Starting phenix.real_space_refine
on Sat Jul 26 00:57:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xou_33359/07_2025/7xou_33359.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xou_33359/07_2025/7xou_33359.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xou_33359/07_2025/7xou_33359.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xou_33359/07_2025/7xou_33359.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xou_33359/07_2025/7xou_33359.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xou_33359/07_2025/7xou_33359.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
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: 4
    Type Number    sf(0)   Gaussians
     S      63      5.16       5
     C    5231      2.51       5
     N    1433      2.21       5
     O    1520      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8247
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "L"
      Number of atoms: 77
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 77
          Classifications: {'peptide': 8}
          Link IDs: {'TRANS': 7}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'TYS:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "L"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 1884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1884
          Classifications: {'peptide': 227}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 220}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "R"
      Number of atoms: 2288
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2288
          Classifications: {'peptide': 287}
          Link IDs: {'PTRANS': 11, 'TRANS': 275}
          Chain breaks: 1
  Time building chain proxies: 4.82, per 1000 atoms: 0.58
  Number of scatterers: 8247
  At special positions: 0
  Unit cell: (90.246, 91.26, 129.792, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      63     16.00
     O    1520      8.00
     N    1433      7.00
     C    5231      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 114 " - pdb=" SG  CYS R 196 " 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.03
  Conformation dependent library (CDL) restraints added in 909.0 milliseconds
  

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1968

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 11 sheets defined
      39.8% alpha, 19.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 38
      removed outlier: 3.545A  pdb=" N   ILE A  26 " --> pdb=" O   ALA A  22 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 59
      removed outlier: 3.729A  pdb=" N   GLN A  59 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 240
      removed outlier: 3.860A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   ASP A 240 " --> pdb=" O   CYS A 237 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 236 through 240'
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 302
      removed outlier: 3.584A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LEU A 302 " --> pdb=" O   ALA A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 318
      removed outlier: 3.917A  pdb=" N   TYR A 318 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.724A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   GLY A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 388
      removed outlier: 3.626A  pdb=" N   ASP A 378 " --> pdb=" O   ARG A 374 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ARG A 385 " --> pdb=" O   ASP A 381 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   MET A 386 " --> pdb=" O   ILE A 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 8 through 22
      removed outlier: 3.670A  pdb=" N   ALA G  12 " --> pdb=" O   SER G   8 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   LYS G  14 " --> pdb=" O   ALA G  10 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.575A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.824A  pdb=" N   ASN N  31 " --> pdb=" O   THR N  28 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 28 through 32'
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.800A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 44 through 69
      removed outlier: 3.976A  pdb=" N   PHE R  52 " --> pdb=" O   TYR R  48 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   SER R  55 " --> pdb=" O   ILE R  51 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   GLY R  58 " --> pdb=" O   LEU R  54 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ASN R  69 " --> pdb=" O   VAL R  65 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 74 through 94
      removed outlier: 3.980A  pdb=" N   PHE R  79 " --> pdb=" O   VAL R  75 " (cutoff:3.500A)
      removed outlier: 5.151A  pdb=" N   LEU R  80 " --> pdb=" O   THR R  76 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 95 through 105
      Proline residue:  R 101  - end of helix
    Processing helix  chain 'R' and resid 110 through 144
      removed outlier: 4.612A  pdb=" N   THR R 116 " --> pdb=" O   ALA R 112 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   THR R 117 " --> pdb=" O   VAL R 113 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   VAL R 125 " --> pdb=" O   MET R 121 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLY R 141 " --> pdb=" O   LEU R 137 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 154 through 173
    Processing helix  chain 'R' and resid 202 through 218
    Processing helix  chain 'R' and resid 219 through 244
      removed outlier: 4.003A  pdb=" N   GLU R 243 " --> pdb=" O   GLY R 239 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 302 through 339
      Proline residue:  R 328  - end of helix
    Processing helix  chain 'R' and resid 350 through 370
      removed outlier: 4.044A  pdb=" N   SER R 359 " --> pdb=" O   ILE R 355 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   THR R 361 " --> pdb=" O   LEU R 357 " (cutoff:3.500A)
      removed outlier: 4.924A  pdb=" N   SER R 362 " --> pdb=" O   LEU R 358 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   SER R 363 " --> pdb=" O   SER R 359 " (cutoff:3.500A)
      Proline residue:  R 367  - end of helix
    Processing helix  chain 'R' and resid 375 through 385
      removed outlier: 4.054A  pdb=" N   LEU R 379 " --> pdb=" O   LYS R 375 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ALA R 383 " --> pdb=" O   LEU R 379 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 3.568A  pdb=" N   LEU A  45 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 9.657A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.690A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.263A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.687A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 61
      removed outlier: 6.861A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.966A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 4.107A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.428A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.388A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.787A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.923A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.713A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.480A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.413A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.506A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.099A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.203A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11
      removed outlier: 6.778A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ASP N  50 " --> pdb=" O   SER N  59 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 179 through 182
      removed outlier: 3.606A  pdb=" N   ARG R 197 " --> pdb=" O   SER R 180 " (cutoff:3.500A)

    394 hydrogen bonds defined for protein.
