Starting phenix.real_space_refine
on Tue Feb  3 18:29:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j9b_61257/02_2026/9j9b_61257.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j9b_61257/02_2026/9j9b_61257.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.83
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j9b_61257/02_2026/9j9b_61257.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j9b_61257/02_2026/9j9b_61257.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j9b_61257/02_2026/9j9b_61257.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j9b_61257/02_2026/9j9b_61257.cif"
  }
  resolution = 3.83
  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=   0.003 sd=   0.042
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      31      5.16       5
     C    3840      2.51       5
     N    1041      2.21       5
     O    1133      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6047
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 985
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 133, 985
          Classifications: {'peptide': 133}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 127}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "B"
      Number of atoms: 614
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 614
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 4, 'TRANS': 78}
    Chain: "C"
      Number of atoms: 2094
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 2094
          Classifications: {'peptide': 264}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 7, 'TRANS': 256}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 13
    Chain: "D"
      Number of atoms: 479
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 67, 479
          Classifications: {'peptide': 67}
          Link IDs: {'PTRANS': 3, 'TRANS': 63}
    Chain: "H"
      Number of atoms: 901
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 901
          Classifications: {'peptide': 117}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 113}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "L"
      Number of atoms: 837
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 837
          Classifications: {'peptide': 111}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 103}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "E"
      Number of atoms: 74
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 74
          Classifications: {'peptide': 15}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 14}
          Link IDs: {'TRANS': 14}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'UNK:plan-1': 15}
          Unresolved non-hydrogen planarities: 15
    Chain: "A"
      Number of atoms: 63
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 63
          Unusual residues: {'CDL': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 37
  Time building chain proxies: 1.31, per 1000 atoms: 0.22
  Number of scatterers: 6047
  At special positions: 0
  Unit cell: (94.05, 91.2, 115.9, 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      31     16.00
     P       2     15.00
     O    1133      8.00
     N    1041      7.00
     C    3840      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  10 " - pdb=" SG  CYS A  77 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  41 " - pdb=" SG  CYS H 114 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  43 " - pdb=" SG  CYS L 112 " 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=0, symmetry=0
  Time building additional restraints: 0.45
  Conformation dependent library (CDL) restraints added in 158.2 milliseconds
  

