Starting phenix.real_space_refine
on Thu Jul  2 21:24:01 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7v6a_31740/07_2026/7v6a_31740.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v6a_31740/07_2026/7v6a_31740.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v6a_31740/07_2026/7v6a_31740.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v6a_31740/07_2026/7v6a_31740.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v6a_31740/07_2026/7v6a_31740.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v6a_31740/07_2026/7v6a_31740.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7v6a_31740/07_2026/7v6a_31740.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7v6a_31740/07_2026/7v6a_31740.cif"
  }
  resolution = 3.6
  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=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2132 atoms to isotropic.
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      65      5.16       5
     C    5497      2.51       5
     N    1460      2.21       5
     O    1562      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8584
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1646
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 110
          Unresolved non-hydrogen angles: 131
          Unresolved non-hydrogen dihedrals: 89
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 8, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 72
    Chain: "B"
      Number of atoms: 2562
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2562
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 28
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 3}
          Unresolved non-hydrogen planarities: 38
    Chain: "C"
      Number of atoms: 435
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 435
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "S"
      Number of atoms: 1746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1746
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "R"
      Number of atoms: 2168
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 2168
          Classifications: {'peptide': 277}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 10, 'TRANS': 266}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "R"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'5XI': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.79, per 1000 atoms: 0.21
  Number of scatterers: 8584
  At special positions: 0
  Unit cell: (94.2936, 123.414, 123.414, 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      65     16.00
     O    1562      8.00
     N    1460      7.00
     C    5497      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 105 " - pdb=" SG  CYS R 185 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 426 " - pdb=" SG  CYS R 429 " 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: 2.18
  Conformation dependent library (CDL) restraints added in 424.1 milliseconds
  

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2104

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 14 sheets defined
      35.9% alpha, 15.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 4.087A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.887A  pdb=" N   MET A  53 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 205
      removed outlier: 4.124A  pdb=" N   ARG A 205 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 202 through 205'
    Processing helix  chain 'A' and resid 211 through 216
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 281
    Processing helix  chain 'A' and resid 295 through 308
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 10 through 24
    Processing helix  chain 'C' and resid 29 through 34
    Processing helix  chain 'C' and resid 34 through 42
      removed outlier: 3.558A  pdb=" N   CYS C  41 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLU C  42 " --> pdb=" O   MET C  38 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 30 through 55
    Processing helix  chain 'R' and resid 55 through 60
    Processing helix  chain 'R' and resid 65 through 67
      No H-bonds generated for 'chain 'R' and resid 65 through 67'
    Processing helix  chain 'R' and resid 68 through 91
      removed outlier: 5.378A  pdb=" N   MET R  86 " --> pdb=" O   GLY R  82 " (cutoff:3.500A)
      removed outlier: 5.635A  pdb=" N   ASN R  87 " --> pdb=" O   ALA R  83 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 92 through 94
      No H-bonds generated for 'chain 'R' and resid 92 through 94'
    Processing helix  chain 'R' and resid 101 through 136
      removed outlier: 4.149A  pdb=" N   TYR R 113 " --> pdb=" O   LEU R 109 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   VAL R 114 " --> pdb=" O   ALA R 110 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ASN R 117 " --> pdb=" O   TYR R 113 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 138 through 144
    Processing helix  chain 'R' and resid 145 through 165
    Processing helix  chain 'R' and resid 165 through 176
      removed outlier: 4.291A  pdb=" N   LEU R 169 " --> pdb=" O   ALA R 165 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 192 through 204
      removed outlier: 3.929A  pdb=" N   THR R 196 " --> pdb=" O   ASN R 192 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   ALA R 202 " --> pdb=" O   GLY R 198 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 204 through 222
    Processing helix  chain 'R' and resid 392 through 413
      removed outlier: 3.654A  pdb=" N   LEU R 406 " --> pdb=" O   ILE R 402 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 415 through 420
    Processing helix  chain 'R' and resid 431 through 441
    Processing helix  chain 'R' and resid 443 through 455
      Proline residue:  R 450  - end of helix
    Processing helix  chain 'R' and resid 457 through 463
    Processing helix  chain 'R' and resid 465 through 470
      removed outlier: 3.823A  pdb=" N   CYS R 470 " --> pdb=" O   HIS R 466 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 190
      removed outlier: 3.503A  pdb=" N   PHE A 189 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.714A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 225 through 226
      removed outlier: 7.147A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51
      removed outlier: 3.731A  pdb=" N   ARG B  46 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.435A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105
      removed outlier: 6.084A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.796A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.881A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   VAL B 200 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 232 through 234
      removed outlier: 3.648A  pdb=" N   CYS B 233 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   CYS B 250 " --> pdb=" O   TYR B 264 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 275
      removed outlier: 6.322A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU B 308 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 6 through 7
      removed outlier: 3.513A  pdb=" N   ARG S  18 " --> pdb=" O   MET S  83 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU S  81 " --> pdb=" O   LEU S  20 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   LEU S  79 " --> pdb=" O   CYS S  22 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12
    Processing sheet with id=AB3, first strand: chain 'S' and resid 58 through 60
      removed outlier: 5.691A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ALA S  49 " --> pdb=" O   TRP S  36 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   TRP S  36 " --> pdb=" O   ALA S  49 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 143 through 146
      removed outlier: 3.599A  pdb=" N   VAL S 143 " --> pdb=" O   ILE S 204 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 174 through 177
      removed outlier: 6.782A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)

    368 hydrogen bonds defined for protein.
