Starting phenix.real_space_refine
on Thu Mar 13 18:49:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ew4_31347/03_2025/7ew4_31347.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ew4_31347/03_2025/7ew4_31347.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ew4_31347/03_2025/7ew4_31347.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ew4_31347/03_2025/7ew4_31347.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ew4_31347/03_2025/7ew4_31347.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ew4_31347/03_2025/7ew4_31347.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.097
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 48 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    5692      2.51       5
     N    1508      2.21       5
     O    1664      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8929
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1820
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1820
          Classifications: {'peptide': 228}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 2, 'TRANS': 225}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "B"
      Number of atoms: 2611
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2611
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
    Chain: "C"
      Number of atoms: 445
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 445
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "R"
      Number of atoms: 2211
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2211
          Classifications: {'peptide': 287}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 8, 'TRANS': 278}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 94
          Unresolved non-hydrogen angles: 114
          Unresolved non-hydrogen dihedrals: 87
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 57
    Chain: "S"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1783
          Classifications: {'peptide': 232}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 59
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 59
          Unusual residues: {'JF9': 1, 'PLM': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 5.72, per 1000 atoms: 0.64
  Number of scatterers: 8929
  At special positions: 0
  Unit cell: (92.34, 122.265, 129.96, 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    1664      8.00
     N    1508      7.00
     C    5692      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 178 " - pdb=" SG  CYS R 185 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 269 " - pdb=" SG  CYS R 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.85
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2146

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 14 sheets defined
      38.3% alpha, 22.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 45 through 55
    Processing helix  chain 'A' and resid 207 through 211
    Processing helix  chain 'A' and resid 212 through 216
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 241 through 255
      removed outlier: 3.718A  pdb=" N   GLU A 245 " --> pdb=" O   ASN A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.519A  pdb=" N   PHE A 259 " --> pdb=" O   ASN A 256 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 256 through 260'
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.539A  pdb=" N   PHE A 274 " --> pdb=" O   LYS A 270 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 3.542A  pdb=" N   ALA A 299 " --> pdb=" O   THR A 295 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 351
      removed outlier: 4.121A  pdb=" N   ASN A 331 " --> pdb=" O   THR A 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 26
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'C' and resid 8 through 23
      removed outlier: 4.357A  pdb=" N   ALA C  12 " --> pdb=" O   SER C   8 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.557A  pdb=" N   ALA C  33 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 17 through 25
      removed outlier: 3.783A  pdb=" N   VAL R  25 " --> pdb=" O   HIS R  21 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 40 through 67
      removed outlier: 3.672A  pdb=" N   ASN R  67 " --> pdb=" O   ALA R  63 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 73 through 102
      removed outlier: 3.848A  pdb=" N   PHE R  77 " --> pdb=" O   ARG R  73 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 107 through 125
      removed outlier: 3.602A  pdb=" N   PHE R 112 " --> pdb=" O   PRO R 108 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   MET R 118 " --> pdb=" O   ARG R 114 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 126 through 142
      removed outlier: 3.746A  pdb=" N   LYS R 142 " --> pdb=" O   LEU R 138 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 150 through 175
      removed outlier: 4.142A  pdb=" N   VAL R 154 " --> pdb=" O   LYS R 150 " (cutoff:3.500A)
      Proline residue:  R 172  - end of helix
    Processing helix  chain 'R' and resid 193 through 228
      removed outlier: 3.580A  pdb=" N   ILE R 197 " --> pdb=" O   SER R 193 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   LYS R 228 " --> pdb=" O   SER R 224 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 231 through 269
      Proline residue:  R 258  - end of helix
    Processing helix  chain 'R' and resid 279 through 301
      removed outlier: 3.816A  pdb=" N   PHE R 283 " --> pdb=" O   LYS R 279 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   LEU R 286 " --> pdb=" O   TRP R 282 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   SER R 291 " --> pdb=" O   ALA R 287 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ALA R 292 " --> pdb=" O   VAL R 288 " (cutoff:3.500A)
      Proline residue:  R 295  - end of helix
      removed outlier: 3.765A  pdb=" N   ALA R 301 " --> pdb=" O   ILE R 297 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 302 through 312
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 3.993A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 62 through 65
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 3.687A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 7.560A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191
      removed outlier: 3.687A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 52
      removed outlier: 6.853A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.171A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.075A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.244A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.161A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.123A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.125A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.995A  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: 3.536A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.332A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 7.235A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.731A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.890A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 7.090A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.694A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12
      removed outlier: 6.874A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141
      removed outlier: 3.516A  pdb=" N   THR S 141 " --> pdb=" O   ARG S 160 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 194 through 195
      removed outlier: 5.484A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 225 through 227