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1394

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 8 sheets defined
      54.3% alpha, 25.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 41
    Processing helix  chain 'A' and resid 45 through 84
      Proline residue:  A  59  - end of helix
    Processing helix  chain 'A' and resid 88 through 103
      removed outlier: 3.508A  pdb=" N   ILE A  92 " --> pdb=" O   PRO A  88 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   GLY A  95 " --> pdb=" O   ALA A  91 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ALA A 103 " --> pdb=" O   GLY A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 136
      removed outlier: 3.999A  pdb=" N   LEU A 130 " --> pdb=" O   GLU A 126 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   MET A 131 " --> pdb=" O   GLY A 127 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   PHE A 132 " --> pdb=" O   VAL A 128 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ALA A 136 " --> pdb=" O   PHE A 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 122
      removed outlier: 3.643A  pdb=" N   VAL B 104 " --> pdb=" O   GLY B 100 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   LEU B 107 " --> pdb=" O   ALA B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 166
      Proline residue:  B 146  - end of helix
      removed outlier: 4.131A  pdb=" N   ASN B 151 " --> pdb=" O   PHE B 147 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   ALA B 152 " --> pdb=" O   LEU B 148 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ILE B 166 " --> pdb=" O   ILE B 162 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 103
      No H-bonds generated for 'chain 'C' and resid 101 through 103'
    Processing helix  chain 'C' and resid 104 through 125
      removed outlier: 3.806A  pdb=" N   THR C 108 " --> pdb=" O   ILE C 104 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   LYS C 110 " --> pdb=" O   GLY C 106 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   LYS C 111 " --> pdb=" O   LYS C 107 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   THR C 112 " --> pdb=" O   THR C 108 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   MET C 116 " --> pdb=" O   THR C 112 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   HIS C 118 " --> pdb=" O   GLU C 114 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   ILE C 119 " --> pdb=" O   THR C 115 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 126 through 147
    Processing helix  chain 'C' and resid 147 through 152
    Processing helix  chain 'C' and resid 153 through 164
    Processing helix  chain 'C' and resid 165 through 172
      removed outlier: 3.911A  pdb=" N   SER C 168 " --> pdb=" O   ASP C 165 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   GLY C 172 " --> pdb=" O   SER C 169 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 176 through 193
    Processing helix  chain 'C' and resid 257 through 263
      removed outlier: 3.845A  pdb=" N   VAL C 261 " --> pdb=" O   ILE C 257 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 264 through 266
      No H-bonds generated for 'chain 'C' and resid 264 through 266'
    Processing helix  chain 'C' and resid 268 through 281
    Processing helix  chain 'C' and resid 285 through 296
    Processing helix  chain 'C' and resid 296 through 308
    Processing helix  chain 'C' and resid 309 through 317
      removed outlier: 3.873A  pdb=" N   LEU C 313 " --> pdb=" O   ASP C 309 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   LYS C 315 " --> pdb=" O   LYS C 311 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   TRP C 316 " --> pdb=" O   VAL C 312 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   PHE C 317 " --> pdb=" O   LEU C 313 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 318 through 335
      removed outlier: 3.634A  pdb=" N   PHE C 322 " --> pdb=" O   SER C 318 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ILE C 331 " --> pdb=" O   ALA C 327 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   PHE C 332 " --> pdb=" O   GLN C 328 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 14 through 46
      removed outlier: 3.595A  pdb=" N   CYS D  32 " --> pdb=" O   THR D  28 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ILE D  35 " --> pdb=" O   VAL D  31 " (cutoff:3.500A)
      removed outlier: 4.856A  pdb=" N   PHE D  40 " --> pdb=" O   LEU D  36 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ALA D  41 " --> pdb=" O   PHE D  37 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   ILE D  42 " --> pdb=" O   GLY D  38 " (cutoff:3.500A)
      removed outlier: 5.038A  pdb=" N   ALA D  43 " --> pdb=" O   GLY D  39 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 51 through 77
      removed outlier: 3.544A  pdb=" N   LEU D  56 " --> pdb=" O   VAL D  52 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   PHE D  70 " --> pdb=" O   THR D  66 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   ILE D  76 " --> pdb=" O   SER D  72 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 105 through 109
      removed outlier: 4.139A  pdb=" N   THR H 109 " --> pdb=" O   ALA H 106 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 138 through 148
      removed outlier: 3.745A  pdb=" N   UNK E 145 " --> pdb=" O   UNK E 141 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   UNK E 146 " --> pdb=" O   UNK E 142 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 337 through 356
      removed outlier: 6.973A  pdb=" N   ASP C 340 " --> pdb=" O   ARG C 378 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   ARG C 378 " --> pdb=" O   ASP C 340 " (cutoff:3.500A)
      removed outlier: 7.935A  pdb=" N   ARG C 342 " --> pdb=" O   LEU C 376 " (cutoff:3.500A)
      removed outlier: 8.345A  pdb=" N   LEU C 376 " --> pdb=" O   ARG C 342 " (cutoff:3.500A)
      removed outlier: 8.169A  pdb=" N   LEU C 344 " --> pdb=" O   ILE C 374 " (cutoff:3.500A)
      removed outlier: 9.709A  pdb=" N   ILE C 374 " --> pdb=" O   LEU C 344 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   ILE C 346 " --> pdb=" O   GLN C 372 " (cutoff:3.500A)
      removed outlier: 7.476A  pdb=" N   GLN C 372 " --> pdb=" O   ILE C 346 " (cutoff:3.500A)
      removed outlier: 5.242A  pdb=" N   GLY C 348 " --> pdb=" O   ARG C 370 " (cutoff:3.500A)
      removed outlier: 4.687A  pdb=" N   ARG C 370 " --> pdb=" O   GLY C 348 " (cutoff:3.500A)
      removed outlier: 7.050A  pdb=" N   VAL C 366 " --> pdb=" O   VAL C 352 " (cutoff:3.500A)
      removed outlier: 5.106A  pdb=" N   ALA C 354 " --> pdb=" O   VAL C 364 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   VAL C 364 " --> pdb=" O   ALA C 354 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   TYR C 377 " --> pdb=" O   ALA C 386 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 337 through 356
      removed outlier: 6.973A  pdb=" N   ASP C 340 " --> pdb=" O   ARG C 378 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   ARG C 378 " --> pdb=" O   ASP C 340 " (cutoff:3.500A)
      removed outlier: 7.935A  pdb=" N   ARG C 342 " --> pdb=" O   LEU C 376 " (cutoff:3.500A)
      removed outlier: 8.345A  pdb=" N   LEU C 376 " --> pdb=" O   ARG C 342 " (cutoff:3.500A)
      removed outlier: 8.169A  pdb=" N   LEU C 344 " --> pdb=" O   ILE C 374 " (cutoff:3.500A)
      removed outlier: 9.709A  pdb=" N   ILE C 374 " --> pdb=" O   LEU C 344 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   ILE C 346 " --> pdb=" O   GLN C 372 " (cutoff:3.500A)
      removed outlier: 7.476A  pdb=" N   GLN C 372 " --> pdb=" O   ILE C 346 " (cutoff:3.500A)
      removed outlier: 5.242A  pdb=" N   GLY C 348 " --> pdb=" O   ARG C 370 " (cutoff:3.500A)
      removed outlier: 4.687A  pdb=" N   ARG C 370 " --> pdb=" O   GLY C 348 " (cutoff:3.500A)
      removed outlier: 7.050A  pdb=" N   VAL C 366 " --> pdb=" O   VAL C 352 " (cutoff:3.500A)
      removed outlier: 5.106A  pdb=" N   ALA C 354 " --> pdb=" O   VAL C 364 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   VAL C 364 " --> pdb=" O   ALA C 354 " (cutoff:3.500A)
      removed outlier: 5.238A  pdb=" N   ARG C 404 " --> pdb=" O   PRO C 363 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   SER C 397 " --> pdb=" O   ARG C 424 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   ARG C 424 " --> pdb=" O   SER C 397 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   ALA C 399 " --> pdb=" O   PHE C 422 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   PHE C 422 " --> pdb=" O   ALA C 399 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   VAL C 401 " --> pdb=" O   LEU C 420 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 22 through 25
    Processing sheet with id=AA4, first strand: chain 'H' and resid 76 through 78
      removed outlier: 4.843A  pdb=" N   LEU H  64 " --> pdb=" O   SER H  59 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   SER H  59 " --> pdb=" O   LEU H  64 " (cutoff:3.500A)
      removed outlier: 5.453A  pdb=" N   TRP H  66 " --> pdb=" O   ARG H  57 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ARG H  57 " --> pdb=" O   TRP H  66 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLY H  68 " --> pdb=" O   TRP H  55 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   GLY H  52 " --> pdb=" O   TYR H 117 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   TYR H 117 " --> pdb=" O   GLY H  52 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ILE H 111 " --> pdb=" O   GLN H  58 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   TYR H 125 " --> pdb=" O   ARG H 116 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 76 through 78
      removed outlier: 4.843A  pdb=" N   LEU H  64 " --> pdb=" O   SER H  59 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   SER H  59 " --> pdb=" O   LEU H  64 " (cutoff:3.500A)
      removed outlier: 5.453A  pdb=" N   TRP H  66 " --> pdb=" O   ARG H  57 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ARG H  57 " --> pdb=" O   TRP H  66 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLY H  68 " --> pdb=" O   TRP H  55 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   GLY H  52 " --> pdb=" O   TYR H 117 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   TYR H 117 " --> pdb=" O   GLY H  52 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ILE H 111 " --> pdb=" O   GLN H  58 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 25 through 26
    Processing sheet with id=AA7, first strand: chain 'L' and resid 30 through 33
      removed outlier: 7.016A  pdb=" N   MET L  57 " --> pdb=" O   TYR L  73 " (cutoff:3.500A)
      removed outlier: 5.079A  pdb=" N   TYR L  73 " --> pdb=" O   MET L  57 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   TRP L  59 " --> pdb=" O   LEU L  71 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 50 through 51

    375 hydrogen bonds defined for protein.
    1071 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: 0.96

