Starting phenix.real_space_refine
on Sat May  2 22:10:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rsj_54220/05_2026/9rsj_54220.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rsj_54220/05_2026/9rsj_54220.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rsj_54220/05_2026/9rsj_54220.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rsj_54220/05_2026/9rsj_54220.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rsj_54220/05_2026/9rsj_54220.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rsj_54220/05_2026/9rsj_54220.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.017
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      41      5.16       5
     C    5568      2.51       5
     N    1441      2.21       5
     O    1614      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8664
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3472
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 456, 3472
          Classifications: {'peptide': 456}
          Link IDs: {'PTRANS': 16, 'TRANS': 439}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 1722
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1722
          Classifications: {'peptide': 228}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 216}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "L"
      Number of atoms: 1582
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 1582
          Classifications: {'peptide': 208}
          Link IDs: {'PTRANS': 10, 'TRANS': 197}
    Chain: "N"
      Number of atoms: 919
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 919
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 4, 'TRANS': 117}
    Chain: "K"
      Number of atoms: 930
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 120, 922
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
      Conformer: "B"
        Number of residues, atoms: 120, 922
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
          bond proxies already assigned to first conformer: 931
    Chain: "A"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 39
          Unusual residues: {'DM2': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.10, per 1000 atoms: 0.24
  Number of scatterers: 8664
  At special positions: 0
  Unit cell: (69.68, 79.73, 163.48, 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      41     16.00
     O    1614      8.00
     N    1441      7.00
     C    5568      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 140 " - pdb=" SG  CYS H 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 134 " - pdb=" SG  CYS L 194 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  92 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.70
  Conformation dependent library (CDL) restraints added in 273.3 milliseconds
  

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2076

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 15 sheets defined
      39.7% alpha, 26.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 17
    Processing helix  chain 'A' and resid 19 through 41
      removed outlier: 3.797A  pdb=" N   GLY A  33 " --> pdb=" O   GLN A  29 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ASP A  36 " --> pdb=" O   MET A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 69
      removed outlier: 3.594A  pdb=" N   ALA A  55 " --> pdb=" O   VAL A  51 " (cutoff:3.500A)
      Proline residue:  A  60  - end of helix
      removed outlier: 3.770A  pdb=" N   PHE A  64 " --> pdb=" O   PRO A  60 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   GLY A  65 " --> pdb=" O   SER A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 83
      removed outlier: 3.549A  pdb=" N   VAL A  75 " --> pdb=" O   ALA A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 112
      removed outlier: 4.107A  pdb=" N   VAL A 104 " --> pdb=" O   LEU A 100 " (cutoff:3.500A)
      Proline residue:  A 105  - end of helix
    Processing helix  chain 'A' and resid 112 through 117
      removed outlier: 3.623A  pdb=" N   ILE A 116 " --> pdb=" O   GLN A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 138
    Processing helix  chain 'A' and resid 139 through 157
      removed outlier: 4.597A  pdb=" N   ALA A 143 " --> pdb=" O   PHE A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 183
      removed outlier: 3.697A  pdb=" N   MET A 164 " --> pdb=" O   THR A 160 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ILE A 175 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
      Proline residue:  A 176  - end of helix
    Processing helix  chain 'A' and resid 191 through 193
      No H-bonds generated for 'chain 'A' and resid 191 through 193'
    Processing helix  chain 'A' and resid 194 through 218
      removed outlier: 3.537A  pdb=" N   VAL A 198 " --> pdb=" O   VAL A 194 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ILE A 202 " --> pdb=" O   VAL A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 229
      removed outlier: 3.926A  pdb=" N   GLU A 228 " --> pdb=" O   LYS A 225 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   THR A 229 " --> pdb=" O   VAL A 226 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 225 through 229'
    Processing helix  chain 'A' and resid 234 through 244
    Processing helix  chain 'A' and resid 246 through 267
      removed outlier: 3.500A  pdb=" N   ALA A 251 " --> pdb=" O   PRO A 247 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   LEU A 252 " --> pdb=" O   VAL A 248 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   VAL A 256 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 270
      No H-bonds generated for 'chain 'A' and resid 268 through 270'
    Processing helix  chain 'A' and resid 271 through 308
      removed outlier: 3.749A  pdb=" N   ALA A 275 " --> pdb=" O   SER A 271 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ALA A 276 " --> pdb=" O   THR A 272 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LEU A 286 " --> pdb=" O   ASN A 282 " (cutoff:3.500A)
      Proline residue:  A 291  - end of helix
      removed outlier: 4.122A  pdb=" N   ILE A 294 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 339
      removed outlier: 3.662A  pdb=" N   LEU A 326 " --> pdb=" O   LEU A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 348
      removed outlier: 3.630A  pdb=" N   TYR A 347 " --> pdb=" O   ILE A 343 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   THR A 348 " --> pdb=" O   ALA A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 384
      removed outlier: 4.074A  pdb=" N   LEU A 362 " --> pdb=" O   MET A 358 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   PHE A 363 " --> pdb=" O   GLN A 359 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ALA A 365 " --> pdb=" O   LEU A 361 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   ILE A 366 " --> pdb=" O   LEU A 362 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ALA A 372 " --> pdb=" O   GLN A 368 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   VAL A 373 " --> pdb=" O   CYS A 369 " (cutoff:3.500A)
      removed outlier: 4.886A  pdb=" N   VAL A 375 " --> pdb=" O   ASP A 371 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA A 377 " --> pdb=" O   VAL A 373 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   TYR A 384 " --> pdb=" O   SER A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 399
      removed outlier: 3.659A  pdb=" N   ILE A 390 " --> pdb=" O   ASP A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 410
    Processing helix  chain 'A' and resid 421 through 448
      removed outlier: 3.803A  pdb=" N   PHE A 425 " --> pdb=" O   GLY A 421 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LEU A 427 " --> pdb=" O   LYS A 423 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   ALA A 435 " --> pdb=" O   ILE A 431 " (cutoff:3.500A)
      removed outlier: 5.824A  pdb=" N   LEU A 438 " --> pdb=" O   SER A 434 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   GLY A 441 " --> pdb=" O   ALA A 437 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   LEU A 444 " --> pdb=" O   LEU A 440 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   TYR A 445 " --> pdb=" O   GLY A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 461
    Processing helix  chain 'H' and resid 61 through 64
      removed outlier: 3.519A  pdb=" N   LYS H  64 " --> pdb=" O   ASP H  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 61 through 64'
    Processing helix  chain 'H' and resid 98 through 100C
    Processing helix  chain 'H' and resid 187 through 192
      removed outlier: 3.572A  pdb=" N   GLN H 192 " --> pdb=" O   LEU H 189 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 121 through 128
      removed outlier: 3.677A  pdb=" N   LEU L 125 " --> pdb=" O   SER L 121 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   LYS L 126 " --> pdb=" O   ASP L 122 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   SER L 127 " --> pdb=" O   SER L 123 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 183 through 189
    Processing helix  chain 'N' and resid 60 through 64
      removed outlier: 3.808A  pdb=" N   VAL N  63 " --> pdb=" O   ALA N  60 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LYS N  64 " --> pdb=" O   ASP N  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 60 through 64'
    Processing helix  chain 'N' and resid 83 through 87
      removed outlier: 3.947A  pdb=" N   THR N  87 " --> pdb=" O   PRO N  84 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 83 through 87
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.028A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 110 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ALA H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 6.066A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.214A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 120 through 124
      removed outlier: 6.005A  pdb=" N   TYR H 176 " --> pdb=" O   ASP H 144 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 120 through 124
      removed outlier: 6.005A  pdb=" N   TYR H 176 " --> pdb=" O   ASP H 144 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 151 through 154
      removed outlier: 4.344A  pdb=" N   TYR H 194 " --> pdb=" O   VAL H 211 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   HIS H 200 " --> pdb=" O   THR H 205 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 6
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.096A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.096A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 114 through 118
      removed outlier: 6.279A  pdb=" N   TYR L 173 " --> pdb=" O   ASN L 138 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 153 through 154
    Processing sheet with id=AB2, first strand: chain 'N' and resid 4 through 7
      removed outlier: 3.608A  pdb=" N   THR N  77 " --> pdb=" O   ASP N  72 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 12
      removed outlier: 3.662A  pdb=" N   GLY N  10 " --> pdb=" O   PRO N 108 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   MET N  34 " --> pdb=" O   GLY N  50 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   GLY N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'N' and resid 10 through 12
      removed outlier: 3.662A  pdb=" N   GLY N  10 " --> pdb=" O   PRO N 108 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'K' and resid 3 through 7
      removed outlier: 3.558A  pdb=" N   VAL K  78 " --> pdb=" O   CYS K  22 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'K' and resid 10 through 12
      removed outlier: 6.247A  pdb=" N   GLY K  10 " --> pdb=" O   THR K 110 " (cutoff:3.500A)
      removed outlier: 5.629A  pdb=" N   ARG K  38 " --> pdb=" O   PHE K  47 " (cutoff:3.500A)
      removed outlier: 5.493A  pdb=" N   PHE K  47 " --> pdb=" O   ARG K  38 " (cutoff:3.500A)