    460 hydrogen bonds defined for protein.
    1287 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.50

  Time building geometry restraints manager: 2.63 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1448
        1.31 -     1.43: 2470
        1.43 -     1.56: 5093
        1.56 -     1.69: 2
        1.69 -     1.82: 93
  Bond restraints: 9106
  Sorted by residual:
  bond pdb=" C14 JF9 R 401 "
       pdb=" N7  JF9 R 401 "
    ideal  model  delta    sigma   weight residual
    1.338  1.497 -0.159 2.00e-02 2.50e+03 6.28e+01
  bond pdb=" C19 JF9 R 401 "
       pdb=" C21 JF9 R 401 "
    ideal  model  delta    sigma   weight residual
    1.459  1.540 -0.081 2.00e-02 2.50e+03 1.64e+01
  bond pdb=" C8  JF9 R 401 "
       pdb=" N7  JF9 R 401 "
    ideal  model  delta    sigma   weight residual
    1.467  1.516 -0.049 2.00e-02 2.50e+03 6.09e+00
  bond pdb=" C14 JF9 R 401 "
       pdb=" O15 JF9 R 401 "
    ideal  model  delta    sigma   weight residual
    1.223  1.178  0.045 2.00e-02 2.50e+03 4.96e+00
  bond pdb=" C14 JF9 R 401 "
       pdb=" C16 JF9 R 401 "
    ideal  model  delta    sigma   weight residual
    1.500  1.542 -0.042 2.00e-02 2.50e+03 4.36e+00
  ... (remaining 9101 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.58: 12257
        2.58 -     5.17: 59
        5.17 -     7.75: 6
        7.75 -    10.33: 1
       10.33 -    12.92: 1
  Bond angle restraints: 12324
  Sorted by residual:
  angle pdb=" C19 JF9 R 401 "
        pdb=" C21 JF9 R 401 "
        pdb=" C22 JF9 R 401 "
      ideal   model   delta    sigma   weight residual
     121.01  133.93  -12.92 3.00e+00 1.11e-01 1.85e+01
  angle pdb=" CA  LEU R  97 "
        pdb=" CB  LEU R  97 "
        pdb=" CG  LEU R  97 "
      ideal   model   delta    sigma   weight residual
     116.30  124.60   -8.30 3.50e+00 8.16e-02 5.63e+00
  angle pdb=" C12 JF9 R 401 "
        pdb=" C13 JF9 R 401 "
        pdb=" C8  JF9 R 401 "
      ideal   model   delta    sigma   weight residual
     109.43  116.39   -6.96 3.00e+00 1.11e-01 5.38e+00
  angle pdb=" C14 JF9 R 401 "
        pdb=" C16 JF9 R 401 "
        pdb=" N17 JF9 R 401 "
      ideal   model   delta    sigma   weight residual
     120.71  127.21   -6.50 3.00e+00 1.11e-01 4.69e+00
  angle pdb=" C   LYS A  54 "
        pdb=" N   ILE A  55 "
        pdb=" CA  ILE A  55 "
      ideal   model   delta    sigma   weight residual
     121.70  125.54   -3.84 1.80e+00 3.09e-01 4.56e+00
  ... (remaining 12319 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.98: 4891
       16.98 -    33.95: 445
       33.95 -    50.93: 89
       50.93 -    67.91: 9
       67.91 -    84.88: 8
  Dihedral angle restraints: 5442
    sinusoidal: 2120
      harmonic: 3322
  Sorted by residual:
  dihedral pdb=" CB  CYS S 159 "
           pdb=" SG  CYS S 159 "
           pdb=" SG  CYS S 229 "
           pdb=" CB  CYS S 229 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   52.64   40.36     1      1.00e+01 1.00e-02 2.28e+01
  dihedral pdb=" CB  CYS R 178 "
           pdb=" SG  CYS R 178 "
           pdb=" SG  CYS R 185 "
           pdb=" CB  CYS R 185 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -114.71   28.71     1      1.00e+01 1.00e-02 1.18e+01
  dihedral pdb=" CA  ASP B 195 "
           pdb=" CB  ASP B 195 "
           pdb=" CG  ASP B 195 "
           pdb=" OD1 ASP B 195 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.19   57.19     1      2.00e+01 2.50e-03 1.10e+01
  ... (remaining 5439 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1161
       0.050 -    0.100: 211
       0.100 -    0.150: 36
       0.150 -    0.200: 3
       0.200 -    0.250: 1
  Chirality restraints: 1412
  Sorted by residual:
  chirality pdb=" C8  JF9 R 401 "
            pdb=" C13 JF9 R 401 "
            pdb=" C9  JF9 R 401 "
            pdb=" N7  JF9 R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.37    2.62   -0.25 2.00e-01 2.50e+01 1.56e+00
  chirality pdb=" C21 JF9 R 401 "
            pdb=" C19 JF9 R 401 "
            pdb=" C22 JF9 R 401 "
            pdb=" C23 JF9 R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.30   -2.10    0.20 2.00e-01 2.50e+01 9.59e-01
  chirality pdb=" CB  THR S  91 "
            pdb=" CA  THR S  91 "
            pdb=" OG1 THR S  91 "
            pdb=" CG2 THR S  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.16 2.00e-01 2.50e+01 6.02e-01
  ... (remaining 1409 not shown)

