Starting phenix.real_space_refine
on Wed Mar  4 03:08:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v6a_31740/03_2026/7v6a_31740.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v6a_31740/03_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v6a_31740/03_2026/7v6a_31740.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v6a_31740/03_2026/7v6a_31740.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v6a_31740/03_2026/7v6a_31740.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v6a_31740/03_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-5986/lib/python3.9/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: 2.01, per 1000 atoms: 0.23
  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: 0.76
  Conformation dependent library (CDL) restraints added in 339.0 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: 0.27
  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: 1.08

  Time building geometry restraints manager: 0.96 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: 4695
       17.90 -    35.80: 373
       35.80 -    53.70: 78
       53.70 -    71.60: 11
       71.60 -    89.49: 10
  Dihedral angle restraints: 5167
    sinusoidal: 1908
      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 5164 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:             0.440
  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:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.720
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6809
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  : 14.081  89.494   3057
  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
  covalent geometry    : bond        0.00393 ( 8770)
  covalent geometry    : angle       0.70647 (11923)
  SS BOND              : bond        0.00166 (    2)
  SS BOND              : angle       0.81040 (    4)
  hydrogen bonds       : bond        0.17222 (  368)
  hydrogen bonds       : angle       7.27066 ( 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  : 0.288 
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: 0.1023
  time to fit residues: 36.6722
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  : 0.294 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3885 r_free = 0.3885 target = 0.150692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.133139 restraints weight = 13609.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.136622 restraints weight = 6266.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.138873 restraints weight = 3507.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.140317 restraints weight = 2243.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.141095 restraints weight = 1607.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6775
moved from start:          0.1389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8772  Z= 0.147
  Angle     :  0.607  10.832  11927  Z= 0.319
  Chirality :  0.043   0.199   1387
  Planarity :  0.004   0.054   1488
  Dihedral  :  6.123  59.116   1242
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 12.36 %
    Favored  : 86.08 %
  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: -1.72 (0.25), residues: 1104
  helix:  0.62 (0.27), residues: 392
  sheet: -2.34 (0.30), residues: 238
  loop : -1.95 (0.27), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG S 190 
 TYR   0.012   0.001   TYR S 223 
 PHE   0.012   0.002   PHE B 234 
 TRP   0.014   0.002   TRP B 339 
 HIS   0.005   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 8770)
  covalent geometry    : angle       0.60641 (11923)
  SS BOND              : bond        0.00212 (    2)
  SS BOND              : angle       1.09848 (    4)
  hydrogen bonds       : bond        0.03939 (  368)
  hydrogen bonds       : angle       5.19775 ( 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
  257 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 243
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.7409 (tm-30) cc_final: 0.6919 (tm-30)
REVERT: A  210 LYS cc_start: 0.7722 (tptt) cc_final: 0.7501 (tptt)
REVERT: A  211 TRP cc_start: 0.7699 (p-90) cc_final: 0.7142 (p-90)
REVERT: A  252 SER cc_start: 0.7381 (p) cc_final: 0.7088 (p)
REVERT: A  255 ASN cc_start: 0.7142 (m-40) cc_final: 0.6732 (m-40)
REVERT: A  337 ASP cc_start: 0.6990 (t70) cc_final: 0.6756 (t70)
REVERT: A  351 CYS cc_start: 0.7248 (m) cc_final: 0.6705 (m)
REVERT: B  105 TYR cc_start: 0.8097 (t80) cc_final: 0.7823 (t80)
REVERT: B  110 ASN cc_start: 0.8365 (m-40) cc_final: 0.8118 (m110)
REVERT: B  125 ASN cc_start: 0.8468 (t0) cc_final: 0.8085 (t0)
REVERT: B  228 ASP cc_start: 0.6862 (p0) cc_final: 0.6155 (p0)
REVERT: B  249 THR cc_start: 0.7597 (m) cc_final: 0.7307 (p)
REVERT: B  297 TRP cc_start: 0.8459 (m100) cc_final: 0.8046 (m100)
REVERT: B  301 LYS cc_start: 0.7320 (mttp) cc_final: 0.7105 (mtpp)
REVERT: B  339 TRP cc_start: 0.8159 (m100) cc_final: 0.7920 (m100)
REVERT: S  110 PHE cc_start: 0.7797 (t80) cc_final: 0.7524 (t80)
REVERT: S  190 ARG cc_start: 0.7549 (mtm110) cc_final: 0.7303 (mtm110)
REVERT: S  202 LEU cc_start: 0.8238 (tp) cc_final: 0.7998 (tt)
REVERT: R  152 MET cc_start: 0.5845 (tpt) cc_final: 0.5572 (tpt)
