Starting phenix.real_space_refine
on Thu Mar 13 11:17:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yuu_39583/03_2025/8yuu_39583.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yuu_39583/03_2025/8yuu_39583.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yuu_39583/03_2025/8yuu_39583.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yuu_39583/03_2025/8yuu_39583.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yuu_39583/03_2025/8yuu_39583.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yuu_39583/03_2025/8yuu_39583.cif"
  }
  resolution = 2.7
  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=  -0.000 sd=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C    5762      2.51       5
     N    1537      2.21       5
     O    1678      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 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: 9037
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2344
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2344
          Classifications: {'peptide': 289}
          Link IDs: {'PTRANS': 9, 'TRANS': 279}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1811
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 2, 'TRANS': 222}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2607
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
    Chain: "G"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 444
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "S"
      Number of atoms: 1795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1795
          Classifications: {'peptide': 234}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 36
          Unusual residues: {'CLR': 1, 'HSM': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.52, per 1000 atoms: 0.61
  Number of scatterers: 9037
  At special positions: 0
  Unit cell: (106.47, 121.68, 115.596, 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      60     16.00
     O    1678      8.00
     N    1537      7.00
     C    5762      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 107 " - pdb=" SG  CYS R 188 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 384 " - pdb=" SG  CYS R 388 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.04

  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: 2.27
  Conformation dependent library (CDL) restraints added in 976.8 milliseconds
  

  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:  2142

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 14 sheets defined
      41.7% alpha, 24.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'R' and resid 33 through 62
      removed outlier: 3.502A  pdb=" N   LEU R  37 " --> pdb=" O   TRP R  33 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   VAL R  49 " --> pdb=" O   ILE R  45 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 67 through 86
    Processing helix  chain 'R' and resid 86 through 98
      Proline residue:  R  93  - end of helix
    Processing helix  chain 'R' and resid 106 through 138
      removed outlier: 3.782A  pdb=" N   VAL R 136 " --> pdb=" O   ARG R 132 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   THR R 137 " --> pdb=" O   PHE R 133 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 138 through 146
    Processing helix  chain 'R' and resid 149 through 173
      removed outlier: 3.911A  pdb=" N   TYR R 167 " --> pdb=" O   ALA R 163 " (cutoff:3.500A)
      Proline residue:  R 169  - end of helix
    Processing helix  chain 'R' and resid 174 through 179
    Processing helix  chain 'R' and resid 195 through 207
      removed outlier: 3.713A  pdb=" N   LEU R 199 " --> pdb=" O   ASN R 195 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 207 through 235
    Processing helix  chain 'R' and resid 344 through 384
      Proline residue:  R 373  - end of helix
    Processing helix  chain 'R' and resid 390 through 416
      removed outlier: 3.542A  pdb=" N   TYR R 394 " --> pdb=" O   PRO R 390 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LEU R 401 " --> pdb=" O   SER R 397 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   TRP R 402 " --> pdb=" O   PHE R 398 " (cutoff:3.500A)
      Proline residue:  R 409  - end of helix
      Proline residue:  R 413  - end of helix
    Processing helix  chain 'R' and resid 416 through 427
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.839A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.729A  pdb=" N   LYS A 210 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.627A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 232
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 4.125A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 4.329A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.640A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 3 through 25
      removed outlier: 3.572A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 6 through 24
      removed outlier: 3.592A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.568A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 62 through 65
    Processing helix  chain 'S' and resid 87 through 91
    Processing helix  chain 'S' and resid 220 through 224
      removed outlier: 3.611A  pdb=" N   VAL S 224 " --> pdb=" O   ALA S 221 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 3.604A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.323A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.234A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.428A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.568A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.906A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.034A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.060A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.219A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.852A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.033A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.804A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.175A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.437A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.758A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.973A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.221A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.486A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   MET B 217 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.423A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.803A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.672A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.045A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.045A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141
    Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148
      removed outlier: 4.944A  pdb=" N   LEU S 174 " --> pdb=" O   TYR S 190 " (cutoff:3.500A)
      removed outlier: 4.974A  pdb=" N   TYR S 190 " --> pdb=" O   LEU S 174 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   TRP S 176 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   ARG S 191 " --> pdb=" O   ASN S 194 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148
      removed outlier: 4.023A  pdb=" N   THR S 238 " --> pdb=" O   GLN S 231 " (cutoff:3.500A)

    486 hydrogen bonds defined for protein.
    1341 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: 3.13