    1128 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.32

  Time building geometry restraints manager: 2.39 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2680
        1.34 -     1.46: 1989
        1.46 -     1.58: 3647
        1.58 -     1.70: 1
        1.70 -     1.82: 92
  Bond restraints: 8409
  Sorted by residual:
  bond pdb=" O1  TYS L   2 "
       pdb=" S   TYS L   2 "
    ideal  model  delta    sigma   weight residual
    1.462  1.630 -0.168 2.00e-02 2.50e+03 7.07e+01
  bond pdb=" OH  TYS L   2 "
       pdb=" S   TYS L   2 "
    ideal  model  delta    sigma   weight residual
    1.679  1.531  0.148 2.00e-02 2.50e+03 5.48e+01
  bond pdb=" N   TRP L   5 "
       pdb=" CA  TRP L   5 "
    ideal  model  delta    sigma   weight residual
    1.458  1.432  0.027 1.08e-02 8.57e+03 6.04e+00
  bond pdb=" C   VAL R 183 "
       pdb=" N   PRO R 184 "
    ideal  model  delta    sigma   weight residual
    1.334  1.376 -0.042 2.34e-02 1.83e+03 3.19e+00
  bond pdb=" C   GLY L   4 "
       pdb=" N   TRP L   5 "
    ideal  model  delta    sigma   weight residual
    1.336  1.313  0.023 1.55e-02 4.16e+03 2.30e+00
  ... (remaining 8404 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.96: 11120
        1.96 -     3.92: 212
        3.92 -     5.88: 30
        5.88 -     7.84: 15
        7.84 -     9.79: 2
  Bond angle restraints: 11379
  Sorted by residual:
  angle pdb=" N   TRP L   5 "
        pdb=" CA  TRP L   5 "
        pdb=" C   TRP L   5 "
      ideal   model   delta    sigma   weight residual
     112.30  105.02    7.28 1.36e+00 5.41e-01 2.87e+01
  angle pdb=" C   MET L   6 "
        pdb=" CA  MET L   6 "
        pdb=" CB  MET L   6 "
      ideal   model   delta    sigma   weight residual
     116.54  110.40    6.14 1.15e+00 7.56e-01 2.85e+01
  angle pdb=" CA  MET L   6 "
        pdb=" C   MET L   6 "
        pdb=" N   ASP L   7 "
      ideal   model   delta    sigma   weight residual
     119.52  115.50    4.02 7.90e-01 1.60e+00 2.58e+01
  angle pdb=" N   SER R 180 "
        pdb=" CA  SER R 180 "
        pdb=" C   SER R 180 "
      ideal   model   delta    sigma   weight residual
     108.45  114.06   -5.61 1.26e+00 6.30e-01 1.98e+01
  angle pdb=" N   VAL R 183 "
        pdb=" CA  VAL R 183 "
        pdb=" C   VAL R 183 "
      ideal   model   delta    sigma   weight residual
     108.88  116.53   -7.65 2.16e+00 2.14e-01 1.25e+01
  ... (remaining 11374 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.06: 4464
       16.06 -    32.12: 461
       32.12 -    48.18: 83
       48.18 -    64.24: 17
       64.24 -    80.31: 7
  Dihedral angle restraints: 5032
    sinusoidal: 1998
      harmonic: 3034
  Sorted by residual:
  dihedral pdb=" CB  CYS R 114 "
           pdb=" SG  CYS R 114 "
           pdb=" SG  CYS R 196 "
           pdb=" CB  CYS R 196 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  173.31  -80.31     1      1.00e+01 1.00e-02 7.98e+01
  dihedral pdb=" CA  LEU R 200 "
           pdb=" C   LEU R 200 "
           pdb=" N   PRO R 201 "
           pdb=" CA  PRO R 201 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -147.78  -32.22     0      5.00e+00 4.00e-02 4.15e+01
  dihedral pdb=" CA  CYS R  94 "
           pdb=" C   CYS R  94 "
           pdb=" N   MET R  95 "
           pdb=" CA  MET R  95 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.11  -28.89     0      5.00e+00 4.00e-02 3.34e+01
  ... (remaining 5029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 795
       0.035 -    0.069: 333
       0.069 -    0.104: 118
       0.104 -    0.139: 37
       0.139 -    0.174: 4
  Chirality restraints: 1287
  Sorted by residual:
  chirality pdb=" CA  THR R 350 "
            pdb=" N   THR R 350 "
            pdb=" C   THR R 350 "
            pdb=" CB  THR R 350 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.35    0.17 2.00e-01 2.50e+01 7.53e-01
  chirality pdb=" CA  PRO R 201 "
            pdb=" N   PRO R 201 "
            pdb=" C   PRO R 201 "
            pdb=" CB  PRO R 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 7.24e-01
  chirality pdb=" CA  THR R 174 "
            pdb=" N   THR R 174 "
            pdb=" C   THR R 174 "
            pdb=" CB  THR R 174 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.36    0.17 2.00e-01 2.50e+01 7.01e-01
  ... (remaining 1284 not shown)

  Planarity restraints: 1445
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET R  95 "    0.010 2.00e-02 2.50e+03   2.01e-02 4.06e+00
        pdb=" C   MET R  95 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   MET R  95 "    0.013 2.00e-02 2.50e+03
        pdb=" N   PRO R  96 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET L   3 "   -0.010 2.00e-02 2.50e+03   1.97e-02 3.90e+00
        pdb=" C   MET L   3 "    0.034 2.00e-02 2.50e+03
        pdb=" O   MET L   3 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   GLY L   4 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R 242 "    0.010 2.00e-02 2.50e+03   1.44e-02 3.63e+00
        pdb=" CG  PHE R 242 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 PHE R 242 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE R 242 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 PHE R 242 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE R 242 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE R 242 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1442 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 783
        2.74 -     3.28: 8415
        3.28 -     3.82: 13572
        3.82 -     4.36: 16321
        4.36 -     4.90: 28075
  Nonbonded interactions: 67166
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" OD2 ASP B 247 "
            pdb=" NH2 ARG B 251 "
     model   vdw
     2.206 3.120
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" OE2 GLU A 230 "