  Planarity restraints: 1550
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 182 "   -0.062 5.00e-02 4.00e+02   9.57e-02 1.46e+01
        pdb=" N   PRO R 183 "    0.166 5.00e-02 4.00e+02
        pdb=" CA  PRO R 183 "   -0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO R 183 "   -0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN S  13 "    0.032 5.00e-02 4.00e+02   4.89e-02 3.83e+00
        pdb=" N   PRO S  14 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO S  14 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO S  14 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.031 5.00e-02 4.00e+02   4.77e-02 3.64e+00
        pdb=" N   PRO B 236 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 1547 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1467
        2.77 -     3.30: 8300
        3.30 -     3.83: 14500
        3.83 -     4.37: 16511
        4.37 -     4.90: 29776
  Nonbonded interactions: 70554
  Sorted by model distance:
  nonbonded pdb=" OG  SER R 186 "
            pdb=" O   LEU R 189 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" O   ILE S 138 "
            pdb=" OG1 THR S 238 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP C  48 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" O   PHE S  29 "
            pdb=" NH2 ARG S  72 "
     model   vdw
     2.291 3.120
  ... (remaining 70549 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.910
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7114
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      :  0.003   0.159   9106  Z= 0.210
  Angle     :  0.515  12.917  12324  Z= 0.277
  Chirality :  0.040   0.250   1412
  Planarity :  0.004   0.096   1550
  Dihedral  : 13.407  84.884   3287
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.25), residues: 1129
  helix:  2.98 (0.26), residues: 399
  sheet:  0.26 (0.31), residues: 288
  loop : -1.21 (0.27), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B  54 
 PHE   0.018   0.001   PHE R  52 
 TYR   0.019   0.001   TYR R  24 
 ARG   0.006   0.000   ARG S  18 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.975 
Fit side-chains
REVERT: A   18 MET cc_start: 0.7675 (mtp) cc_final: 0.7467 (mtt)
REVERT: R  106 LEU cc_start: 0.7822 (tp) cc_final: 0.7600 (tp)
REVERT: R  257 SER cc_start: 0.7327 (m) cc_final: 0.7054 (m)
REVERT: S  220 GLU cc_start: 0.7713 (mp0) cc_final: 0.7511 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.2764
  time to fit residues: 50.9612
Evaluate side-chains
  101 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 1.004 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    4.9990
   chunk 84 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 87 optimal weight:    8.9990
   chunk 33 optimal weight:    4.9990
   chunk 53 optimal weight:    0.6980
   chunk 65 optimal weight:    0.0170
   chunk 101 optimal weight:    3.9990
   overall best weight:    0.9422