    1050 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: 1.38

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2252
        1.33 -     1.45: 1739
        1.45 -     1.57: 4685
        1.57 -     1.70: 0
        1.70 -     1.82: 94
  Bond restraints: 8770
  Sorted by residual:
  bond pdb=" C19 5XI R 601 "
       pdb=" N4  5XI R 601 "
    ideal  model  delta    sigma   weight residual
    1.351  1.479 -0.128 2.00e-02 2.50e+03 4.10e+01
  bond pdb=" C19 5XI R 601 "
       pdb=" O3  5XI R 601 "
    ideal  model  delta    sigma   weight residual
    1.337  1.428 -0.091 2.00e-02 2.50e+03 2.08e+01
  bond pdb=" C8  5XI R 601 "
       pdb=" N1  5XI R 601 "
    ideal  model  delta    sigma   weight residual
    1.439  1.480 -0.041 2.00e-02 2.50e+03 4.22e+00
  bond pdb=" C9  5XI R 601 "
       pdb=" N2  5XI R 601 "
    ideal  model  delta    sigma   weight residual
    1.452  1.493 -0.041 2.00e-02 2.50e+03 4.12e+00
  bond pdb=" CA  THR B 181 "
       pdb=" CB  THR B 181 "
    ideal  model  delta    sigma   weight residual
    1.523  1.548 -0.025 1.35e-02 5.49e+03 3.35e+00
  ... (remaining 8765 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 11425
        1.54 -     3.08: 407
        3.08 -     4.62: 70
        4.62 -     6.16: 16
        6.16 -     7.70: 5
  Bond angle restraints: 11923
  Sorted by residual:
  angle pdb=" N   VAL R 418 "
        pdb=" CA  VAL R 418 "
        pdb=" C   VAL R 418 "
      ideal   model   delta    sigma   weight residual
     112.96  108.07    4.89 1.00e+00 1.00e+00 2.39e+01
  angle pdb=" CA  TRP R 435 "
        pdb=" CB  TRP R 435 "
        pdb=" CG  TRP R 435 "
      ideal   model   delta    sigma   weight residual
     113.60  119.04   -5.44 1.90e+00 2.77e-01 8.20e+00
  angle pdb=" N   TRP R 435 "
        pdb=" CA  TRP R 435 "
        pdb=" C   TRP R 435 "
      ideal   model   delta    sigma   weight residual
     111.33  107.91    3.42 1.21e+00 6.83e-01 8.00e+00
  angle pdb=" N   ASP B 246 "
        pdb=" CA  ASP B 246 "
        pdb=" C   ASP B 246 "
      ideal   model   delta    sigma   weight residual
     113.38  110.13    3.25 1.23e+00 6.61e-01 6.96e+00
  angle pdb=" C   ARG S 179 "
        pdb=" N   MET S 180 "
        pdb=" CA  MET S 180 "
      ideal   model   delta    sigma   weight residual
     122.19  118.54    3.65 1.41e+00 5.03e-01 6.71e+00
  ... (remaining 11918 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 4687
       17.90 -    35.80: 369
       35.80 -    53.70: 76
       53.70 -    71.60: 11
       71.60 -    89.49: 8
  Dihedral angle restraints: 5151
    sinusoidal: 1892
      harmonic: 3259
  Sorted by residual:
  dihedral pdb=" CB  CYS R 426 "
           pdb=" SG  CYS R 426 "
           pdb=" SG  CYS R 429 "
           pdb=" CB  CYS R 429 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  136.93  -43.93     1      1.00e+01 1.00e-02 2.69e+01
  dihedral pdb=" CA  VAL R 434 "
           pdb=" C   VAL R 434 "
           pdb=" N   TRP R 435 "
           pdb=" CA  TRP R 435 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.63   21.37     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  MET S  93 "
           pdb=" C   MET S  93 "
           pdb=" N   TYR S  94 "
           pdb=" CA  TYR S  94 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.11  -19.89     0      5.00e+00 4.00e-02 1.58e+01
  ... (remaining 5148 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 1222
       0.069 -    0.137: 156
       0.137 -    0.206: 7
       0.206 -    0.274: 0
       0.274 -    0.343: 2
  Chirality restraints: 1387
  Sorted by residual:
  chirality pdb=" C9  5XI R 601 "
            pdb=" C10 5XI R 601 "
            pdb=" C13 5XI R 601 "
            pdb=" N2  5XI R 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.30   -2.65    0.34 2.00e-01 2.50e+01 2.94e+00
  chirality pdb=" C14 5XI R 601 "
            pdb=" C15 5XI R 601 "
            pdb=" C18 5XI R 601 "
            pdb=" N3  5XI R 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.29   -2.62    0.33 2.00e-01 2.50e+01 2.79e+00
  chirality pdb=" CB  ILE R  93 "
            pdb=" CA  ILE R  93 "
            pdb=" CG1 ILE R  93 "
            pdb=" CG2 ILE R  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.83   -0.18 2.00e-01 2.50e+01 8.34e-01
  ... (remaining 1384 not shown)

  Planarity restraints: 1488
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR R 414 "   -0.037 5.00e-02 4.00e+02   5.65e-02 5.10e+00
        pdb=" N   PRO R 415 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO R 415 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO R 415 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA S  40 "    0.037 5.00e-02 4.00e+02   5.57e-02 4.96e+00
        pdb=" N   PRO S  41 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO S  41 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO S  41 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R 201 "   -0.009 2.00e-02 2.50e+03   1.82e-02 3.31e+00
        pdb=" C   ILE R 201 "    0.031 2.00e-02 2.50e+03
        pdb=" O   ILE R 201 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ALA R 202 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1485 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 182
        2.67 -     3.23: 8623
        3.23 -     3.79: 13522
        3.79 -     4.34: 17889
        4.34 -     4.90: 29286
  Nonbonded interactions: 69502
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.113 3.040
  nonbonded pdb=" OH  TYR A 290 "
            pdb=" O   SER A 293 "
     model   vdw
     2.163 3.040
  nonbonded pdb=" OH  TYR R 439 "
            pdb=" OH  TYR R 443 "
     model   vdw
     2.179 3.040
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   SER B 160 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OG1 THR B  65 "
            pdb=" O   PRO B 107 "
     model   vdw
     2.210 3.040
  ... (remaining 69497 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.960
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  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:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6959
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   0.128   8772  Z= 0.196
  Angle     :  0.707   7.697  11927  Z= 0.397
  Chirality :  0.045   0.343   1387
  Planarity :  0.004   0.056   1488
  Dihedral  : 13.929  89.494   3041
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 14.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -1.88 (0.25), residues: 1104
  helix:  0.44 (0.27), residues: 398
  sheet: -2.68 (0.30), residues: 230
  loop : -1.90 (0.27), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG S 190 
 TYR   0.020   0.002   TYR S 103 
 PHE   0.029   0.002   PHE B 235 
 TRP   0.029   0.002   TRP B  82 
 HIS   0.005   0.001   HIS S  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00393 /  0.20 ( 8770)
  covalent geometry    : angle       0.70647 /  0.40 (11923)
  SS BOND              : bond        0.00166 /  0.08 (    2)
  SS BOND              : angle       0.81040 /  0.39 (    4)
  hydrogen bonds       : bond        0.17222 / 11.81 (  368)
  hydrogen bonds       : angle       7.27066 /  4.97 ( 1050)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 268
  time to evaluate  : 0.309 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6878 (tm-30)
REVERT: A  210 LYS cc_start: 0.7389 (tptt) cc_final: 0.6844 (mmtm)
REVERT: A  252 SER cc_start: 0.7474 (p) cc_final: 0.7193 (p)