  Time building geometry restraints manager: 2.72 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: 2068
        1.33 -     1.45: 2075
        1.45 -     1.57: 5004
        1.57 -     1.69: 5
        1.69 -     1.82: 85
  Bond restraints: 9237
  Sorted by residual:
  bond pdb=" CA  TYR A 296 "
       pdb=" C   TYR A 296 "
    ideal  model  delta    sigma   weight residual
    1.523  1.483  0.040 1.30e-02 5.92e+03 9.62e+00
  bond pdb=" C23 CLR R 502 "
       pdb=" C24 CLR R 502 "
    ideal  model  delta    sigma   weight residual
    1.525  1.578 -0.053 2.00e-02 2.50e+03 6.98e+00
  bond pdb=" C16 CLR R 502 "
       pdb=" C17 CLR R 502 "
    ideal  model  delta    sigma   weight residual
    1.554  1.607 -0.053 2.00e-02 2.50e+03 6.90e+00
  bond pdb=" CA  ALA R  53 "
       pdb=" C   ALA R  53 "
    ideal  model  delta    sigma   weight residual
    1.524  1.492  0.032 1.27e-02 6.20e+03 6.29e+00
  bond pdb=" C   GLN S  13 "
       pdb=" N   PRO S  14 "
    ideal  model  delta    sigma   weight residual
    1.332  1.364 -0.032 1.30e-02 5.92e+03 6.06e+00
  ... (remaining 9232 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.11: 12137
        2.11 -     4.21: 319
        4.21 -     6.32: 48
        6.32 -     8.43: 10
        8.43 -    10.54: 6
  Bond angle restraints: 12520
  Sorted by residual:
  angle pdb=" N   ASP B  76 "
        pdb=" CA  ASP B  76 "
        pdb=" C   ASP B  76 "
      ideal   model   delta    sigma   weight residual
     112.92  102.38   10.54 1.23e+00 6.61e-01 7.34e+01
  angle pdb=" N   GLY S 114 "
        pdb=" CA  GLY S 114 "
        pdb=" C   GLY S 114 "
      ideal   model   delta    sigma   weight residual
     112.18  122.53  -10.35 1.34e+00 5.57e-01 5.97e+01
  angle pdb=" N   LEU R 172 "
        pdb=" CA  LEU R 172 "
        pdb=" C   LEU R 172 "
      ideal   model   delta    sigma   weight residual
     111.07  117.03   -5.96 1.07e+00 8.73e-01 3.10e+01
  angle pdb=" N   GLY B 282 "
        pdb=" CA  GLY B 282 "
        pdb=" C   GLY B 282 "
      ideal   model   delta    sigma   weight residual
     115.27  107.68    7.59 1.41e+00 5.03e-01 2.90e+01
  angle pdb=" N   LYS B  78 "
        pdb=" CA  LYS B  78 "
        pdb=" C   LYS B  78 "
      ideal   model   delta    sigma   weight residual
     109.50  117.94   -8.44 1.58e+00 4.01e-01 2.85e+01
  ... (remaining 12515 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 5237
       17.99 -    35.97: 229
       35.97 -    53.96: 22
       53.96 -    71.94: 5
       71.94 -    89.93: 6
  Dihedral angle restraints: 5499
    sinusoidal: 2176
      harmonic: 3323
  Sorted by residual:
  dihedral pdb=" N   SER S 193 "
           pdb=" C   SER S 193 "
           pdb=" CA  SER S 193 "
           pdb=" CB  SER S 193 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  131.92   -9.12     0      2.50e+00 1.60e-01 1.33e+01
  dihedral pdb=" CA  SER S 208 "
           pdb=" C   SER S 208 "
           pdb=" N   GLY S 209 "
           pdb=" CA  GLY S 209 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.52   17.48     0      5.00e+00 4.00e-02 1.22e+01
  dihedral pdb=" C   SER S 193 "
           pdb=" N   SER S 193 "
           pdb=" CA  SER S 193 "
           pdb=" CB  SER S 193 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.11    8.51     0      2.50e+00 1.60e-01 1.16e+01
  ... (remaining 5496 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 1187
       0.075 -    0.150: 184
       0.150 -    0.225: 24
       0.225 -    0.300: 11
       0.300 -    0.375: 2
  Chirality restraints: 1408
  Sorted by residual:
  chirality pdb=" CA  SER S 193 "
            pdb=" N   SER S 193 "
            pdb=" C   SER S 193 "
            pdb=" CB  SER S 193 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.51e+00
  chirality pdb=" C13 CLR R 502 "
            pdb=" C12 CLR R 502 "
            pdb=" C14 CLR R 502 "
            pdb=" C17 CLR R 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -3.24    0.31 2.00e-01 2.50e+01 2.36e+00
  chirality pdb=" C17 CLR R 502 "
            pdb=" C13 CLR R 502 "
            pdb=" C16 CLR R 502 "
            pdb=" C20 CLR R 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.85   -0.30 2.00e-01 2.50e+01 2.23e+00
  ... (remaining 1405 not shown)