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
R  57 ASN
** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.190146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.152877 restraints weight = 11260.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3843 rms_B_bonded: 2.05
r_work: 0.3572 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.3444 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.1146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9106  Z= 0.175
  Angle     :  0.503  12.270  12324  Z= 0.262
  Chirality :  0.040   0.206   1412
  Planarity :  0.004   0.055   1550
  Dihedral  :  3.959  25.765   1294
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  8.23 %
    Favored  : 91.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.25), residues: 1129
  helix:  3.29 (0.25), residues: 389
  sheet:  0.41 (0.31), residues: 287
  loop : -1.24 (0.27), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 211 
 HIS   0.007   0.001   HIS B 225 
 PHE   0.014   0.001   PHE R  52 
 TYR   0.010   0.001   TYR R  24 
 ARG   0.011   0.000   ARG S  67 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 112
  time to evaluate  : 0.878 
Fit side-chains
REVERT: C   42 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7856 (mm-30)
REVERT: R  257 SER cc_start: 0.7979 (m) cc_final: 0.7639 (m)
REVERT: R  293 MET cc_start: 0.7734 (mmt) cc_final: 0.7330 (mmp)
  outliers start: 4
  outliers final: 2
  residues processed: 115
  average time/residue: 0.2648
  time to fit residues: 41.8605
Evaluate side-chains
  100 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 98
  time to evaluate  : 1.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  161 CYS
Chi-restraints excluded: chain S residue  197 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 18 optimal weight:    7.9990
   chunk 101 optimal weight:    0.5980
   chunk 58 optimal weight:   30.0000
   chunk 88 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 54 optimal weight:    0.0570
   chunk 32 optimal weight:    0.7980
   chunk 61 optimal weight:   30.0000
   chunk 13 optimal weight:    0.8980
   chunk 65 optimal weight:    8.9990
   overall best weight:    0.6700

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

Flipped N/Q/H residues before XYZ refinement:
** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.188757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.154038 restraints weight = 11229.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3869 rms_B_bonded: 1.93
r_work: 0.3576 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.3453 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.1463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9106  Z= 0.142
  Angle     :  0.464  12.212  12324  Z= 0.241
  Chirality :  0.040   0.213   1412
  Planarity :  0.003   0.049   1550
  Dihedral  :  3.863  28.836   1294
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 10.73 %
    Favored  : 87.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.25), residues: 1129
  helix:  3.12 (0.25), residues: 398
  sheet:  0.41 (0.31), residues: 285
  loop : -1.22 (0.26), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 211 
 HIS   0.007   0.001   HIS R  21 
 PHE   0.011   0.001   PHE R  52 
 TYR   0.011   0.001   TYR R  24 
 ARG   0.005   0.000   ARG S  67 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
REVERT: C   42 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7927 (mm-30)
REVERT: R  257 SER cc_start: 0.8059 (m) cc_final: 0.7687 (m)
REVERT: R  293 MET cc_start: 0.7675 (mmt) cc_final: 0.7313 (mmm)
  outliers start: 13
  outliers final: 6
  residues processed: 115
  average time/residue: 0.2372
  time to fit residues: 36.9268
Evaluate side-chains
  102 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 96
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain R residue   97 LEU
Chi-restraints excluded: chain R residue  161 CYS
Chi-restraints excluded: chain S residue   96 CYS
Chi-restraints excluded: chain S residue  197 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 103 optimal weight:    9.9990
   chunk 95 optimal weight:    0.0370
   chunk 28 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 14 optimal weight:    5.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    5.9990
   chunk 108 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    0.9462