REVERT: A  255 ASN cc_start: 0.6919 (m-40) cc_final: 0.6498 (m-40)
REVERT: A  337 ASP cc_start: 0.6790 (t70) cc_final: 0.6584 (t70)
REVERT: A  345 LYS cc_start: 0.8149 (tptt) cc_final: 0.7755 (tptt)
REVERT: A  353 LEU cc_start: 0.8697 (tp) cc_final: 0.8402 (tp)
REVERT: B  110 ASN cc_start: 0.8503 (m110) cc_final: 0.8224 (m110)
REVERT: B  125 ASN cc_start: 0.8332 (t0) cc_final: 0.8092 (t0)
REVERT: B  161 SER cc_start: 0.8108 (p) cc_final: 0.7846 (p)
REVERT: B  228 ASP cc_start: 0.6713 (p0) cc_final: 0.6192 (p0)
REVERT: B  239 ASN cc_start: 0.7808 (m110) cc_final: 0.7303 (m-40)
REVERT: B  279 SER cc_start: 0.7990 (t) cc_final: 0.7480 (p)
REVERT: B  294 CYS cc_start: 0.7277 (t) cc_final: 0.7023 (t)
REVERT: B  297 TRP cc_start: 0.8425 (m100) cc_final: 0.8143 (m100)
REVERT: C   15 LEU cc_start: 0.8064 (tt) cc_final: 0.7775 (tt)
REVERT: S   45 LEU cc_start: 0.7481 (mp) cc_final: 0.7278 (mt)
REVERT: S  128 MET cc_start: 0.7325 (mtp) cc_final: 0.6859 (mtp)
REVERT: S  179 ARG cc_start: 0.7552 (tpp-160) cc_final: 0.7326 (tpp-160)
REVERT: S  214 VAL cc_start: 0.8351 (t) cc_final: 0.8149 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 268
  average time/residue: 0.1015
  time to fit residues: 36.4080
Evaluate side-chains
  241 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 241
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0870
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.6980
   chunk 106 optimal weight:    0.7980
   overall best weight:    0.6358

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  52 GLN
A 331 ASN
B  88 ASN
B 110 ASN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 174 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.150492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.132983 restraints weight = 13635.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.136427 restraints weight = 6270.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.138625 restraints weight = 3516.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.140080 restraints weight = 2258.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 55)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.141054 restraints weight = 1628.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6915
moved from start:          0.1313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8772  Z= 0.149
  Angle     :  0.606  11.010  11927  Z= 0.319
  Chirality :  0.043   0.196   1387
  Planarity :  0.004   0.053   1488
  Dihedral  :  5.089  33.372   1226
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 12.25 %
    Favored  : 86.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -1.70 (0.25), residues: 1104
  helix:  0.62 (0.27), residues: 392
  sheet: -2.30 (0.31), residues: 232
  loop : -1.96 (0.27), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG S 190 
 TYR   0.011   0.001   TYR S  50 
 PHE   0.012   0.002   PHE B 234 
 TRP   0.013   0.002   TRP R 435 
 HIS   0.005   0.001   HIS S  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.15 ( 8770)
  covalent geometry    : angle       0.60591 /  0.32 (11923)
  SS BOND              : bond        0.00176 /  0.08 (    2)
  SS BOND              : angle       1.11354 /  0.53 (    4)
  hydrogen bonds       : bond        0.04110 /  2.77 (  368)
  hydrogen bonds       : angle       5.25302 /  3.64 ( 1050)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 243
  time to evaluate  : 0.315 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.7419 (tm-30) cc_final: 0.6926 (tm-30)
REVERT: A  210 LYS cc_start: 0.7718 (tptt) cc_final: 0.7497 (tptt)
REVERT: A  211 TRP cc_start: 0.7704 (p-90) cc_final: 0.7137 (p-90)
REVERT: A  249 LEU cc_start: 0.8147 (tt) cc_final: 0.7901 (tp)
REVERT: A  252 SER cc_start: 0.7375 (p) cc_final: 0.7103 (p)
REVERT: A  255 ASN cc_start: 0.7005 (m-40) cc_final: 0.6618 (m-40)
REVERT: A  337 ASP cc_start: 0.6986 (t70) cc_final: 0.6752 (t70)
REVERT: A  351 CYS cc_start: 0.7256 (m) cc_final: 0.6714 (m)
REVERT: B  105 TYR cc_start: 0.8084 (t80) cc_final: 0.7775 (t80)
REVERT: B  110 ASN cc_start: 0.8362 (m-40) cc_final: 0.8100 (m110)
REVERT: B  125 ASN cc_start: 0.8459 (t0) cc_final: 0.8077 (t0)
REVERT: B  228 ASP cc_start: 0.6871 (p0) cc_final: 0.6162 (p0)
REVERT: B  249 THR cc_start: 0.7604 (m) cc_final: 0.7308 (p)
REVERT: B  297 TRP cc_start: 0.8455 (m100) cc_final: 0.8019 (m100)
REVERT: B  301 LYS cc_start: 0.7320 (mttp) cc_final: 0.7108 (mtpp)
REVERT: B  339 TRP cc_start: 0.8193 (m100) cc_final: 0.7990 (m100)
REVERT: S  110 PHE cc_start: 0.7773 (t80) cc_final: 0.7539 (t80)
REVERT: S  190 ARG cc_start: 0.7540 (mtm110) cc_final: 0.7293 (mtm110)
REVERT: S  202 LEU cc_start: 0.8238 (tp) cc_final: 0.7998 (tt)
REVERT: R  152 MET cc_start: 0.5851 (tpt) cc_final: 0.5572 (tpt)
REVERT: R  190 LEU cc_start: 0.6685 (mm) cc_final: 0.6432 (mp)
REVERT: R  459 THR cc_start: 0.6447 (t) cc_final: 0.6202 (m)
  outliers start: 13
  outliers final: 11
  residues processed: 247
  average time/residue: 0.1055
  time to fit residues: 34.7740
Evaluate side-chains
  245 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 234
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain S residue   55 SER
Chi-restraints excluded: chain S residue  174 GLN
Chi-restraints excluded: chain R residue  398 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 88 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 97 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 12 optimal weight:    0.1980
   chunk 2 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 331 ASN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S 174 GLN
** R 449 ASN ** 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 = 0.3866 r_free = 0.3866 target = 0.149227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.131659 restraints weight = 13584.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.135154 restraints weight = 6309.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.137370 restraints weight = 3534.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.138775 restraints weight = 2283.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.139740 restraints weight = 1643.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6937
moved from start:          0.1793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8772  Z= 0.161
  Angle     :  0.603  11.289  11927  Z= 0.316
  Chirality :  0.043   0.177   1387
  Planarity :  0.004   0.054   1488
  Dihedral  :  5.062  33.174   1226
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 16.59 %
    Favored  : 80.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -1.58 (0.25), residues: 1104
  helix:  0.69 (0.27), residues: 392
  sheet: -2.14 (0.31), residues: 247
  loop : -1.88 (0.27), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 283 
 TYR   0.013   0.002   TYR S 102 
 PHE   0.016   0.002   PHE R 409 
 TRP   0.018   0.002   TRP R 435 
 HIS   0.006   0.001   HIS S  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00350 /  0.16 ( 8770)
  covalent geometry    : angle       0.60297 /  0.32 (11923)
  SS BOND              : bond        0.00204 /  0.10 (    2)
  SS BOND              : angle       0.98797 /  0.48 (    4)
  hydrogen bonds       : bond        0.03727 /  2.49 (  368)
  hydrogen bonds       : angle       4.96697 /  3.45 ( 1050)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 235
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6858 (mt-10)
REVERT: A   14 GLU cc_start: 0.7371 (tm-30) cc_final: 0.6903 (tm-30)