  Planarity restraints: 1577
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B  75 "    0.018 2.00e-02 2.50e+03   3.60e-02 1.30e+01
        pdb=" C   GLN B  75 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   GLN B  75 "    0.023 2.00e-02 2.50e+03
        pdb=" N   ASP B  76 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS S  35 "   -0.012 2.00e-02 2.50e+03   2.45e-02 5.98e+00
        pdb=" C   HIS S  35 "    0.042 2.00e-02 2.50e+03
        pdb=" O   HIS S  35 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   TRP S  36 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR S 190 "    0.012 2.00e-02 2.50e+03   2.40e-02 5.76e+00
        pdb=" C   TYR S 190 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   TYR S 190 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ARG S 191 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1574 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 77
        2.64 -     3.21: 8124
        3.21 -     3.77: 13503
        3.77 -     4.34: 19935
        4.34 -     4.90: 33421
  Nonbonded interactions: 75060
  Sorted by model distance:
  nonbonded pdb=" O   THR B  86 "
            pdb=" OG1 THR B  87 "
     model   vdw
     2.076 3.040
  nonbonded pdb=" O   CYS A   3 "
            pdb=" OG1 THR A   4 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" O   ASP B 154 "
            pdb=" OD1 ASP B 154 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" O   GLY A 352 "
            pdb=" N   PHE A 354 "
     model   vdw
     2.258 3.120
  nonbonded pdb=" OD1 ASP R  62 "
            pdb=" OG  SER R  64 "
     model   vdw
     2.315 3.040
  ... (remaining 75055 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:             3.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.830
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  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:             0.010
  Load rotamer database and sin/cos tables:54.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   81.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   9237  Z= 0.338
  Angle     :  0.834  10.537  12520  Z= 0.527
  Chirality :  0.059   0.375   1408
  Planarity :  0.004   0.053   1577
  Dihedral  : 10.474  89.929   3345
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.48 (0.26), residues: 1129
  helix:  2.09 (0.26), residues: 418
  sheet:  1.03 (0.30), residues: 286
  loop : -0.12 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 211 
 HIS   0.007   0.001   HIS B  91 
 PHE   0.017   0.002   PHE B 199 
 TYR   0.014   0.002   TYR S 103 
 ARG   0.005   0.001   ARG S  72 

*********************** 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
  188 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  197 TYR cc_start: 0.6279 (m-80) cc_final: 0.6078 (m-10)
REVERT: R  354 ARG cc_start: 0.6585 (ttt180) cc_final: 0.5941 (ttp-110)
REVERT: A   47 ASN cc_start: 0.7235 (m-40) cc_final: 0.6777 (p0)
REVERT: A  228 SER cc_start: 0.7781 (p) cc_final: 0.6761 (m)
REVERT: A  306 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7758 (mp10)
REVERT: B  254 ASP cc_start: 0.7427 (t70) cc_final: 0.7188 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 188
  average time/residue: 1.3305
  time to fit residues: 266.1433
Evaluate side-chains
  138 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.0670
   chunk 84 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0570
   chunk 28 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 87 optimal weight:    0.0770
   chunk 33 optimal weight:    6.9990
   chunk 52 optimal weight:    8.9990
   chunk 64 optimal weight:    0.4980
   chunk 100 optimal weight:    7.9990
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.174485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.114558 restraints weight = 9420.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 2.04
r_work: 0.3101 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2965 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.1758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.061   9237  Z= 0.153
  Angle     :  0.526   8.862  12520  Z= 0.285
  Chirality :  0.041   0.171   1408
  Planarity :  0.004   0.043   1577
  Dihedral  :  5.421  77.184   1314
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 10.14 %
    Favored  : 87.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.89 (0.25), residues: 1129
  helix:  2.76 (0.25), residues: 419
  sheet:  0.98 (0.29), residues: 278
  loop : -0.05 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.002   0.001   HIS S  35 
 PHE   0.017   0.001   PHE R 192 
 TYR   0.010   0.001   TYR R 189 
 ARG   0.011   0.000   ARG R  99 