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

Flipped N/Q/H residues before XYZ refinement:
** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.186916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.149798 restraints weight = 11198.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.3798 rms_B_bonded: 1.98
r_work: 0.3526 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3400 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.1806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9106  Z= 0.171
  Angle     :  0.483  12.683  12324  Z= 0.252
  Chirality :  0.040   0.233   1412
  Planarity :  0.003   0.049   1550
  Dihedral  :  3.964  31.529   1294
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 11.77 %
    Favored  : 86.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.25), residues: 1129
  helix:  3.11 (0.25), residues: 398
  sheet:  0.36 (0.31), residues: 286
  loop : -1.24 (0.27), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 211 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.011   0.001   PHE A 189 
 TYR   0.012   0.001   TYR S 102 
 ARG   0.008   0.000   ARG S  67 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 1.322 
Fit side-chains
   revert: symmetry clash
REVERT: C   42 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7880 (mm-30)
REVERT: C   58 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7324 (mp0)
REVERT: R  257 SER cc_start: 0.8062 (m) cc_final: 0.7664 (m)
REVERT: R  293 MET cc_start: 0.7759 (mmt) cc_final: 0.7394 (mmm)
REVERT: S   67 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.5559 (tmm160)
REVERT: S  230 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.5555 (tmm)
  outliers start: 14
  outliers final: 7
  residues processed: 106
  average time/residue: 0.2583
  time to fit residues: 37.5005
Evaluate side-chains
  101 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue   97 LEU
Chi-restraints excluded: chain R residue  161 CYS
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   96 CYS
Chi-restraints excluded: chain S residue  197 SER
Chi-restraints excluded: chain S residue  230 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 107 optimal weight:    3.9990
   chunk 95 optimal weight:    2.9990
   chunk 97 optimal weight:    0.7980
   chunk 87 optimal weight:    9.9990
   chunk 71 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 88 optimal weight:    0.0040
   chunk 61 optimal weight:   20.0000
   chunk 80 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0980
   overall best weight:    0.7594