            pdb=" NH1 ARG A 232 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" O   ASP A 368 "
            pdb=" ND2 ASN A 371 "
     model   vdw
     2.221 3.120
  ... (remaining 67161 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.240
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.040
  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:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6435
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   0.168   8413  Z= 0.225
  Angle     :  0.707   9.794  11385  Z= 0.395
  Chirality :  0.045   0.174   1287
  Planarity :  0.005   0.047   1445
  Dihedral  : 13.469  76.468   3055
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  3.45 %
    Favored  : 96.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.52 (0.22), residues: 1021
  helix: -1.72 (0.22), residues: 384
  sheet: -2.12 (0.30), residues: 221
  loop : -2.94 (0.25), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 234 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.033   0.002   PHE R 242 
 TYR   0.014   0.001   TYR B  59 
 ARG   0.005   0.000   ARG B 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13363 (  394)
  hydrogen bonds       : angle       6.63465 ( 1128)
  SS BOND              : bond        0.00371 (    3)
  SS BOND              : angle       0.67087 (    6)
  covalent geometry    : bond        0.00386 ( 8409)
  covalent geometry    : angle       0.70718 (11379)
  Misc. bond           : bond        0.10101 (    1)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 192
  time to evaluate  : 1.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  291 LEU cc_start: 0.8099 (mp) cc_final: 0.7885 (mp)
REVERT: B  155 ASN cc_start: 0.8405 (t0) cc_final: 0.7831 (t0)
REVERT: N   72 ARG cc_start: 0.6911 (ptm160) cc_final: 0.5861 (ptp-170)
REVERT: R  105 LYS cc_start: 0.4547 (mttm) cc_final: 0.4273 (mptt)
REVERT: R  306 MET cc_start: 0.6633 (tpp) cc_final: 0.6323 (tpp)
REVERT: R  309 LYS cc_start: 0.6598 (ttpp) cc_final: 0.6389 (ptmt)
  outliers start: 1
  outliers final: 0
  residues processed: 192
  average time/residue: 0.2733
  time to fit residues: 68.5350
Evaluate side-chains
  152 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 40 optimal weight:    9.9990
   chunk 79 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 91 optimal weight:    1.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 387 HIS
A 390 GLN
B 110 ASN
B 259 GLN
N 120 GLN
** R  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 102 ASN
R 181 ASN
R 194 ASN
R 238 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4820 r_free = 0.4820 target = 0.243883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4578 r_free = 0.4578 target = 0.211547 restraints weight = 8864.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.4559 rms_B_bonded: 2.53
r_work: 0.4390 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.4390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6611
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8413  Z= 0.136
  Angle     :  0.618   7.942  11385  Z= 0.324
  Chirality :  0.043   0.160   1287
  Planarity :  0.004   0.047   1445
  Dihedral  :  5.166  41.371   1133
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 12.46 %
    Favored  : 85.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.81 (0.25), residues: 1021
  helix:  0.09 (0.27), residues: 383
  sheet: -1.35 (0.33), residues: 234
  loop : -2.33 (0.28), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP L   5 
 HIS   0.005   0.001   HIS A 387 
 PHE   0.017   0.002   PHE R 242 
 TYR   0.025   0.002   TYR N  60 
 ARG   0.005   0.000   ARG B 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04053 (  394)
  hydrogen bonds       : angle       5.19456 ( 1128)
  SS BOND              : bond        0.00724 (    3)
  SS BOND              : angle       1.48971 (    6)
  covalent geometry    : bond        0.00307 ( 8409)
  covalent geometry    : angle       0.61705 (11379)
  Misc. bond           : bond        0.00041 (    1)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 164
  time to evaluate  : 0.833 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  291 LEU cc_start: 0.8190 (mp) cc_final: 0.7772 (mp)
REVERT: B  155 ASN cc_start: 0.8626 (t0) cc_final: 0.7920 (t0)
REVERT: G   48 ASP cc_start: 0.7644 (t70) cc_final: 0.7100 (p0)
REVERT: R  105 LYS cc_start: 0.4661 (mttm) cc_final: 0.4461 (mttt)
REVERT: R  326 TRP cc_start: 0.7668 (m100) cc_final: 0.7334 (m100)
  outliers start: 14
  outliers final: 6
  residues processed: 170
  average time/residue: 0.2236
  time to fit residues: 50.8584
Evaluate side-chains
  154 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 148
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain R residue  150 ARG
Chi-restraints excluded: chain R residue  153 GLN
Chi-restraints excluded: chain R residue  340 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 32 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 33 optimal weight:   10.0000
   chunk 7 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 61 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9980
   chunk 25 optimal weight:    7.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
N  53 GLN
N 120 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4806 r_free = 0.4806 target = 0.242016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4554 r_free = 0.4554 target = 0.208987 restraints weight = 9062.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.4525 rms_B_bonded: 2.57
r_work: 0.4364 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.4364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6623
moved from start:          0.2127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8413  Z= 0.136
