Starting phenix.real_space_refine
on Tue Mar  3 19:19:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s8m_24897/03_2026/7s8m_24897.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s8m_24897/03_2026/7s8m_24897.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s8m_24897/03_2026/7s8m_24897.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s8m_24897/03_2026/7s8m_24897.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s8m_24897/03_2026/7s8m_24897.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s8m_24897/03_2026/7s8m_24897.cif"
  }
  resolution = 2.54
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      63      5.16       5
     C    5343      2.51       5
     N    1408      2.21       5
     O    1532      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8346
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 1707
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1707
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 61
          Unresolved non-hydrogen dihedrals: 41
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 35
    Chain: "C"
      Number of atoms: 2564
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2564
          Classifications: {'peptide': 339}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 42
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 34
          Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 2, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 34
    Chain: "D"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 401
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "E"
      Number of atoms: 1743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1743
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 49
          Unresolved non-hydrogen dihedrals: 31
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 31
    Chain: "R"
      Number of atoms: 1892
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1892
          Classifications: {'peptide': 253}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 8, 'TRANS': 244}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 134
          Unresolved non-hydrogen angles: 170
          Unresolved non-hydrogen dihedrals: 121
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 7, 'TRP:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 84
    Chain: "A"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 39
          Classifications: {'peptide': 5}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 4}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
  Time building chain proxies: 1.70, per 1000 atoms: 0.20
  Number of scatterers: 8346
  At special positions: 0
  Unit cell: (102.08, 117.92, 117.92, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      63     16.00
     O    1532      8.00
     N    1408      7.00
     C    5343      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 168 " - pdb=" SG  CYS R 180 " 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: 0.85
  Conformation dependent library (CDL) restraints added in 330.8 milliseconds
  

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2052

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 13 sheets defined
      36.9% alpha, 23.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'B' and resid 6 through 31
    Processing helix  chain 'B' and resid 46 through 54
    Processing helix  chain 'B' and resid 207 through 216
      removed outlier: 4.667A  pdb=" N   ILE B 212 " --> pdb=" O   LYS B 209 " (cutoff:3.500A)
      removed outlier: 5.719A  pdb=" N   HIS B 213 " --> pdb=" O   LYS B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 255
    Processing helix  chain 'B' and resid 270 through 281
      removed outlier: 4.144A  pdb=" N   LYS B 279 " --> pdb=" O   GLU B 275 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   LYS B 280 " --> pdb=" O   GLU B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 286
      removed outlier: 3.541A  pdb=" N   ILE B 285 " --> pdb=" O   PRO B 282 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 310
      removed outlier: 3.683A  pdb=" N   LEU B 310 " --> pdb=" O   GLN B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 330 through 351
      removed outlier: 3.633A  pdb=" N   ASP B 341 " --> pdb=" O   ASP B 337 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   VAL B 342 " --> pdb=" O   ALA B 338 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 3 through 24
    Processing helix  chain 'C' and resid 29 through 34
    Processing helix  chain 'D' and resid 9 through 24
      removed outlier: 3.501A  pdb=" N   ASN D  24 " --> pdb=" O   LYS D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 44
    Processing helix  chain 'D' and resid 55 through 59
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.823A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 30 through 57
      removed outlier: 3.966A  pdb=" N   VAL R  34 " --> pdb=" O   THR R  30 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   VAL R  43 " --> pdb=" O   PHE R  39 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   GLY R  44 " --> pdb=" O   ILE R  40 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   PHE R  57 " --> pdb=" O   TRP R  53 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 64 through 95
      removed outlier: 3.779A  pdb=" N   VAL R  68 " --> pdb=" O   PHE R  64 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 103 through 133