    482 hydrogen bonds defined for protein.
    1319 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.49

  Time building geometry restraints manager: 0.85 seconds

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

  Histogram of bond lengths:
        1.15 -     1.28: 1358
        1.28 -     1.41: 2271
        1.41 -     1.55: 5163
        1.55 -     1.68: 8
        1.68 -     1.81: 66
  Bond restraints: 8866
  Sorted by residual:
  bond pdb=" C4  DM2 A 501 "
       pdb=" O4  DM2 A 501 "
    ideal  model  delta    sigma   weight residual
    1.333  1.450 -0.117 2.00e-02 2.50e+03 3.42e+01
  bond pdb=" C1' DM2 A 501 "
       pdb=" O5' DM2 A 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.492 -0.095 2.00e-02 2.50e+03 2.27e+01
  bond pdb=" C15 DM2 A 501 "
       pdb=" C16 DM2 A 501 "
    ideal  model  delta    sigma   weight residual
    1.502  1.589 -0.087 2.00e-02 2.50e+03 1.91e+01
  bond pdb=" C19 DM2 A 501 "
       pdb=" C20 DM2 A 501 "
    ideal  model  delta    sigma   weight residual
    1.477  1.556 -0.079 2.00e-02 2.50e+03 1.55e+01
  bond pdb=" C17 DM2 A 501 "
       pdb=" O17 DM2 A 501 "
    ideal  model  delta    sigma   weight residual
    1.330  1.408 -0.078 2.00e-02 2.50e+03 1.54e+01
  ... (remaining 8861 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.37: 11934
        2.37 -     4.73: 96
        4.73 -     7.10: 25
        7.10 -     9.47: 2
        9.47 -    11.83: 2
  Bond angle restraints: 12059
  Sorted by residual:
  angle pdb=" C18 DM2 A 501 "
        pdb=" C17 DM2 A 501 "
        pdb=" O17 DM2 A 501 "
      ideal   model   delta    sigma   weight residual
     122.66  110.83   11.83 3.00e+00 1.11e-01 1.56e+01
  angle pdb=" C16 DM2 A 501 "
        pdb=" C17 DM2 A 501 "
        pdb=" O17 DM2 A 501 "
      ideal   model   delta    sigma   weight residual
     117.23  126.61   -9.38 3.00e+00 1.11e-01 9.78e+00
  angle pdb=" N   PRO L 141 "
        pdb=" CA  PRO L 141 "
        pdb=" C   PRO L 141 "
      ideal   model   delta    sigma   weight residual
     112.47  106.51    5.96 2.06e+00 2.36e-01 8.37e+00
  angle pdb=" N   TYR L 140 "
        pdb=" CA  TYR L 140 "
        pdb=" C   TYR L 140 "
      ideal   model   delta    sigma   weight residual
     108.76  112.81   -4.05 1.44e+00 4.82e-01 7.91e+00
  angle pdb=" C7  DM2 A 501 "
        pdb=" C8  DM2 A 501 "
        pdb=" C9  DM2 A 501 "
      ideal   model   delta    sigma   weight residual
     120.12  128.44   -8.32 3.00e+00 1.11e-01 7.70e+00
  ... (remaining 12054 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.83: 4857
       15.83 -    31.66: 283
       31.66 -    47.49: 67
       47.49 -    63.32: 21
       63.32 -    79.15: 6
  Dihedral angle restraints: 5234
    sinusoidal: 1975
      harmonic: 3259
  Sorted by residual:
  dihedral pdb=" CA  TYR L 140 "
           pdb=" C   TYR L 140 "
           pdb=" N   PRO L 141 "
           pdb=" CA  PRO L 141 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  109.00   71.00     0      5.00e+00 4.00e-02 2.02e+02
  dihedral pdb=" CA  ALA A 435 "
           pdb=" C   ALA A 435 "
           pdb=" N   ALA A 436 "
           pdb=" CA  ALA A 436 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.43   24.57     0      5.00e+00 4.00e-02 2.41e+01
  dihedral pdb=" CA  GLN A 450 "
           pdb=" C   GLN A 450 "
           pdb=" N   SER A 451 "
           pdb=" CA  SER A 451 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.76   21.24     0      5.00e+00 4.00e-02 1.80e+01
  ... (remaining 5231 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 1225
       0.063 -    0.127: 145
       0.127 -    0.190: 9
       0.190 -    0.253: 0
       0.253 -    0.317: 2
  Chirality restraints: 1381
  Sorted by residual:
  chirality pdb=" C10 DM2 A 501 "
            pdb=" C11 DM2 A 501 "
            pdb=" C9  DM2 A 501 "
            pdb=" O10 DM2 A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.64    0.32 2.00e-01 2.50e+01 2.51e+00
  chirality pdb=" C1' DM2 A 501 "
            pdb=" C2' DM2 A 501 "
            pdb=" O10 DM2 A 501 "
            pdb=" O5' DM2 A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.16    2.43   -0.27 2.00e-01 2.50e+01 1.84e+00
  chirality pdb=" CA  PHE A 290 "
            pdb=" N   PHE A 290 "
            pdb=" C   PHE A 290 "
            pdb=" CB  PHE A 290 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.70e-01
  ... (remaining 1378 not shown)