REVERT: R  190 LEU cc_start: 0.6956 (mm) cc_final: 0.6711 (mp)
  outliers start: 14
  outliers final: 12
  residues processed: 247
  average time/residue: 0.1014
  time to fit residues: 32.9312
Evaluate side-chains
  249 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 237
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
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  126 ILE
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:    0.4980
   chunk 88 optimal weight:    2.9990
   chunk 67 optimal weight:    0.0970
   chunk 22 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S 174 GLN
R 417 ASN
** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.148193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.130747 restraints weight = 13581.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.134225 restraints weight = 6304.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.136439 restraints weight = 3522.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.137888 restraints weight = 2250.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.138711 restraints weight = 1618.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6801
moved from start:          0.1839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8772  Z= 0.168
  Angle     :  0.608  11.145  11927  Z= 0.319
  Chirality :  0.043   0.177   1387
  Planarity :  0.004   0.055   1488
  Dihedral  :  6.157  59.063   1242
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 16.15 %
    Favored  : 81.18 %
  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: -1.61 (0.25), residues: 1104
  helix:  0.69 (0.27), residues: 392
  sheet: -2.17 (0.30), residues: 249
  loop : -1.91 (0.27), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 283 
 TYR   0.012   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
  covalent geometry    : bond        0.00366 ( 8770)
  covalent geometry    : angle       0.60787 (11923)
  SS BOND              : bond        0.00206 (    2)
  SS BOND              : angle       1.01783 (    4)
  hydrogen bonds       : bond        0.03740 (  368)
  hydrogen bonds       : angle       4.96818 ( 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
  262 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 238
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7068 (mt-10) cc_final: 0.6834 (mt-10)
REVERT: A   14 GLU cc_start: 0.7371 (tm-30) cc_final: 0.6928 (tm-30)
REVERT: A   53 MET cc_start: 0.5338 (mpp) cc_final: 0.4722 (mpp)
REVERT: A  210 LYS cc_start: 0.7813 (tptt) cc_final: 0.7563 (tptt)
REVERT: A  252 SER cc_start: 0.7340 (p) cc_final: 0.6993 (p)
REVERT: A  255 ASN cc_start: 0.7261 (m-40) cc_final: 0.6767 (m110)
REVERT: A  337 ASP cc_start: 0.7089 (t70) cc_final: 0.6847 (t70)
REVERT: A  351 CYS cc_start: 0.7221 (m) cc_final: 0.6713 (m)
REVERT: B  105 TYR cc_start: 0.8210 (t80) cc_final: 0.7987 (t80)
REVERT: B  125 ASN cc_start: 0.8477 (t0) cc_final: 0.8093 (t0)
REVERT: B  137 ARG cc_start: 0.7762 (tpp-160) cc_final: 0.7391 (tpp-160)
REVERT: B  228 ASP cc_start: 0.6907 (p0) cc_final: 0.6236 (p0)
REVERT: B  249 THR cc_start: 0.7616 (m) cc_final: 0.7340 (p)
REVERT: B  297 TRP cc_start: 0.8480 (m100) cc_final: 0.8192 (m100)
REVERT: B  339 TRP cc_start: 0.8183 (m100) cc_final: 0.7791 (m100)
REVERT: C   62 ARG cc_start: 0.5924 (mtm-85) cc_final: 0.5634 (mtt180)
REVERT: S   27 PHE cc_start: 0.7892 (p90) cc_final: 0.7687 (p90)
REVERT: S  110 PHE cc_start: 0.8025 (t80) cc_final: 0.7781 (t80)
REVERT: S  128 MET cc_start: 0.7575 (mtp) cc_final: 0.7005 (mtp)
REVERT: S  190 ARG cc_start: 0.7507 (mtm110) cc_final: 0.7294 (mtm110)
REVERT: S  202 LEU cc_start: 0.8229 (tp) cc_final: 0.7973 (tt)
REVERT: R   53 VAL cc_start: 0.7155 (m) cc_final: 0.6946 (p)
REVERT: R  419 MET cc_start: 0.4850 (ppp) cc_final: 0.4407 (ppp)
  outliers start: 24
  outliers final: 17
  residues processed: 246
  average time/residue: 0.1025
  time to fit residues: 33.4977
Evaluate side-chains
  247 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 230
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
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  335 VAL
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:    0.2980
   chunk 84 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 107 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 97 optimal weight:    3.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
B 142 HIS
** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  68 ASN
** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.147403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.129596 restraints weight = 13715.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.133112 restraints weight = 6341.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.135320 restraints weight = 3566.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.136805 restraints weight = 2297.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.137669 restraints weight = 1641.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6847
moved from start:          0.2208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   8772  Z= 0.219
