  520 ASN cc_start: 0.7563 (t0) cc_final: 0.7287 (t0)
REVERT: B  268 THR cc_start: 0.8547 (t) cc_final: 0.8294 (m)
REVERT: C   41 TYR cc_start: 0.6295 (p90) cc_final: 0.6046 (p90)
REVERT: D   93 ASP cc_start: 0.8091 (m-30) cc_final: 0.7728 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 1.0079
  time to fit residues: 149.9737
Evaluate side-chains
  110 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:    0.0980
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    1.4188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 244 GLN
A 561 GLN
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 230 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.172032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.127940 restraints weight = 35450.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 2.00
r_work: 0.3234 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3110 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.0572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  12071  Z= 0.172
  Angle     :  0.533   7.299  16405  Z= 0.284
  Chirality :  0.044   0.149   1783
  Planarity :  0.004   0.042   2158
  Dihedral  :  4.258  20.124   1651
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  5.70 %
    Favored  : 93.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.21), residues: 1487
  helix:  2.28 (0.28), residues: 326
  sheet:  0.36 (0.25), residues: 440
  loop : -1.00 (0.21), residues: 721

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 583 
 TYR   0.010   0.001   TYR A 787 
 PHE   0.015   0.001   PHE A 426 
 TRP   0.021   0.002   TRP A 546 
 HIS   0.006   0.001   HIS D 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00415 /  0.17 (12068)
  covalent geometry    : angle       0.53297 /  0.28 (16403)
  SS BOND              : bond        0.00394 /  0.21 (    1)
  SS BOND              : angle       1.65087 /  0.97 (    2)
  hydrogen bonds       : bond        0.04866 /  3.32 (  521)
  hydrogen bonds       : angle       4.66581 /  3.34 ( 1467)
  Misc. bond           : bond        0.00428 /  0.20 (    2)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 0.635 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  224 GLU cc_start: 0.6891 (mm-30) cc_final: 0.6648 (mm-30)
REVERT: A  286 GLN cc_start: 0.7456 (mp10) cc_final: 0.6524 (tm130)
REVERT: A  520 ASN cc_start: 0.8041 (t0) cc_final: 0.7569 (t0)
REVERT: B   70 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.8162 (t0)
REVERT: B  268 THR cc_start: 0.8520 (t) cc_final: 0.8252 (m)
REVERT: C   41 TYR cc_start: 0.6790 (p90) cc_final: 0.6167 (p90)
REVERT: C   76 VAL cc_start: 0.7880 (OUTLIER) cc_final: 0.7595 (p)
REVERT: D   93 ASP cc_start: 0.8218 (m-30) cc_final: 0.7742 (m-30)
  outliers start: 16
  outliers final: 10
  residues processed: 120
  average time/residue: 0.9948
  time to fit residues: 132.4064
Evaluate side-chains
  118 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  562 ASP
Chi-restraints excluded: chain A residue  702 SER
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain B residue   28 ASP
Chi-restraints excluded: chain B residue   70 ASN
Chi-restraints excluded: chain B residue  138 ASP
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain E residue   42 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 132 optimal weight:    0.9980
   chunk 146 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 129 optimal weight:    1.9990
   chunk 101 optimal weight:    2.9990
   chunk 56 optimal weight:    0.6980
   chunk 78 optimal weight:    0.0570
   chunk 85 optimal weight:    0.4980
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.8500

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 244 GLN
B 266 ASN
B 319 GLN
D 230 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.172342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.125990 restraints weight = 35254.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 2.20
r_work: 0.3230 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3100 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.0732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  12071  Z= 0.121
  Angle     :  0.485   6.724  16405  Z= 0.258
  Chirality :  0.042   0.146   1783
  Planarity :  0.004   0.042   2158
  Dihedral  :  4.115  18.426   1651
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 2.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  7.13 %