  Time building geometry restraints manager: 0.57 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1015
        1.32 -     1.45: 1643
        1.45 -     1.57: 3453
        1.57 -     1.69: 4
        1.69 -     1.82: 51
  Bond restraints: 6166
  Sorted by residual:
  bond pdb=" C   GLN D  12 "
       pdb=" N   PRO D  13 "
    ideal  model  delta    sigma   weight residual
    1.334  1.385 -0.051 2.34e-02 1.83e+03 4.81e+00
  bond pdb=" C   HIS L 100 "
       pdb=" N   PRO L 101 "
    ideal  model  delta    sigma   weight residual
    1.334  1.371 -0.037 2.34e-02 1.83e+03 2.49e+00
  bond pdb=" CA  ALA A  58 "
       pdb=" C   ALA A  58 "
    ideal  model  delta    sigma   weight residual
    1.520  1.538 -0.018 1.23e-02 6.61e+03 2.12e+00
  bond pdb=" C   VAL L 118 "
       pdb=" N   PRO L 119 "
    ideal  model  delta    sigma   weight residual
    1.334  1.368 -0.034 2.34e-02 1.83e+03 2.07e+00
  bond pdb=" C   ALA A  58 "
       pdb=" N   PRO A  59 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 1.25e-02 6.40e+03 2.01e+00
  ... (remaining 6161 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 8125
        1.98 -     3.96: 155
        3.96 -     5.94: 13
        5.94 -     7.92: 11
        7.92 -     9.90: 6
  Bond angle restraints: 8310
  Sorted by residual:
  angle pdb=" C   GLU L 117 "
        pdb=" N   VAL L 118 "
        pdb=" CA  VAL L 118 "
      ideal   model   delta    sigma   weight residual
     120.24  123.35   -3.11 6.30e-01 2.52e+00 2.43e+01
  angle pdb=" C   TRP B  93 "
        pdb=" N   THR B  94 "
        pdb=" CA  THR B  94 "
      ideal   model   delta    sigma   weight residual
     121.54  129.83   -8.29 1.91e+00 2.74e-01 1.88e+01
  angle pdb=" C   GLY B  92 "
        pdb=" N   TRP B  93 "
        pdb=" CA  TRP B  93 "
      ideal   model   delta    sigma   weight residual
     121.54  129.52   -7.98 1.91e+00 2.74e-01 1.75e+01
  angle pdb=" N   GLY H  27 "
        pdb=" CA  GLY H  27 "
        pdb=" C   GLY H  27 "
      ideal   model   delta    sigma   weight residual
     112.34  120.71   -8.37 2.04e+00 2.40e-01 1.69e+01
  angle pdb=" C   GLU C 407 "
        pdb=" N   GLN C 408 "
        pdb=" CA  GLN C 408 "
      ideal   model   delta    sigma   weight residual
     121.54  128.46   -6.92 1.91e+00 2.74e-01 1.31e+01
  ... (remaining 8305 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.12: 3262
       15.12 -    30.25: 263
       30.25 -    45.37: 86
       45.37 -    60.49: 40
       60.49 -    75.62: 6
  Dihedral angle restraints: 3657
    sinusoidal: 1458
      harmonic: 2199
  Sorted by residual:
  dihedral pdb=" CB  CYS A  10 "
           pdb=" SG  CYS A  10 "
           pdb=" SG  CYS A  77 "
           pdb=" CB  CYS A  77 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  136.60  -43.60     1      1.00e+01 1.00e-02 2.65e+01
  dihedral pdb=" CA  ALA C 358 "
           pdb=" C   ALA C 358 "
           pdb=" N   PRO C 359 "
           pdb=" CA  PRO C 359 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.78   24.22     0      5.00e+00 4.00e-02 2.35e+01
  dihedral pdb=" CA  ILE A  92 "
           pdb=" C   ILE A  92 "
           pdb=" N   ILE A  93 "
           pdb=" CA  ILE A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.90  -22.10     0      5.00e+00 4.00e-02 1.95e+01
  ... (remaining 3654 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 591
       0.039 -    0.077: 210
       0.077 -    0.116: 73
       0.116 -    0.155: 24
       0.155 -    0.193: 2
  Chirality restraints: 900
  Sorted by residual:
  chirality pdb=" CA  THR B  94 "
            pdb=" N   THR B  94 "
            pdb=" C   THR B  94 "
            pdb=" CB  THR B  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.33    0.19 2.00e-01 2.50e+01 9.34e-01
  chirality pdb=" CA  SER L  27 "
            pdb=" N   SER L  27 "
            pdb=" C   SER L  27 "
            pdb=" CB  SER L  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.40e-01
  chirality pdb=" CA  GLN C 408 "
            pdb=" N   GLN C 408 "
            pdb=" C   GLN C 408 "
            pdb=" CB  GLN C 408 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.70e-01
  ... (remaining 897 not shown)