  Angle     :  0.645  11.977  11927  Z= 0.338
  Chirality :  0.044   0.187   1387
  Planarity :  0.004   0.059   1488
  Dihedral  :  6.337  55.923   1242
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 17.04 %
    Favored  : 78.29 %
  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: -1.72 (0.25), residues: 1104
  helix:  0.58 (0.27), residues: 389
  sheet: -2.39 (0.29), residues: 271
  loop : -1.77 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 283 
 TYR   0.014   0.002   TYR S 102 
 PHE   0.013   0.002   PHE R  70 
 TRP   0.022   0.002   TRP R 435 
 HIS   0.005   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 ( 8770)
  covalent geometry    : angle       0.64446 (11923)
  SS BOND              : bond        0.00197 (    2)
  SS BOND              : angle       1.18362 (    4)
  hydrogen bonds       : bond        0.03825 (  368)
  hydrogen bonds       : angle       5.01337 ( 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
  281 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 239
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.7421 (tm-30) cc_final: 0.6970 (tm-30)
REVERT: A  252 SER cc_start: 0.6552 (p) cc_final: 0.6223 (p)
REVERT: A  255 ASN cc_start: 0.7463 (m-40) cc_final: 0.6943 (m110)
REVERT: A  270 LYS cc_start: 0.7329 (mmmt) cc_final: 0.6961 (mmtp)
REVERT: A  337 ASP cc_start: 0.7145 (t70) cc_final: 0.6921 (t70)
REVERT: B  105 TYR cc_start: 0.8319 (t80) cc_final: 0.8071 (t80)
REVERT: B  125 ASN cc_start: 0.8548 (t0) cc_final: 0.8121 (t0)
REVERT: B  228 ASP cc_start: 0.7000 (p0) cc_final: 0.6434 (p0)
REVERT: B  249 THR cc_start: 0.7546 (m) cc_final: 0.7218 (p)
REVERT: B  308 LEU cc_start: 0.7414 (tp) cc_final: 0.6940 (mp)
REVERT: B  339 TRP cc_start: 0.8187 (m100) cc_final: 0.7869 (m100)
REVERT: C   62 ARG cc_start: 0.5870 (mtm-85) cc_final: 0.5615 (mtt180)
REVERT: S   27 PHE cc_start: 0.7916 (p90) cc_final: 0.7701 (p90)
REVERT: S  128 MET cc_start: 0.7609 (mtp) cc_final: 0.7016 (mtp)
REVERT: S  174 GLN cc_start: 0.7033 (OUTLIER) cc_final: 0.6694 (pt0)
REVERT: S  190 ARG cc_start: 0.7518 (mtm110) cc_final: 0.7215 (mtm110)
REVERT: S  202 LEU cc_start: 0.8218 (tp) cc_final: 0.8005 (tt)
REVERT: R   53 VAL cc_start: 0.7272 (m) cc_final: 0.7063 (p)
REVERT: R  152 MET cc_start: 0.5916 (tpt) cc_final: 0.5706 (tpt)
  outliers start: 42
  outliers final: 30
  residues processed: 255
  average time/residue: 0.1010
  time to fit residues: 34.4161
Evaluate side-chains
  260 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 229
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  329 THR
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   42 GLU
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  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:    0.6980
   chunk 73 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 100 optimal weight:    0.5980
   chunk 66 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 106 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
B 142 HIS
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
R  68 ASN
R 423 ASN
** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.149264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.131840 restraints weight = 13538.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.135299 restraints weight = 6204.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.137450 restraints weight = 3465.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.138815 restraints weight = 2237.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.139751 restraints weight = 1614.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6809
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      :  0.003   0.048   8772  Z= 0.156
  Angle     :  0.617  12.361  11927  Z= 0.318
  Chirality :  0.043   0.188   1387
  Planarity :  0.004   0.057   1488
  Dihedral  :  6.176  55.413   1242
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 19.71 %
    Favored  : 75.72 %
  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: -1.48 (0.26), residues: 1104
  helix:  0.68 (0.27), residues: 392
  sheet: -2.16 (0.29), residues: 275
  loop : -1.59 (0.30), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 256 
 TYR   0.014   0.001   TYR S 102 
 PHE   0.014   0.001   PHE S  29 
 TRP   0.019   0.002   TRP R 435 
 HIS   0.006   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 8770)
  covalent geometry    : angle       0.61683 (11923)
  SS BOND              : bond        0.00267 (    2)
  SS BOND              : angle       0.92679 (    4)
  hydrogen bonds       : bond        0.03595 (  368)
  hydrogen bonds       : angle       4.78104 ( 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
  280 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 239
  time to evaluate  : 0.192 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6897 (mt-10)
REVERT: A   14 GLU cc_start: 0.7407 (tm-30) cc_final: 0.6956 (tm-30)
REVERT: A  210 LYS cc_start: 0.7856 (tptt) cc_final: 0.7607 (tptt)
REVERT: A  252 SER cc_start: 0.6512 (p) cc_final: 0.6184 (p)
REVERT: A  255 ASN cc_start: 0.7319 (m-40) cc_final: 0.6927 (m110)
REVERT: A  270 LYS cc_start: 0.7370 (mmmt) cc_final: 0.7048 (mmtp)