  Planarity restraints: 1507
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR L 140 "   -0.089 5.00e-02 4.00e+02   1.34e-01 2.89e+01
        pdb=" N   PRO L 141 "    0.232 5.00e-02 4.00e+02
        pdb=" CA  PRO L 141 "   -0.074 5.00e-02 4.00e+02
        pdb=" CD  PRO L 141 "   -0.070 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 435 "   -0.017 2.00e-02 2.50e+03   3.44e-02 1.18e+01
        pdb=" C   ALA A 435 "    0.060 2.00e-02 2.50e+03
        pdb=" O   ALA A 435 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   ALA A 436 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE H 146 "   -0.035 5.00e-02 4.00e+02   5.31e-02 4.51e+00
        pdb=" N   PRO H 147 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO H 147 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO H 147 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 1504 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 791
        2.74 -     3.28: 8645
        3.28 -     3.82: 13839
        3.82 -     4.36: 16535
        4.36 -     4.90: 29192
  Nonbonded interactions: 69002
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 110 "
            pdb=" OG1 THR A 113 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" OG1 THR H 131 "
            pdb=" O   THR H 135 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" OG  SER K   7 "
            pdb=" OG  SER K  21 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O   HIS L 189 "
            pdb=" NH2 ARG L 211 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" OG  SER L  63 "
            pdb=" OG1 THR L  74 "
     model   vdw
     2.251 3.040
  ... (remaining 68997 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.36 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:             6.400
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.070
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
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      :  0.005   0.117   8871  Z= 0.228
  Angle     :  0.621  11.832  12069  Z= 0.306
  Chirality :  0.043   0.317   1381
  Planarity :  0.006   0.134   1507
  Dihedral  : 11.712  79.147   3143
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.37 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  :  7.44 %
    Favored  : 89.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.63 (0.25), residues: 1124
  helix: -0.18 (0.26), residues: 385
  sheet:  0.57 (0.31), residues: 265
  loop : -1.12 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  61 
 TYR   0.022   0.001   TYR L 140 
 PHE   0.017   0.001   PHE A 259 
 TRP   0.010   0.001   TRP A 426 
 HIS   0.002   0.001   HIS A  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 ( 8866)
  covalent geometry    : angle       0.62125 (12059)
  SS BOND              : bond        0.00400 (    5)
  SS BOND              : angle       0.52075 (   10)
  hydrogen bonds       : bond        0.14111 (  461)
  hydrogen bonds       : angle       6.71142 ( 1319)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 171
  time to evaluate  : 0.332 
Fit side-chains
REVERT: A   78 GLN cc_start: 0.7396 (tt0) cc_final: 0.6931 (mt0)
REVERT: A  323 MET cc_start: 0.6593 (mmm) cc_final: 0.6040 (mtm)
REVERT: A  358 MET cc_start: 0.8148 (ttt) cc_final: 0.7911 (ttm)
REVERT: A  362 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8230 (mp)
REVERT: A  371 ASP cc_start: 0.8172 (t70) cc_final: 0.7912 (t0)
REVERT: A  449 LYS cc_start: 0.8045 (tttt) cc_final: 0.7682 (tppt)
REVERT: H    2 VAL cc_start: 0.7221 (p) cc_final: 0.6999 (p)
REVERT: H    3 GLN cc_start: 0.7862 (tt0) cc_final: 0.7355 (mt0)
REVERT: H   83 ARG cc_start: 0.8119 (mtm-85) cc_final: 0.7728 (mtt-85)
REVERT: H  199 ASN cc_start: 0.7322 (t0) cc_final: 0.7107 (t0)
REVERT: L   42 LYS cc_start: 0.8002 (mttt) cc_final: 0.7648 (mttp)
REVERT: L   82 ASP cc_start: 0.8039 (m-30) cc_final: 0.7763 (m-30)
REVERT: L  126 LYS cc_start: 0.7864 (mmmt) cc_final: 0.7626 (mmtm)
REVERT: N   43 LYS cc_start: 0.8481 (mttt) cc_final: 0.8212 (mtpp)
REVERT: N   56 ARG cc_start: 0.7262 (mtt-85) cc_final: 0.6902 (ttp80)
REVERT: N   82 SER cc_start: 0.9058 (m) cc_final: 0.8760 (t)
REVERT: N   85 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8045 (mp0)
REVERT: K   34 MET cc_start: 0.6956 (mtp) cc_final: 0.6316 (mmm)
  outliers start: 33
  outliers final: 9
  residues processed: 198
  average time/residue: 0.0780
  time to fit residues: 22.0922
Evaluate side-chains
  126 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 116
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 PHE
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain H residue   50 TYR
Chi-restraints excluded: chain H residue  109 VAL
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain L residue   33 VAL
Chi-restraints excluded: chain L residue  132 VAL
Chi-restraints excluded: chain N residue   87 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    8.9990
   chunk 106 optimal weight:   10.0000
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 278 GLN
A 368 GLN
A 418 GLN
H 171 GLN
** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L   6 GLN
L  38 GLN
L 147 GLN
** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  32 ASN
N 100DGLN
K   5 GLN
K  13 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.164727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.127073 restraints weight = 20731.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 3.99
r_work: 0.3242 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3248
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3248 r_free = 0.3248    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3248 r_free = 0.3248    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3248
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.1730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   8871  Z= 0.160
  Angle     :  0.605   8.079  12069  Z= 0.312
  Chirality :  0.042   0.153   1381
  Planarity :  0.006   0.123   1507
  Dihedral  :  7.529  68.163   1282
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.01 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 10.02 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.23 (0.25), residues: 1124
  helix:  0.42 (0.26), residues: 390
  sheet:  0.71 (0.30), residues: 273
  loop : -1.13 (0.29), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A   7 
 TYR   0.017   0.001   TYR L 140 
 PHE   0.017   0.001   PHE A 259 
 TRP   0.011   0.001   TRP A  58 
 HIS   0.004   0.001   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 8866)
  covalent geometry    : angle       0.60418 (12059)
  SS BOND              : bond        0.00750 (    5)
  SS BOND              : angle       1.01295 (   10)
  hydrogen bonds       : bond        0.04529 (  461)
  hydrogen bonds       : angle       5.06358 ( 1319)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 119
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 TRP cc_start: 0.8567 (OUTLIER) cc_final: 0.7074 (t-100)
REVERT: A  208 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8098 (tp)
REVERT: A  323 MET cc_start: 0.6746 (mmm) cc_final: 0.6428 (mtm)
REVERT: A  362 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8391 (mp)
REVERT: A  396 ILE cc_start: 0.7724 (tt) cc_final: 0.7439 (tt)
REVERT: A  449 LYS cc_start: 0.7892 (tttt) cc_final: 0.7675 (tppt)
REVERT: H    3 GLN cc_start: 0.8225 (tt0) cc_final: 0.7894 (mt0)
REVERT: L  147 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.7203 (mt0)
REVERT: L  175 LEU cc_start: 0.8318 (pp) cc_final: 0.7655 (tt)
REVERT: K   34 MET cc_start: 0.7134 (mtp) cc_final: 0.6549 (mmm)
  outliers start: 41
  outliers final: 22
  residues processed: 153
  average time/residue: 0.0797
  time to fit residues: 17.4940
Evaluate side-chains
  128 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 102
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 TRP
Chi-restraints excluded: chain A residue  111 PHE
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   50 TYR
Chi-restraints excluded: chain H residue  109 VAL
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  138 LEU
Chi-restraints excluded: chain H residue  150 VAL
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   33 VAL
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue  132 VAL
Chi-restraints excluded: chain L residue  135 LEU
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  147 GLN
Chi-restraints excluded: chain N residue   70 SER
Chi-restraints excluded: chain N residue   87 THR
Chi-restraints excluded: chain N residue   94 SER
Chi-restraints excluded: chain K residue   11 LEU
Chi-restraints excluded: chain K residue   94 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 69 optimal weight:    3.9990
   chunk 43 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 37 optimal weight:    0.0070
   chunk 11 optimal weight:    0.0970
   chunk 7 optimal weight:    0.8980
   chunk 42 optimal weight:    0.2980
   chunk 6 optimal weight:    0.9980
   chunk 83 optimal weight:    3.9990
   overall best weight:    0.3796