    Favored  : 91.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.31 (0.22), residues: 1487
  helix:  2.46 (0.29), residues: 327
  sheet:  0.33 (0.25), residues: 439
  loop : -0.95 (0.22), residues: 721

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 583 
 TYR   0.012   0.001   TYR D  79 
 PHE   0.015   0.001   PHE A 426 
 TRP   0.012   0.001   TRP B 348 
 HIS   0.006   0.001   HIS B 347 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.12 (12068)
  covalent geometry    : angle       0.48485 /  0.26 (16403)
  SS BOND              : bond        0.00299 /  0.16 (    1)
  SS BOND              : angle       1.59550 /  0.94 (    2)
  hydrogen bonds       : bond        0.04150 /  2.86 (  521)
  hydrogen bonds       : angle       4.47773 /  3.20 ( 1467)
  Misc. bond           : bond        0.00455 /  0.22 (    2)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 0.573 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7399 (mp10) cc_final: 0.6429 (tm130)
REVERT: A  520 ASN cc_start: 0.7984 (t0) cc_final: 0.7449 (t0)
REVERT: A  614 ASP cc_start: 0.8314 (m-30) cc_final: 0.8015 (m-30)
REVERT: B   70 ASN cc_start: 0.8418 (OUTLIER) cc_final: 0.8153 (t0)
REVERT: B  266 ASN cc_start: 0.7022 (OUTLIER) cc_final: 0.6602 (p0)
REVERT: B  268 THR cc_start: 0.8512 (t) cc_final: 0.8198 (m)
REVERT: C   41 TYR cc_start: 0.6793 (p90) cc_final: 0.6206 (p90)
REVERT: C   76 VAL cc_start: 0.7811 (OUTLIER) cc_final: 0.7524 (p)
REVERT: D   93 ASP cc_start: 0.8221 (m-30) cc_final: 0.7744 (m-30)
  outliers start: 16
  outliers final: 10
  residues processed: 121
  average time/residue: 1.0140
  time to fit residues: 136.1942
Evaluate side-chains
  119 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  562 ASP
Chi-restraints excluded: chain A residue  702 SER
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain B residue   28 ASP
Chi-restraints excluded: chain B residue   70 ASN
Chi-restraints excluded: chain B residue  138 ASP
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  255 ASN
Chi-restraints excluded: chain B residue  266 ASN
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain D residue  134 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   chunk 96 optimal weight:    2.9990
   chunk 26 optimal weight:    0.3980
   chunk 78 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   chunk 1 optimal weight:   30.0000
   chunk 93 optimal weight:    2.9990
   chunk 4 optimal weight:   20.0000
   chunk 22 optimal weight:    2.9990
   chunk 66 optimal weight:    5.9990
   overall best weight:    2.0786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 244 GLN
B 359 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.170396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.125185 restraints weight = 35487.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 2.13
r_work: 0.3193 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.0900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  12071  Z= 0.228
  Angle     :  0.558   8.383  16405  Z= 0.297
  Chirality :  0.045   0.148   1783
  Planarity :  0.004   0.046   2158
  Dihedral  :  4.377  19.922   1651
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  :  8.23 %
    Favored  : 90.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.01 (0.21), residues: 1487
  helix:  2.08 (0.28), residues: 330
  sheet:  0.11 (0.24), residues: 447
  loop : -1.07 (0.21), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 583 
 TYR   0.012   0.002   TYR D  79 
 PHE   0.017   0.002   PHE A 791 
 TRP   0.011   0.002   TRP B 143 
 HIS   0.006   0.001   HIS B 347 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00553 /  0.23 (12068)
  covalent geometry    : angle       0.55750 /  0.30 (16403)
  SS BOND              : bond        0.00445 /  0.23 (    1)
  SS BOND              : angle       1.65317 /  0.97 (    2)
  hydrogen bonds       : bond        0.05028 /  3.49 (  521)
  hydrogen bonds       : angle       4.62322 /  3.30 ( 1467)
  Misc. bond           : bond        0.00439 /  0.21 (    2)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 ASP cc_start: 0.8430 (p0) cc_final: 0.8204 (p0)
REVERT: A  286 GLN cc_start: 0.7423 (mp10) cc_final: 0.6514 (tm130)
REVERT: A  520 ASN cc_start: 0.8120 (t0) cc_final: 0.7600 (t0)
REVERT: A  521 GLU cc_start: 0.7413 (tt0) cc_final: 0.7099 (pt0)