REVERT: A  337 ASP cc_start: 0.7081 (t70) cc_final: 0.6833 (t70)
REVERT: B   70 LEU cc_start: 0.8387 (mm) cc_final: 0.8184 (mp)
REVERT: B  105 TYR cc_start: 0.8322 (t80) cc_final: 0.8098 (t80)
REVERT: B  125 ASN cc_start: 0.8513 (t0) cc_final: 0.8093 (t0)
REVERT: B  137 ARG cc_start: 0.7731 (tpp-160) cc_final: 0.7407 (tpp-160)
REVERT: B  169 TRP cc_start: 0.8275 (m100) cc_final: 0.8024 (m100)
REVERT: B  228 ASP cc_start: 0.7026 (p0) cc_final: 0.6403 (p0)
REVERT: B  249 THR cc_start: 0.7392 (m) cc_final: 0.7121 (p)
REVERT: B  308 LEU cc_start: 0.7375 (tp) cc_final: 0.7008 (mp)
REVERT: B  339 TRP cc_start: 0.8141 (m100) cc_final: 0.7817 (m100)
REVERT: S   27 PHE cc_start: 0.7927 (p90) cc_final: 0.7613 (p90)
REVERT: S   67 ARG cc_start: 0.5264 (mtp180) cc_final: 0.4401 (mtp180)
REVERT: S  128 MET cc_start: 0.7582 (mtp) cc_final: 0.7022 (mtp)
REVERT: S  162 LEU cc_start: 0.8038 (tt) cc_final: 0.7760 (tt)
REVERT: S  190 ARG cc_start: 0.7537 (mtm110) cc_final: 0.7217 (mtm110)
REVERT: S  202 LEU cc_start: 0.8224 (tp) cc_final: 0.7993 (tt)
REVERT: R  121 MET cc_start: 0.7094 (mmt) cc_final: 0.6859 (mmt)
REVERT: R  152 MET cc_start: 0.5908 (tpt) cc_final: 0.5651 (tpt)
  outliers start: 41
  outliers final: 34
  residues processed: 254
  average time/residue: 0.0987
  time to fit residues: 33.3943
Evaluate side-chains
  270 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 236
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue  225 VAL
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   84 SER
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   88 ASN
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 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   55 SER
Chi-restraints excluded: chain S residue   63 THR
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  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:    0.7980
   chunk 98 optimal weight:    0.1980
   chunk 40 optimal weight:    0.0870
   chunk 18 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0980
   chunk 70 optimal weight:    0.8980
   chunk 66 optimal weight:    0.6980
   chunk 91 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.3758

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
S 167 GLN
R  68 ASN
R 423 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.151071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.133238 restraints weight = 13824.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.136818 restraints weight = 6346.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.139096 restraints weight = 3537.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.140549 restraints weight = 2261.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.141458 restraints weight = 1635.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6768
moved from start:          0.2477

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= 0.118
  Angle     :  0.595  12.158  11927  Z= 0.303
  Chirality :  0.042   0.190   1387
  Planarity :  0.004   0.056   1488
  Dihedral  :  5.999  55.986   1242
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 20.49 %
    Favored  : 74.50 %
  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: -1.19 (0.26), residues: 1104
  helix:  0.82 (0.27), residues: 398
  sheet: -1.86 (0.30), residues: 271
  loop : -1.48 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG S  67 
 TYR   0.011   0.001   TYR B 264 
 PHE   0.016   0.001   PHE R 186 
 TRP   0.018   0.001   TRP R 435 
 HIS   0.006   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 8770)
  covalent geometry    : angle       0.59471 (11923)
  SS BOND              : bond        0.00259 (    2)
  SS BOND              : angle       0.89647 (    4)
  hydrogen bonds       : bond        0.03374 (  368)
  hydrogen bonds       : angle       4.59572 ( 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
  290 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 245
  time to evaluate  : 0.190 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6762 (mt-10)
REVERT: A   14 GLU cc_start: 0.7392 (tm-30) cc_final: 0.6930 (tm-30)
REVERT: A  210 LYS cc_start: 0.7840 (tptt) cc_final: 0.7630 (tptt)
REVERT: A  249 LEU cc_start: 0.8247 (tt) cc_final: 0.7966 (tp)
REVERT: A  252 SER cc_start: 0.6470 (p) cc_final: 0.6258 (p)
REVERT: A  270 LYS cc_start: 0.7316 (mmmt) cc_final: 0.7034 (mmtp)
REVERT: A  337 ASP cc_start: 0.7075 (t70) cc_final: 0.6805 (t70)
REVERT: A  351 CYS cc_start: 0.7233 (m) cc_final: 0.6739 (m)
REVERT: B   70 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8161 (mp)
REVERT: B  105 TYR cc_start: 0.8335 (t80) cc_final: 0.8057 (t80)
REVERT: B  125 ASN cc_start: 0.8494 (t0) cc_final: 0.8063 (t0)
REVERT: B  137 ARG cc_start: 0.7704 (tpp-160) cc_final: 0.7401 (tpp-160)
REVERT: B  228 ASP cc_start: 0.7006 (p0) cc_final: 0.6614 (p0)
REVERT: B  249 THR cc_start: 0.7376 (m) cc_final: 0.7120 (p)
REVERT: B  297 TRP cc_start: 0.8430 (m100) cc_final: 0.8202 (m100)
REVERT: B  308 LEU cc_start: 0.7322 (tp) cc_final: 0.6922 (mp)
REVERT: B  339 TRP cc_start: 0.8090 (m100) cc_final: 0.7802 (m100)
REVERT: S   18 ARG cc_start: 0.5590 (OUTLIER) cc_final: 0.5320 (mmm160)