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 418 GLN
** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 147 GLN
** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  32 ASN
N 100DGLN
K  13 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.166537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.129621 restraints weight = 22296.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 4.48
r_work: 0.3267 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3267
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3267 r_free = 0.3267    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3267 r_free = 0.3267    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3267
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.2238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8871  Z= 0.115
  Angle     :  0.555   7.049  12069  Z= 0.284
  Chirality :  0.041   0.146   1381
  Planarity :  0.005   0.116   1507
  Dihedral  :  7.000  63.616   1278
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.01 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 11.85 %
    Favored  : 84.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.25), residues: 1124
  helix:  0.89 (0.27), residues: 394
  sheet:  0.85 (0.31), residues: 273
  loop : -1.04 (0.29), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  83 
 TYR   0.014   0.001   TYR L 140 
 PHE   0.015   0.001   PHE A 259 
 TRP   0.011   0.001   TRP A  58 
 HIS   0.003   0.001   HIS L 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 8866)
  covalent geometry    : angle       0.55460 (12059)
  SS BOND              : bond        0.00439 (    5)
  SS BOND              : angle       0.71897 (   10)
  hydrogen bonds       : bond        0.03953 (  461)
  hydrogen bonds       : angle       4.77898 ( 1319)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 113
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 TRP cc_start: 0.8516 (OUTLIER) cc_final: 0.6976 (t-100)
REVERT: A   87 LYS cc_start: 0.7137 (mttt) cc_final: 0.6408 (tttm)
REVERT: A  208 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8018 (tp)
REVERT: A  323 MET cc_start: 0.6695 (mmm) cc_final: 0.6340 (mtm)
REVERT: A  396 ILE cc_start: 0.7694 (tt) cc_final: 0.7387 (tt)
REVERT: A  444 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.8037 (tt)
REVERT: A  449 LYS cc_start: 0.7895 (tttt) cc_final: 0.7669 (tppt)
REVERT: H    3 GLN cc_start: 0.8159 (tt0) cc_final: 0.7774 (mt0)
REVERT: H    6 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8083 (mp0)
REVERT: H  117 LYS cc_start: 0.7887 (tttt) cc_final: 0.7655 (tttm)
REVERT: H  138 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7537 (pp)
REVERT: L  147 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7212 (mt0)
REVERT: L  161 GLU cc_start: 0.7663 (pt0) cc_final: 0.7239 (tt0)
REVERT: L  203 SER cc_start: 0.7434 (p) cc_final: 0.7178 (m)
REVERT: K   34 MET cc_start: 0.7079 (mtp) cc_final: 0.6502 (mmm)
  outliers start: 31
  outliers final: 20
  residues processed: 141
  average time/residue: 0.0757
  time to fit residues: 15.4810
Evaluate side-chains
  127 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 102
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   58 TRP
Chi-restraints excluded: chain A residue  111 PHE
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain H residue   50 TYR
Chi-restraints excluded: chain H residue   77 THR
Chi-restraints excluded: chain H residue  109 VAL
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain H residue  138 LEU
Chi-restraints excluded: chain H residue  150 VAL
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   33 VAL
Chi-restraints excluded: chain L residue   85 THR
Chi-restraints excluded: chain L residue  132 VAL
Chi-restraints excluded: chain L residue  136 LEU
Chi-restraints excluded: chain L residue  147 GLN
Chi-restraints excluded: chain N residue   70 SER
Chi-restraints excluded: chain K residue   11 LEU
Chi-restraints excluded: chain K residue   94 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 69 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   chunk 47 optimal weight:    4.9990
   chunk 44 optimal weight:    4.9990
   chunk 102 optimal weight:    1.9990
   chunk 106 optimal weight:    7.9990
   chunk 71 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 6 optimal weight:    4.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 418 GLN
A 450 GLN
** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.160170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.122063 restraints weight = 13044.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 2.37
r_work: 0.3238 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3098 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3114
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3114 r_free = 0.3114    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3114 r_free = 0.3114    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3114
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.2707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8871  Z= 0.188
  Angle     :  0.612   8.251  12069  Z= 0.314
  Chirality :  0.043   0.156   1381
  Planarity :  0.006   0.119   1507
  Dihedral  :  6.495  62.362   1275
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.55 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 12.39 %
    Favored  : 83.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.25), residues: 1124
  helix:  0.72 (0.26), residues: 399
  sheet:  0.67 (0.29), residues: 302
  loop : -1.09 (0.30), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG N  19 
 TYR   0.021   0.002   TYR L 140 
 PHE   0.024   0.002   PHE H 122 
 TRP   0.016   0.001   TRP A  58 
 HIS   0.004   0.001   HIS A  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 ( 8866)
  covalent geometry    : angle       0.61158 (12059)
  SS BOND              : bond        0.00425 (    5)
  SS BOND              : angle       0.97867 (   10)
  hydrogen bonds       : bond        0.04577 (  461)
  hydrogen bonds       : angle       4.83279 ( 1319)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 106
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 TRP cc_start: 0.8659 (OUTLIER) cc_final: 0.6998 (t-100)
REVERT: A   87 LYS cc_start: 0.7475 (mttt) cc_final: 0.6643 (tttm)
REVERT: A  208 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8122 (tp)
REVERT: A  323 MET cc_start: 0.6867 (mmm) cc_final: 0.6533 (mtt)
REVERT: A  449 LYS cc_start: 0.8059 (tttt) cc_final: 0.7800 (tppt)
REVERT: L  161 GLU cc_start: 0.7967 (pt0) cc_final: 0.7736 (tt0)
REVERT: L  190 LYS cc_start: 0.7391 (tptt) cc_final: 0.7065 (tppt)
REVERT: L  203 SER cc_start: 0.7461 (p) cc_final: 0.7159 (m)
  outliers start: 42
  outliers final: 29
  residues processed: 142
  average time/residue: 0.0941
  time to fit residues: 18.9827
Evaluate side-chains
  127 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 96
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   58 TRP
Chi-restraints excluded: chain A residue  111 PHE
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   50 TYR
Chi-restraints excluded: chain H residue   77 THR
Chi-restraints excluded: chain H residue  109 VAL
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  138 LEU
Chi-restraints excluded: chain H residue  150 VAL
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   33 VAL
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   85 THR
Chi-restraints excluded: chain L residue  132 VAL
Chi-restraints excluded: chain L residue  135 LEU
Chi-restraints excluded: chain N residue   70 SER
Chi-restraints excluded: chain N residue   87 THR
Chi-restraints excluded: chain N residue   94 SER
Chi-restraints excluded: chain K residue   11 LEU
Chi-restraints excluded: chain K residue   94 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 62 optimal weight:    0.2980
   chunk 80 optimal weight:    1.9990
   chunk 107 optimal weight:    6.9990
   chunk 78 optimal weight:    3.9990
   chunk 108 optimal weight:   10.0000
   chunk 35 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   chunk 36 optimal weight:    0.7980
   chunk 81 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
A  80 ASN
A 231 HIS
H  13 GLN
H  39 GLN
H 197 ASN
** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.157549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.119506 restraints weight = 22312.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 4.11
r_work: 0.3103 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3130
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3130 r_free = 0.3130    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3130 r_free = 0.3130    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3130
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.3336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   8871  Z= 0.206
  Angle     :  0.637   8.473  12069  Z= 0.327
  Chirality :  0.044   0.157   1381
  Planarity :  0.006   0.112   1507
  Dihedral  :  6.242  63.276   1275
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.99 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 12.61 %
    Favored  : 82.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.03 (0.25), residues: 1124
  helix:  0.69 (0.26), residues: 396
  sheet:  0.80 (0.29), residues: 291
  loop : -1.24 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG N  71 
 TYR   0.025   0.002   TYR L 140 
 PHE   0.018   0.002   PHE H 122 
 TRP   0.016   0.001   TRP A  58 
 HIS   0.004   0.001   HIS A  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 ( 8866)
  covalent geometry    : angle       0.63670 (12059)
  SS BOND              : bond        0.00398 (    5)
  SS BOND              : angle       0.85909 (   10)
  hydrogen bonds       : bond        0.04676 (  461)
  hydrogen bonds       : angle       4.86871 ( 1319)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 104
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 TRP cc_start: 0.8617 (OUTLIER) cc_final: 0.6859 (t-100)
REVERT: A   87 LYS cc_start: 0.7528 (mttt) cc_final: 0.6672 (tttm)
REVERT: A  175 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.7949 (mm)
REVERT: A  208 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8035 (tp)
REVERT: A  269 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7714 (mp)
REVERT: A  323 MET cc_start: 0.6780 (mmm) cc_final: 0.6482 (mtm)
REVERT: A  449 LYS cc_start: 0.8039 (tttt) cc_final: 0.7763 (tppt)
REVERT: L  141 PRO cc_start: 0.7020 (Cg_exo) cc_final: 0.6682 (Cg_endo)
REVERT: L  142 ARG cc_start: 0.7290 (tpt90) cc_final: 0.6721 (tpt-90)
REVERT: L  161 GLU cc_start: 0.8100 (pt0) cc_final: 0.7797 (tt0)
REVERT: L  190 LYS cc_start: 0.7052 (tptt) cc_final: 0.6728 (tppt)
REVERT: L  203 SER cc_start: 0.7209 (p) cc_final: 0.6786 (m)
REVERT: K   81 GLN cc_start: 0.5735 (tm-30) cc_final: 0.5199 (tt0)
  outliers start: 50
  outliers final: 37
  residues processed: 144
  average time/residue: 0.0950
  time to fit residues: 19.2668
Evaluate side-chains
  136 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 95
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   58 TRP
Chi-restraints excluded: chain A residue   80 ASN
Chi-restraints excluded: chain A residue  111 PHE
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  289 MET
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   50 TYR
Chi-restraints excluded: chain H residue   77 THR
Chi-restraints excluded: chain H residue  101 ASP
Chi-restraints excluded: chain H residue  109 VAL
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  138 LEU
Chi-restraints excluded: chain H residue  150 VAL
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   33 VAL
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue  132 VAL
Chi-restraints excluded: chain L residue  135 LEU
Chi-restraints excluded: chain L residue  175 LEU
Chi-restraints excluded: chain L residue  205 VAL
Chi-restraints excluded: chain N residue   70 SER
Chi-restraints excluded: chain N residue   87 THR
Chi-restraints excluded: chain N residue   94 SER
Chi-restraints excluded: chain K residue   11 LEU
Chi-restraints excluded: chain K residue   35 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 83 optimal weight:    4.9990
   chunk 92 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 85 optimal weight:    0.3980
   chunk 101 optimal weight:   10.0000
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.159536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.122617 restraints weight = 14329.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 2.50
r_work: 0.3246 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3105 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3117
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3117 r_free = 0.3117    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3117 r_free = 0.3117    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3117
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.3524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8871  Z= 0.143
  Angle     :  0.578   7.370  12069  Z= 0.295
  Chirality :  0.041   0.146   1381
  Planarity :  0.005   0.111   1507
  Dihedral  :  5.850  59.922   1275
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.81 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 14.98 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.25), residues: 1124
  helix:  0.95 (0.26), residues: 397
  sheet:  0.78 (0.29), residues: 290
  loop : -1.12 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG N  19 
 TYR   0.020   0.001   TYR L 140 
 PHE   0.016   0.001   PHE A 259 
 TRP   0.015   0.001   TRP A  58 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 8866)
  covalent geometry    : angle       0.57778 (12059)
  SS BOND              : bond        0.00441 (    5)
  SS BOND              : angle       0.69722 (   10)
  hydrogen bonds       : bond        0.04106 (  461)
  hydrogen bonds       : angle       4.69299 ( 1319)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 101
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 TRP cc_start: 0.8575 (OUTLIER) cc_final: 0.6798 (t-100)
REVERT: A   80 ASN cc_start: 0.8248 (t0) cc_final: 0.7947 (t0)
REVERT: A   87 LYS cc_start: 0.7443 (mttt) cc_final: 0.6577 (tttm)
REVERT: A  175 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.7965 (mm)
REVERT: A  208 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8007 (tp)
REVERT: A  269 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7647 (mp)
REVERT: A  323 MET cc_start: 0.6859 (mmm) cc_final: 0.6504 (mtm)
REVERT: A  396 ILE cc_start: 0.7710 (tt) cc_final: 0.7449 (tt)
REVERT: H   82 ASN cc_start: 0.7909 (p0) cc_final: 0.7603 (m-40)
REVERT: L  141 PRO cc_start: 0.6906 (Cg_exo) cc_final: 0.6586 (Cg_endo)
REVERT: L  161 GLU cc_start: 0.8159 (pt0) cc_final: 0.7818 (tt0)
REVERT: L  190 LYS cc_start: 0.6986 (tptt) cc_final: 0.6686 (tppt)
REVERT: L  203 SER cc_start: 0.7148 (p) cc_final: 0.6700 (m)
REVERT: N    7 SER cc_start: 0.8643 (t) cc_final: 0.8244 (m)
REVERT: K   45 ARG cc_start: 0.6059 (ttm170) cc_final: 0.5670 (ttm170)
REVERT: K   81 GLN cc_start: 0.5714 (tm-30) cc_final: 0.5181 (tt0)
  outliers start: 40
  outliers final: 28
  residues processed: 139
  average time/residue: 0.0900
  time to fit residues: 18.1180
Evaluate side-chains
  128 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 96
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   58 TRP
Chi-restraints excluded: chain A residue  111 PHE
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   50 TYR
Chi-restraints excluded: chain H residue   77 THR
Chi-restraints excluded: chain H residue  109 VAL
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain H residue  138 LEU
Chi-restraints excluded: chain H residue  150 VAL
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   33 VAL
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue  132 VAL
Chi-restraints excluded: chain L residue  135 LEU
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain L residue  205 VAL
Chi-restraints excluded: chain N residue   70 SER
Chi-restraints excluded: chain N residue   87 THR
Chi-restraints excluded: chain N residue   94 SER
Chi-restraints excluded: chain K residue   11 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 18 optimal weight:    0.0370
   chunk 91 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 80 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 81 optimal weight:    0.8980
   chunk 107 optimal weight:    9.9990
   chunk 16 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 43 optimal weight:    0.5980
   chunk 76 optimal weight:    0.8980
   overall best weight:    0.6860