      removed outlier: 3.874A  pdb=" N   THR R 107 " --> pdb=" O   SER R 103 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   VAL R 108 " --> pdb=" O   PHE R 104 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   LEU R 120 " --> pdb=" O   GLY R 116 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   SER R 121 " --> pdb=" O   LEU R 117 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 133 through 139
    Processing helix  chain 'R' and resid 144 through 167
    Processing helix  chain 'R' and resid 177 through 212
    Processing helix  chain 'R' and resid 217 through 236
    Processing helix  chain 'R' and resid 236 through 250
      removed outlier: 4.291A  pdb=" N   GLY R 240 " --> pdb=" O   GLY R 236 " (cutoff:3.500A)
      removed outlier: 4.855A  pdb=" N   LEU R 247 " --> pdb=" O   TRP R 243 " (cutoff:3.500A)
      removed outlier: 5.403A  pdb=" N   TRP R 248 " --> pdb=" O   PHE R 244 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 257 through 280
      Proline residue:  R 262  - end of helix
      Proline residue:  R 276  - end of helix
    Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 190
    Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 51
      removed outlier: 6.293A  pdb=" N   THR C  47 " --> pdb=" O   ASN C 340 " (cutoff:3.500A)
      removed outlier: 7.227A  pdb=" N   ASN C 340 " --> pdb=" O   THR C  47 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ARG C  49 " --> pdb=" O   ILE C 338 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   CYS C 317 " --> pdb=" O   GLY C 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63
      removed outlier: 6.826A  pdb=" N   ALA C  73 " --> pdb=" O   TYR C  59 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   MET C  61 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   VAL C  71 " --> pdb=" O   MET C  61 " (cutoff:3.500A)
      removed outlier: 5.212A  pdb=" N   TRP C  63 " --> pdb=" O   LEU C  69 " (cutoff:3.500A)
      removed outlier: 7.430A  pdb=" N   LEU C  69 " --> pdb=" O   TRP C  63 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   LEU C  79 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   ALA C  92 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   ILE C  81 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105
      removed outlier: 6.908A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 5.165A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 7.331A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 6.020A  pdb=" N   ASN C 125 " --> pdb=" O   VAL C 135 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   VAL C 135 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151
      removed outlier: 3.585A  pdb=" N   CYS C 148 " --> pdb=" O   SER C 160 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   ILE C 157 " --> pdb=" O   TRP C 169 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   THR C 165 " --> pdb=" O   SER C 161 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192
      removed outlier: 6.992A  pdb=" N   GLY C 202 " --> pdb=" O   MET C 188 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   LEU C 190 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   VAL C 200 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
      removed outlier: 5.476A  pdb=" N   LEU C 192 " --> pdb=" O   LEU C 198 " (cutoff:3.500A)
      removed outlier: 7.642A  pdb=" N   LEU C 198 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   ALA C 208 " --> pdb=" O   THR C 221 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   THR C 221 " --> pdb=" O   ALA C 208 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   LEU C 210 " --> pdb=" O   ARG C 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234
      removed outlier: 6.522A  pdb=" N   CYS C 250 " --> pdb=" O   THR C 263 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   THR C 263 " --> pdb=" O   CYS C 250 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   LEU C 252 " --> pdb=" O   LEU C 261 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLN C 259 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278
      removed outlier: 3.554A  pdb=" N   SER C 275 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   ASP C 298 " --> pdb=" O   ARG C 304 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   ARG C 304 " --> pdb=" O   ASP C 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 5.996A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.524A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12
      removed outlier: 5.996A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 129
    Processing sheet with id=AB4, first strand: chain 'E' and resid 135 through 136
      removed outlier: 6.338A  pdb=" N   VAL E 135 " --> pdb=" O   GLU E 234 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   TRP E 164 " --> pdb=" O   LEU E 176 " (cutoff:3.500A)

    445 hydrogen bonds defined for protein.
    1239 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: 1.46

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2666
        1.34 -     1.46: 1967
        1.46 -     1.58: 3802
        1.58 -     1.69: 0
        1.69 -     1.81: 87
  Bond restraints: 8522
  Sorted by residual:
  bond pdb=" CB  ASP R  75 "
       pdb=" CG  ASP R  75 "
    ideal  model  delta    sigma   weight residual
    1.516  1.478  0.038 2.50e-02 1.60e+03 2.37e+00
  bond pdb=" CG1 ILE C  58 "
       pdb=" CD1 ILE C  58 "
    ideal  model  delta    sigma   weight residual
    1.513  1.470  0.043 3.90e-02 6.57e+02 1.22e+00
  bond pdb=" CG  LEU R 237 "
       pdb=" CD1 LEU R 237 "
    ideal  model  delta    sigma   weight residual
    1.521  1.488  0.033 3.30e-02 9.18e+02 1.02e+00
  bond pdb=" C   GLU E 222 "
       pdb=" N   TYR E 223 "
    ideal  model  delta    sigma   weight residual