  Angle     :  0.604   7.726  11385  Z= 0.317
  Chirality :  0.043   0.156   1287
  Planarity :  0.004   0.045   1445
  Dihedral  :  5.035  44.457   1133
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 16.24 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.26), residues: 1021
  helix:  0.56 (0.27), residues: 382
  sheet: -1.07 (0.34), residues: 234
  loop : -2.05 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP L   5 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.015   0.001   PHE R 107 
 TYR   0.017   0.001   TYR N  60 
 ARG   0.005   0.000   ARG A 380 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03901 (  394)
  hydrogen bonds       : angle       4.96498 ( 1128)
  SS BOND              : bond        0.00356 (    3)
  SS BOND              : angle       0.52221 (    6)
  covalent geometry    : bond        0.00307 ( 8409)
  covalent geometry    : angle       0.60368 (11379)
  Misc. bond           : bond        0.00004 (    1)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 157
  time to evaluate  : 1.052 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L    7 ASP cc_start: 0.7120 (OUTLIER) cc_final: 0.6688 (m-30)
REVERT: A  291 LEU cc_start: 0.8105 (mp) cc_final: 0.7694 (mp)
REVERT: B   86 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8074 (p)
REVERT: B  155 ASN cc_start: 0.8597 (t0) cc_final: 0.7921 (t0)
REVERT: G   48 ASP cc_start: 0.7636 (t70) cc_final: 0.7074 (p0)
REVERT: R  105 LYS cc_start: 0.4676 (mttm) cc_final: 0.4276 (mptt)
  outliers start: 22
  outliers final: 13
  residues processed: 166
  average time/residue: 0.2285
  time to fit residues: 51.2026
Evaluate side-chains
  156 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 141
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    7 ASP
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue  102 ASN
Chi-restraints excluded: chain R residue  129 THR
Chi-restraints excluded: chain R residue  150 ARG
Chi-restraints excluded: chain R residue  153 GLN
Chi-restraints excluded: chain R residue  340 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 34 optimal weight:    7.9990
   chunk 41 optimal weight:    0.6980
   chunk 4 optimal weight:    9.9990
   chunk 63 optimal weight:    0.9980
   chunk 79 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9980
   chunk 76 optimal weight:    0.4980
   chunk 96 optimal weight:    0.9980
   chunk 25 optimal weight:   20.0000
   chunk 94 optimal weight:    5.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B   6 GLN
N  35 ASN
N 120 GLN
** R  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4816 r_free = 0.4816 target = 0.242977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4579 r_free = 0.4579 target = 0.211255 restraints weight = 8903.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.4560 rms_B_bonded: 2.49
r_work: 0.4401 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.4401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6563
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8413  Z= 0.116
  Angle     :  0.570   7.405  11385  Z= 0.300
  Chirality :  0.042   0.161   1287
  Planarity :  0.004   0.043   1445
  Dihedral  :  4.821  43.318   1133
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 17.91 %
    Favored  : 78.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.26), residues: 1021
  helix:  0.97 (0.28), residues: 378
  sheet: -0.83 (0.35), residues: 208
  loop : -1.89 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP L   5 
 HIS   0.002   0.001   HIS A 357 
 PHE   0.020   0.001   PHE A 363 
 TYR   0.017   0.001   TYR R 179 
 ARG   0.004   0.000   ARG A 380 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03611 (  394)
  hydrogen bonds       : angle       4.75608 ( 1128)
  SS BOND              : bond        0.00292 (    3)
  SS BOND              : angle       1.61210 (    6)
  covalent geometry    : bond        0.00258 ( 8409)
  covalent geometry    : angle       0.56852 (11379)
  Misc. bond           : bond        0.00003 (    1)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 153
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  291 LEU cc_start: 0.7888 (mp) cc_final: 0.7452 (mp)
REVERT: B   86 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8138 (p)
REVERT: B  155 ASN cc_start: 0.8514 (t0) cc_final: 0.7779 (t0)
REVERT: G   48 ASP cc_start: 0.7638 (t70) cc_final: 0.6982 (p0)
REVERT: N   72 ARG cc_start: 0.7015 (ptt90) cc_final: 0.5711 (ptp-170)
REVERT: R  105 LYS cc_start: 0.4660 (mttm) cc_final: 0.4253 (mptt)
REVERT: R  199 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7131 (mm)
  outliers start: 29
  outliers final: 18
  residues processed: 171
  average time/residue: 0.2140
  time to fit residues: 49.3715
Evaluate side-chains
  165 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 145
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue  102 ASN
Chi-restraints excluded: chain R residue  150 ARG
Chi-restraints excluded: chain R residue  153 GLN
Chi-restraints excluded: chain R residue  199 LEU
Chi-restraints excluded: chain R residue  340 THR
Chi-restraints excluded: chain R residue  365 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 93 optimal weight:    8.9990
   chunk 65 optimal weight:    1.9990
   chunk 23 optimal weight:    9.9990
   chunk 52 optimal weight:    9.9990
   chunk 71 optimal weight:    5.9990
   chunk 64 optimal weight:    8.9990
   chunk 63 optimal weight:    0.6980
   chunk 0 optimal weight:    6.9990
   chunk 57 optimal weight:   20.0000
   chunk 4 optimal weight:    7.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    4.1388

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 362 HIS
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 183 HIS
B 259 GLN
B 268 ASN
B 295 ASN
N 120 GLN