REVERT: A   53 MET cc_start: 0.5367 (mpp) cc_final: 0.4757 (mpp)
REVERT: A  210 LYS cc_start: 0.7792 (tptt) cc_final: 0.7547 (tptt)
REVERT: A  252 SER cc_start: 0.7343 (p) cc_final: 0.7038 (p)
REVERT: A  255 ASN cc_start: 0.7231 (m-40) cc_final: 0.6968 (m-40)
REVERT: A  337 ASP cc_start: 0.7082 (t70) cc_final: 0.6845 (t70)
REVERT: A  351 CYS cc_start: 0.7215 (m) cc_final: 0.6700 (m)
REVERT: B  105 TYR cc_start: 0.8170 (t80) cc_final: 0.7949 (t80)
REVERT: B  125 ASN cc_start: 0.8471 (t0) cc_final: 0.8080 (t0)
REVERT: B  137 ARG cc_start: 0.7762 (tpp-160) cc_final: 0.7382 (tpp-160)
REVERT: B  228 ASP cc_start: 0.6912 (p0) cc_final: 0.6266 (p0)
REVERT: B  239 ASN cc_start: 0.7758 (m110) cc_final: 0.7556 (m-40)
REVERT: B  249 THR cc_start: 0.7618 (m) cc_final: 0.7330 (p)
REVERT: B  297 TRP cc_start: 0.8460 (m100) cc_final: 0.8140 (m100)
REVERT: B  339 TRP cc_start: 0.8155 (m100) cc_final: 0.7767 (m100)
REVERT: C   62 ARG cc_start: 0.5906 (mtm-85) cc_final: 0.5616 (mtt180)
REVERT: S  110 PHE cc_start: 0.7989 (t80) cc_final: 0.7508 (t80)
REVERT: S  128 MET cc_start: 0.7542 (mtp) cc_final: 0.6966 (mtp)
REVERT: S  190 ARG cc_start: 0.7478 (mtm110) cc_final: 0.7277 (mtm110)
REVERT: S  202 LEU cc_start: 0.8226 (tp) cc_final: 0.7973 (tt)
REVERT: R   53 VAL cc_start: 0.7149 (m) cc_final: 0.6936 (p)
REVERT: R  419 MET cc_start: 0.4939 (ppp) cc_final: 0.4459 (ppp)
  outliers start: 22
  outliers final: 17
  residues processed: 243
  average time/residue: 0.1052
  time to fit residues: 33.9060
Evaluate side-chains
  245 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 228
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain S residue   55 SER
Chi-restraints excluded: chain S residue  174 GLN
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue  398 VAL
Chi-restraints excluded: chain R residue  421 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 84 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 107 optimal weight:    0.0670
   chunk 24 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 97 optimal weight:    5.9990
   overall best weight:    1.1122

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 331 ASN
B 142 HIS
** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  68 ASN
R 417 ASN
** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.147197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.129504 restraints weight = 13732.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.133029 restraints weight = 6304.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.135294 restraints weight = 3508.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.136796 restraints weight = 2235.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.137702 restraints weight = 1588.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6974
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   8772  Z= 0.203
  Angle     :  0.636  12.091  11927  Z= 0.333
  Chirality :  0.044   0.188   1387
  Planarity :  0.004   0.058   1488
  Dihedral  :  5.285  33.257   1226
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 16.48 %
    Favored  : 78.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -1.69 (0.25), residues: 1104
  helix:  0.60 (0.27), residues: 389
  sheet: -2.32 (0.29), residues: 267
  loop : -1.81 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 283 
 TYR   0.015   0.002   TYR S 102 
 PHE   0.013   0.002   PHE R  70 
 TRP   0.021   0.002   TRP R 435 
 HIS   0.003   0.001   HIS R 217 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00438 /  0.20 ( 8770)
  covalent geometry    : angle       0.63536 /  0.33 (11923)
  SS BOND              : bond        0.00209 /  0.10 (    2)
  SS BOND              : angle       1.13902 /  0.56 (    4)
  hydrogen bonds       : bond        0.03788 /  2.50 (  368)
  hydrogen bonds       : angle       4.97786 /  3.49 ( 1050)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 241
  time to evaluate  : 0.300 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6982 (mt-10)
REVERT: A   14 GLU cc_start: 0.7415 (tm-30) cc_final: 0.6985 (tm-30)
REVERT: A  252 SER cc_start: 0.7180 (p) cc_final: 0.6798 (p)
REVERT: A  255 ASN cc_start: 0.7282 (m-40) cc_final: 0.6690 (m110)
REVERT: A  270 LYS cc_start: 0.7324 (mmmt) cc_final: 0.6960 (mmtp)
REVERT: A  337 ASP cc_start: 0.7153 (t70) cc_final: 0.6919 (t70)
REVERT: B  105 TYR cc_start: 0.8309 (t80) cc_final: 0.8065 (t80)
REVERT: B  125 ASN cc_start: 0.8533 (t0) cc_final: 0.8101 (t0)
REVERT: B  228 ASP cc_start: 0.7013 (p0) cc_final: 0.6361 (p0)
REVERT: B  249 THR cc_start: 0.7552 (m) cc_final: 0.7250 (p)
REVERT: B  339 TRP cc_start: 0.8193 (m100) cc_final: 0.7805 (m100)
REVERT: S   27 PHE cc_start: 0.7915 (p90) cc_final: 0.7715 (p90)
REVERT: S  128 MET cc_start: 0.7611 (mtp) cc_final: 0.7022 (mtp)
REVERT: S  174 GLN cc_start: 0.6955 (OUTLIER) cc_final: 0.6679 (pt0)
REVERT: S  190 ARG cc_start: 0.7516 (mtm110) cc_final: 0.7205 (mtm110)
REVERT: S  202 LEU cc_start: 0.8223 (tp) cc_final: 0.8003 (tt)
REVERT: R   53 VAL cc_start: 0.7265 (m) cc_final: 0.7044 (p)
REVERT: R  138 LEU cc_start: 0.6535 (OUTLIER) cc_final: 0.6291 (mt)
REVERT: R  152 MET cc_start: 0.5907 (tpt) cc_final: 0.5700 (tpt)
  outliers start: 43
  outliers final: 31
  residues processed: 258
  average time/residue: 0.0979
  time to fit residues: 33.9112
Evaluate side-chains
  266 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 233
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue   55 SER
Chi-restraints excluded: chain S residue  126 ILE
Chi-restraints excluded: chain S residue  174 GLN
Chi-restraints excluded: chain S residue  217 CYS
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue   68 ASN
Chi-restraints excluded: chain R residue  138 LEU
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  398 VAL
Chi-restraints excluded: chain R residue  421 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 100 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 106 optimal weight:    0.8980
   overall best weight:    0.9382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 331 ASN
B 142 HIS
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  68 ASN
R 423 ASN
** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.148162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.130488 restraints weight = 13518.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.133940 restraints weight = 6331.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.136163 restraints weight = 3583.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.137628 restraints weight = 2318.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.138493 restraints weight = 1663.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6975
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8772  Z= 0.180
  Angle     :  0.625  12.485  11927  Z= 0.324
  Chirality :  0.043   0.195   1387
  Planarity :  0.004   0.058   1488
  Dihedral  :  5.246  33.990   1226
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 18.82 %
    Favored  : 76.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -1.56 (0.25), residues: 1104
  helix:  0.60 (0.27), residues: 392
  sheet: -2.15 (0.29), residues: 273
  loop : -1.67 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 283 
 TYR   0.014   0.002   TYR R 113 
 PHE   0.013   0.002   PHE S  29 
 TRP   0.021   0.002   TRP R 435 
 HIS   0.003   0.001   HIS S  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00393 /  0.18 ( 8770)