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

Flipped N/Q/H residues before XYZ refinement:
S 194 ASN
** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.187228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.152313 restraints weight = 11108.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3846 rms_B_bonded: 1.89
r_work: 0.3572 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3441 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.1915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9106  Z= 0.151
  Angle     :  0.467  12.603  12324  Z= 0.244
  Chirality :  0.040   0.241   1412
  Planarity :  0.003   0.048   1550
  Dihedral  :  3.907  31.298   1294
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 12.40 %
    Favored  : 86.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.25), residues: 1129
  helix:  3.09 (0.25), residues: 398
  sheet:  0.32 (0.30), residues: 291
  loop : -1.20 (0.27), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 211 
 HIS   0.007   0.001   HIS R  21 
 PHE   0.010   0.001   PHE A 189 
 TYR   0.013   0.001   TYR R  24 
 ARG   0.006   0.000   ARG S  67 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
REVERT: B   14 LEU cc_start: 0.6184 (OUTLIER) cc_final: 0.5942 (mt)
REVERT: B   43 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8123 (pt)
REVERT: C   42 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7824 (mm-30)
REVERT: C   58 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7344 (mp0)
REVERT: R  293 MET cc_start: 0.7602 (mmt) cc_final: 0.7231 (mmm)
REVERT: S   67 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.6055 (tmm160)
REVERT: S   83 MET cc_start: 0.7667 (mtm) cc_final: 0.7342 (mtp)
  outliers start: 14
  outliers final: 7
  residues processed: 108
  average time/residue: 0.3324
  time to fit residues: 48.0151
Evaluate side-chains
  103 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 1.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain R residue   97 LEU
Chi-restraints excluded: chain R residue  161 CYS
Chi-restraints excluded: chain R residue  221 LEU
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   96 CYS
Chi-restraints excluded: chain S residue  197 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 56 optimal weight:    7.9990
   chunk 110 optimal weight:    7.9990
   chunk 7 optimal weight:    0.9980
   chunk 25 optimal weight:    9.9990
   chunk 6 optimal weight:    0.9990
   chunk 79 optimal weight:    2.9990
   chunk 98 optimal weight:    5.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 232 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.181709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.140439 restraints weight = 11153.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3694 rms_B_bonded: 2.16
r_work: 0.3430 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3289 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.2298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9106  Z= 0.241
  Angle     :  0.537  13.151  12324  Z= 0.277
  Chirality :  0.041   0.262   1412
  Planarity :  0.004   0.049   1550
  Dihedral  :  4.288  33.703   1294
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 13.54 %
    Favored  : 84.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.25), residues: 1129
  helix:  2.91 (0.26), residues: 399
  sheet:  0.16 (0.30), residues: 290
  loop : -1.35 (0.26), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP S  36 
 HIS   0.007   0.001   HIS S  35 
 PHE   0.013   0.002   PHE A 189 
 TYR   0.011   0.001   TYR R 219 
 ARG   0.006   0.000   ARG S  67 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 1.005 
Fit side-chains
   revert: symmetry clash
REVERT: B   43 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.8073 (pt)
REVERT: C   42 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7787 (mm-30)
REVERT: C   58 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7380 (mp0)
REVERT: R  143 MET cc_start: 0.7642 (mmt) cc_final: 0.7270 (mmp)
REVERT: R  293 MET cc_start: 0.7527 (mmt) cc_final: 0.7164 (mmm)
REVERT: S    6 GLU cc_start: 0.7383 (mp0) cc_final: 0.7078 (mp0)
REVERT: S   67 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.6179 (tmm160)
REVERT: S  230 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6092 (tmm)
  outliers start: 19
  outliers final: 8
  residues processed: 112
  average time/residue: 0.2414
  time to fit residues: 36.6667
Evaluate side-chains
  103 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue   97 LEU
Chi-restraints excluded: chain R residue  161 CYS
Chi-restraints excluded: chain R residue  221 LEU
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   96 CYS
Chi-restraints excluded: chain S residue  197 SER
Chi-restraints excluded: chain S residue  230 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 106 optimal weight:    0.0000
   chunk 92 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 11 optimal weight:    7.9990
   chunk 95 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 57 optimal weight:    7.9990
   chunk 58 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    1.1788

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

Flipped N/Q/H residues before XYZ refinement:
** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.182526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.140923 restraints weight = 11247.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3701 rms_B_bonded: 2.26
r_work: 0.3441 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3299 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.2358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9106  Z= 0.197
  Angle     :  0.516  13.216  12324  Z= 0.266
  Chirality :  0.041   0.276   1412
  Planarity :  0.003   0.048   1550
  Dihedral  :  4.232  33.857   1294
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 14.38 %
    Favored  : 83.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.25), residues: 1129
  helix:  3.02 (0.25), residues: 393
  sheet:  0.13 (0.30), residues: 289
  loop : -1.28 (0.26), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP S  36 
 HIS   0.008   0.001   HIS R  21 
 PHE   0.011   0.001   PHE A 189 
 TYR   0.013   0.001   TYR R 219 
 ARG   0.006   0.000   ARG S  67 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.801 
Fit side-chains
   revert: symmetry clash
REVERT: B   43 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.8042 (pt)
REVERT: B  338 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8038 (mp)
REVERT: C   42 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7813 (mm-30)
REVERT: C   58 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7375 (mp0)
REVERT: R  143 MET cc_start: 0.7679 (mmt) cc_final: 0.7337 (mmp)
REVERT: R  293 MET cc_start: 0.7503 (mmt) cc_final: 0.7159 (mmp)
REVERT: S    6 GLU cc_start: 0.7335 (mp0) cc_final: 0.7121 (mp0)
REVERT: S   67 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.6246 (tmm160)
REVERT: S  230 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.5864 (tmm)
  outliers start: 16
  outliers final: 8
  residues processed: 106
  average time/residue: 0.2455
  time to fit residues: 35.5469
Evaluate side-chains
  106 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain R residue   97 LEU
Chi-restraints excluded: chain R residue  161 CYS
Chi-restraints excluded: chain R residue  221 LEU
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   96 CYS
Chi-restraints excluded: chain S residue  197 SER
Chi-restraints excluded: chain S residue  230 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 99 optimal weight:    1.9990
   chunk 29 optimal weight:    0.2980
   chunk 67 optimal weight:    0.9980
   chunk 32 optimal weight:    0.3980
   chunk 36 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9990
   chunk 102 optimal weight:    0.0970
   chunk 66 optimal weight:    0.8980
   chunk 52 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   overall best weight:    0.4978