R 131 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4702 r_free = 0.4702 target = 0.228694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.195330 restraints weight = 9048.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.4414 rms_B_bonded: 2.48
r_work: 0.4249 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.4249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6769
moved from start:          0.2735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.058   8413  Z= 0.286
  Angle     :  0.771   9.105  11385  Z= 0.406
  Chirality :  0.050   0.166   1287
  Planarity :  0.005   0.044   1445
  Dihedral  :  5.789  50.522   1133
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 15.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.93 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 18.69 %
    Favored  : 76.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.59 (0.26), residues: 1021
  helix:  0.14 (0.27), residues: 381
  sheet: -1.27 (0.34), residues: 226
  loop : -2.02 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP L   5 
 HIS   0.010   0.002   HIS B  91 
 PHE   0.037   0.003   PHE R 377 
 TYR   0.029   0.002   TYR B 105 
 ARG   0.005   0.001   ARG B 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04897 (  394)
  hydrogen bonds       : angle       5.47671 ( 1128)
  SS BOND              : bond        0.00580 (    3)
  SS BOND              : angle       1.89689 (    6)
  covalent geometry    : bond        0.00670 ( 8409)
  covalent geometry    : angle       0.77009 (11379)
  Misc. bond           : bond        0.00038 (    1)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 150
  time to evaluate  : 1.051 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L    7 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7162 (m-30)
REVERT: A  344 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7351 (mp0)
REVERT: B   86 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8439 (m)
REVERT: B  118 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7373 (m-30)
REVERT: R   54 LEU cc_start: 0.6987 (mp) cc_final: 0.6755 (mp)
REVERT: R  199 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7569 (mm)
REVERT: R  314 MET cc_start: 0.6491 (OUTLIER) cc_final: 0.6252 (ttp)
  outliers start: 42
  outliers final: 23
  residues processed: 176
  average time/residue: 0.2457
  time to fit residues: 57.7010
Evaluate side-chains
  169 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 140
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    7 ASP
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  241 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue  129 THR
Chi-restraints excluded: chain R residue  150 ARG
Chi-restraints excluded: chain R residue  165 THR
Chi-restraints excluded: chain R residue  185 PHE
Chi-restraints excluded: chain R residue  199 LEU
Chi-restraints excluded: chain R residue  314 MET
Chi-restraints excluded: chain R residue  318 ILE
Chi-restraints excluded: chain R residue  340 THR
Chi-restraints excluded: chain R residue  365 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 96 optimal weight:    0.8980
   chunk 64 optimal weight:   20.0000
   chunk 45 optimal weight:    2.9990
   chunk 69 optimal weight:    7.9990
   chunk 73 optimal weight:    0.5980
   chunk 81 optimal weight:    0.7980
   chunk 95 optimal weight:    0.9990
   chunk 61 optimal weight:    9.9990
   chunk 70 optimal weight:   10.0000
   chunk 16 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 362 HIS
G  18 GLN
N 120 GLN
** R  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 102 ASN
R 131 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4789 r_free = 0.4789 target = 0.239050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4541 r_free = 0.4541 target = 0.206555 restraints weight = 8931.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.4526 rms_B_bonded: 2.47
r_work: 0.4368 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.4368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6602
moved from start:          0.2740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8413  Z= 0.125
  Angle     :  0.593   7.189  11385  Z= 0.314
  Chirality :  0.043   0.156   1287
  Planarity :  0.004   0.043   1445
  Dihedral  :  5.116  48.016   1133
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 21.58 %
    Favored  : 75.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.26), residues: 1021
  helix:  0.76 (0.27), residues: 381
  sheet: -0.82 (0.36), residues: 208
  loop : -1.87 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP R 209 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.013   0.001   PHE N 108 
 TYR   0.021   0.001   TYR N  60 
 ARG   0.004   0.000   ARG A 380 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03789 (  394)
  hydrogen bonds       : angle       4.91552 ( 1128)
  SS BOND              : bond        0.00288 (    3)
  SS BOND              : angle       1.18909 (    6)
  covalent geometry    : bond        0.00279 ( 8409)
  covalent geometry    : angle       0.59244 (11379)
  Misc. bond           : bond        0.00016 (    1)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 143
  time to evaluate  : 1.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L    7 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7133 (m-30)
REVERT: A  291 LEU cc_start: 0.7951 (mp) cc_final: 0.7720 (mp)
REVERT: A  344 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7281 (mp0)
REVERT: A  380 ARG cc_start: 0.7099 (mtp85) cc_final: 0.6732 (mtp-110)
REVERT: B  118 ASP cc_start: 0.7499 (m-30) cc_final: 0.7289 (m-30)
REVERT: B  155 ASN cc_start: 0.8591 (t0) cc_final: 0.7908 (t0)
REVERT: B  259 GLN cc_start: 0.6270 (OUTLIER) cc_final: 0.6041 (mt0)
REVERT: N   72 ARG cc_start: 0.6961 (ptt90) cc_final: 0.5683 (ptp-170)