  covalent geometry    : angle       0.62510 /  0.32 (11923)
  SS BOND              : bond        0.00252 /  0.12 (    2)
  SS BOND              : angle       1.03234 /  0.51 (    4)
  hydrogen bonds       : bond        0.03693 /  2.45 (  368)
  hydrogen bonds       : angle       4.85802 /  3.41 ( 1050)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 243
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6937 (mt-10)
REVERT: A   14 GLU cc_start: 0.7407 (tm-30) cc_final: 0.6963 (tm-30)
REVERT: A  252 SER cc_start: 0.6511 (p) cc_final: 0.6173 (p)
REVERT: A  255 ASN cc_start: 0.7256 (m-40) cc_final: 0.6704 (m110)
REVERT: A  270 LYS cc_start: 0.7377 (mmmt) cc_final: 0.7061 (mmtp)
REVERT: A  337 ASP cc_start: 0.7105 (t70) cc_final: 0.6875 (t70)
REVERT: B   13 GLN cc_start: 0.6063 (OUTLIER) cc_final: 0.5834 (tp40)
REVERT: B   70 LEU cc_start: 0.8391 (mm) cc_final: 0.8179 (mp)
REVERT: B  105 TYR cc_start: 0.8323 (t80) cc_final: 0.8100 (t80)
REVERT: B  125 ASN cc_start: 0.8524 (t0) cc_final: 0.8103 (t0)
REVERT: B  137 ARG cc_start: 0.7731 (tpp-160) cc_final: 0.7421 (tpp-160)
REVERT: B  169 TRP cc_start: 0.8284 (m100) cc_final: 0.8044 (m100)
REVERT: B  228 ASP cc_start: 0.7060 (p0) cc_final: 0.6632 (p0)
REVERT: B  249 THR cc_start: 0.7542 (m) cc_final: 0.7216 (p)
REVERT: B  339 TRP cc_start: 0.8181 (m100) cc_final: 0.7865 (m100)
REVERT: S   18 ARG cc_start: 0.5724 (OUTLIER) cc_final: 0.5417 (mmm160)
REVERT: S   27 PHE cc_start: 0.7919 (p90) cc_final: 0.7620 (p90)
REVERT: S  128 MET cc_start: 0.7583 (mtp) cc_final: 0.7039 (mtp)
REVERT: S  162 LEU cc_start: 0.8039 (tt) cc_final: 0.7731 (tt)
REVERT: S  190 ARG cc_start: 0.7527 (mtm110) cc_final: 0.7203 (mtm110)
REVERT: S  202 LEU cc_start: 0.8228 (tp) cc_final: 0.8008 (tt)
REVERT: R   53 VAL cc_start: 0.7252 (m) cc_final: 0.7046 (p)
REVERT: R  121 MET cc_start: 0.7098 (mmt) cc_final: 0.6875 (mmt)
REVERT: R  138 LEU cc_start: 0.6538 (OUTLIER) cc_final: 0.5874 (pp)
REVERT: R  152 MET cc_start: 0.5924 (tpt) cc_final: 0.5657 (tpt)
  outliers start: 41
  outliers final: 32
  residues processed: 258
  average time/residue: 0.0949
  time to fit residues: 33.0678
Evaluate side-chains
  270 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 235
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue   18 ARG
Chi-restraints excluded: chain S residue   55 SER
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  217 CYS
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue   68 ASN
Chi-restraints excluded: chain R residue  138 LEU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  398 VAL
Chi-restraints excluded: chain R residue  421 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 56 optimal weight:    0.2980
   chunk 98 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0770
   chunk 18 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0970
   chunk 70 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0980
   chunk 91 optimal weight:    4.9990
   chunk 44 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.2536

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 331 ASN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
C  11 GLN
S 130 GLN
** S 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  68 ASN
R 423 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.151060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.133296 restraints weight = 13829.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.136850 restraints weight = 6357.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.139138 restraints weight = 3546.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.140570 restraints weight = 2274.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.141322 restraints weight = 1628.293|
|-----------------------------------------------------------------------------|
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6911
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   8772  Z= 0.113
  Angle     :  0.587  12.491  11927  Z= 0.301
  Chirality :  0.041   0.191   1387
  Planarity :  0.003   0.056   1488
  Dihedral  :  4.877  32.393   1226
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 19.82 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -1.21 (0.26), residues: 1104
  helix:  0.79 (0.27), residues: 398
  sheet: -1.84 (0.30), residues: 271
  loop : -1.50 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  46 
 TYR   0.009   0.001   TYR S  95 
 PHE   0.016   0.001   PHE S  29 
 TRP   0.015   0.001   TRP R 435 
 HIS   0.007   0.001   HIS S  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.11 ( 8770)
  covalent geometry    : angle       0.58723 /  0.30 (11923)
  SS BOND              : bond        0.00287 /  0.14 (    2)
  SS BOND              : angle       0.87309 /  0.42 (    4)
  hydrogen bonds       : bond        0.03358 /  2.25 (  368)
  hydrogen bonds       : angle       4.58278 /  3.21 ( 1050)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 250
  time to evaluate  : 0.302 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6803 (mt-10)
REVERT: A   14 GLU cc_start: 0.7399 (tm-30) cc_final: 0.6899 (tm-30)
REVERT: A  210 LYS cc_start: 0.7714 (tptt) cc_final: 0.7223 (mmtm)
REVERT: A  249 LEU cc_start: 0.8236 (tt) cc_final: 0.7948 (tp)
REVERT: A  252 SER cc_start: 0.6463 (p) cc_final: 0.6239 (p)
REVERT: A  270 LYS cc_start: 0.7321 (mmmt) cc_final: 0.7025 (mmtp)
REVERT: A  337 ASP cc_start: 0.7087 (t70) cc_final: 0.6811 (t70)
REVERT: A  351 CYS cc_start: 0.7193 (m) cc_final: 0.6699 (m)
REVERT: B   70 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8131 (mp)
REVERT: B  105 TYR cc_start: 0.8315 (t80) cc_final: 0.8044 (t80)
REVERT: B  125 ASN cc_start: 0.8445 (t0) cc_final: 0.8005 (t0)
REVERT: B  137 ARG cc_start: 0.7707 (tpp-160) cc_final: 0.7407 (tpp-160)
REVERT: B  228 ASP cc_start: 0.7126 (p0) cc_final: 0.6794 (p0)
REVERT: B  249 THR cc_start: 0.7361 (m) cc_final: 0.7139 (p)
REVERT: B  297 TRP cc_start: 0.8521 (m100) cc_final: 0.8190 (m100)
REVERT: B  339 TRP cc_start: 0.8084 (m100) cc_final: 0.7741 (m100)
REVERT: S   18 ARG cc_start: 0.5532 (OUTLIER) cc_final: 0.5272 (mmm160)
REVERT: S   38 ARG cc_start: 0.8340 (ptt180) cc_final: 0.7744 (ptp90)
REVERT: S  128 MET cc_start: 0.7570 (mtp) cc_final: 0.7064 (mtp)
REVERT: S  166 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7147 (tt)
REVERT: S  174 GLN cc_start: 0.7594 (pm20) cc_final: 0.7264 (pm20)
REVERT: S  190 ARG cc_start: 0.7555 (mtm110) cc_final: 0.7296 (mtm110)
REVERT: S  202 LEU cc_start: 0.8206 (tp) cc_final: 0.7964 (tt)
REVERT: R   86 MET cc_start: 0.6334 (OUTLIER) cc_final: 0.6011 (mpt)
REVERT: R  138 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6171 (mt)
REVERT: R  152 MET cc_start: 0.5895 (tpt) cc_final: 0.5626 (tpt)
  outliers start: 45
  outliers final: 29
  residues processed: 266
  average time/residue: 0.0973
  time to fit residues: 34.8704
Evaluate side-chains
  277 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 243
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue   18 ARG
Chi-restraints excluded: chain S residue   55 SER
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  126 ILE
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  200 PHE
Chi-restraints excluded: chain S residue  217 CYS
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue   68 ASN
Chi-restraints excluded: chain R residue   71 LEU
Chi-restraints excluded: chain R residue   86 MET
Chi-restraints excluded: chain R residue   93 ILE