REVERT: S   38 ARG cc_start: 0.8307 (ptt180) cc_final: 0.7757 (ptp90)
REVERT: S  128 MET cc_start: 0.7516 (mtp) cc_final: 0.7002 (mtp)
REVERT: S  166 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7140 (tt)
REVERT: S  174 GLN cc_start: 0.7614 (pm20) cc_final: 0.7250 (pm20)
REVERT: S  190 ARG cc_start: 0.7559 (mtm110) cc_final: 0.7317 (mtm110)
REVERT: S  202 LEU cc_start: 0.8212 (tp) cc_final: 0.7963 (tt)
REVERT: R   86 MET cc_start: 0.6349 (OUTLIER) cc_final: 0.6002 (mpt)
REVERT: R  152 MET cc_start: 0.5851 (tpt) cc_final: 0.5614 (tpt)
REVERT: R  419 MET cc_start: 0.5169 (ppp) cc_final: 0.4820 (ppp)
  outliers start: 45
  outliers final: 34
  residues processed: 263
  average time/residue: 0.0939
  time to fit residues: 33.1056
Evaluate side-chains
  277 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 239
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  222 ILE
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   88 ASN
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 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  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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 82 optimal weight:    0.0470
   chunk 79 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9990
   overall best weight:    0.7278

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  68 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.149515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.131817 restraints weight = 13841.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.135336 restraints weight = 6392.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.137579 restraints weight = 3591.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.139038 restraints weight = 2312.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.139991 restraints weight = 1658.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6795
moved from start:          0.2585

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= 0.154
  Angle     :  0.630  12.480  11927  Z= 0.320
  Chirality :  0.043   0.252   1387
  Planarity :  0.004   0.055   1488
  Dihedral  :  6.035  53.316   1242
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 21.05 %
    Favored  : 73.05 %
  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:  0.77 (0.27), residues: 398
  sheet: -1.81 (0.30), residues: 272
  loop : -1.50 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG S  67 
 TYR   0.013   0.001   TYR R 113 
 PHE   0.018   0.001   PHE S  29 
 TRP   0.021   0.002   TRP R 435 
 HIS   0.005   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 8770)
  covalent geometry    : angle       0.62939 (11923)
  SS BOND              : bond        0.00214 (    2)
  SS BOND              : angle       0.91335 (    4)
  hydrogen bonds       : bond        0.03436 (  368)
  hydrogen bonds       : angle       4.58896 ( 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
  300 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 247
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.6967 (mt-10) cc_final: 0.6728 (mt-10)
REVERT: A   14 GLU cc_start: 0.7399 (tm-30) cc_final: 0.6938 (tm-30)
REVERT: A  249 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8043 (tp)
REVERT: A  252 SER cc_start: 0.6471 (p) cc_final: 0.6238 (p)
REVERT: A  270 LYS cc_start: 0.7333 (mmmt) cc_final: 0.7032 (mmtp)
REVERT: A  317 LYS cc_start: 0.7721 (ptmt) cc_final: 0.7521 (ptmt)
REVERT: A  337 ASP cc_start: 0.7089 (t70) cc_final: 0.6869 (t70)
REVERT: B   70 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8253 (mp)
REVERT: B  105 TYR cc_start: 0.8325 (t80) cc_final: 0.8092 (t80)
REVERT: B  125 ASN cc_start: 0.8499 (t0) cc_final: 0.8053 (t0)
REVERT: B  137 ARG cc_start: 0.7702 (tpp-160) cc_final: 0.7386 (tpp-160)
REVERT: B  169 TRP cc_start: 0.8293 (m100) cc_final: 0.6787 (m100)
REVERT: B  228 ASP cc_start: 0.7008 (p0) cc_final: 0.6740 (p0)
REVERT: B  249 THR cc_start: 0.7387 (m) cc_final: 0.7071 (p)
REVERT: B  255 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7429 (mm)
REVERT: B  308 LEU cc_start: 0.7367 (tp) cc_final: 0.6884 (mp)
REVERT: B  339 TRP cc_start: 0.8142 (m100) cc_final: 0.7846 (m100)
REVERT: S   18 ARG cc_start: 0.5590 (OUTLIER) cc_final: 0.5310 (mmm160)
REVERT: S  128 MET cc_start: 0.7552 (mtp) cc_final: 0.7304 (mtt)
REVERT: S  162 LEU cc_start: 0.8094 (tt) cc_final: 0.7734 (tt)
REVERT: S  166 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7141 (tt)
REVERT: S  190 ARG cc_start: 0.7579 (mtm110) cc_final: 0.7320 (mtm110)
REVERT: S  202 LEU cc_start: 0.8220 (tp) cc_final: 0.7983 (tt)
REVERT: R   86 MET cc_start: 0.6365 (OUTLIER) cc_final: 0.6044 (mpt)
  outliers start: 53
  outliers final: 41
  residues processed: 268
  average time/residue: 0.0973
  time to fit residues: 34.5375
Evaluate side-chains
  286 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 239
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
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  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  329 THR
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  335 VAL