REVERT: A  614 ASP cc_start: 0.8381 (m-30) cc_final: 0.8104 (m-30)
REVERT: B   70 ASN cc_start: 0.8391 (OUTLIER) cc_final: 0.8148 (t0)
REVERT: B  266 ASN cc_start: 0.6781 (p0) cc_final: 0.6088 (m110)
REVERT: B  268 THR cc_start: 0.8534 (t) cc_final: 0.8223 (m)
REVERT: C   41 TYR cc_start: 0.6849 (p90) cc_final: 0.6343 (p90)
REVERT: D   93 ASP cc_start: 0.8157 (m-30) cc_final: 0.7693 (m-30)
  outliers start: 19
  outliers final: 13
  residues processed: 119
  average time/residue: 1.0292
  time to fit residues: 135.6645
Evaluate side-chains
  119 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  562 ASP
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  702 SER
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain B residue   28 ASP
Chi-restraints excluded: chain B residue   70 ASN
Chi-restraints excluded: chain B residue  138 ASP
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  359 GLN
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain E residue   42 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 146 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 105 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 143 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 120 optimal weight:    8.9990
   chunk 121 optimal weight:    0.8980
   chunk 9 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 244 GLN
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 230 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.169978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.124013 restraints weight = 35154.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3433 rms_B_bonded: 2.11
r_work: 0.3204 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.1008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12071  Z= 0.164
  Angle     :  0.519   7.829  16405  Z= 0.277
  Chirality :  0.043   0.145   1783
  Planarity :  0.004   0.047   2158
  Dihedral  :  4.322  18.274   1651
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  9.18 %
    Favored  : 89.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.21), residues: 1487
  helix:  2.13 (0.28), residues: 330
  sheet:  0.10 (0.24), residues: 454
  loop : -1.07 (0.22), residues: 703

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 583 
 TYR   0.011   0.001   TYR D  79 
 PHE   0.016   0.001   PHE A 426 
 TRP   0.012   0.001   TRP B 348 
 HIS   0.005   0.001   HIS B 347 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00396 /  0.16 (12068)
  covalent geometry    : angle       0.51912 /  0.28 (16403)
  SS BOND              : bond        0.00378 /  0.20 (    1)
  SS BOND              : angle       1.49770 /  0.88 (    2)
  hydrogen bonds       : bond        0.04555 /  3.17 (  521)
  hydrogen bonds       : angle       4.56031 /  3.25 ( 1467)
  Misc. bond           : bond        0.00421 /  0.20 (    2)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 ASP cc_start: 0.8359 (p0) cc_final: 0.8139 (p0)
REVERT: A  286 GLN cc_start: 0.7333 (mp10) cc_final: 0.6356 (tm130)
REVERT: A  520 ASN cc_start: 0.7974 (t0) cc_final: 0.7401 (t0)
REVERT: A  521 GLU cc_start: 0.7327 (tt0) cc_final: 0.7014 (pt0)
REVERT: A  614 ASP cc_start: 0.8353 (m-30) cc_final: 0.8062 (m-30)
REVERT: B   32 MET cc_start: 0.6932 (tpp) cc_final: 0.6721 (tpp)
REVERT: B   70 ASN cc_start: 0.8384 (OUTLIER) cc_final: 0.8123 (t0)
REVERT: B  268 THR cc_start: 0.8489 (t) cc_final: 0.8204 (m)
REVERT: C   41 TYR cc_start: 0.6828 (p90) cc_final: 0.6219 (p90)
REVERT: D   93 ASP cc_start: 0.8224 (m-30) cc_final: 0.7748 (m-30)
  outliers start: 18
  outliers final: 14
  residues processed: 121
  average time/residue: 0.9892
  time to fit residues: 133.2792
Evaluate side-chains
  122 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  562 ASP
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  702 SER
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain B residue   28 ASP
Chi-restraints excluded: chain B residue   70 ASN
Chi-restraints excluded: chain B residue  138 ASP
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  226 MET
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain E residue   42 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 135 optimal weight:    0.9990
   chunk 14 optimal weight:    8.9990
   chunk 15 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 130 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 61 optimal weight:    0.6980