Chi-restraints excluded: chain R residue  138 LEU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  398 VAL
Chi-restraints excluded: chain R residue  421 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    0.2980
   chunk 76 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 82 optimal weight:    8.9990
   chunk 79 optimal weight:    4.9990
   chunk 12 optimal weight:    0.0060
   chunk 50 optimal weight:    0.9980
   chunk 54 optimal weight:    4.9990
   chunk 99 optimal weight:    0.9990
   overall best weight:    0.5996

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
B 340 ASN
R  68 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.150326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.132797 restraints weight = 13807.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.136352 restraints weight = 6312.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.138616 restraints weight = 3509.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.140055 restraints weight = 2230.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.140816 restraints weight = 1591.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6929
moved from start:          0.2526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8772  Z= 0.141
  Angle     :  0.622  12.380  11927  Z= 0.315
  Chirality :  0.042   0.248   1387
  Planarity :  0.004   0.055   1488
  Dihedral  :  4.947  32.111   1226
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 20.04 %
    Favored  : 74.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -1.16 (0.26), residues: 1104
  helix:  0.82 (0.27), residues: 398
  sheet: -1.75 (0.31), residues: 271
  loop : -1.51 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  46 
 TYR   0.013   0.001   TYR S 102 
 PHE   0.018   0.001   PHE S  29 
 TRP   0.020   0.002   TRP R 435 
 HIS   0.005   0.001   HIS S  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00316 /  0.14 ( 8770)
  covalent geometry    : angle       0.62231 /  0.31 (11923)
  SS BOND              : bond        0.00223 /  0.11 (    2)
  SS BOND              : angle       0.90552 /  0.44 (    4)
  hydrogen bonds       : bond        0.03374 /  2.25 (  368)
  hydrogen bonds       : angle       4.54344 /  3.18 ( 1050)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 248
  time to evaluate  : 0.261 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6957 (mt-10)
REVERT: A   14 GLU cc_start: 0.7395 (tm-30) cc_final: 0.6935 (tm-30)
REVERT: A  249 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8038 (tp)
REVERT: A  252 SER cc_start: 0.6481 (p) cc_final: 0.6234 (p)
REVERT: A  270 LYS cc_start: 0.7293 (mmmt) cc_final: 0.7006 (mmtp)
REVERT: A  337 ASP cc_start: 0.7116 (t70) cc_final: 0.6865 (t70)
REVERT: A  351 CYS cc_start: 0.7250 (m) cc_final: 0.6738 (m)
REVERT: B   70 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8202 (mp)
REVERT: B  105 TYR cc_start: 0.8326 (t80) cc_final: 0.8046 (t80)
REVERT: B  125 ASN cc_start: 0.8497 (t0) cc_final: 0.8050 (t0)
REVERT: B  137 ARG cc_start: 0.7705 (tpp-160) cc_final: 0.7372 (tpp-160)
REVERT: B  169 TRP cc_start: 0.8271 (m100) cc_final: 0.6772 (m100)
REVERT: B  228 ASP cc_start: 0.7079 (p0) cc_final: 0.6798 (p0)
REVERT: B  249 THR cc_start: 0.7396 (m) cc_final: 0.7117 (p)
REVERT: B  255 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7366 (mm)
REVERT: B  339 TRP cc_start: 0.8143 (m100) cc_final: 0.7766 (m100)
REVERT: S   18 ARG cc_start: 0.5581 (OUTLIER) cc_final: 0.5301 (mmm160)
REVERT: S   38 ARG cc_start: 0.8248 (ptt180) cc_final: 0.7916 (ptp90)
REVERT: S  128 MET cc_start: 0.7592 (mtp) cc_final: 0.7041 (mtp)
REVERT: S  162 LEU cc_start: 0.8030 (tt) cc_final: 0.7727 (tt)
REVERT: S  166 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7159 (tt)
REVERT: S  190 ARG cc_start: 0.7584 (mtm110) cc_final: 0.7323 (mtm110)
REVERT: S  202 LEU cc_start: 0.8202 (tp) cc_final: 0.7961 (tt)
REVERT: R   86 MET cc_start: 0.6350 (OUTLIER) cc_final: 0.5982 (mpt)
REVERT: R  138 LEU cc_start: 0.6469 (OUTLIER) cc_final: 0.6223 (mt)
REVERT: R  419 MET cc_start: 0.5158 (ppp) cc_final: 0.4947 (ppp)
  outliers start: 51
  outliers final: 39
  residues processed: 272
  average time/residue: 0.0949
  time to fit residues: 34.3834
Evaluate side-chains
  290 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 244
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue   18 ARG
Chi-restraints excluded: chain S residue   55 SER
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  200 PHE
Chi-restraints excluded: chain S residue  217 CYS
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue   68 ASN
Chi-restraints excluded: chain R residue   71 LEU
Chi-restraints excluded: chain R residue   86 MET
Chi-restraints excluded: chain R residue   93 ILE
Chi-restraints excluded: chain R residue  109 LEU
Chi-restraints excluded: chain R residue  138 LEU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  398 VAL
Chi-restraints excluded: chain R residue  421 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 14 optimal weight:    0.4980
   chunk 100 optimal weight:    0.5980
   chunk 67 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 105 optimal weight:    3.9990
   chunk 108 optimal weight:    0.5980
   chunk 39 optimal weight:    0.4980
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
B 340 ASN
** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  68 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.150542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.133173 restraints weight = 13662.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.136695 restraints weight = 6318.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.138968 restraints weight = 3553.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.140451 restraints weight = 2262.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.141409 restraints weight = 1592.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6917
moved from start:          0.2676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8772  Z= 0.136
  Angle     :  0.634  12.739  11927  Z= 0.320
  Chirality :  0.042   0.238   1387
  Planarity :  0.004   0.055   1488
  Dihedral  :  4.907  31.545   1226
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 21.05 %
    Favored  : 73.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: 1104
  helix:  0.85 (0.27), residues: 397
  sheet: -1.79 (0.30), residues: 282
  loop : -1.40 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  46 
 TYR   0.013   0.001   TYR R 113 
 PHE   0.020   0.001   PHE S  29 
 TRP   0.020   0.001   TRP R 435 
 HIS   0.005   0.001   HIS S  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.14 ( 8770)
  covalent geometry    : angle       0.63351 /  0.32 (11923)
  SS BOND              : bond        0.00221 /  0.11 (    2)
  SS BOND              : angle       0.87550 /  0.42 (    4)
  hydrogen bonds       : bond        0.03361 /  2.24 (  368)
  hydrogen bonds       : angle       4.51470 /  3.16 ( 1050)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 245
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6955 (mt-10)
REVERT: A   14 GLU cc_start: 0.7381 (tm-30) cc_final: 0.6944 (tm-30)
REVERT: A  210 LYS cc_start: 0.7755 (tptt) cc_final: 0.7433 (mmtm)
REVERT: A  249 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8036 (tp)
REVERT: A  252 SER cc_start: 0.6458 (p) cc_final: 0.6218 (p)
REVERT: A  270 LYS cc_start: 0.7246 (mmmt) cc_final: 0.6962 (mmtp)