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  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 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  126 ILE
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  166 LEU
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  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:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 100 optimal weight:    0.8980
   chunk 67 optimal weight:    0.0050
   chunk 19 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   chunk 105 optimal weight:    0.9990
   chunk 108 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   overall best weight:    0.5594

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
S  39 GLN
S 167 GLN
** 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 = 0.3879 r_free = 0.3879 target = 0.150128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.132621 restraints weight = 13636.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.136157 restraints weight = 6325.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.138410 restraints weight = 3545.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.139864 restraints weight = 2273.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.140815 restraints weight = 1626.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6778
moved from start:          0.2689

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= 0.138
  Angle     :  0.635  12.529  11927  Z= 0.321
  Chirality :  0.042   0.239   1387
  Planarity :  0.004   0.055   1488
  Dihedral  :  6.017  53.374   1242
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 21.60 %
    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: -1.16 (0.26), residues: 1104
  helix:  0.84 (0.27), residues: 398
  sheet: -1.83 (0.30), residues: 281
  loop : -1.45 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 256 
 TYR   0.013   0.001   TYR R 113 
 PHE   0.020   0.001   PHE S  29 
 TRP   0.019   0.001   TRP R 435 
 HIS   0.005   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8770)
  covalent geometry    : angle       0.63520 (11923)
  SS BOND              : bond        0.00221 (    2)
  SS BOND              : angle       0.86184 (    4)
  hydrogen bonds       : bond        0.03377 (  368)
  hydrogen bonds       : angle       4.52332 ( 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
  300 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 249
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.7372 (tm-30) cc_final: 0.6937 (tm-30)
REVERT: A  249 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8024 (tp)
REVERT: A  252 SER cc_start: 0.6445 (p) cc_final: 0.6216 (p)
REVERT: A  270 LYS cc_start: 0.7262 (mmmt) cc_final: 0.6971 (mmtp)
REVERT: A  337 ASP cc_start: 0.7099 (t70) cc_final: 0.6887 (t70)
REVERT: A  351 CYS cc_start: 0.7271 (m) cc_final: 0.6811 (m)
REVERT: B   70 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8237 (mp)
REVERT: B  105 TYR cc_start: 0.8329 (t80) cc_final: 0.8053 (t80)
REVERT: B  125 ASN cc_start: 0.8479 (t0) cc_final: 0.8058 (t0)
REVERT: B  126 LEU cc_start: 0.8219 (mp) cc_final: 0.7966 (mt)
REVERT: B  169 TRP cc_start: 0.8258 (m100) cc_final: 0.6810 (m100)
REVERT: B  228 ASP cc_start: 0.6995 (p0) cc_final: 0.6729 (p0)
REVERT: B  249 THR cc_start: 0.7365 (m) cc_final: 0.7099 (p)
REVERT: B  255 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7366 (mm)
REVERT: B  308 LEU cc_start: 0.7350 (tp) cc_final: 0.6877 (mp)
REVERT: B  339 TRP cc_start: 0.8133 (m100) cc_final: 0.7855 (m100)
REVERT: S   18 ARG cc_start: 0.5540 (OUTLIER) cc_final: 0.5273 (mmm160)
REVERT: S  179 ARG cc_start: 0.7366 (tpp-160) cc_final: 0.7162 (tpp-160)
REVERT: S  190 ARG cc_start: 0.7566 (mtm110) cc_final: 0.7290 (mtm110)
REVERT: S  202 LEU cc_start: 0.8216 (tp) cc_final: 0.7981 (tt)
REVERT: R   86 MET cc_start: 0.6348 (OUTLIER) cc_final: 0.6027 (mpt)
  outliers start: 51
  outliers final: 41
  residues processed: 271
  average time/residue: 0.0990
  time to fit residues: 35.9066
Evaluate side-chains
  289 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 243
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
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  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  329 THR
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  335 VAL
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  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  255 LEU
Chi-restraints excluded: chain B residue  279 SER
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  127 VAL
Chi-restraints excluded: chain S residue  135 VAL
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  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:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 92 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 76 optimal weight:    0.4980
   chunk 99 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 87 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 84 optimal weight:    0.0000
   overall best weight:    0.5984

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  68 ASN