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

Flipped N/Q/H residues before XYZ refinement:
A  80 ASN
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  13 GLN
** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.160285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.123087 restraints weight = 21470.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 4.23
r_work: 0.3145 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3174
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3174 r_free = 0.3174    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3174 r_free = 0.3174    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3174
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.3661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8871  Z= 0.133
  Angle     :  0.572   7.035  12069  Z= 0.291
  Chirality :  0.041   0.142   1381
  Planarity :  0.005   0.107   1507
  Dihedral  :  5.645  58.355   1275
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.90 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 14.76 %
    Favored  : 80.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.25), residues: 1124
  helix:  1.14 (0.26), residues: 398
  sheet:  0.88 (0.29), residues: 291
  loop : -1.08 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG N  19 
 TYR   0.019   0.001   TYR L 140 
 PHE   0.015   0.001   PHE A 259 
 TRP   0.014   0.001   TRP A  58 
 HIS   0.003   0.001   HIS A  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8866)
  covalent geometry    : angle       0.57188 (12059)
  SS BOND              : bond        0.00368 (    5)
  SS BOND              : angle       0.64680 (   10)
  hydrogen bonds       : bond        0.03883 (  461)
  hydrogen bonds       : angle       4.55267 ( 1319)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 101
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 LYS cc_start: 0.7395 (mttt) cc_final: 0.6593 (tttm)
REVERT: A  175 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.7916 (mm)
REVERT: A  208 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7990 (tp)
REVERT: A  269 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7649 (mp)
REVERT: A  323 MET cc_start: 0.6761 (mmm) cc_final: 0.6467 (mtm)
REVERT: A  396 ILE cc_start: 0.7715 (tt) cc_final: 0.7458 (tt)
REVERT: H   82 ASN cc_start: 0.7927 (p0) cc_final: 0.7646 (m-40)
REVERT: L  142 ARG cc_start: 0.6824 (tpt90) cc_final: 0.6252 (tpt-90)
REVERT: L  143 GLU cc_start: 0.6810 (mm-30) cc_final: 0.6401 (mp0)
REVERT: L  161 GLU cc_start: 0.8090 (pt0) cc_final: 0.7791 (tt0)
REVERT: L  190 LYS cc_start: 0.6904 (tptt) cc_final: 0.6651 (tppt)
REVERT: L  203 SER cc_start: 0.7142 (p) cc_final: 0.6683 (m)
REVERT: N    7 SER cc_start: 0.8593 (t) cc_final: 0.8206 (m)
REVERT: K   81 GLN cc_start: 0.5732 (tm-30) cc_final: 0.5225 (tt0)
  outliers start: 44
  outliers final: 31
  residues processed: 138
  average time/residue: 0.0935
  time to fit residues: 18.3790
Evaluate side-chains
  133 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 99
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   58 TRP
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   50 TYR
Chi-restraints excluded: chain H residue   77 THR
Chi-restraints excluded: chain H residue  109 VAL
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  138 LEU
Chi-restraints excluded: chain H residue  150 VAL
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   33 VAL
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue  132 VAL
Chi-restraints excluded: chain L residue  135 LEU
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  175 LEU
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain L residue  205 VAL
Chi-restraints excluded: chain N residue   70 SER
Chi-restraints excluded: chain N residue   87 THR
Chi-restraints excluded: chain N residue   94 SER
Chi-restraints excluded: chain K residue   11 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 110 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 85 optimal weight:    0.4980
   chunk 9 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 103 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   chunk 95 optimal weight:    1.9990
   chunk 18 optimal weight:    0.2980
   chunk 93 optimal weight:    0.0270
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.5038