  Planarity restraints: 1065
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  99 "   -0.012 2.00e-02 2.50e+03   2.46e-02 6.05e+00
        pdb=" C   GLY A  99 "    0.043 2.00e-02 2.50e+03
        pdb=" O   GLY A  99 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   GLY A 100 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A   8 "   -0.034 5.00e-02 4.00e+02   5.18e-02 4.29e+00
        pdb=" N   PRO A   9 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A   9 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A   9 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 358 "   -0.031 5.00e-02 4.00e+02   4.67e-02 3.49e+00
        pdb=" N   PRO C 359 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO C 359 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO C 359 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1062 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1494
        2.80 -     3.32: 5178
        3.32 -     3.85: 9633
        3.85 -     4.37: 10053
        4.37 -     4.90: 18523
  Nonbonded interactions: 44881
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C 296 "
            pdb=" OE2 GLU C 413 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" OG1 THR C 176 "
            pdb=" OE1 GLN C 179 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" O   ILE B 161 "
            pdb=" OG1 THR B 165 "
     model   vdw
     2.325 3.040
  nonbonded pdb=" O   GLY A  37 "
            pdb=" OG  SER A  41 "
     model   vdw
     2.336 3.040
  nonbonded pdb=" O   ASN C 286 "
            pdb=" OG1 THR C 290 "
     model   vdw
     2.342 3.040
  ... (remaining 44876 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.500
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.910
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6169  Z= 0.205
  Angle     :  0.738   9.895   8316  Z= 0.404
  Chirality :  0.048   0.193    900
  Planarity :  0.006   0.052   1065
  Dihedral  : 14.206  75.616   2254
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 2.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  :  9.55 %
    Favored  : 84.79 %
  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: -1.43 (0.27), residues: 761
  helix: -0.41 (0.23), residues: 364
  sheet: -0.30 (0.44), residues: 152
  loop : -2.00 (0.35), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 180 
 TYR   0.016   0.002   TYR H 117 
 PHE   0.019   0.002   PHE H  99 
 TRP   0.010   0.001   TRP H  66 
 HIS   0.002   0.001   HIS L 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 6166)
  covalent geometry    : angle       0.73679 ( 8310)
  SS BOND              : bond        0.00467 (    3)
  SS BOND              : angle       1.46305 (    6)
  hydrogen bonds       : bond        0.14168 (  362)
  hydrogen bonds       : angle       6.21413 ( 1071)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 201
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8507 (pt)
REVERT: A   97 PHE cc_start: 0.7915 (m-10) cc_final: 0.7694 (m-10)
REVERT: A  105 ARG cc_start: 0.6332 (ttm170) cc_final: 0.5387 (tpt170)
REVERT: A  109 ARG cc_start: 0.8100 (mpt-90) cc_final: 0.7828 (mtm-85)
REVERT: B   95 ASP cc_start: 0.6354 (t0) cc_final: 0.5759 (t0)
REVERT: C  264 PHE cc_start: 0.8648 (t80) cc_final: 0.8261 (t80)
REVERT: C  423 VAL cc_start: 0.9090 (t) cc_final: 0.8836 (m)
REVERT: D   24 MET cc_start: 0.7018 (mtt) cc_final: 0.6785 (ttt)
REVERT: H  124 ASP cc_start: 0.9039 (OUTLIER) cc_final: 0.8807 (p0)
REVERT: L   35 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7787 (tp)
  outliers start: 35
  outliers final: 8
  residues processed: 220
  average time/residue: 0.0876
  time to fit residues: 24.5464
Evaluate side-chains
  148 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 137
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue   41 SER
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain D residue   67 PHE
Chi-restraints excluded: chain H residue   89 THR
Chi-restraints excluded: chain H residue  109 THR
Chi-restraints excluded: chain H residue  124 ASP
Chi-restraints excluded: chain L residue   35 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.2980
   chunk 33 optimal weight:    0.4980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 329 GLN
H  35 GLN
H  92 ASN
L  26 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.139598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.110604 restraints weight = 12059.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.110743 restraints weight = 8943.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.111475 restraints weight = 8565.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.112516 restraints weight = 5985.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.112953 restraints weight = 5221.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.2637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6169  Z= 0.135
  Angle     :  0.645  12.968   8316  Z= 0.325
  Chirality :  0.042   0.163    900
  Planarity :  0.005   0.042   1065
  Dihedral  :  9.442  59.484    917
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 16.50 %
    Favored  : 79.45 %
  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:  0.17 (0.30), residues: 761
  helix:  1.23 (0.26), residues: 368
  sheet:  0.10 (0.46), residues: 141
  loop : -1.54 (0.36), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 180 
 TYR   0.015   0.002   TYR C 156 
 PHE   0.018   0.002   PHE A  96 
 TRP   0.014   0.001   TRP B  93 
 HIS   0.001   0.000   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 6166)
  covalent geometry    : angle       0.64530 ( 8310)
  SS BOND              : bond        0.00673 (    3)
  SS BOND              : angle       0.73792 (    6)
  hydrogen bonds       : bond        0.03979 (  362)
  hydrogen bonds       : angle       4.24870 ( 1071)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 156
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A   36 LYS cc_start: 0.9358 (mmmm) cc_final: 0.8944 (mmmm)
REVERT: A  105 ARG cc_start: 0.6689 (ttm170) cc_final: 0.5437 (tpt170)
REVERT: A  109 ARG cc_start: 0.8100 (mpt-90) cc_final: 0.7875 (mmm-85)
REVERT: A  131 MET cc_start: 0.7653 (mpp) cc_final: 0.7132 (mpp)
REVERT: A  135 TYR cc_start: 0.7264 (m-80) cc_final: 0.6906 (m-10)
REVERT: A  138 TRP cc_start: 0.5137 (p-90) cc_final: 0.3138 (m100)
REVERT: B   95 ASP cc_start: 0.6474 (t0) cc_final: 0.6180 (t0)
REVERT: C  264 PHE cc_start: 0.8621 (t80) cc_final: 0.8268 (t80)
REVERT: H  124 ASP cc_start: 0.8881 (p0) cc_final: 0.8672 (p0)
REVERT: L   35 LEU cc_start: 0.8251 (mm) cc_final: 0.7875 (tp)
  outliers start: 25
  outliers final: 16
  residues processed: 170
  average time/residue: 0.0823
  time to fit residues: 18.2186
Evaluate side-chains
  158 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 142
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ILE
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  159 TYR
Chi-restraints excluded: chain C residue  118 HIS
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain C residue  393 ILE
Chi-restraints excluded: chain D residue   67 PHE
Chi-restraints excluded: chain H residue   69 VAL
Chi-restraints excluded: chain H residue   89 THR
Chi-restraints excluded: chain H residue  109 THR
Chi-restraints excluded: chain H residue  133 THR
Chi-restraints excluded: chain L residue   23 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 44 optimal weight:    0.1980
   chunk 26 optimal weight:    0.0670
   chunk 73 optimal weight:    2.9990
   chunk 75 optimal weight:   10.0000
   chunk 7 optimal weight:    5.9990
   chunk 13 optimal weight:    0.6980
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:    0.5980
   chunk 36 optimal weight:    0.3980
   chunk 23 optimal weight:    5.9990
   overall best weight:    0.3918