*********************** 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
  162 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  376 LEU cc_start: 0.7998 (mm) cc_final: 0.7730 (mm)
REVERT: A   47 ASN cc_start: 0.7037 (m-40) cc_final: 0.6369 (p0)
REVERT: A   53 MET cc_start: 0.7089 (OUTLIER) cc_final: 0.6771 (mmm)
REVERT: A  197 LYS cc_start: 0.8954 (mttt) cc_final: 0.8585 (mttm)
REVERT: A  273 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7958 (mm)
REVERT: A  306 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7670 (mp10)
REVERT: B   44 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8012 (mt0)
REVERT: B  134 ARG cc_start: 0.8242 (mtm110) cc_final: 0.7943 (ptp90)
REVERT: B  325 MET cc_start: 0.8912 (mmt) cc_final: 0.8351 (tpp)
REVERT: G   46 LYS cc_start: 0.8339 (mttt) cc_final: 0.8020 (mmtm)
REVERT: S   85 SER cc_start: 0.8881 (m) cc_final: 0.8384 (t)
  outliers start: 22
  outliers final: 5
  residues processed: 149
  average time/residue: 1.4313
  time to fit residues: 226.2925
Evaluate side-chains
  137 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 129
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   56 MET
Chi-restraints excluded: chain R residue   95 VAL
Chi-restraints excluded: chain R residue  392 TYR
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain S residue  158 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 25 optimal weight:    8.9990
   chunk 20 optimal weight:   20.0000
   chunk 10 optimal weight:    6.9990
   chunk 18 optimal weight:    0.8980
   chunk 91 optimal weight:    0.3980
   chunk 64 optimal weight:    3.9990
   chunk 102 optimal weight:   20.0000
   chunk 9 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 71 optimal weight:    8.9990
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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 = 0.3955 r_free = 0.3955 target = 0.174403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.119553 restraints weight = 9560.604|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 2.11
r_work: 0.3089 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.1979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9237  Z= 0.188
  Angle     :  0.533   8.406  12520  Z= 0.284
  Chirality :  0.042   0.169   1408
  Planarity :  0.004   0.038   1577
  Dihedral  :  5.326  72.699   1314
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.04 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 10.25 %
    Favored  : 86.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.88 (0.25), residues: 1129
  helix:  2.93 (0.25), residues: 413
  sheet:  0.86 (0.29), residues: 279
  loop : -0.12 (0.30), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B  91 
 PHE   0.017   0.001   PHE R 192 
 TYR   0.011   0.001   TYR S 103 
 ARG   0.006   0.000   ARG R 154 

*********************** 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
  158 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 130
  time to evaluate  : 1.029 
Fit side-chains
   revert: symmetry clash
REVERT: R  161 VAL cc_start: 0.7212 (t) cc_final: 0.7009 (m)
REVERT: R  376 LEU cc_start: 0.8294 (mm) cc_final: 0.7985 (mm)
REVERT: A  194 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.8014 (tp)
REVERT: A  197 LYS cc_start: 0.8983 (mttt) cc_final: 0.8638 (mttm)
REVERT: A  207 GLU cc_start: 0.7145 (tp30) cc_final: 0.6197 (mt-10)
REVERT: A  248 LYS cc_start: 0.8034 (mtmm) cc_final: 0.7808 (mtpt)
REVERT: A  306 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7712 (mp10)
REVERT: B   44 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8015 (mt0)
REVERT: B  134 ARG cc_start: 0.8260 (mtm110) cc_final: 0.7969 (ptp90)
REVERT: B  153 ASP cc_start: 0.7762 (t0) cc_final: 0.7539 (t70)
REVERT: B  212 ASP cc_start: 0.8256 (t0) cc_final: 0.7970 (t0)
REVERT: G   46 LYS cc_start: 0.8378 (mttt) cc_final: 0.8059 (mmtm)
REVERT: S   85 SER cc_start: 0.8924 (m) cc_final: 0.8447 (t)
  outliers start: 28
  outliers final: 13
  residues processed: 143
  average time/residue: 1.3379
  time to fit residues: 203.4559
Evaluate side-chains
  134 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   63 SER
Chi-restraints excluded: chain R residue  159 VAL
Chi-restraints excluded: chain R residue  233 LEU
Chi-restraints excluded: chain R residue  392 TYR
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain S residue   23 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  245 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 5 optimal weight:    0.3980
   chunk 62 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 2 optimal weight:    7.9990
   chunk 47 optimal weight:    3.9990
   chunk 14 optimal weight:    7.9990
   chunk 65 optimal weight:    0.6980
   chunk 50 optimal weight:    7.9990
   chunk 89 optimal weight:    1.9990
   chunk 109 optimal weight:    5.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
S 186 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.172328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.117178 restraints weight = 9497.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 1.99
r_work: 0.3073 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2942 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.2141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9237  Z= 0.182
  Angle     :  0.519   8.997  12520  Z= 0.274
  Chirality :  0.041   0.162   1408
  Planarity :  0.004   0.038   1577
  Dihedral  :  5.076  61.165   1314
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.04 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 11.89 %
    Favored  : 85.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.88 (0.25), residues: 1129
  helix:  3.01 (0.25), residues: 412
  sheet:  0.79 (0.29), residues: 279
  loop : -0.17 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.018   0.001   PHE R 192 
 TYR   0.013   0.001   TYR S 190 
 ARG   0.006   0.000   ARG B 219 