R 423 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 = 0.150283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.132763 restraints weight = 13651.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.136355 restraints weight = 6242.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.138583 restraints weight = 3465.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.140078 restraints weight = 2221.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.141079 restraints weight = 1573.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6773
moved from start:          0.2774

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     :  0.644  12.670  11927  Z= 0.323
  Chirality :  0.043   0.213   1387
  Planarity :  0.004   0.055   1488
  Dihedral  :  6.033  52.568   1242
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 21.16 %
    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: -1.13 (0.26), residues: 1104
  helix:  0.80 (0.27), residues: 403
  sheet: -1.72 (0.30), residues: 275
  loop : -1.48 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 256 
 TYR   0.013   0.001   TYR R 113 
 PHE   0.022   0.001   PHE S  29 
 TRP   0.019   0.002   TRP R 435 
 HIS   0.005   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8770)
  covalent geometry    : angle       0.64376 (11923)
  SS BOND              : bond        0.00211 (    2)
  SS BOND              : angle       0.83156 (    4)
  hydrogen bonds       : bond        0.03378 (  368)
  hydrogen bonds       : angle       4.53555 ( 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
  301 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 250
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.7370 (tm-30) cc_final: 0.6908 (tm-30)
REVERT: A  249 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8023 (tp)
REVERT: A  252 SER cc_start: 0.6426 (p) cc_final: 0.6169 (p)
REVERT: A  270 LYS cc_start: 0.7273 (mmmt) cc_final: 0.6983 (mmtp)
REVERT: A  351 CYS cc_start: 0.7305 (m) cc_final: 0.6868 (m)
REVERT: B   70 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8234 (mp)
REVERT: B  105 TYR cc_start: 0.8333 (t80) cc_final: 0.8045 (t80)
REVERT: B  125 ASN cc_start: 0.8470 (t0) cc_final: 0.8030 (t0)
REVERT: B  137 ARG cc_start: 0.7643 (tpp-160) cc_final: 0.7188 (tpp80)
REVERT: B  169 TRP cc_start: 0.8279 (m100) cc_final: 0.6807 (m100)
REVERT: B  228 ASP cc_start: 0.7032 (p0) cc_final: 0.6713 (p0)
REVERT: B  249 THR cc_start: 0.7378 (m) cc_final: 0.7103 (p)
REVERT: B  255 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7359 (mm)
REVERT: B  297 TRP cc_start: 0.8471 (m100) cc_final: 0.8163 (m100)
REVERT: B  308 LEU cc_start: 0.7365 (tp) cc_final: 0.6892 (mp)
REVERT: B  339 TRP cc_start: 0.8140 (m100) cc_final: 0.7860 (m100)
REVERT: S   18 ARG cc_start: 0.5527 (OUTLIER) cc_final: 0.5271 (mmm160)
REVERT: S   38 ARG cc_start: 0.8260 (ptt180) cc_final: 0.7760 (ptp90)
REVERT: S   67 ARG cc_start: 0.5221 (mtp180) cc_final: 0.5021 (mtp180)
REVERT: S  174 GLN cc_start: 0.7770 (pm20) cc_final: 0.7320 (pm20)
REVERT: S  182 ASN cc_start: 0.7400 (OUTLIER) cc_final: 0.7172 (t0)
REVERT: S  202 LEU cc_start: 0.8223 (tp) cc_final: 0.7956 (tt)
REVERT: R   86 MET cc_start: 0.6398 (OUTLIER) cc_final: 0.6047 (mpt)
  outliers start: 51
  outliers final: 41
  residues processed: 273
  average time/residue: 0.0985
  time to fit residues: 36.0191
Evaluate side-chains
  295 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 248
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
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  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  329 THR
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  335 VAL
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  255 LEU
Chi-restraints excluded: chain B residue  279 SER
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  182 ASN
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 103 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 97 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 98 optimal weight:    0.0770
   chunk 29 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
B 230 ASN
** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3879 r_free = 0.3879 target = 0.149916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.132322 restraints weight = 13642.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.135872 restraints weight = 6340.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.138079 restraints weight = 3553.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.139557 restraints weight = 2301.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.140567 restraints weight = 1655.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6783
moved from start:          0.2839

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= 0.146
  Angle     :  0.662  12.426  11927  Z= 0.332
  Chirality :  0.043   0.217   1387
  Planarity :  0.004   0.055   1488
  Dihedral  :  6.016  51.923   1242
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 22.38 %
    Favored  : 72.16 %
  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:  0.81 (0.27), residues: 403
  sheet: -1.68 (0.30), residues: 272
  loop : -1.42 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG S  67 