REVERT: A  337 ASP cc_start: 0.7300 (t70) cc_final: 0.7085 (t70)
REVERT: A  351 CYS cc_start: 0.7264 (m) cc_final: 0.6767 (m)
REVERT: B   70 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8200 (mp)
REVERT: B  105 TYR cc_start: 0.8325 (t80) cc_final: 0.8057 (t80)
REVERT: B  125 ASN cc_start: 0.8473 (t0) cc_final: 0.8047 (t0)
REVERT: B  228 ASP cc_start: 0.7136 (p0) cc_final: 0.6801 (p0)
REVERT: B  239 ASN cc_start: 0.7568 (m-40) cc_final: 0.7096 (m-40)
REVERT: B  249 THR cc_start: 0.7379 (m) cc_final: 0.7112 (p)
REVERT: B  255 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7282 (mm)
REVERT: B  297 TRP cc_start: 0.8526 (m100) cc_final: 0.8120 (m100)
REVERT: B  339 TRP cc_start: 0.8131 (m100) cc_final: 0.7784 (m100)
REVERT: S   18 ARG cc_start: 0.5555 (OUTLIER) cc_final: 0.5293 (mmm160)
REVERT: S   38 ARG cc_start: 0.8245 (ptt180) cc_final: 0.7778 (ptp90)
REVERT: S  128 MET cc_start: 0.7493 (mtp) cc_final: 0.7292 (mtt)
REVERT: S  162 LEU cc_start: 0.8059 (tt) cc_final: 0.7726 (tt)
REVERT: S  177 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7491 (mm)
REVERT: S  190 ARG cc_start: 0.7559 (mtm110) cc_final: 0.7290 (mtm110)
REVERT: S  202 LEU cc_start: 0.8199 (tp) cc_final: 0.7978 (tt)
REVERT: R   86 MET cc_start: 0.6342 (OUTLIER) cc_final: 0.5980 (mpt)
REVERT: R  138 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.6196 (mt)
REVERT: R  419 MET cc_start: 0.5136 (ppp) cc_final: 0.4923 (ppp)
  outliers start: 52
  outliers final: 38
  residues processed: 268
  average time/residue: 0.0922
  time to fit residues: 33.5175
Evaluate side-chains
  286 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 241
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue   18 ARG
Chi-restraints excluded: chain S residue   55 SER
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  126 ILE
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  135 VAL
Chi-restraints excluded: chain S residue  177 ILE
Chi-restraints excluded: chain S residue  217 CYS
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue   68 ASN
Chi-restraints excluded: chain R residue   71 LEU
Chi-restraints excluded: chain R residue   86 MET
Chi-restraints excluded: chain R residue   93 ILE
Chi-restraints excluded: chain R residue  138 LEU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  398 VAL
Chi-restraints excluded: chain R residue  421 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 92 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 76 optimal weight:    0.3980
   chunk 99 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 87 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 94 optimal weight:    2.9990
   chunk 84 optimal weight:    0.0030
   overall best weight:    0.5390

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
B 340 ASN
** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  68 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.150899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.133185 restraints weight = 13697.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.136728 restraints weight = 6343.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.139042 restraints weight = 3587.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.140575 restraints weight = 2307.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.141573 restraints weight = 1623.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6916
moved from start:          0.2766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8772  Z= 0.136
  Angle     :  0.649  12.686  11927  Z= 0.325
  Chirality :  0.042   0.230   1387
  Planarity :  0.004   0.055   1488
  Dihedral  :  4.891  31.101   1226
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 21.05 %
    Favored  : 73.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: 1104
  helix:  0.85 (0.27), residues: 403
  sheet: -1.73 (0.30), residues: 281
  loop : -1.41 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  52 
 TYR   0.013   0.001   TYR R 113 
 PHE   0.022   0.001   PHE S  29 
 TRP   0.020   0.001   TRP R 435 
 HIS   0.005   0.001   HIS S  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.14 ( 8770)
  covalent geometry    : angle       0.64905 /  0.32 (11923)
  SS BOND              : bond        0.00218 /  0.10 (    2)
  SS BOND              : angle       0.84613 /  0.41 (    4)
  hydrogen bonds       : bond        0.03319 /  2.21 (  368)
  hydrogen bonds       : angle       4.50121 /  3.14 ( 1050)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 245
  time to evaluate  : 0.329 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6954 (mt-10)
REVERT: A   14 GLU cc_start: 0.7388 (tm-30) cc_final: 0.6941 (tm-30)
REVERT: A  210 LYS cc_start: 0.7749 (tptt) cc_final: 0.7406 (mmtm)
REVERT: A  249 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8039 (tp)
REVERT: A  252 SER cc_start: 0.6441 (p) cc_final: 0.6192 (p)
REVERT: A  270 LYS cc_start: 0.7248 (mmmt) cc_final: 0.6975 (mmtp)
REVERT: A  351 CYS cc_start: 0.7291 (m) cc_final: 0.6852 (m)
REVERT: B   70 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8214 (mp)
REVERT: B  105 TYR cc_start: 0.8317 (t80) cc_final: 0.8045 (t80)
REVERT: B  125 ASN cc_start: 0.8462 (t0) cc_final: 0.8027 (t0)
REVERT: B  137 ARG cc_start: 0.7639 (tpp-160) cc_final: 0.7322 (tpp-160)
REVERT: B  145 TYR cc_start: 0.7669 (p90) cc_final: 0.7403 (p90)
REVERT: B  228 ASP cc_start: 0.7130 (p0) cc_final: 0.6778 (p0)
REVERT: B  239 ASN cc_start: 0.7593 (m-40) cc_final: 0.7138 (m-40)
REVERT: B  249 THR cc_start: 0.7358 (m) cc_final: 0.7088 (p)
REVERT: B  255 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7429 (mm)
REVERT: B  297 TRP cc_start: 0.8531 (m100) cc_final: 0.8307 (m100)
REVERT: B  339 TRP cc_start: 0.8127 (m100) cc_final: 0.7775 (m100)
REVERT: S   18 ARG cc_start: 0.5518 (OUTLIER) cc_final: 0.5265 (mmm160)
REVERT: S   38 ARG cc_start: 0.8253 (ptt180) cc_final: 0.7747 (ptp90)
REVERT: S  128 MET cc_start: 0.7502 (mtp) cc_final: 0.7290 (mtt)
REVERT: S  174 GLN cc_start: 0.7730 (pm20) cc_final: 0.7292 (pm20)
REVERT: S  177 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7494 (mm)
REVERT: S  190 ARG cc_start: 0.7552 (mtm110) cc_final: 0.7313 (mtm110)
REVERT: S  202 LEU cc_start: 0.8216 (tp) cc_final: 0.7960 (tt)
REVERT: R   86 MET cc_start: 0.6273 (OUTLIER) cc_final: 0.5885 (mpt)
REVERT: R  138 LEU cc_start: 0.6481 (OUTLIER) cc_final: 0.6124 (mt)
REVERT: R  419 MET cc_start: 0.5142 (ppp) cc_final: 0.4790 (ppp)
  outliers start: 52
  outliers final: 41
  residues processed: 267
  average time/residue: 0.1078
  time to fit residues: 38.5233
Evaluate side-chains
  289 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 241
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue   18 ARG
Chi-restraints excluded: chain S residue   55 SER
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  135 VAL
Chi-restraints excluded: chain S residue  177 ILE
Chi-restraints excluded: chain S residue  217 CYS
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue   68 ASN
Chi-restraints excluded: chain R residue   71 LEU
Chi-restraints excluded: chain R residue   86 MET
Chi-restraints excluded: chain R residue   93 ILE
Chi-restraints excluded: chain R residue  109 LEU
Chi-restraints excluded: chain R residue  138 LEU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  398 VAL
Chi-restraints excluded: chain R residue  421 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 54 optimal weight:    0.0270