    1.330  1.318  0.012 1.47e-02 4.63e+03 7.05e-01
  bond pdb=" CG  LEU R  45 "
       pdb=" CD2 LEU R  45 "
    ideal  model  delta    sigma   weight residual
    1.521  1.494  0.027 3.30e-02 9.18e+02 6.66e-01
  ... (remaining 8517 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 11209
        1.41 -     2.81: 294
        2.81 -     4.22: 48
        4.22 -     5.63: 17
        5.63 -     7.04: 5
  Bond angle restraints: 11573
  Sorted by residual:
  angle pdb=" N   PRO E 224 "
        pdb=" CA  PRO E 224 "
        pdb=" C   PRO E 224 "
      ideal   model   delta    sigma   weight residual
     112.10  118.27   -6.17 2.60e+00 1.48e-01 5.64e+00
  angle pdb=" N   GLY B 352 "
        pdb=" CA  GLY B 352 "
        pdb=" C   GLY B 352 "
      ideal   model   delta    sigma   weight residual
     114.67  117.97   -3.30 1.41e+00 5.03e-01 5.47e+00
  angle pdb=" N   ASP C 291 "
        pdb=" CA  ASP C 291 "
        pdb=" C   ASP C 291 "
      ideal   model   delta    sigma   weight residual
     112.97  110.60    2.37 1.06e+00 8.90e-01 5.01e+00
  angle pdb=" CA  TYR E 178 "
        pdb=" CB  TYR E 178 "
        pdb=" CG  TYR E 178 "
      ideal   model   delta    sigma   weight residual
     113.90  117.79   -3.89 1.80e+00 3.09e-01 4.66e+00
  angle pdb=" CA  ARG E 206 "
        pdb=" CB  ARG E 206 "
        pdb=" CG  ARG E 206 "
      ideal   model   delta    sigma   weight residual
     114.10  118.19   -4.09 2.00e+00 2.50e-01 4.19e+00
  ... (remaining 11568 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.95: 4587
       16.95 -    33.89: 316
       33.89 -    50.84: 68
       50.84 -    67.78: 11
       67.78 -    84.73: 5
  Dihedral angle restraints: 4987
    sinusoidal: 1808
      harmonic: 3179
  Sorted by residual:
  dihedral pdb=" CA  ARG E 179 "
           pdb=" C   ARG E 179 "
           pdb=" N   MET E 180 "
           pdb=" CA  MET E 180 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.06  -25.94     0      5.00e+00 4.00e-02 2.69e+01
  dihedral pdb=" CA  ASN B 347 "
           pdb=" C   ASN B 347 "
           pdb=" N   LEU B 348 "
           pdb=" CA  LEU B 348 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.57   22.43     0      5.00e+00 4.00e-02 2.01e+01
  dihedral pdb=" CA  PHE C 234 "
           pdb=" C   PHE C 234 "
           pdb=" N   PHE C 235 "
           pdb=" CA  PHE C 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.41   19.59     0      5.00e+00 4.00e-02 1.54e+01
  ... (remaining 4984 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 838
       0.033 -    0.066: 344
       0.066 -    0.099: 105
       0.099 -    0.133: 49
       0.133 -    0.166: 8
  Chirality restraints: 1344
  Sorted by residual:
  chirality pdb=" CA  TYR E 178 "
            pdb=" N   TYR E 178 "
            pdb=" C   TYR E 178 "
            pdb=" CB  TYR E 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.87e-01
  chirality pdb=" CA  VAL E  37 "
            pdb=" N   VAL E  37 "
            pdb=" C   VAL E  37 "
            pdb=" CB  VAL E  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.69e-01
  chirality pdb=" CA  PRO E 224 "
            pdb=" N   PRO E 224 "
            pdb=" C   PRO E 224 "
            pdb=" CB  PRO E 224 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.49e-01
  ... (remaining 1341 not shown)

  Planarity restraints: 1452
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 129 "   -0.008 2.00e-02 2.50e+03   1.67e-02 2.80e+00
        pdb=" C   LEU R 129 "    0.029 2.00e-02 2.50e+03
        pdb=" O   LEU R 129 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   SER R 130 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN R 242 "   -0.008 2.00e-02 2.50e+03   1.67e-02 2.79e+00
        pdb=" C   GLN R 242 "    0.029 2.00e-02 2.50e+03
        pdb=" O   GLN R 242 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   TRP R 243 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R 123 "   -0.008 2.00e-02 2.50e+03   1.61e-02 2.58e+00
        pdb=" C   VAL R 123 "    0.028 2.00e-02 2.50e+03
        pdb=" O   VAL R 123 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   SER R 124 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1449 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 268
        2.72 -     3.26: 8118
        3.26 -     3.81: 13659
        3.81 -     4.35: 16864
        4.35 -     4.90: 29665
  Nonbonded interactions: 68574
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B  14 "
            pdb=" OG1 THR E  57 "
     model   vdw
     2.171 3.040
  nonbonded pdb=" OG  SER C 281 "
            pdb=" OD2 ASP D  48 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OG1 THR C 274 "
            pdb=" O   VAL C 315 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" O   CYS B 254 "
            pdb=" NZ  LYS B 317 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" OD1 ASP B 272 "
            pdb=" N   LEU B 273 "
     model   vdw
     2.249 3.120
  ... (remaining 68569 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.220
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     8.970
  Find NCS groups from input model:        0.060
  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:9.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8523  Z= 0.162
  Angle     :  0.589   7.037  11575  Z= 0.326
  Chirality :  0.043   0.166   1344
  Planarity :  0.004   0.031   1452
  Dihedral  : 12.635  84.726   2932
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.46 (0.26), residues: 1082
  helix:  2.00 (0.28), residues: 369
  sheet:  0.15 (0.29), residues: 276