REVERT: N   76 LYS cc_start: 0.7122 (mmtm) cc_final: 0.6710 (mmmt)
REVERT: R  105 LYS cc_start: 0.4926 (mttm) cc_final: 0.4392 (mptt)
REVERT: R  199 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7121 (mm)
  outliers start: 30
  outliers final: 18
  residues processed: 159
  average time/residue: 0.2388
  time to fit residues: 52.8216
Evaluate side-chains
  162 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 1.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    7 ASP
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain R residue  102 ASN
Chi-restraints excluded: chain R residue  150 ARG
Chi-restraints excluded: chain R residue  165 THR
Chi-restraints excluded: chain R residue  199 LEU
Chi-restraints excluded: chain R residue  312 ILE
Chi-restraints excluded: chain R residue  340 THR
Chi-restraints excluded: chain R residue  365 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 74 optimal weight:    0.8980
   chunk 73 optimal weight:    0.8980
   chunk 85 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 68 optimal weight:   10.0000
   chunk 83 optimal weight:    0.7980
   chunk 19 optimal weight:    7.9990
   chunk 87 optimal weight:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 227 GLN
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 120 GLN
** R  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 102 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4823 r_free = 0.4823 target = 0.243667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4580 r_free = 0.4580 target = 0.211363 restraints weight = 8983.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.4546 rms_B_bonded: 2.48
r_work: 0.4389 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.4389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6581
moved from start:          0.2868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8413  Z= 0.123
  Angle     :  0.601  10.514  11385  Z= 0.317
  Chirality :  0.042   0.166   1287
  Planarity :  0.004   0.042   1445
  Dihedral  :  4.985  49.709   1133
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 22.47 %
    Favored  : 74.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.27), residues: 1021
  helix:  1.01 (0.27), residues: 379
  sheet: -0.66 (0.36), residues: 208
  loop : -1.80 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP R 209 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.022   0.001   PHE R 198 
 TYR   0.018   0.001   TYR N  60 
 ARG   0.003   0.000   ARG N  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03694 (  394)
  hydrogen bonds       : angle       4.72662 ( 1128)
  SS BOND              : bond        0.00288 (    3)
  SS BOND              : angle       0.97866 (    6)
  covalent geometry    : bond        0.00271 ( 8409)
  covalent geometry    : angle       0.60122 (11379)
  Misc. bond           : bond        0.00016 (    1)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 146
  time to evaluate  : 1.051 
Fit side-chains
   revert: symmetry clash
REVERT: L    7 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.7124 (m-30)
REVERT: A  291 LEU cc_start: 0.7992 (mp) cc_final: 0.7722 (mp)
REVERT: A  344 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7260 (mp0)
REVERT: A  380 ARG cc_start: 0.7109 (mtp85) cc_final: 0.6623 (mtp85)
REVERT: B  118 ASP cc_start: 0.7459 (m-30) cc_final: 0.7245 (m-30)
REVERT: B  155 ASN cc_start: 0.8587 (t0) cc_final: 0.7898 (t0)
REVERT: N   72 ARG cc_start: 0.6944 (ptt90) cc_final: 0.5810 (ptp-170)
REVERT: N   76 LYS cc_start: 0.7146 (mmtm) cc_final: 0.6750 (mmmt)
REVERT: N   80 TYR cc_start: 0.7152 (m-80) cc_final: 0.6935 (m-80)
REVERT: R  105 LYS cc_start: 0.4758 (mttm) cc_final: 0.4208 (mptt)
REVERT: R  199 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7190 (mm)
  outliers start: 26
  outliers final: 19
  residues processed: 160
  average time/residue: 0.2511
  time to fit residues: 55.5511
Evaluate side-chains
  166 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 144
  time to evaluate  : 1.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    7 ASP
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain R residue  150 ARG
Chi-restraints excluded: chain R residue  153 GLN
Chi-restraints excluded: chain R residue  165 THR
Chi-restraints excluded: chain R residue  199 LEU
Chi-restraints excluded: chain R residue  312 ILE
Chi-restraints excluded: chain R residue  340 THR
Chi-restraints excluded: chain R residue  365 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 70 optimal weight:    6.9990
   chunk 55 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 96 optimal weight:    0.6980
   chunk 85 optimal weight:    0.8980
   chunk 77 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 14 optimal weight:    5.9990
   chunk 60 optimal weight:    8.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 227 GLN
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
N 120 GLN
R 102 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4809 r_free = 0.4809 target = 0.241829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4557 r_free = 0.4557 target = 0.208830 restraints weight = 9010.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.4527 rms_B_bonded: 2.55
r_work: 0.4371 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.4371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6584
moved from start:          0.2942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8413  Z= 0.139
  Angle     :  0.616  10.361  11385  Z= 0.324
  Chirality :  0.043   0.161   1287
  Planarity :  0.004   0.042   1445
  Dihedral  :  4.983  50.104   1133
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 22.58 %
    Favored  : 74.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.27), residues: 1021
  helix:  0.96 (0.27), residues: 381