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.186628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.145671 restraints weight = 11348.059|
|-----------------------------------------------------------------------------|
r_work (start): 0.3715 rms_B_bonded: 2.41
r_work: 0.3448 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9106  Z= 0.139
  Angle     :  0.485  12.962  12324  Z= 0.248
  Chirality :  0.040   0.288   1412
  Planarity :  0.003   0.047   1550
  Dihedral  :  3.967  31.449   1294
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 14.79 %
    Favored  : 83.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.25), residues: 1129
  helix:  3.13 (0.26), residues: 394
  sheet:  0.22 (0.30), residues: 287
  loop : -1.18 (0.27), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 211 
 HIS   0.006   0.001   HIS R  21 
 PHE   0.010   0.001   PHE A 189 
 TYR   0.011   0.001   TYR R 219 
 ARG   0.005   0.000   ARG S  67 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
REVERT: B  338 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.7860 (mp)
REVERT: C   42 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7774 (mm-30)
REVERT: R  293 MET cc_start: 0.7337 (mmt) cc_final: 0.6994 (mmp)
REVERT: S   67 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6099 (tmm160)
REVERT: S  230 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.5596 (tmm)
  outliers start: 14
  outliers final: 9
  residues processed: 112
  average time/residue: 0.2479
  time to fit residues: 37.3272
Evaluate side-chains
  107 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain R residue   97 LEU
Chi-restraints excluded: chain R residue  161 CYS
Chi-restraints excluded: chain R residue  221 LEU
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   96 CYS
Chi-restraints excluded: chain S residue  197 SER
Chi-restraints excluded: chain S residue  230 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 96 optimal weight:    0.7980
   chunk 111 optimal weight:    0.2980
   chunk 95 optimal weight:    0.9990
   chunk 9 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 98 optimal weight:    0.9990
   chunk 76 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.184231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.143441 restraints weight = 11051.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.3683 rms_B_bonded: 2.31
r_work: 0.3412 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9106  Z= 0.166
  Angle     :  0.510  13.287  12324  Z= 0.263
  Chirality :  0.041   0.295   1412
  Planarity :  0.003   0.048   1550
  Dihedral  :  3.976  31.558   1294
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 15.10 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.25), residues: 1129
  helix:  3.08 (0.25), residues: 393
  sheet:  0.19 (0.30), residues: 287
  loop : -1.14 (0.27), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 211 
 HIS   0.006   0.001   HIS R  21 
 PHE   0.010   0.001   PHE A 189 
 TYR   0.010   0.001   TYR R 219 
 ARG   0.005   0.000   ARG S  67 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 1.017 
Fit side-chains
   revert: symmetry clash
REVERT: A  309 ASP cc_start: 0.6762 (m-30) cc_final: 0.6489 (t0)
REVERT: B   43 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.8019 (pt)
REVERT: B  338 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.7894 (mp)
REVERT: C   42 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7769 (mm-30)
REVERT: R  293 MET cc_start: 0.7337 (mmt) cc_final: 0.6984 (mmp)
REVERT: S    6 GLU cc_start: 0.7045 (mp0) cc_final: 0.6804 (mp0)
REVERT: S   67 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.6098 (tmm160)
REVERT: S  230 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.5546 (tmm)
  outliers start: 16
  outliers final: 11
  residues processed: 106
  average time/residue: 0.2479
  time to fit residues: 35.6874
Evaluate side-chains
  108 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain R residue   97 LEU
Chi-restraints excluded: chain R residue  161 CYS
Chi-restraints excluded: chain R residue  221 LEU
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   96 CYS
Chi-restraints excluded: chain S residue  197 SER
Chi-restraints excluded: chain S residue  230 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 93 optimal weight:    0.0980
   chunk 95 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 77 optimal weight:    7.9990
   chunk 71 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 72 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0470
   overall best weight:    0.5880