   overall best weight:    1.3186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 244 GLN
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 230 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.169689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.123159 restraints weight = 35404.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 2.15
r_work: 0.3198 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.1105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12071  Z= 0.160
  Angle     :  0.513   7.851  16405  Z= 0.273
  Chirality :  0.043   0.144   1783
  Planarity :  0.004   0.053   2158
  Dihedral  :  4.274  17.513   1651
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 2.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 10.06 %
    Favored  : 88.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.05 (0.21), residues: 1487
  helix:  2.16 (0.28), residues: 330
  sheet:  0.10 (0.24), residues: 454
  loop : -1.06 (0.22), residues: 703

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 583 
 TYR   0.011   0.001   TYR D  79 
 PHE   0.016   0.001   PHE A 426 
 TRP   0.010   0.001   TRP B 143 
 HIS   0.005   0.001   HIS B 347 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00386 /  0.16 (12068)
  covalent geometry    : angle       0.51241 /  0.27 (16403)
  SS BOND              : bond        0.00339 /  0.18 (    1)
  SS BOND              : angle       1.50855 /  0.89 (    2)
  hydrogen bonds       : bond        0.04444 /  3.10 (  521)
  hydrogen bonds       : angle       4.51356 /  3.22 ( 1467)
  Misc. bond           : bond        0.00400 /  0.19 (    2)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 0.639 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 ASP cc_start: 0.8338 (p0) cc_final: 0.8117 (p0)
REVERT: A  286 GLN cc_start: 0.7292 (mp10) cc_final: 0.6313 (tm130)
REVERT: A  520 ASN cc_start: 0.8054 (t0) cc_final: 0.7513 (t0)
REVERT: A  521 GLU cc_start: 0.7349 (tt0) cc_final: 0.7044 (pt0)
REVERT: A  614 ASP cc_start: 0.8360 (m-30) cc_final: 0.8051 (m-30)
REVERT: B   70 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.8148 (t0)
REVERT: B  268 THR cc_start: 0.8447 (t) cc_final: 0.8191 (m)
REVERT: C   41 TYR cc_start: 0.6687 (p90) cc_final: 0.6075 (p90)
REVERT: C   76 VAL cc_start: 0.7898 (OUTLIER) cc_final: 0.7619 (p)
REVERT: D   93 ASP cc_start: 0.8213 (m-30) cc_final: 0.7738 (m-30)
  outliers start: 19
  outliers final: 13
  residues processed: 120
  average time/residue: 1.0041
  time to fit residues: 133.8724
Evaluate side-chains
  122 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  562 ASP
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  702 SER
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain B residue   28 ASP
Chi-restraints excluded: chain B residue   70 ASN
Chi-restraints excluded: chain B residue  138 ASP
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  226 MET
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain D residue  134 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 143 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 137 optimal weight:    0.9990
   chunk 145 optimal weight:    0.7980
   chunk 115 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0980
   chunk 99 optimal weight:    0.7980
   chunk 131 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 133 optimal weight:    0.9980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 244 GLN
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 230 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.171670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.124646 restraints weight = 35267.072|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 2.09
r_work: 0.3233 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3103 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.1214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  12071  Z= 0.106
  Angle     :  0.473   7.703  16405  Z= 0.251
  Chirality :  0.042   0.141   1783
  Planarity :  0.004   0.057   2158
  Dihedral  :  4.099  16.712   1651
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 1.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 10.37 %
    Favored  : 88.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.22), residues: 1487
  helix:  2.55 (0.29), residues: 327
  sheet:  0.17 (0.24), residues: 462