   chunk 33 optimal weight:    0.7980
   chunk 103 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 97 optimal weight:    0.0030
   chunk 83 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9980
   chunk 98 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.4448

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  52 GLN
A 331 ASN
B 230 ASN
** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  68 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.151299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.133578 restraints weight = 13706.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.137125 restraints weight = 6414.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.139422 restraints weight = 3637.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.140894 restraints weight = 2347.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.141656 restraints weight = 1683.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6912
moved from start:          0.2850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8772  Z= 0.128
  Angle     :  0.648  12.611  11927  Z= 0.323
  Chirality :  0.042   0.221   1387
  Planarity :  0.003   0.054   1488
  Dihedral  :  4.822  30.756   1226
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  5.23 %
    Allowed  : 22.05 %
    Favored  : 72.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: 1104
  helix:  0.88 (0.27), residues: 396
  sheet: -1.69 (0.30), residues: 281
  loop : -1.41 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  52 
 TYR   0.013   0.001   TYR R 113 
 PHE   0.023   0.001   PHE S  29 
 TRP   0.018   0.001   TRP R 435 
 HIS   0.005   0.001   HIS S  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.13 ( 8770)
  covalent geometry    : angle       0.64788 /  0.32 (11923)
  SS BOND              : bond        0.00226 /  0.11 (    2)
  SS BOND              : angle       0.80004 /  0.38 (    4)
  hydrogen bonds       : bond        0.03285 /  2.19 (  368)
  hydrogen bonds       : angle       4.46951 /  3.12 ( 1050)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 244
  time to evaluate  : 0.325 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6725 (mt-10)
REVERT: A   14 GLU cc_start: 0.7365 (tm-30) cc_final: 0.6928 (tm-30)
REVERT: A  210 LYS cc_start: 0.7724 (tptt) cc_final: 0.7376 (mmtm)
REVERT: A  249 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8026 (tp)
REVERT: A  252 SER cc_start: 0.6453 (p) cc_final: 0.6203 (p)
REVERT: A  270 LYS cc_start: 0.7250 (mmmt) cc_final: 0.6986 (mmtp)
REVERT: B   70 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8157 (mp)
REVERT: B  105 TYR cc_start: 0.8268 (t80) cc_final: 0.7994 (t80)
REVERT: B  125 ASN cc_start: 0.8420 (t0) cc_final: 0.8035 (t0)
REVERT: B  137 ARG cc_start: 0.7650 (tpp-160) cc_final: 0.7248 (tpp80)
REVERT: B  145 TYR cc_start: 0.7669 (p90) cc_final: 0.7139 (p90)
REVERT: B  186 ASP cc_start: 0.7605 (p0) cc_final: 0.6910 (p0)
REVERT: B  228 ASP cc_start: 0.7139 (p0) cc_final: 0.6782 (p0)
REVERT: B  239 ASN cc_start: 0.7605 (m-40) cc_final: 0.7145 (m-40)
REVERT: B  249 THR cc_start: 0.7350 (m) cc_final: 0.7085 (p)
REVERT: B  255 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7446 (mm)
REVERT: B  297 TRP cc_start: 0.8528 (m100) cc_final: 0.8306 (m100)
REVERT: B  339 TRP cc_start: 0.8118 (m100) cc_final: 0.7789 (m100)
REVERT: S   18 ARG cc_start: 0.5448 (OUTLIER) cc_final: 0.5224 (mmm160)
REVERT: S   38 ARG cc_start: 0.8234 (ptt180) cc_final: 0.7898 (ptp-170)
REVERT: S  108 PHE cc_start: 0.8012 (m-80) cc_final: 0.7796 (m-80)
REVERT: S  174 GLN cc_start: 0.7731 (pm20) cc_final: 0.7298 (pm20)
REVERT: S  179 ARG cc_start: 0.7126 (tpp-160) cc_final: 0.6926 (tpp-160)
REVERT: S  190 ARG cc_start: 0.7550 (mtm110) cc_final: 0.7316 (mtm110)
REVERT: S  202 LEU cc_start: 0.8215 (tp) cc_final: 0.7988 (tt)
REVERT: R   86 MET cc_start: 0.6372 (OUTLIER) cc_final: 0.5969 (mpt)
REVERT: R  138 LEU cc_start: 0.6492 (OUTLIER) cc_final: 0.6160 (mt)
REVERT: R  215 TYR cc_start: 0.7692 (m-10) cc_final: 0.7367 (m-80)
REVERT: R  419 MET cc_start: 0.5140 (ppp) cc_final: 0.4770 (ppp)
  outliers start: 47
  outliers final: 39
  residues processed: 265
  average time/residue: 0.1067
  time to fit residues: 37.9902
Evaluate side-chains
  284 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 239
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain S residue    3 GLN
Chi-restraints excluded: chain S residue   18 ARG
Chi-restraints excluded: chain S residue   55 SER
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  135 VAL
Chi-restraints excluded: chain S residue  177 ILE
Chi-restraints excluded: chain S residue  217 CYS
Chi-restraints excluded: chain R residue   65 THR
Chi-restraints excluded: chain R residue   68 ASN
Chi-restraints excluded: chain R residue   71 LEU
Chi-restraints excluded: chain R residue   86 MET
Chi-restraints excluded: chain R residue   93 ILE
Chi-restraints excluded: chain R residue  109 LEU
Chi-restraints excluded: chain R residue  138 LEU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  398 VAL
Chi-restraints excluded: chain R residue  421 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 89 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0020
   chunk 16 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 108 optimal weight:    4.9990
   chunk 83 optimal weight:    0.9980
   chunk 103 optimal weight:    0.5980
   chunk 22 optimal weight:    0.7980
   chunk 78 optimal weight:    3.9990
   chunk 29 optimal weight:    0.0770
   overall best weight:    0.4146

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 230 ASN
B 340 ASN
** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  68 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.151555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.133803 restraints weight = 13792.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.137386 restraints weight = 6408.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.139668 restraints weight = 3611.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.141151 restraints weight = 2325.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.142032 restraints weight = 1657.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6899
moved from start:          0.2909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8772  Z= 0.124
  Angle     :  0.646  12.490  11927  Z= 0.322
  Chirality :  0.042   0.213   1387
  Planarity :  0.003   0.055   1488
  Dihedral  :  4.824  30.595   1226
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 22.05 %
    Favored  : 72.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -1.01 (0.26), residues: 1104
  helix:  0.90 (0.27), residues: 396
  sheet: -1.57 (0.30), residues: 276
  loop : -1.44 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  52 
 TYR   0.012   0.001   TYR R 113 
 PHE   0.023   0.001   PHE S  29 
 TRP   0.028   0.002   TRP B 169 
 HIS   0.005   0.001   HIS S  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.12 ( 8770)
  covalent geometry    : angle       0.64612 /  0.32 (11923)
  SS BOND              : bond        0.00230 /  0.11 (    2)
  SS BOND              : angle       0.77169 /  0.37 (    4)
  hydrogen bonds       : bond        0.03231 /  2.16 (  368)
  hydrogen bonds       : angle       4.42591 /  3.08 ( 1050)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1645.82 seconds
wall clock time: 29 minutes 15.13 seconds (1755.13 seconds total)