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

Flipped N/Q/H residues before XYZ refinement:
C 179 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.140291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.110557 restraints weight = 12247.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.109419 restraints weight = 8591.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.110570 restraints weight = 7785.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.110896 restraints weight = 5867.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.111188 restraints weight = 5839.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.3055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6169  Z= 0.115
  Angle     :  0.589  11.485   8316  Z= 0.294
  Chirality :  0.041   0.144    900
  Planarity :  0.004   0.039   1065
  Dihedral  :  8.635  56.881    909
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 18.12 %
    Favored  : 77.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.58 (0.30), residues: 761
  helix:  1.72 (0.27), residues: 368
  sheet:  0.21 (0.45), residues: 145
  loop : -1.57 (0.36), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 181 
 TYR   0.013   0.001   TYR C 296 
 PHE   0.011   0.001   PHE A  18 
 TRP   0.018   0.001   TRP B  93 
 HIS   0.002   0.001   HIS H  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 6166)
  covalent geometry    : angle       0.58824 ( 8310)
  SS BOND              : bond        0.00524 (    3)
  SS BOND              : angle       1.30239 (    6)
  hydrogen bonds       : bond        0.03523 (  362)
  hydrogen bonds       : angle       3.95070 ( 1071)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 153
  time to evaluate  : 0.300 
Fit side-chains
REVERT: A   36 LYS cc_start: 0.9347 (mmmm) cc_final: 0.9080 (mmmm)
REVERT: A  105 ARG cc_start: 0.6433 (ttm170) cc_final: 0.5594 (tpt170)
REVERT: A  109 ARG cc_start: 0.8122 (mpt-90) cc_final: 0.7811 (mmm-85)
REVERT: A  131 MET cc_start: 0.7794 (mpp) cc_final: 0.7224 (mpp)
REVERT: C  264 PHE cc_start: 0.8624 (t80) cc_final: 0.8243 (t80)
REVERT: D   24 MET cc_start: 0.7744 (mtt) cc_final: 0.7082 (ttt)
REVERT: D   25 MET cc_start: 0.7939 (mmm) cc_final: 0.7625 (tpp)
REVERT: H  124 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.8445 (p0)
REVERT: L   35 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7884 (tp)
  outliers start: 29
  outliers final: 16
  residues processed: 167
  average time/residue: 0.0837
  time to fit residues: 18.1753
Evaluate side-chains
  160 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 142
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ILE
Chi-restraints excluded: chain A residue  108 TRP
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain C residue  118 HIS
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain C residue  393 ILE
Chi-restraints excluded: chain D residue   67 PHE
Chi-restraints excluded: chain H residue   69 VAL
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue   89 THR
Chi-restraints excluded: chain H residue  109 THR
Chi-restraints excluded: chain H residue  124 ASP
Chi-restraints excluded: chain H residue  133 THR
Chi-restraints excluded: chain H residue  134 VAL
Chi-restraints excluded: chain L residue   22 ILE
Chi-restraints excluded: chain L residue   23 VAL
Chi-restraints excluded: chain L residue   35 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 42 optimal weight:    0.7980
   chunk 12 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9990
   chunk 56 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0020
   chunk 24 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9990
   chunk 21 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0040
   overall best weight:    0.5604

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

Flipped N/Q/H residues before XYZ refinement:
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  92 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.140076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.111024 restraints weight = 12320.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.108914 restraints weight = 9067.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.110084 restraints weight = 8129.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.110510 restraints weight = 6331.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.111063 restraints weight = 6069.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.3370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6169  Z= 0.119
  Angle     :  0.582  11.406   8316  Z= 0.291
  Chirality :  0.041   0.155    900
  Planarity :  0.004   0.041   1065
  Dihedral  :  8.079  56.030    906
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 19.90 %
    Favored  : 75.73 %
  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:  0.82 (0.31), residues: 761
  helix:  1.92 (0.26), residues: 375
  sheet:  0.23 (0.45), residues: 145
  loop : -1.48 (0.37), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 181 
 TYR   0.013   0.001   TYR C 296 
 PHE   0.017   0.001   PHE A  96 
 TRP   0.022   0.001   TRP B  93 
 HIS   0.003   0.001   HIS C 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 6166)
  covalent geometry    : angle       0.58110 ( 8310)
  SS BOND              : bond        0.00552 (    3)
  SS BOND              : angle       1.18944 (    6)
  hydrogen bonds       : bond        0.03398 (  362)
  hydrogen bonds       : angle       3.75074 ( 1071)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 150
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A   36 LYS cc_start: 0.9320 (mmmm) cc_final: 0.9042 (mmmm)
REVERT: A  105 ARG cc_start: 0.6708 (ttm170) cc_final: 0.5408 (tpt170)
REVERT: A  109 ARG cc_start: 0.8211 (mpt-90) cc_final: 0.7900 (mmm-85)
REVERT: A  131 MET cc_start: 0.7794 (mpp) cc_final: 0.7283 (mpp)
REVERT: C  264 PHE cc_start: 0.8637 (t80) cc_final: 0.8282 (t80)
REVERT: C  332 PHE cc_start: 0.8294 (m-10) cc_final: 0.8056 (m-10)
REVERT: D   24 MET cc_start: 0.7762 (mtt) cc_final: 0.7142 (ttt)
REVERT: D   25 MET cc_start: 0.8079 (mmm) cc_final: 0.7827 (tpp)
REVERT: L   35 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7909 (tp)
  outliers start: 27
  outliers final: 19
  residues processed: 161
  average time/residue: 0.0668
  time to fit residues: 14.0631
Evaluate side-chains
  161 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 141
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ILE
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  138 TRP
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  158 SER
Chi-restraints excluded: chain C residue  118 HIS
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain C residue  393 ILE
Chi-restraints excluded: chain D residue   67 PHE
Chi-restraints excluded: chain H residue   69 VAL
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue   89 THR
Chi-restraints excluded: chain H residue  109 THR
Chi-restraints excluded: chain H residue  133 THR
Chi-restraints excluded: chain H residue  134 VAL
Chi-restraints excluded: chain L residue   23 VAL
Chi-restraints excluded: chain L residue   35 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0770
   chunk 19 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   chunk 60 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    1.3142