  loop : -1.08 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 219 
 TYR   0.018   0.002   TYR E 178 
 PHE   0.019   0.002   PHE B 189 
 TRP   0.014   0.002   TRP C  82 
 HIS   0.004   0.001   HIS C 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 8522)
  covalent geometry    : angle       0.58860 (11573)
  SS BOND              : bond        0.00042 (    1)
  SS BOND              : angle       0.79996 (    2)
  hydrogen bonds       : bond        0.12524 (  441)
  hydrogen bonds       : angle       5.87440 ( 1239)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
REVERT: B   17 LYS cc_start: 0.7754 (mmtp) cc_final: 0.7520 (mmtp)
REVERT: C   25 CYS cc_start: 0.7535 (p) cc_final: 0.7145 (p)
REVERT: C  254 ASP cc_start: 0.7040 (t70) cc_final: 0.6790 (t0)
REVERT: R  109 MET cc_start: 0.6736 (ttp) cc_final: 0.6462 (ttm)
REVERT: R  280 PHE cc_start: 0.7849 (t80) cc_final: 0.7147 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 200
  average time/residue: 0.4321
  time to fit residues: 93.1677
Evaluate side-chains
  183 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 49 optimal weight:    0.1980
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    0.1980
   chunk 106 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B 255 ASN
C  75 GLN
C 268 ASN
R  48 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.131709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.117215 restraints weight = 11092.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3601 rms_B_bonded: 1.63
r_work: 0.3499 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3358 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.0855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8523  Z= 0.154
  Angle     :  0.564   7.669  11575  Z= 0.296
  Chirality :  0.043   0.150   1344
  Planarity :  0.003   0.031   1452
  Dihedral  :  4.469  24.520   1173
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  :  8.24 %
    Favored  : 90.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.92 (0.26), residues: 1082
  helix:  2.65 (0.28), residues: 373
  sheet:  0.32 (0.29), residues: 273
  loop : -1.04 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 197 
 TYR   0.020   0.002   TYR E 178 
 PHE   0.018   0.002   PHE B 189 
 TRP   0.010   0.001   TRP R 243 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 8522)
  covalent geometry    : angle       0.56430 (11573)
  SS BOND              : bond        0.00141 (    1)
  SS BOND              : angle       0.29806 (    2)
  hydrogen bonds       : bond        0.03916 (  441)
  hydrogen bonds       : angle       4.53274 ( 1239)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 192
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
REVERT: B  249 LEU cc_start: 0.8426 (tt) cc_final: 0.8226 (tt)
REVERT: C   25 CYS cc_start: 0.7918 (p) cc_final: 0.7537 (p)
REVERT: C  197 ARG cc_start: 0.7791 (mmt180) cc_final: 0.7551 (mmt180)
REVERT: E   30 SER cc_start: 0.8230 (m) cc_final: 0.8019 (t)
REVERT: R   45 LEU cc_start: 0.7610 (mm) cc_final: 0.7217 (mm)
REVERT: R  109 MET cc_start: 0.6814 (ttp) cc_final: 0.6591 (ttp)
REVERT: R  280 PHE cc_start: 0.8167 (t80) cc_final: 0.7690 (t80)
  outliers start: 11
  outliers final: 9
  residues processed: 196
  average time/residue: 0.4264
  time to fit residues: 90.3114
Evaluate side-chains
  193 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 184
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain D residue   21 MET
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain R residue  186 ILE
Chi-restraints excluded: chain R residue  192 ILE
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 105 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0770
   chunk 89 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 15 optimal weight:    0.0870
   chunk 66 optimal weight:    1.9990
   chunk 93 optimal weight:    0.5980
   overall best weight:    0.3916

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

Flipped N/Q/H residues before XYZ refinement:
C 268 ASN
E 182 ASN
R  48 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.132355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.117947 restraints weight = 11036.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3616 rms_B_bonded: 1.64
r_work: 0.3513 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3372 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.1120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8523  Z= 0.116
  Angle     :  0.509   6.013  11575  Z= 0.269
  Chirality :  0.041   0.142   1344
  Planarity :  0.003   0.032   1452
  Dihedral  :  4.218  22.369   1173
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 10.98 %
    Favored  : 87.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.08 (0.26), residues: 1082
  helix:  2.80 (0.28), residues: 375
  sheet:  0.33 (0.29), residues: 279
  loop : -0.93 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 127 
 TYR   0.015   0.001   TYR E 178 
 PHE   0.017   0.001   PHE B 189 
 TRP   0.011   0.001   TRP C 297 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 8522)
  covalent geometry    : angle       0.50891 (11573)
  SS BOND              : bond        0.00115 (    1)
  SS BOND              : angle       0.28816 (    2)
  hydrogen bonds       : bond        0.03427 (  441)
  hydrogen bonds       : angle       4.27926 ( 1239)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 187
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
REVERT: B  271 LYS cc_start: 0.7998 (ptmm) cc_final: 0.7666 (ptmm)
REVERT: B  279 LYS cc_start: 0.8641 (mtmm) cc_final: 0.8261 (mtmm)