  sheet: -0.66 (0.36), residues: 208
  loop : -1.82 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP L   5 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.022   0.002   PHE A 363 
 TYR   0.016   0.001   TYR R 176 
 ARG   0.002   0.000   ARG N  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03737 (  394)
  hydrogen bonds       : angle       4.81863 ( 1128)
  SS BOND              : bond        0.00323 (    3)
  SS BOND              : angle       0.97093 (    6)
  covalent geometry    : bond        0.00318 ( 8409)
  covalent geometry    : angle       0.61545 (11379)
  Misc. bond           : bond        0.00020 (    1)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 148
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
REVERT: L    7 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7154 (m-30)
REVERT: A  291 LEU cc_start: 0.7970 (mp) cc_final: 0.7618 (mp)
REVERT: A  344 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7302 (mp0)
REVERT: A  380 ARG cc_start: 0.7108 (mtp85) cc_final: 0.6632 (mtp85)
REVERT: B  118 ASP cc_start: 0.7488 (m-30) cc_final: 0.7278 (m-30)
REVERT: B  155 ASN cc_start: 0.8589 (t0) cc_final: 0.7893 (t0)
REVERT: N   72 ARG cc_start: 0.6899 (ptt90) cc_final: 0.5765 (ptp-170)
REVERT: N   76 LYS cc_start: 0.7217 (mmtm) cc_final: 0.6873 (mmmt)
REVERT: R  105 LYS cc_start: 0.4793 (mttm) cc_final: 0.4220 (mptt)
REVERT: R  162 ILE cc_start: 0.7262 (mt) cc_final: 0.7061 (mt)
REVERT: R  199 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7095 (mm)
  outliers start: 27
  outliers final: 22
  residues processed: 163
  average time/residue: 0.2117
  time to fit residues: 46.8140
Evaluate side-chains
  167 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 142
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    7 ASP
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain R residue   47 LEU
Chi-restraints excluded: chain R residue  102 ASN
Chi-restraints excluded: chain R residue  150 ARG
Chi-restraints excluded: chain R residue  165 THR
Chi-restraints excluded: chain R residue  199 LEU
Chi-restraints excluded: chain R residue  312 ILE
Chi-restraints excluded: chain R residue  318 ILE
Chi-restraints excluded: chain R residue  340 THR
Chi-restraints excluded: chain R residue  365 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0770
   chunk 93 optimal weight:   10.0000
   chunk 30 optimal weight:    3.9990
   chunk 75 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 89 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 82 optimal weight:    0.5980
   chunk 6 optimal weight:    7.9990
   overall best weight:    1.3344

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

Flipped N/Q/H residues before XYZ refinement:
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  18 GLN
N 120 GLN
R 102 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4802 r_free = 0.4802 target = 0.241277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.207693 restraints weight = 9074.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.4529 rms_B_bonded: 2.58
r_work: 0.4371 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.4371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6592
moved from start:          0.3021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8413  Z= 0.139
  Angle     :  0.618  10.027  11385  Z= 0.325
  Chirality :  0.043   0.159   1287
  Planarity :  0.004   0.043   1445
  Dihedral  :  4.979  50.487   1133
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 23.14 %
    Favored  : 73.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.27), residues: 1021
  helix:  1.01 (0.27), residues: 379
  sheet: -0.63 (0.36), residues: 208
  loop : -1.77 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP L   5 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.024   0.002   PHE A 363 
 TYR   0.017   0.001   TYR R 176 
 ARG   0.003   0.000   ARG B 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03801 (  394)
  hydrogen bonds       : angle       4.84187 ( 1128)
  SS BOND              : bond        0.00312 (    3)
  SS BOND              : angle       0.96176 (    6)
  covalent geometry    : bond        0.00320 ( 8409)
  covalent geometry    : angle       0.61810 (11379)
  Misc. bond           : bond        0.00021 (    1)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 147
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
REVERT: L    7 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7152 (m-30)
REVERT: A  291 LEU cc_start: 0.7964 (mp) cc_final: 0.7525 (mp)
REVERT: A  344 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7513 (mp0)
REVERT: A  380 ARG cc_start: 0.7116 (mtp85) cc_final: 0.6643 (mtp85)
REVERT: B  118 ASP cc_start: 0.7480 (m-30) cc_final: 0.7267 (m-30)
REVERT: B  155 ASN cc_start: 0.8594 (t0) cc_final: 0.7880 (t0)
REVERT: N   72 ARG cc_start: 0.6906 (ptt90) cc_final: 0.5793 (ptp-170)
REVERT: N   76 LYS cc_start: 0.7217 (mmtm) cc_final: 0.6915 (mmmt)
REVERT: R  105 LYS cc_start: 0.4996 (mttm) cc_final: 0.4347 (mptt)
REVERT: R  199 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7047 (mm)
  outliers start: 31
  outliers final: 26
  residues processed: 163
  average time/residue: 0.2048
  time to fit residues: 45.5813
Evaluate side-chains
  173 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 144
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    7 ASP
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain R residue  102 ASN
Chi-restraints excluded: chain R residue  150 ARG
Chi-restraints excluded: chain R residue  153 GLN
Chi-restraints excluded: chain R residue  165 THR
Chi-restraints excluded: chain R residue  199 LEU
Chi-restraints excluded: chain R residue  312 ILE
Chi-restraints excluded: chain R residue  318 ILE
Chi-restraints excluded: chain R residue  340 THR