  loop : -0.92 (0.22), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 583 
 TYR   0.009   0.001   TYR D  79 
 PHE   0.016   0.001   PHE A 426 
 TRP   0.012   0.001   TRP B 348 
 HIS   0.005   0.001   HIS D 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.11 (12068)
  covalent geometry    : angle       0.47252 /  0.25 (16403)
  SS BOND              : bond        0.00254 /  0.13 (    1)
  SS BOND              : angle       1.34803 /  0.79 (    2)
  hydrogen bonds       : bond        0.03813 /  2.66 (  521)
  hydrogen bonds       : angle       4.36896 /  3.11 ( 1467)
  Misc. bond           : bond        0.00372 /  0.18 (    2)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.649 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7246 (mp10) cc_final: 0.6286 (tm130)
REVERT: A  520 ASN cc_start: 0.8006 (t0) cc_final: 0.7404 (t0)
REVERT: A  521 GLU cc_start: 0.7222 (tt0) cc_final: 0.6941 (pt0)
REVERT: A  614 ASP cc_start: 0.8318 (m-30) cc_final: 0.8005 (m-30)
REVERT: B   41 GLN cc_start: 0.7444 (tm-30) cc_final: 0.6919 (mt0)
REVERT: B  268 THR cc_start: 0.8438 (t) cc_final: 0.8200 (m)
REVERT: C   41 TYR cc_start: 0.6637 (p90) cc_final: 0.6038 (p90)
REVERT: C   76 VAL cc_start: 0.7801 (OUTLIER) cc_final: 0.7522 (p)
REVERT: D   93 ASP cc_start: 0.8198 (m-30) cc_final: 0.7726 (m-30)
  outliers start: 16
  outliers final: 10
  residues processed: 118
  average time/residue: 1.0559
  time to fit residues: 138.1939
Evaluate side-chains
  118 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  702 SER
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain B residue   28 ASP
Chi-restraints excluded: chain B residue  138 ASP
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain D residue  134 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 112 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0970
   chunk 109 optimal weight:    2.9990
   chunk 144 optimal weight:    0.9980
   chunk 117 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 129 optimal weight:    0.0980
   chunk 145 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 127 optimal weight:    2.9990
   chunk 102 optimal weight:    4.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 244 GLN
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 230 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.170669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.125202 restraints weight = 35158.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 2.10
r_work: 0.3219 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3088 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.1249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12071  Z= 0.133
  Angle     :  0.489   7.313  16405  Z= 0.259
  Chirality :  0.043   0.141   1783
  Planarity :  0.004   0.062   2158
  Dihedral  :  4.108  16.770   1651
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 2.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 10.69 %
    Favored  : 87.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.22), residues: 1487
  helix:  2.45 (0.29), residues: 331
  sheet:  0.18 (0.24), residues: 449
  loop : -0.96 (0.22), residues: 707

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 583 
 TYR   0.009   0.001   TYR D  79 
 PHE   0.015   0.001   PHE A 426 
 TRP   0.010   0.001   TRP B 143 
 HIS   0.005   0.001   HIS B 347 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.13 (12068)
  covalent geometry    : angle       0.48904 /  0.26 (16403)
  SS BOND              : bond        0.00309 /  0.16 (    1)
  SS BOND              : angle       1.33534 /  0.78 (    2)
  hydrogen bonds       : bond        0.04054 /  2.83 (  521)
  hydrogen bonds       : angle       4.37493 /  3.12 ( 1467)
  Misc. bond           : bond        0.00370 /  0.18 (    2)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.640 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7291 (mp10) cc_final: 0.6382 (tm130)
REVERT: A  520 ASN cc_start: 0.8094 (t0) cc_final: 0.7604 (t0)
REVERT: A  521 GLU cc_start: 0.7366 (tt0) cc_final: 0.7065 (pt0)
REVERT: A  614 ASP cc_start: 0.8332 (m-30) cc_final: 0.8031 (m-30)
REVERT: B  268 THR cc_start: 0.8499 (t) cc_final: 0.8248 (m)
REVERT: C   41 TYR cc_start: 0.6682 (p90) cc_final: 0.6157 (p90)
REVERT: C   76 VAL cc_start: 0.7893 (OUTLIER) cc_final: 0.7594 (p)
REVERT: D   93 ASP cc_start: 0.8228 (m-30) cc_final: 0.7763 (m-30)