REVERT: C   25 CYS cc_start: 0.7937 (p) cc_final: 0.7535 (p)
REVERT: C  197 ARG cc_start: 0.7821 (mmt180) cc_final: 0.7575 (mmt180)
REVERT: C  217 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8217 (pmm)
REVERT: E   30 SER cc_start: 0.8286 (m) cc_final: 0.8034 (t)
REVERT: E  198 THR cc_start: 0.8115 (p) cc_final: 0.7906 (p)
REVERT: R   45 LEU cc_start: 0.7613 (mm) cc_final: 0.7239 (mm)
REVERT: R  280 PHE cc_start: 0.8193 (t80) cc_final: 0.7689 (t80)
  outliers start: 15
  outliers final: 11
  residues processed: 193
  average time/residue: 0.4213
  time to fit residues: 87.9000
Evaluate side-chains
  194 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 182
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain D residue   21 MET
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain R residue   84 ILE
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 104 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   chunk 94 optimal weight:    0.8980
   chunk 96 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
B 269 ASN
C 268 ASN
E 182 ASN
R  48 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.129568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.114992 restraints weight = 11222.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 1.64
r_work: 0.3470 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3328 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.1171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060   8523  Z= 0.234
  Angle     :  0.588   7.868  11575  Z= 0.308
  Chirality :  0.045   0.179   1344
  Planarity :  0.004   0.034   1452
  Dihedral  :  4.517  26.054   1173
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 11.56 %
    Favored  : 84.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.93 (0.26), residues: 1082
  helix:  2.72 (0.28), residues: 375
  sheet:  0.28 (0.30), residues: 274
  loop : -1.09 (0.29), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 127 
 TYR   0.024   0.002   TYR E 178 
 PHE   0.020   0.002   PHE B 189 
 TRP   0.011   0.002   TRP R 190 
 HIS   0.005   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00560 ( 8522)
  covalent geometry    : angle       0.58756 (11573)
  SS BOND              : bond        0.00136 (    1)
  SS BOND              : angle       0.49416 (    2)
  hydrogen bonds       : bond        0.04119 (  441)
  hydrogen bonds       : angle       4.46783 ( 1239)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 184
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: B  279 LYS cc_start: 0.8629 (mtmm) cc_final: 0.8266 (mtmm)
REVERT: C   25 CYS cc_start: 0.7937 (p) cc_final: 0.7513 (p)
REVERT: C  197 ARG cc_start: 0.7832 (mmt180) cc_final: 0.7548 (mmt180)
REVERT: C  217 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8269 (pmm)
REVERT: E   30 SER cc_start: 0.8257 (m) cc_final: 0.8055 (t)
REVERT: R   45 LEU cc_start: 0.7615 (mm) cc_final: 0.7176 (mm)
REVERT: R  280 PHE cc_start: 0.8225 (t80) cc_final: 0.7732 (t80)
  outliers start: 31
  outliers final: 19
  residues processed: 199
  average time/residue: 0.4131
  time to fit residues: 89.1562
Evaluate side-chains
  203 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 183
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  227 SER
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain D residue   38 MET
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain R residue   66 VAL
Chi-restraints excluded: chain R residue   88 VAL
Chi-restraints excluded: chain R residue  186 ILE
Chi-restraints excluded: chain R residue  192 ILE
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  263 VAL
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 94 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0470
   chunk 13 optimal weight:    0.6980
   chunk 91 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0670
   chunk 74 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 72 optimal weight:    3.9990
   chunk 99 optimal weight:    0.5980
   overall best weight:    0.4216

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

Flipped N/Q/H residues before XYZ refinement:
C 268 ASN
E 130 GLN
R  48 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.131914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.117421 restraints weight = 11124.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3609 rms_B_bonded: 1.65
r_work: 0.3506 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3364 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.1266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8523  Z= 0.123
  Angle     :  0.527   9.569  11575  Z= 0.275
  Chirality :  0.042   0.148   1344
  Planarity :  0.003   0.032   1452
  Dihedral  :  4.284  23.177   1173
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 13.62 %
    Favored  : 83.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.02 (0.26), residues: 1082
  helix:  2.81 (0.28), residues: 375
  sheet:  0.28 (0.30), residues: 270
  loop : -1.01 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 251 
 TYR   0.016   0.001   TYR E 178 
 PHE   0.017   0.001   PHE B 189 
 TRP   0.012   0.001   TRP C  82 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 8522)
  covalent geometry    : angle       0.52703 (11573)
  SS BOND              : bond        0.00128 (    1)
  SS BOND              : angle       0.28340 (    2)
  hydrogen bonds       : bond        0.03445 (  441)
  hydrogen bonds       : angle       4.28178 ( 1239)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 179
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
REVERT: C   25 CYS cc_start: 0.7914 (p) cc_final: 0.7509 (p)