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

Flipped N/Q/H residues before XYZ refinement:
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.133856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.102901 restraints weight = 12624.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.102372 restraints weight = 8420.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.103278 restraints weight = 8165.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.103879 restraints weight = 5979.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.104217 restraints weight = 5540.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.3538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6169  Z= 0.169
  Angle     :  0.630   9.400   8316  Z= 0.318
  Chirality :  0.043   0.154    900
  Planarity :  0.004   0.044   1065
  Dihedral  :  8.204  59.330    906
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 19.90 %
    Favored  : 75.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.86 (0.31), residues: 761
  helix:  2.01 (0.26), residues: 372
  sheet:  0.10 (0.44), residues: 149
  loop : -1.46 (0.37), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 180 
 TYR   0.015   0.002   TYR C 296 
 PHE   0.019   0.002   PHE H  99 
 TRP   0.026   0.002   TRP B  93 
 HIS   0.003   0.001   HIS C 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 6166)
  covalent geometry    : angle       0.62968 ( 8310)
  SS BOND              : bond        0.00690 (    3)
  SS BOND              : angle       1.31951 (    6)
  hydrogen bonds       : bond        0.03782 (  362)
  hydrogen bonds       : angle       3.89865 ( 1071)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 143
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A   36 LYS cc_start: 0.9317 (mmmm) cc_final: 0.9051 (mmmm)
REVERT: A  105 ARG cc_start: 0.6928 (ttm170) cc_final: 0.5478 (tpt170)
REVERT: A  109 ARG cc_start: 0.8242 (mpt-90) cc_final: 0.7930 (mmm-85)
REVERT: A  131 MET cc_start: 0.7887 (mpp) cc_final: 0.7419 (mpp)
REVERT: D   24 MET cc_start: 0.7714 (mtt) cc_final: 0.7149 (ttt)
REVERT: L   35 LEU cc_start: 0.8292 (mm) cc_final: 0.7928 (tp)
  outliers start: 30
  outliers final: 25
  residues processed: 158
  average time/residue: 0.0875
  time to fit residues: 17.8046
Evaluate side-chains
  164 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 139
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ILE
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  108 TRP
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  158 SER
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain C residue  118 HIS
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain C residue  295 GLU
Chi-restraints excluded: chain C residue  382 THR
Chi-restraints excluded: chain C residue  393 ILE
Chi-restraints excluded: chain D residue   67 PHE
Chi-restraints excluded: chain H residue   31 VAL
Chi-restraints excluded: chain H residue   69 VAL
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue   89 THR
Chi-restraints excluded: chain H residue  107 ASP
Chi-restraints excluded: chain H residue  109 THR
Chi-restraints excluded: chain H residue  133 THR
Chi-restraints excluded: chain H residue  134 VAL
Chi-restraints excluded: chain L residue   22 ILE
Chi-restraints excluded: chain L residue   23 VAL
Chi-restraints excluded: chain L residue   99 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 46 optimal weight:    0.0170
   chunk 55 optimal weight:    0.7980
   chunk 67 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 2 optimal weight:    7.9990
   chunk 3 optimal weight:    0.2980
   chunk 71 optimal weight:    0.1980
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.4218