  outliers start: 17
  outliers final: 12
  residues processed: 122
  average time/residue: 1.0164
  time to fit residues: 137.6914
Evaluate side-chains
  123 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  562 ASP
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  702 SER
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain B residue   28 ASP
Chi-restraints excluded: chain B residue  138 ASP
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain D residue  134 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 82 optimal weight:    0.2980
   chunk 78 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 101 optimal weight:    3.9990
   chunk 56 optimal weight:    0.8980
   chunk 128 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 123 optimal weight:    7.9990
   chunk 67 optimal weight:    2.9990
   chunk 124 optimal weight:    1.9990
   overall best weight:    1.4386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 244 GLN
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 319 GLN
D 230 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.169344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.122988 restraints weight = 35397.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 2.15
r_work: 0.3196 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3061 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.1310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12071  Z= 0.170
  Angle     :  0.516   7.788  16405  Z= 0.274
  Chirality :  0.043   0.140   1783
  Planarity :  0.004   0.061   2158
  Dihedral  :  4.225  16.880   1651
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 2.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 11.01 %
    Favored  : 87.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.22), residues: 1487
  helix:  2.34 (0.28), residues: 330
  sheet:  0.18 (0.24), residues: 449
  loop : -0.99 (0.22), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 583 
 TYR   0.014   0.001   TYR D  79 
 PHE   0.015   0.001   PHE A 426 
 TRP   0.010   0.001   TRP B 143 
 HIS   0.005   0.001   HIS B 347 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00412 /  0.17 (12068)
  covalent geometry    : angle       0.51563 /  0.27 (16403)
  SS BOND              : bond        0.00307 /  0.16 (    1)
  SS BOND              : angle       1.37167 /  0.81 (    2)
  hydrogen bonds       : bond        0.04411 /  3.08 (  521)
  hydrogen bonds       : angle       4.44153 /  3.16 ( 1467)
  Misc. bond           : bond        0.00376 /  0.18 (    2)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 0.586 
Fit side-chains
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7247 (mp10) cc_final: 0.6326 (tm130)
REVERT: A  520 ASN cc_start: 0.8034 (t0) cc_final: 0.7544 (t0)
REVERT: A  614 ASP cc_start: 0.8368 (m-30) cc_final: 0.8071 (m-30)
REVERT: B  266 ASN cc_start: 0.6926 (p0) cc_final: 0.6707 (p0)
REVERT: B  268 THR cc_start: 0.8482 (t) cc_final: 0.8239 (m)
REVERT: C   41 TYR cc_start: 0.6649 (p90) cc_final: 0.6188 (p90)
REVERT: D   93 ASP cc_start: 0.8106 (m-30) cc_final: 0.7642 (m-30)
  outliers start: 16
  outliers final: 12
  residues processed: 121
  average time/residue: 0.9572
  time to fit residues: 128.7900
Evaluate side-chains
  123 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  702 SER
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain B residue   28 ASP
Chi-restraints excluded: chain B residue  138 ASP
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  226 MET
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain D residue  134 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 112 optimal weight:    0.8980
   chunk 116 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 117 optimal weight:    0.6980
   chunk 133 optimal weight:    0.9980
   chunk 108 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 244 GLN
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 230 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.170975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.125331 restraints weight = 35229.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 2.09
r_work: 0.3226 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3094 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.1359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12071  Z= 0.118