REVERT: C  197 ARG cc_start: 0.7795 (mmt180) cc_final: 0.7524 (mmt180)
REVERT: C  217 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8199 (pmm)
REVERT: E   30 SER cc_start: 0.8253 (m) cc_final: 0.8042 (t)
REVERT: R   45 LEU cc_start: 0.7609 (mm) cc_final: 0.7257 (mm)
REVERT: R  280 PHE cc_start: 0.8211 (t80) cc_final: 0.7718 (t80)
  outliers start: 21
  outliers final: 15
  residues processed: 189
  average time/residue: 0.4276
  time to fit residues: 87.3754
Evaluate side-chains
  191 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 175
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue   33 ILE
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  227 SER
Chi-restraints excluded: chain D residue   21 MET
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain R residue   66 VAL
Chi-restraints excluded: chain R residue  131 VAL
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 52 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 9 optimal weight:    0.4980
   chunk 7 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
C 142 HIS
C 268 ASN
E 182 ASN
R  48 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.131330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.116850 restraints weight = 11075.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3602 rms_B_bonded: 1.63
r_work: 0.3499 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3359 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.1322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8523  Z= 0.151
  Angle     :  0.542   9.111  11575  Z= 0.283
  Chirality :  0.042   0.152   1344
  Planarity :  0.003   0.033   1452
  Dihedral  :  4.286  23.180   1173
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 13.73 %
    Favored  : 83.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.26), residues: 1082
  helix:  2.85 (0.27), residues: 375
  sheet:  0.27 (0.30), residues: 276
  loop : -0.96 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 127 
 TYR   0.020   0.002   TYR E 178 
 PHE   0.017   0.001   PHE B 189 
 TRP   0.012   0.001   TRP C  82 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 8522)
  covalent geometry    : angle       0.54169 (11573)
  SS BOND              : bond        0.00133 (    1)
  SS BOND              : angle       0.34205 (    2)
  hydrogen bonds       : bond        0.03607 (  441)
  hydrogen bonds       : angle       4.28928 ( 1239)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 178
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
REVERT: B  279 LYS cc_start: 0.8629 (mtmm) cc_final: 0.8268 (mtmm)
REVERT: C   25 CYS cc_start: 0.7917 (p) cc_final: 0.7503 (p)
REVERT: C  197 ARG cc_start: 0.7791 (mmt180) cc_final: 0.7562 (mmt180)
REVERT: C  217 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8237 (pmm)
REVERT: E   30 SER cc_start: 0.8236 (m) cc_final: 0.8025 (t)
REVERT: R   45 LEU cc_start: 0.7624 (mm) cc_final: 0.7271 (mm)
REVERT: R  280 PHE cc_start: 0.8220 (t80) cc_final: 0.7729 (t80)
  outliers start: 23
  outliers final: 16
  residues processed: 190
  average time/residue: 0.4133
  time to fit residues: 84.7470
Evaluate side-chains
  194 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 177
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  227 SER
Chi-restraints excluded: chain D residue   21 MET
Chi-restraints excluded: chain D residue   38 MET
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain R residue   66 VAL
Chi-restraints excluded: chain R residue  131 VAL
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  263 VAL
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 66 optimal weight:    0.3980
   chunk 105 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 17 optimal weight:    0.1980
   chunk 49 optimal weight:    0.6980
   chunk 98 optimal weight:    0.6980
   chunk 68 optimal weight:    0.8980
   chunk 106 optimal weight:    0.6980
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
C 142 HIS
C 268 ASN
R  48 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.131689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.117220 restraints weight = 11176.985|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 1.64
r_work: 0.3502 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3361 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.1373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8523  Z= 0.138
  Angle     :  0.539   9.227  11575  Z= 0.279
  Chirality :  0.042   0.148   1344
  Planarity :  0.003   0.031   1452
  Dihedral  :  4.236  22.297   1173
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 14.42 %
    Favored  : 83.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.26), residues: 1082
  helix:  3.00 (0.27), residues: 369
  sheet:  0.24 (0.30), residues: 277
  loop : -0.92 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 127 
 TYR   0.018   0.002   TYR E 178 
 PHE   0.017   0.001   PHE B 189 
 TRP   0.012   0.001   TRP C  82 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 8522)
  covalent geometry    : angle       0.53864 (11573)
  SS BOND              : bond        0.00115 (    1)
  SS BOND              : angle       0.31219 (    2)
  hydrogen bonds       : bond        0.03463 (  441)
  hydrogen bonds       : angle       4.24809 ( 1239)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 179
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: B  279 LYS cc_start: 0.8630 (mtmm) cc_final: 0.8268 (mtmm)
REVERT: C   25 CYS cc_start: 0.7889 (p) cc_final: 0.7485 (p)
REVERT: C  146 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8496 (mt)