Chi-restraints excluded: chain R residue  350 THR
Chi-restraints excluded: chain R residue  365 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 90 optimal weight:    0.9980
   chunk 26 optimal weight:    7.9990
   chunk 52 optimal weight:    4.9990
   chunk 77 optimal weight:    5.9990
   chunk 95 optimal weight:    0.7980
   chunk 67 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 57 optimal weight:    5.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 120 GLN
** R  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 102 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4822 r_free = 0.4822 target = 0.243723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4578 r_free = 0.4578 target = 0.211162 restraints weight = 8949.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.4552 rms_B_bonded: 2.50
r_work: 0.4392 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.4392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6562
moved from start:          0.3136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8413  Z= 0.129
  Angle     :  0.644  13.051  11385  Z= 0.330
  Chirality :  0.043   0.160   1287
  Planarity :  0.004   0.043   1445
  Dihedral  :  4.921  50.459   1133
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 23.69 %
    Favored  : 73.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.27), residues: 1021
  helix:  1.04 (0.28), residues: 375
  sheet: -0.60 (0.36), residues: 208
  loop : -1.79 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP R 209 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.020   0.001   PHE A 363 
 TYR   0.026   0.001   TYR R 360 
 ARG   0.003   0.000   ARG B 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03762 (  394)
  hydrogen bonds       : angle       4.82669 ( 1128)
  SS BOND              : bond        0.00267 (    3)
  SS BOND              : angle       0.89649 (    6)
  covalent geometry    : bond        0.00294 ( 8409)
  covalent geometry    : angle       0.64371 (11379)
  Misc. bond           : bond        0.00012 (    1)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 144
  time to evaluate  : 0.829 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L    7 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.7093 (m-30)
REVERT: A  291 LEU cc_start: 0.7993 (mp) cc_final: 0.7503 (mp)
REVERT: A  380 ARG cc_start: 0.7083 (mtp85) cc_final: 0.6609 (mtp85)
REVERT: B  118 ASP cc_start: 0.7440 (m-30) cc_final: 0.7224 (m-30)
REVERT: B  155 ASN cc_start: 0.8571 (t0) cc_final: 0.7871 (t0)
REVERT: N   72 ARG cc_start: 0.6900 (ptt90) cc_final: 0.5816 (ptp-170)
REVERT: N   76 LYS cc_start: 0.7326 (mmtm) cc_final: 0.7002 (mmmt)
REVERT: N   80 TYR cc_start: 0.7085 (m-80) cc_final: 0.6867 (m-80)
REVERT: R  105 LYS cc_start: 0.4930 (mttm) cc_final: 0.4283 (mptt)
REVERT: R  199 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.6973 (mm)
  outliers start: 28
  outliers final: 25
  residues processed: 159
  average time/residue: 0.2325
  time to fit residues: 49.3203
Evaluate side-chains
  166 residues out of total 899 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 139
  time to evaluate  : 1.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    7 ASP
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain R residue  102 ASN
Chi-restraints excluded: chain R residue  150 ARG
Chi-restraints excluded: chain R residue  153 GLN
Chi-restraints excluded: chain R residue  165 THR
Chi-restraints excluded: chain R residue  199 LEU
Chi-restraints excluded: chain R residue  312 ILE
Chi-restraints excluded: chain R residue  318 ILE
Chi-restraints excluded: chain R residue  340 THR
Chi-restraints excluded: chain R residue  365 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 52 optimal weight:    0.7980
   chunk 8 optimal weight:    5.9990
   chunk 56 optimal weight:    0.3980
   chunk 49 optimal weight:    0.9990
   chunk 25 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9980
   chunk 89 optimal weight:    1.9990
   chunk 9 optimal weight:    0.4980
   chunk 16 optimal weight:    0.6980
   chunk 84 optimal weight:    3.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 102 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4839 r_free = 0.4839 target = 0.245923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4604 r_free = 0.4604 target = 0.214010 restraints weight = 8984.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.4563 rms_B_bonded: 2.49
r_work: 0.4409 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.4409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6557
moved from start:          0.3276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8413  Z= 0.123
  Angle     :  0.637  12.816  11385  Z= 0.328
  Chirality :  0.042   0.161   1287
  Planarity :  0.006   0.150   1445
  Dihedral  :  4.849  50.314   1133
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 23.36 %
    Favored  : 73.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.27), residues: 1021
  helix:  1.13 (0.27), residues: 381
  sheet: -0.48 (0.36), residues: 206
  loop : -1.73 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP R 209 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.020   0.001   PHE R 198 
 TYR   0.021   0.001   TYR R 360 
 ARG   0.020   0.000   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03664 (  394)
  hydrogen bonds       : angle       4.72217 ( 1128)
  SS BOND              : bond        0.00242 (    3)
  SS BOND              : angle       0.83599 (    6)
  covalent geometry    : bond        0.00275 ( 8409)
  covalent geometry    : angle       0.63735 (11379)
  Misc. bond           : bond        0.00016 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4328.14 seconds
wall clock time: 76 minutes 52.55 seconds (4612.55 seconds total)