  Angle     :  0.483   7.882  16405  Z= 0.256
  Chirality :  0.042   0.140   1783
  Planarity :  0.004   0.068   2158
  Dihedral  :  4.107  17.028   1651
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 2.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 11.48 %
    Favored  : 87.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.29 (0.22), residues: 1487
  helix:  2.48 (0.29), residues: 331
  sheet:  0.24 (0.24), residues: 451
  loop : -0.97 (0.22), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 583 
 TYR   0.011   0.001   TYR D  79 
 PHE   0.015   0.001   PHE A 426 
 TRP   0.012   0.001   TRP B 348 
 HIS   0.005   0.001   HIS D 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.12 (12068)
  covalent geometry    : angle       0.48235 /  0.26 (16403)
  SS BOND              : bond        0.00301 /  0.16 (    1)
  SS BOND              : angle       1.23971 /  0.73 (    2)
  hydrogen bonds       : bond        0.03908 /  2.73 (  521)
  hydrogen bonds       : angle       4.35002 /  3.10 ( 1467)
  Misc. bond           : bond        0.00364 /  0.17 (    2)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.622 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 GLN cc_start: 0.7237 (mp10) cc_final: 0.6318 (tm130)
REVERT: A  520 ASN cc_start: 0.8030 (t0) cc_final: 0.7495 (t0)
REVERT: A  521 GLU cc_start: 0.7358 (tt0) cc_final: 0.7033 (pt0)
REVERT: A  614 ASP cc_start: 0.8288 (m-30) cc_final: 0.7987 (m-30)
REVERT: B   41 GLN cc_start: 0.7389 (tm-30) cc_final: 0.6948 (mt0)
REVERT: B  268 THR cc_start: 0.8481 (t) cc_final: 0.8248 (m)
REVERT: C   41 TYR cc_start: 0.6614 (p90) cc_final: 0.6088 (p90)
REVERT: D   93 ASP cc_start: 0.8101 (m-30) cc_final: 0.7642 (m-30)
  outliers start: 12
  outliers final: 10
  residues processed: 116
  average time/residue: 0.9801
  time to fit residues: 126.3351
Evaluate side-chains
  119 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 109
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  702 SER
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain B residue   28 ASP
Chi-restraints excluded: chain B residue  138 ASP
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  226 MET
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain D residue  134 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 120 optimal weight:    7.9990
   chunk 117 optimal weight:    0.0010
   chunk 41 optimal weight:    0.5980
   chunk 115 optimal weight:    0.7980
   chunk 135 optimal weight:    0.5980
   chunk 106 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9990
   chunk 126 optimal weight:    0.0470
   chunk 137 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.3684

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 244 GLN
A 422 ASN
D 230 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.172843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.126854 restraints weight = 35108.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 1.99
r_work: 0.3264 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3133 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.1453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  12071  Z= 0.087
  Angle     :  0.451   7.279  16405  Z= 0.239
  Chirality :  0.042   0.137   1783
  Planarity :  0.004   0.070   2158
  Dihedral  :  3.919  17.083   1651
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 2.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 11.80 %
    Favored  : 87.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.51 (0.22), residues: 1487
  helix:  2.73 (0.29), residues: 331
  sheet:  0.35 (0.24), residues: 458
  loop : -0.86 (0.23), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG A 583 
 TYR   0.010   0.001   TYR D 184 
 PHE   0.015   0.001   PHE A 426 
 TRP   0.016   0.001   TRP B 348 
 HIS   0.004   0.001   HIS D 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00194 /  0.09 (12068)
  covalent geometry    : angle       0.45071 /  0.24 (16403)
  SS BOND              : bond        0.00171 /  0.09 (    1)
  SS BOND              : angle       1.17122 /  0.69 (    2)
  hydrogen bonds       : bond        0.03373 /  2.35 (  521)
  hydrogen bonds       : angle       4.21142 /  3.00 ( 1467)
  Misc. bond           : bond        0.00363 /  0.17 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6981.06 seconds
wall clock time: 118 minutes 46.23 seconds (7126.23 seconds total)