*********************** 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
  152 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 125
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 ARG cc_start: 0.7976 (mtm-85) cc_final: 0.7527 (ttm-80)
REVERT: A  197 LYS cc_start: 0.8972 (mttt) cc_final: 0.8594 (mttm)
REVERT: A  248 LYS cc_start: 0.7999 (mtmm) cc_final: 0.7779 (mtpt)
REVERT: A  306 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7671 (mp10)
REVERT: B   44 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7983 (mt0)
REVERT: B  134 ARG cc_start: 0.8275 (mtm110) cc_final: 0.7988 (ptp90)
REVERT: B  212 ASP cc_start: 0.8195 (t0) cc_final: 0.7960 (t0)
REVERT: B  217 MET cc_start: 0.7669 (ptt) cc_final: 0.7348 (ppp)
REVERT: G   46 LYS cc_start: 0.8366 (mttt) cc_final: 0.8067 (mmtm)
REVERT: S   85 SER cc_start: 0.8978 (m) cc_final: 0.8460 (t)
  outliers start: 27
  outliers final: 14
  residues processed: 141
  average time/residue: 1.2929
  time to fit residues: 194.5156
Evaluate side-chains
  134 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   95 VAL
Chi-restraints excluded: chain R residue  157 LEU
Chi-restraints excluded: chain R residue  159 VAL
Chi-restraints excluded: chain R residue  392 TYR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue   23 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  245 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 30 optimal weight:    0.0670
   chunk 104 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0980
   chunk 51 optimal weight:    9.9990
   chunk 74 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 77 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.7720

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

Flipped N/Q/H residues before XYZ refinement:
S 186 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.173403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.118524 restraints weight = 9469.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 1.96
r_work: 0.3085 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2954 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.2340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   9237  Z= 0.139
  Angle     :  0.483   7.846  12520  Z= 0.256
  Chirality :  0.040   0.159   1408
  Planarity :  0.003   0.038   1577
  Dihedral  :  4.551  37.182   1314
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.04 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 12.81 %
    Favored  : 84.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.95 (0.25), residues: 1129
  helix:  3.12 (0.25), residues: 413
  sheet:  0.77 (0.29), residues: 279
  loop : -0.15 (0.30), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.013   0.001   PHE R 192 
 TYR   0.012   0.001   TYR S 190 
 ARG   0.004   0.000   ARG R 154 