REVERT: C  197 ARG cc_start: 0.7785 (mmt180) cc_final: 0.7561 (mmt180)
REVERT: E   30 SER cc_start: 0.8238 (m) cc_final: 0.8029 (t)
REVERT: R   45 LEU cc_start: 0.7603 (mm) cc_final: 0.7250 (mm)
REVERT: R  280 PHE cc_start: 0.8224 (t80) cc_final: 0.7732 (t80)
  outliers start: 22
  outliers final: 17
  residues processed: 191
  average time/residue: 0.4268
  time to fit residues: 88.0354
Evaluate side-chains
  195 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 177
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  165 THR
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  227 SER
Chi-restraints excluded: chain D residue   21 MET
Chi-restraints excluded: chain D residue   38 MET
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain R residue   66 VAL
Chi-restraints excluded: chain R residue  131 VAL
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  263 VAL
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 100 optimal weight:    0.2980
   chunk 51 optimal weight:    3.9990
   chunk 82 optimal weight:    0.0030
   chunk 27 optimal weight:    0.3980
   chunk 101 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 106 optimal weight:    0.4980
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.4390

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

Flipped N/Q/H residues before XYZ refinement:
C 142 HIS
C 268 ASN
R  48 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.131490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.116662 restraints weight = 11225.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 1.67
r_work: 0.3524 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3385 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.1425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8523  Z= 0.124
  Angle     :  0.527   9.091  11575  Z= 0.272
  Chirality :  0.042   0.155   1344
  Planarity :  0.003   0.031   1452
  Dihedral  :  4.159  20.962   1173
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 14.42 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.17 (0.26), residues: 1082
  helix:  3.04 (0.27), residues: 369
  sheet:  0.28 (0.30), residues: 273
  loop : -0.90 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 127 
 TYR   0.016   0.001   TYR E 178 
 PHE   0.016   0.001   PHE B 189 
 TRP   0.013   0.001   TRP C  82 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 8522)
  covalent geometry    : angle       0.52743 (11573)
  SS BOND              : bond        0.00095 (    1)
  SS BOND              : angle       0.29040 (    2)
  hydrogen bonds       : bond        0.03334 (  441)
  hydrogen bonds       : angle       4.18484 ( 1239)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 176
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
REVERT: B  279 LYS cc_start: 0.8652 (mtmm) cc_final: 0.8292 (mtmm)
REVERT: C   25 CYS cc_start: 0.7942 (p) cc_final: 0.7513 (p)
REVERT: C  146 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8479 (mt)
REVERT: C  197 ARG cc_start: 0.7825 (mmt180) cc_final: 0.7597 (mmt180)
REVERT: R  280 PHE cc_start: 0.8204 (t80) cc_final: 0.7724 (t80)
  outliers start: 21
  outliers final: 16
  residues processed: 187
  average time/residue: 0.4184
  time to fit residues: 84.4961
Evaluate side-chains
  195 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 178
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  227 SER
Chi-restraints excluded: chain D residue   21 MET
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain R residue   66 VAL
Chi-restraints excluded: chain R residue  131 VAL
Chi-restraints excluded: chain R residue  168 CYS
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  263 VAL
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 100 optimal weight:    0.1980
   chunk 38 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 76 optimal weight:    0.7980
   chunk 106 optimal weight:    0.8980
   chunk 96 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
C 142 HIS
C 239 ASN
C 268 ASN
E 182 ASN
R  48 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.130872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.116314 restraints weight = 11066.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3592 rms_B_bonded: 1.63
r_work: 0.3488 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3347 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.1423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8523  Z= 0.180
  Angle     :  0.582  10.595  11575  Z= 0.299
  Chirality :  0.044   0.160   1344
  Planarity :  0.003   0.033   1452
  Dihedral  :  4.354  23.478   1173
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 14.99 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.12 (0.26), residues: 1082
  helix:  2.98 (0.27), residues: 368
  sheet:  0.31 (0.31), residues: 267
  loop : -0.95 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 127 
 TYR   0.021   0.002   TYR E 178 
 PHE   0.018   0.002   PHE B 189 
 TRP   0.012   0.002   TRP C  82 
 HIS   0.004   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 8522)
  covalent geometry    : angle       0.58184 (11573)
  SS BOND              : bond        0.00104 (    1)
  SS BOND              : angle       0.41955 (    2)
  hydrogen bonds       : bond        0.03756 (  441)
  hydrogen bonds       : angle       4.33454 ( 1239)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 176
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: C   25 CYS cc_start: 0.7884 (p) cc_final: 0.7472 (p)
REVERT: C  197 ARG cc_start: 0.7789 (mmt180) cc_final: 0.7561 (mmt180)
REVERT: E   43 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8108 (mttp)