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

Flipped N/Q/H residues before XYZ refinement:
A  80 ASN
A  94 GLN
** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.161885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.124344 restraints weight = 19862.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 3.63
r_work: 0.3210 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3218
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3218
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.3807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8871  Z= 0.116
  Angle     :  0.558   8.695  12069  Z= 0.283
  Chirality :  0.040   0.139   1381
  Planarity :  0.005   0.104   1507
  Dihedral  :  5.350  59.988   1273
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.72 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 16.59 %
    Favored  : 79.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.25), residues: 1124
  helix:  1.31 (0.27), residues: 397
  sheet:  1.11 (0.30), residues: 281
  loop : -0.99 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L 211 
 TYR   0.017   0.001   TYR L 140 
 PHE   0.014   0.001   PHE A 259 
 TRP   0.013   0.001   TRP A  58 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 8866)
  covalent geometry    : angle       0.55800 (12059)
  SS BOND              : bond        0.00358 (    5)
  SS BOND              : angle       0.58520 (   10)
  hydrogen bonds       : bond        0.03647 (  461)
  hydrogen bonds       : angle       4.45512 ( 1319)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 99
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 LYS cc_start: 0.7360 (mttt) cc_final: 0.6628 (tttm)
REVERT: A  175 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.7925 (mm)
REVERT: A  208 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7979 (tp)
REVERT: A  269 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7656 (mp)
REVERT: A  290 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7831 (t80)
REVERT: A  323 MET cc_start: 0.6734 (mmm) cc_final: 0.6475 (mtm)
REVERT: A  396 ILE cc_start: 0.7691 (tt) cc_final: 0.7445 (tt)
REVERT: H   82 ASN cc_start: 0.7899 (p0) cc_final: 0.7683 (m-40)
REVERT: L  142 ARG cc_start: 0.6565 (tpt90) cc_final: 0.5893 (tpt-90)
REVERT: L  161 GLU cc_start: 0.8060 (pt0) cc_final: 0.7816 (tt0)
REVERT: L  190 LYS cc_start: 0.6965 (tptt) cc_final: 0.6699 (tppt)
REVERT: L  203 SER cc_start: 0.7151 (p) cc_final: 0.6685 (m)
REVERT: N    7 SER cc_start: 0.8537 (t) cc_final: 0.8178 (m)
REVERT: K   81 GLN cc_start: 0.5743 (tm-30) cc_final: 0.5250 (tt0)
  outliers start: 34
  outliers final: 26
  residues processed: 130
  average time/residue: 0.0989
  time to fit residues: 17.8893
Evaluate side-chains
  124 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 94
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   36 ASP
Chi-restraints excluded: chain A residue   58 TRP
Chi-restraints excluded: chain A residue   80 ASN
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  290 PHE
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain A residue  457 HIS
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   50 TYR
Chi-restraints excluded: chain H residue  109 VAL
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain H residue  138 LEU
Chi-restraints excluded: chain H residue  150 VAL
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue  132 VAL
Chi-restraints excluded: chain L residue  135 LEU
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain N residue   70 SER
Chi-restraints excluded: chain N residue   87 THR
Chi-restraints excluded: chain K residue   11 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 102 optimal weight:    5.9990
   chunk 34 optimal weight:    0.4980
   chunk 55 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  80 ASN
H 171 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.160356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.122992 restraints weight = 19392.807|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 3.69
r_work: 0.3185 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3191
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3191 r_free = 0.3191    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3191 r_free = 0.3191    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3191
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.3858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8871  Z= 0.144
  Angle     :  0.581   7.943  12069  Z= 0.295
  Chirality :  0.041   0.143   1381
  Planarity :  0.005   0.104   1507
  Dihedral  :  5.375  59.386   1272
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.46 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 16.92 %
    Favored  : 79.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.51 (0.25), residues: 1124
  helix:  1.27 (0.27), residues: 397
  sheet:  1.06 (0.30), residues: 283
  loop : -1.01 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG N  19 
 TYR   0.014   0.001   TYR L 140 
 PHE   0.014   0.001   PHE A 259 
 TRP   0.015   0.001   TRP A  58 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 8866)
  covalent geometry    : angle       0.58103 (12059)
  SS BOND              : bond        0.00390 (    5)
  SS BOND              : angle       0.66768 (   10)
  hydrogen bonds       : bond        0.03897 (  461)
  hydrogen bonds       : angle       4.48888 ( 1319)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 93
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 LYS cc_start: 0.7406 (mttt) cc_final: 0.6654 (tttm)
REVERT: A  175 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.7962 (mm)
REVERT: A  208 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7998 (tp)
REVERT: A  269 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7599 (mp)
REVERT: A  323 MET cc_start: 0.6750 (mmm) cc_final: 0.6494 (mtt)
REVERT: A  396 ILE cc_start: 0.7712 (tt) cc_final: 0.7460 (tt)
REVERT: H   82 ASN cc_start: 0.7903 (p0) cc_final: 0.7671 (m-40)
REVERT: L  161 GLU cc_start: 0.8078 (pt0) cc_final: 0.7802 (tt0)
REVERT: L  190 LYS cc_start: 0.6896 (tptt) cc_final: 0.6632 (tppt)
REVERT: L  203 SER cc_start: 0.7158 (p) cc_final: 0.6690 (m)
REVERT: N    7 SER cc_start: 0.8524 (t) cc_final: 0.8158 (m)
REVERT: K   81 GLN cc_start: 0.5739 (tm-30) cc_final: 0.5224 (tt0)
  outliers start: 37
  outliers final: 33
  residues processed: 126
  average time/residue: 0.0888
  time to fit residues: 16.1830
Evaluate side-chains
  128 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 92
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   36 ASP
Chi-restraints excluded: chain A residue   58 TRP
Chi-restraints excluded: chain A residue   80 ASN
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  289 MET
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain A residue  457 HIS
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   50 TYR
Chi-restraints excluded: chain H residue  109 VAL
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  138 LEU
Chi-restraints excluded: chain H residue  150 VAL
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue  132 VAL
Chi-restraints excluded: chain L residue  135 LEU
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  175 LEU
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain N residue   70 SER
Chi-restraints excluded: chain N residue   87 THR
Chi-restraints excluded: chain N residue   94 SER
Chi-restraints excluded: chain K residue   11 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0060
   chunk 25 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 93 optimal weight:    0.0060
   chunk 41 optimal weight:    0.8980
   chunk 91 optimal weight:    3.9990
   chunk 89 optimal weight:    0.0000
   chunk 50 optimal weight:    0.6980
   chunk 100 optimal weight:    8.9990
   overall best weight:    0.2816