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.185609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.144718 restraints weight = 11145.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.3709 rms_B_bonded: 2.19
r_work: 0.3448 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3308 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.2412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9106  Z= 0.150
  Angle     :  0.503  13.324  12324  Z= 0.257
  Chirality :  0.041   0.302   1412
  Planarity :  0.003   0.047   1550
  Dihedral  :  3.897  30.827   1294
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 15.10 %
    Favored  : 83.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.25), residues: 1129
  helix:  3.12 (0.26), residues: 393
  sheet:  0.20 (0.30), residues: 287
  loop : -1.11 (0.27), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 211 
 HIS   0.005   0.001   HIS R  21 
 PHE   0.010   0.001   PHE A 189 
 TYR   0.013   0.001   TYR R  24 
 ARG   0.004   0.000   ARG S  67 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
REVERT: A  309 ASP cc_start: 0.6817 (m-30) cc_final: 0.6537 (t0)
REVERT: B  338 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.7928 (mp)
REVERT: C   42 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7849 (mm-30)
REVERT: R  293 MET cc_start: 0.7507 (mmt) cc_final: 0.7148 (mmp)
REVERT: S    6 GLU cc_start: 0.7152 (mp0) cc_final: 0.6777 (mp0)
REVERT: S   67 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6023 (tmm160)
REVERT: S  230 MET cc_start: 0.7157 (OUTLIER) cc_final: 0.5743 (tmm)
  outliers start: 14
  outliers final: 11
  residues processed: 107
  average time/residue: 0.2372
  time to fit residues: 34.3549
Evaluate side-chains
  109 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain R residue   97 LEU
Chi-restraints excluded: chain R residue  161 CYS
Chi-restraints excluded: chain R residue  221 LEU
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   96 CYS
Chi-restraints excluded: chain S residue  197 SER
Chi-restraints excluded: chain S residue  230 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 99 optimal weight:    0.0670
   chunk 40 optimal weight:    1.9990
   chunk 65 optimal weight:   10.0000
   chunk 57 optimal weight:    8.9990
   chunk 67 optimal weight:    5.9990
   chunk 93 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9990
   chunk 89 optimal weight:    0.7980
   overall best weight:    0.9724

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

Flipped N/Q/H residues before XYZ refinement:
** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.183467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.142465 restraints weight = 11127.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3670 rms_B_bonded: 2.20
r_work: 0.3406 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3264 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.2524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9106  Z= 0.183
  Angle     :  0.519  13.165  12324  Z= 0.267
  Chirality :  0.041   0.310   1412
  Planarity :  0.003   0.048   1550
  Dihedral  :  4.010  32.015   1294
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 15.31 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.25), residues: 1129
  helix:  3.09 (0.26), residues: 393
  sheet:  0.26 (0.31), residues: 272
  loop : -1.14 (0.26), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 211 
 HIS   0.005   0.001   HIS R  21 
 PHE   0.010   0.001   PHE A 189 
 TYR   0.012   0.001   TYR R  24 
 ARG   0.005   0.000   ARG S  67 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5654.20 seconds
wall clock time: 101 minutes 2.19 seconds (6062.19 seconds total)