 TYR   0.013   0.001   TYR S  94 
 PHE   0.023   0.001   PHE S  29 
 TRP   0.019   0.002   TRP R 435 
 HIS   0.005   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 8770)
  covalent geometry    : angle       0.66233 (11923)
  SS BOND              : bond        0.00213 (    2)
  SS BOND              : angle       0.87409 (    4)
  hydrogen bonds       : bond        0.03391 (  368)
  hydrogen bonds       : angle       4.53585 ( 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
  293 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 244
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6777 (mt-10)
REVERT: A   14 GLU cc_start: 0.7359 (tm-30) cc_final: 0.6914 (tm-30)
REVERT: A  249 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8020 (tp)
REVERT: A  252 SER cc_start: 0.6433 (p) cc_final: 0.6195 (p)
REVERT: A  270 LYS cc_start: 0.7263 (mmmt) cc_final: 0.6984 (mmtp)
REVERT: A  351 CYS cc_start: 0.7271 (m) cc_final: 0.6864 (m)
REVERT: B   70 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8249 (mp)
REVERT: B  105 TYR cc_start: 0.8286 (t80) cc_final: 0.8000 (t80)
REVERT: B  125 ASN cc_start: 0.8471 (t0) cc_final: 0.8037 (t0)
REVERT: B  137 ARG cc_start: 0.7632 (tpp-160) cc_final: 0.7222 (tpp80)
REVERT: B  186 ASP cc_start: 0.7631 (p0) cc_final: 0.7033 (p0)
REVERT: B  228 ASP cc_start: 0.7037 (p0) cc_final: 0.6691 (p0)
REVERT: B  249 THR cc_start: 0.7370 (m) cc_final: 0.7105 (p)
REVERT: B  255 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7372 (mm)
REVERT: B  297 TRP cc_start: 0.8478 (m100) cc_final: 0.8251 (m100)
REVERT: B  308 LEU cc_start: 0.7381 (tp) cc_final: 0.6914 (mp)
REVERT: B  339 TRP cc_start: 0.8142 (m100) cc_final: 0.7882 (m100)
REVERT: S   18 ARG cc_start: 0.5507 (OUTLIER) cc_final: 0.5276 (mmm160)
REVERT: S   38 ARG cc_start: 0.8241 (ptt180) cc_final: 0.7763 (ptp-170)
REVERT: S  166 LEU cc_start: 0.7614 (tt) cc_final: 0.6996 (tt)
REVERT: S  174 GLN cc_start: 0.7679 (pm20) cc_final: 0.7199 (pm20)
REVERT: S  202 LEU cc_start: 0.8229 (tp) cc_final: 0.7983 (tt)
REVERT: R   86 MET cc_start: 0.6399 (OUTLIER) cc_final: 0.6038 (mpt)
REVERT: R  138 LEU cc_start: 0.6809 (OUTLIER) cc_final: 0.6506 (mp)
REVERT: R  215 TYR cc_start: 0.7716 (m-10) cc_final: 0.7486 (m-10)
  outliers start: 49
  outliers final: 41
  residues processed: 267
  average time/residue: 0.1032
  time to fit residues: 36.4768
Evaluate side-chains
  288 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 241
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
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  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  329 THR
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  335 VAL
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  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  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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 89 optimal weight:    0.5980
   chunk 36 optimal weight:    0.5980
   chunk 58 optimal weight:    0.0170
   chunk 16 optimal weight:    0.0170
   chunk 54 optimal weight:    0.0060
   chunk 108 optimal weight:    0.0030
   chunk 83 optimal weight:    0.8980
   chunk 103 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.1282

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
A 346 ASN
B 340 ASN
S 130 GLN
** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 445 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 = 0.3938 r_free = 0.3938 target = 0.154576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.136762 restraints weight = 13833.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.140326 restraints weight = 6474.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.142608 restraints weight = 3682.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.144118 restraints weight = 2373.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.145083 restraints weight = 1707.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6701
moved from start:          0.3044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8772  Z= 0.110
  Angle     :  0.639  12.350  11927  Z= 0.317
  Chirality :  0.041   0.193   1387
  Planarity :  0.004   0.056   1488
  Dihedral  :  5.877  52.935   1242
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 23.94 %
    Favored  : 71.83 %
  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: -0.94 (0.26), residues: 1104
  helix:  0.92 (0.27), residues: 402
  sheet: -1.47 (0.31), residues: 269
  loop : -1.44 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG S  87 
 TYR   0.013   0.001   TYR R  69 
 PHE   0.025   0.001   PHE S  29 
 TRP   0.012   0.001   TRP R 435 
 HIS   0.007   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 8770)
  covalent geometry    : angle       0.63880 (11923)
  SS BOND              : bond        0.00259 (    2)
  SS BOND              : angle       0.73955 (    4)
  hydrogen bonds       : bond        0.03195 (  368)
  hydrogen bonds       : angle       4.36058 ( 1050)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1551.29 seconds
wall clock time: 27 minutes 36.04 seconds (1656.04 seconds total)