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

Flipped N/Q/H residues before XYZ refinement:
A  80 ASN
A 231 HIS
** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.163700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.127788 restraints weight = 23803.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3495 rms_B_bonded: 5.13
r_work: 0.3166 rms_B_bonded: 4.69 restraints_weight: 0.5000
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3170
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3170 r_free = 0.3170    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3170 r_free = 0.3170    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3170
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.3988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8871  Z= 0.107
  Angle     :  0.558   8.603  12069  Z= 0.281
  Chirality :  0.040   0.139   1381
  Planarity :  0.005   0.103   1507
  Dihedral  :  5.203  59.308   1272
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.46 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 17.56 %
    Favored  : 78.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.68 (0.25), residues: 1124
  helix:  1.43 (0.27), residues: 398
  sheet:  1.21 (0.30), residues: 276
  loop : -0.94 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG L 211 
 TYR   0.021   0.001   TYR L 140 
 PHE   0.013   0.001   PHE A 259 
 TRP   0.014   0.001   TRP H 154 
 HIS   0.005   0.001   HIS A 231 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 8866)
  covalent geometry    : angle       0.55817 (12059)
  SS BOND              : bond        0.00349 (    5)
  SS BOND              : angle       0.50637 (   10)
  hydrogen bonds       : bond        0.03413 (  461)
  hydrogen bonds       : angle       4.35482 ( 1319)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 97
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.7525 (tp30) cc_final: 0.7243 (mm-30)
REVERT: A   87 LYS cc_start: 0.7293 (mttt) cc_final: 0.6524 (tttm)
REVERT: A  175 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.7896 (mm)
REVERT: A  208 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7982 (tp)
REVERT: A  323 MET cc_start: 0.6807 (mmm) cc_final: 0.6467 (mtm)
REVERT: A  396 ILE cc_start: 0.7705 (tt) cc_final: 0.7450 (tt)
REVERT: H   82 ASN cc_start: 0.7864 (p0) cc_final: 0.7652 (m-40)
REVERT: L  143 GLU cc_start: 0.6462 (mp0) cc_final: 0.6230 (mp0)
REVERT: L  161 GLU cc_start: 0.8149 (pt0) cc_final: 0.7910 (tt0)
REVERT: L  190 LYS cc_start: 0.6734 (tptt) cc_final: 0.6496 (tppt)
REVERT: L  203 SER cc_start: 0.7074 (p) cc_final: 0.6605 (m)
REVERT: N    7 SER cc_start: 0.8594 (t) cc_final: 0.8208 (m)
REVERT: K   81 GLN cc_start: 0.5669 (tm-30) cc_final: 0.5176 (tt0)
  outliers start: 32
  outliers final: 27
  residues processed: 125
  average time/residue: 0.0884
  time to fit residues: 16.0469
Evaluate side-chains
  121 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 92
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   58 TRP
Chi-restraints excluded: chain A residue   80 ASN
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  289 MET
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain A residue  457 HIS
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   50 TYR
Chi-restraints excluded: chain H residue  109 VAL
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain H residue  150 VAL
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue  132 VAL
Chi-restraints excluded: chain L residue  135 LEU
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain L residue  205 VAL
Chi-restraints excluded: chain N residue   70 SER
Chi-restraints excluded: chain N residue   87 THR
Chi-restraints excluded: chain K residue   11 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 107 optimal weight:    0.0770
   chunk 69 optimal weight:    6.9990
   chunk 36 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.6740

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

Flipped N/Q/H residues before XYZ refinement:
A  80 ASN
H 171 GLN
** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 124 GLN
** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.161862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.126332 restraints weight = 23496.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 5.12
r_work: 0.3146 rms_B_bonded: 4.61 restraints_weight: 0.5000
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3151
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3151 r_free = 0.3151    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3151 r_free = 0.3151    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3151
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.4012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8871  Z= 0.128
  Angle     :  0.569   7.928  12069  Z= 0.287
  Chirality :  0.040   0.139   1381
  Planarity :  0.005   0.104   1507
  Dihedral  :  5.257  59.372   1272
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.46 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 18.10 %
    Favored  : 78.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.25), residues: 1124
  helix:  1.46 (0.27), residues: 398
  sheet:  1.23 (0.31), residues: 276
  loop : -0.93 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG L 211 
 TYR   0.023   0.001   TYR L 140 
 PHE   0.027   0.001   PHE H 122 
 TRP   0.014   0.001   TRP A  58 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 8866)
  covalent geometry    : angle       0.56859 (12059)
  SS BOND              : bond        0.00365 (    5)
  SS BOND              : angle       0.61292 (   10)
  hydrogen bonds       : bond        0.03645 (  461)
  hydrogen bonds       : angle       4.34442 ( 1319)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2527.62 seconds
wall clock time: 44 minutes 5.61 seconds (2645.61 seconds total)