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

Flipped N/Q/H residues before XYZ refinement:
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.136438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.106239 restraints weight = 12455.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.105246 restraints weight = 8262.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.106171 restraints weight = 9153.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.106648 restraints weight = 6225.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.107400 restraints weight = 5662.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.3720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   6169  Z= 0.114
  Angle     :  0.583   9.483   8316  Z= 0.293
  Chirality :  0.041   0.152    900
  Planarity :  0.004   0.042   1065
  Dihedral  :  8.000  57.826    906
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 21.36 %
    Favored  : 74.60 %
  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:  0.98 (0.31), residues: 761
  helix:  2.13 (0.26), residues: 374
  sheet:  0.22 (0.45), residues: 143
  loop : -1.49 (0.36), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 134 
 TYR   0.010   0.001   TYR C 296 
 PHE   0.016   0.001   PHE C 264 
 TRP   0.021   0.001   TRP B  93 
 HIS   0.003   0.001   HIS C 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 6166)
  covalent geometry    : angle       0.58230 ( 8310)
  SS BOND              : bond        0.00522 (    3)
  SS BOND              : angle       1.32406 (    6)
  hydrogen bonds       : bond        0.03390 (  362)
  hydrogen bonds       : angle       3.72393 ( 1071)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 144
  time to evaluate  : 0.253 
Fit side-chains
REVERT: A   36 LYS cc_start: 0.9314 (mmmm) cc_final: 0.8934 (mmmm)
REVERT: A   83 ARG cc_start: 0.7011 (ttp-170) cc_final: 0.6622 (ttp-170)
REVERT: A  105 ARG cc_start: 0.6483 (ttm170) cc_final: 0.5453 (tpt170)
REVERT: A  109 ARG cc_start: 0.8165 (mpt-90) cc_final: 0.7887 (mmm-85)
REVERT: C  274 TYR cc_start: 0.9049 (m-80) cc_final: 0.8781 (m-80)
REVERT: C  328 GLN cc_start: 0.8205 (tp-100) cc_final: 0.7837 (tp-100)
REVERT: C  332 PHE cc_start: 0.8360 (m-10) cc_final: 0.7859 (m-80)
REVERT: D   24 MET cc_start: 0.7336 (mtt) cc_final: 0.6993 (ttt)
REVERT: D   67 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.8404 (t80)
REVERT: L   35 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7951 (tp)
  outliers start: 25
  outliers final: 18
  residues processed: 156
  average time/residue: 0.0705
  time to fit residues: 14.3682
Evaluate side-chains
  161 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 141
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ILE
Chi-restraints excluded: chain A residue  108 TRP
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  158 SER
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain C residue  118 HIS
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain C residue  295 GLU
Chi-restraints excluded: chain C residue  393 ILE
Chi-restraints excluded: chain D residue   67 PHE
Chi-restraints excluded: chain H residue   69 VAL
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue   89 THR
Chi-restraints excluded: chain H residue  109 THR
Chi-restraints excluded: chain H residue  134 VAL
Chi-restraints excluded: chain L residue   23 VAL
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain L residue   99 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 57 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   chunk 59 optimal weight:    0.0970
   chunk 32 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.135811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.100380 restraints weight = 12397.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.103047 restraints weight = 7675.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.104863 restraints weight = 5676.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.105969 restraints weight = 4669.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.106606 restraints weight = 4135.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.3852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6169  Z= 0.126
  Angle     :  0.617  16.190   8316  Z= 0.303
  Chirality :  0.042   0.154    900
  Planarity :  0.004   0.042   1065
  Dihedral  :  7.896  56.454    906
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 22.33 %
    Favored  : 73.46 %
  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:  0.99 (0.31), residues: 761
  helix:  2.12 (0.26), residues: 377
  sheet:  0.09 (0.44), residues: 147
  loop : -1.42 (0.37), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  91 
 TYR   0.009   0.001   TYR C 338 
 PHE   0.012   0.001   PHE H  99 
 TRP   0.020   0.001   TRP B  93 
 HIS   0.004   0.001   HIS C 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 6166)
  covalent geometry    : angle       0.61625 ( 8310)
  SS BOND              : bond        0.00316 (    3)
  SS BOND              : angle       1.08357 (    6)
  hydrogen bonds       : bond        0.03399 (  362)
  hydrogen bonds       : angle       3.71803 ( 1071)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 148
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 LYS cc_start: 0.9329 (mmmm) cc_final: 0.9108 (mmmm)
REVERT: A  105 ARG cc_start: 0.6520 (ttm170) cc_final: 0.5444 (tpt170)
REVERT: B   96 ASP cc_start: 0.7424 (m-30) cc_final: 0.7208 (m-30)
REVERT: B  161 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8568 (tt)
REVERT: C  118 HIS cc_start: 0.7079 (OUTLIER) cc_final: 0.6859 (p90)
REVERT: C  328 GLN cc_start: 0.8234 (tp-100) cc_final: 0.7826 (tp-100)
REVERT: C  332 PHE cc_start: 0.8369 (m-10) cc_final: 0.7831 (m-80)
REVERT: D   24 MET cc_start: 0.7767 (mtt) cc_final: 0.7243 (ttt)
REVERT: D   67 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8212 (t80)
REVERT: D   71 MET cc_start: 0.8364 (mmm) cc_final: 0.7809 (mmm)
REVERT: L   35 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7998 (tp)
  outliers start: 26
  outliers final: 18
  residues processed: 160
  average time/residue: 0.0824
  time to fit residues: 16.9304
Evaluate side-chains
  162 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ILE
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  158 SER
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain C residue  118 HIS
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain C residue  295 GLU
Chi-restraints excluded: chain C residue  393 ILE
Chi-restraints excluded: chain D residue   67 PHE
Chi-restraints excluded: chain H residue   69 VAL
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue   89 THR
Chi-restraints excluded: chain H residue  109 THR
Chi-restraints excluded: chain H residue  133 THR
Chi-restraints excluded: chain H residue  134 VAL
Chi-restraints excluded: chain L residue   23 VAL
Chi-restraints excluded: chain L residue   35 LEU
Chi-restraints excluded: chain L residue   99 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 31 optimal weight:    6.9990
   chunk 55 optimal weight:    0.8980
   chunk 43 optimal weight:    5.9990
   chunk 27 optimal weight:    8.9990
   chunk 32 optimal weight:    0.9990
   chunk 75 optimal weight:   10.0000
   chunk 58 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 21 optimal weight:   20.0000
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.132963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.097691 restraints weight = 12608.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.100312 restraints weight = 7745.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.102086 restraints weight = 5703.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.103163 restraints weight = 4695.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.103836 restraints weight = 4175.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.4024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   6169  Z= 0.211
  Angle     :  0.686  13.628   8316  Z= 0.344
  Chirality :  0.044   0.159    900
  Planarity :  0.004   0.043   1065
  Dihedral  :  8.246  55.402    906
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 22.33 %
    Favored  : 72.98 %
  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:  0.77 (0.30), residues: 761
  helix:  2.00 (0.26), residues: 376
  sheet: -0.04 (0.44), residues: 147
  loop : -1.60 (0.37), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 404 
 TYR   0.018   0.002   TYR H 117 
 PHE   0.020   0.002   PHE H  99 
 TRP   0.015   0.001   TRP B  93 
 HIS   0.003   0.001   HIS C 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 ( 6166)
  covalent geometry    : angle       0.68512 ( 8310)
  SS BOND              : bond        0.00815 (    3)
  SS BOND              : angle       1.33243 (    6)
  hydrogen bonds       : bond        0.03976 (  362)
  hydrogen bonds       : angle       4.03312 ( 1071)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 139
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 LYS cc_start: 0.9340 (mmmm) cc_final: 0.9126 (mmmm)
REVERT: A   83 ARG cc_start: 0.6513 (ttp-170) cc_final: 0.6240 (ttp-170)
REVERT: B  161 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8584 (tt)
REVERT: C  156 TYR cc_start: 0.6139 (m-80) cc_final: 0.5443 (m-80)
REVERT: C  332 PHE cc_start: 0.8501 (m-10) cc_final: 0.8179 (m-80)
REVERT: D   24 MET cc_start: 0.7697 (mtt) cc_final: 0.7223 (ttt)
REVERT: D   67 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8428 (t80)
REVERT: H   70 MET cc_start: 0.7941 (tmm) cc_final: 0.7571 (tmm)
REVERT: L   35 LEU cc_start: 0.8308 (mm) cc_final: 0.8090 (tp)
  outliers start: 29
  outliers final: 18
  residues processed: 156
  average time/residue: 0.0758
  time to fit residues: 15.4430
Evaluate side-chains
  156 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 136
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ILE
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  158 SER
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain C residue  118 HIS
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain C residue  295 GLU
Chi-restraints excluded: chain C residue  382 THR
Chi-restraints excluded: chain C residue  393 ILE
Chi-restraints excluded: chain D residue   67 PHE
Chi-restraints excluded: chain H residue   69 VAL
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue   89 THR
Chi-restraints excluded: chain H residue  109 THR
Chi-restraints excluded: chain H residue  133 THR
Chi-restraints excluded: chain L residue   23 VAL
Chi-restraints excluded: chain L residue   54 ILE
Chi-restraints excluded: chain L residue   99 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 67 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 53 optimal weight:    0.4980
   chunk 57 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  37 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.134883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.099924 restraints weight = 12519.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.102568 restraints weight = 7809.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.104330 restraints weight = 5772.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.105437 restraints weight = 4759.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.105956 restraints weight = 4212.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.4125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6169  Z= 0.130
  Angle     :  0.651  12.436   8316  Z= 0.322
  Chirality :  0.042   0.154    900
  Planarity :  0.004   0.043   1065
  Dihedral  :  8.114  58.917    906
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 23.62 %
    Favored  : 72.33 %
  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:  1.00 (0.31), residues: 761
  helix:  2.15 (0.26), residues: 375
  sheet:  0.04 (0.44), residues: 147
  loop : -1.38 (0.38), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  91 
 TYR   0.010   0.001   TYR C 377 
 PHE   0.016   0.001   PHE A 132 
 TRP   0.027   0.001   TRP B  93 
 HIS   0.004   0.001   HIS C 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 6166)
  covalent geometry    : angle       0.65015 ( 8310)
  SS BOND              : bond        0.00369 (    3)
  SS BOND              : angle       1.04453 (    6)
  hydrogen bonds       : bond        0.03485 (  362)
  hydrogen bonds       : angle       3.81886 ( 1071)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 143
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 ILE cc_start: 0.8637 (pt) cc_final: 0.8287 (mt)
REVERT: A   36 LYS cc_start: 0.9330 (mmmm) cc_final: 0.9106 (mmmm)
REVERT: A  105 ARG cc_start: 0.6664 (ttm170) cc_final: 0.5422 (tpt170)
REVERT: B   96 ASP cc_start: 0.7356 (m-30) cc_final: 0.7136 (m-30)
REVERT: C  156 TYR cc_start: 0.6221 (m-80) cc_final: 0.5571 (m-80)
REVERT: C  274 TYR cc_start: 0.9081 (m-80) cc_final: 0.8869 (m-80)
REVERT: D   24 MET cc_start: 0.7412 (mtt) cc_final: 0.7028 (ttt)
REVERT: D   67 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8441 (t80)
REVERT: L   35 LEU cc_start: 0.8318 (mm) cc_final: 0.8013 (tp)
  outliers start: 25
  outliers final: 19
  residues processed: 156
  average time/residue: 0.0841
  time to fit residues: 17.0592
Evaluate side-chains
  160 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 140
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ILE
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  158 SER
Chi-restraints excluded: chain C residue  118 HIS
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain C residue  295 GLU
Chi-restraints excluded: chain C residue  382 THR
Chi-restraints excluded: chain C residue  393 ILE
Chi-restraints excluded: chain D residue   25 MET
Chi-restraints excluded: chain D residue   67 PHE
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue   89 THR
Chi-restraints excluded: chain H residue  109 THR
Chi-restraints excluded: chain H residue  133 THR
Chi-restraints excluded: chain H residue  134 VAL
Chi-restraints excluded: chain L residue   23 VAL
Chi-restraints excluded: chain L residue   99 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 40 optimal weight:    0.0570
   chunk 18 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   chunk 30 optimal weight:    5.9990
   chunk 70 optimal weight:    0.5980
   chunk 12 optimal weight:    3.9990
   chunk 74 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.6700