REVERT: E  180 MET cc_start: 0.6525 (OUTLIER) cc_final: 0.6273 (ptt)
REVERT: R   45 LEU cc_start: 0.7635 (mm) cc_final: 0.7294 (mm)
  outliers start: 22
  outliers final: 18
  residues processed: 186
  average time/residue: 0.4269
  time to fit residues: 85.6869
Evaluate side-chains
  196 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 176
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  165 THR
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  227 SER
Chi-restraints excluded: chain D residue   21 MET
Chi-restraints excluded: chain D residue   38 MET
Chi-restraints excluded: chain E residue   43 LYS
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain R residue   66 VAL
Chi-restraints excluded: chain R residue  168 CYS
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  263 VAL
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 31 optimal weight:    0.4980
   chunk 101 optimal weight:    0.7980
   chunk 45 optimal weight:    0.5980
   chunk 87 optimal weight:    0.5980
   chunk 54 optimal weight:    2.9990
   chunk 105 optimal weight:    0.8980
   chunk 95 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
C 142 HIS
C 239 ASN
C 268 ASN
R  48 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.131526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.117055 restraints weight = 11087.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.3599 rms_B_bonded: 1.62
r_work: 0.3496 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3356 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.1456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8523  Z= 0.156
  Angle     :  0.558   9.277  11575  Z= 0.290
  Chirality :  0.043   0.156   1344
  Planarity :  0.003   0.032   1452
  Dihedral  :  4.321  22.791   1173
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 15.22 %
    Favored  : 82.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.26), residues: 1082
  helix:  3.01 (0.27), residues: 368
  sheet:  0.37 (0.31), residues: 266
  loop : -0.91 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 127 
 TYR   0.019   0.002   TYR E 178 
 PHE   0.017   0.002   PHE B 189 
 TRP   0.014   0.001   TRP C  82 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 8522)
  covalent geometry    : angle       0.55836 (11573)
  SS BOND              : bond        0.00119 (    1)
  SS BOND              : angle       0.31644 (    2)
  hydrogen bonds       : bond        0.03593 (  441)
  hydrogen bonds       : angle       4.27002 ( 1239)

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 177
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: C   25 CYS cc_start: 0.7873 (p) cc_final: 0.7468 (p)
REVERT: C  197 ARG cc_start: 0.7788 (mmt180) cc_final: 0.7550 (mmt180)
REVERT: E   43 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8094 (mttp)
REVERT: E  180 MET cc_start: 0.6457 (OUTLIER) cc_final: 0.6194 (ptt)
REVERT: R   45 LEU cc_start: 0.7645 (mm) cc_final: 0.7308 (mm)
REVERT: R  280 PHE cc_start: 0.8143 (t80) cc_final: 0.7836 (t80)
  outliers start: 21
  outliers final: 19
  residues processed: 187
  average time/residue: 0.4299
  time to fit residues: 86.8777
Evaluate side-chains
  197 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 176
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  165 THR
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  227 SER
Chi-restraints excluded: chain D residue   21 MET
Chi-restraints excluded: chain D residue   38 MET
Chi-restraints excluded: chain E residue   43 LYS
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain R residue   66 VAL
Chi-restraints excluded: chain R residue  131 VAL
Chi-restraints excluded: chain R residue  168 CYS
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  263 VAL
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 86 optimal weight:    0.6980
   chunk 72 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 63 optimal weight:    0.2980
   chunk 26 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0060
   chunk 33 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.5798

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

Flipped N/Q/H residues before XYZ refinement:
C 142 HIS
C 268 ASN
R  48 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.134404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.119452 restraints weight = 11153.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 1.71
r_work: 0.3509 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3369 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.1488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8523  Z= 0.147
  Angle     :  0.553   9.182  11575  Z= 0.287
  Chirality :  0.043   0.152   1344
  Planarity :  0.003   0.032   1452
  Dihedral  :  4.276  22.294   1173
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 15.68 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.26), residues: 1082
  helix:  3.03 (0.27), residues: 368
  sheet:  0.38 (0.31), residues: 266
  loop : -0.93 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 127 
 TYR   0.019   0.002   TYR E 178 
 PHE   0.019   0.001   PHE R 280 
 TRP   0.014   0.001   TRP C  82 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 8522)
  covalent geometry    : angle       0.55306 (11573)
  SS BOND              : bond        0.00128 (    1)
  SS BOND              : angle       0.27605 (    2)
  hydrogen bonds       : bond        0.03523 (  441)
  hydrogen bonds       : angle       4.25666 ( 1239)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3393.37 seconds
wall clock time: 58 minutes 27.07 seconds (3507.07 seconds total)