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

Flipped N/Q/H residues before XYZ refinement:
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.135131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.104703 restraints weight = 12400.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.105362 restraints weight = 8987.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.105899 restraints weight = 7331.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.106433 restraints weight = 6033.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.106483 restraints weight = 5673.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.4194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6169  Z= 0.130
  Angle     :  0.648  11.172   8316  Z= 0.321
  Chirality :  0.042   0.157    900
  Planarity :  0.004   0.044   1065
  Dihedral  :  8.028  57.386    906
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 23.79 %
    Favored  : 72.65 %
  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:  1.03 (0.31), residues: 761
  helix:  2.14 (0.26), residues: 378
  sheet:  0.35 (0.45), residues: 137
  loop : -1.50 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  91 
 TYR   0.008   0.001   TYR C 398 
 PHE   0.019   0.002   PHE B 114 
 TRP   0.025   0.001   TRP B  93 
 HIS   0.003   0.001   HIS C 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 6166)
  covalent geometry    : angle       0.64554 ( 8310)
  SS BOND              : bond        0.00758 (    3)
  SS BOND              : angle       2.27574 (    6)
  hydrogen bonds       : bond        0.03403 (  362)
  hydrogen bonds       : angle       3.78306 ( 1071)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 138
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 ILE cc_start: 0.8699 (pt) cc_final: 0.8388 (mt)
REVERT: A   36 LYS cc_start: 0.9316 (mmmm) cc_final: 0.9081 (mmmm)
REVERT: A  105 ARG cc_start: 0.6659 (ttm170) cc_final: 0.5352 (tpt170)
REVERT: C  156 TYR cc_start: 0.6174 (m-80) cc_final: 0.5495 (m-80)
REVERT: C  274 TYR cc_start: 0.9083 (m-80) cc_final: 0.8830 (m-80)
REVERT: C  332 PHE cc_start: 0.8184 (m-10) cc_final: 0.7970 (m-10)
REVERT: D   24 MET cc_start: 0.7236 (mtt) cc_final: 0.7007 (ttt)
REVERT: D   67 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.8284 (t80)
REVERT: L   35 LEU cc_start: 0.8265 (mm) cc_final: 0.8017 (tp)
  outliers start: 22
  outliers final: 18
  residues processed: 149
  average time/residue: 0.0868
  time to fit residues: 16.8052
Evaluate side-chains
  155 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ILE
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  158 SER
Chi-restraints excluded: chain C residue  118 HIS
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain C residue  295 GLU
Chi-restraints excluded: chain C residue  382 THR
Chi-restraints excluded: chain C residue  393 ILE
Chi-restraints excluded: chain D residue   67 PHE
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue   89 THR
Chi-restraints excluded: chain H residue  109 THR
Chi-restraints excluded: chain H residue  133 THR
Chi-restraints excluded: chain H residue  134 VAL
Chi-restraints excluded: chain L residue   99 ILE
Chi-restraints excluded: chain L residue  128 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 75 optimal weight:    9.9990
   chunk 12 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0770
   chunk 5 optimal weight:    0.9980
   chunk 50 optimal weight:    0.0870
   chunk 10 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0040
   overall best weight:    0.3328

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

Flipped N/Q/H residues before XYZ refinement:
** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.136783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.106584 restraints weight = 12398.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.107444 restraints weight = 8677.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.107906 restraints weight = 7128.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.108213 restraints weight = 6001.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.109105 restraints weight = 5263.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.4327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6169  Z= 0.123
  Angle     :  0.652  13.387   8316  Z= 0.324
  Chirality :  0.042   0.153    900
  Planarity :  0.004   0.042   1065
  Dihedral  :  7.817  59.510    906
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 24.60 %
    Favored  : 72.01 %
  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:  1.17 (0.31), residues: 761
  helix:  2.26 (0.26), residues: 377
  sheet:  0.39 (0.45), residues: 141
  loop : -1.42 (0.38), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  91 
 TYR   0.010   0.001   TYR C 398 
 PHE   0.018   0.001   PHE C 264 
 TRP   0.027   0.001   TRP B  93 
 HIS   0.005   0.001   HIS H  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 6166)
  covalent geometry    : angle       0.65061 ( 8310)
  SS BOND              : bond        0.00542 (    3)
  SS BOND              : angle       1.79147 (    6)
  hydrogen bonds       : bond        0.03240 (  362)
  hydrogen bonds       : angle       3.73938 ( 1071)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1173.68 seconds
wall clock time: 20 minutes 57.52 seconds (1257.52 seconds total)