*********************** 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
  153 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 131
  time to evaluate  : 1.057 
Fit side-chains
   revert: symmetry clash
REVERT: R  378 MET cc_start: 0.6382 (ttp) cc_final: 0.6131 (tpp)
REVERT: A   24 ARG cc_start: 0.7812 (mtm-85) cc_final: 0.7356 (ttm-80)
REVERT: A  197 LYS cc_start: 0.8964 (mttt) cc_final: 0.8555 (mttp)
REVERT: A  207 GLU cc_start: 0.6931 (tp30) cc_final: 0.5980 (mt-10)
REVERT: A  248 LYS cc_start: 0.7859 (mtmm) cc_final: 0.7640 (mtpt)
REVERT: A  306 GLN cc_start: 0.7827 (mm-40) cc_final: 0.7487 (mp10)
REVERT: B   44 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7933 (mt0)
REVERT: B  134 ARG cc_start: 0.8221 (mtm110) cc_final: 0.7993 (ptp90)
REVERT: B  153 ASP cc_start: 0.7753 (t0) cc_final: 0.7518 (t70)
REVERT: B  212 ASP cc_start: 0.8125 (t0) cc_final: 0.7919 (t0)
REVERT: B  217 MET cc_start: 0.7525 (ptt) cc_final: 0.7129 (ppp)
REVERT: B  219 ARG cc_start: 0.8373 (mtp180) cc_final: 0.7606 (mmm160)
REVERT: G   46 LYS cc_start: 0.8299 (mttt) cc_final: 0.7959 (mmtt)
REVERT: S   85 SER cc_start: 0.8990 (m) cc_final: 0.8446 (t)
  outliers start: 22
  outliers final: 9
  residues processed: 143
  average time/residue: 1.3287
  time to fit residues: 202.7864
Evaluate side-chains
  135 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 125
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  159 VAL
Chi-restraints excluded: chain R residue  233 LEU
Chi-restraints excluded: chain R residue  392 TYR
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue  158 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 77 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 93 optimal weight:    0.2980
   chunk 102 optimal weight:   20.0000
   chunk 40 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 53 optimal weight:    0.0070
   chunk 55 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   chunk 90 optimal weight:    6.9990
   chunk 5 optimal weight:    0.3980
   overall best weight:    1.3402

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

Flipped N/Q/H residues before XYZ refinement:
S 186 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.171500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.116531 restraints weight = 9448.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 2.12
r_work: 0.3081 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2948 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.2317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9237  Z= 0.190
  Angle     :  0.514   9.465  12520  Z= 0.271
  Chirality :  0.041   0.168   1408
  Planarity :  0.004   0.039   1577
  Dihedral  :  4.505  28.913   1314
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.04 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 13.32 %
    Favored  : 83.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.89 (0.25), residues: 1129
  helix:  3.07 (0.25), residues: 413
  sheet:  0.71 (0.29), residues: 278
  loop : -0.15 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.020   0.001   PHE R 192 
 TYR   0.016   0.001   TYR S 190 
 ARG   0.003   0.000   ARG R 154 

*********************** 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
  156 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 126
  time to evaluate  : 1.000 
Fit side-chains
   revert: symmetry clash
REVERT: R  378 MET cc_start: 0.6435 (ttp) cc_final: 0.6204 (tpp)
REVERT: A   24 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7472 (ttm-80)
REVERT: A  197 LYS cc_start: 0.8990 (mttt) cc_final: 0.8618 (mttp)
REVERT: A  248 LYS cc_start: 0.7932 (mtmm) cc_final: 0.7716 (mtpt)
REVERT: A  306 GLN cc_start: 0.7949 (mm-40) cc_final: 0.7606 (mp10)
REVERT: B   44 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7979 (mt0)
REVERT: B  134 ARG cc_start: 0.8280 (mtm110) cc_final: 0.8041 (ptp90)
REVERT: B  153 ASP cc_start: 0.7836 (t0) cc_final: 0.7622 (t70)
REVERT: B  212 ASP cc_start: 0.8193 (t0) cc_final: 0.7949 (t0)
REVERT: G   46 LYS cc_start: 0.8381 (mttt) cc_final: 0.8019 (mmtt)
REVERT: S   85 SER cc_start: 0.9012 (m) cc_final: 0.8488 (t)
  outliers start: 30
  outliers final: 15
  residues processed: 143
  average time/residue: 1.3148
  time to fit residues: 200.3328
Evaluate side-chains
  136 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   63 SER
Chi-restraints excluded: chain R residue  159 VAL
Chi-restraints excluded: chain R residue  233 LEU
Chi-restraints excluded: chain R residue  392 TYR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue   23 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  245 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 83 optimal weight:    9.9990
   chunk 77 optimal weight:    0.8980
   chunk 50 optimal weight:    8.9990
   chunk 21 optimal weight:    6.9990
   chunk 70 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 107 optimal weight:    4.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
S 186 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.172497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.111560 restraints weight = 9523.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 2.03
r_work: 0.3028 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2893 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.2344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9237  Z= 0.208
  Angle     :  0.524  10.010  12520  Z= 0.277
  Chirality :  0.042   0.163   1408
  Planarity :  0.004   0.039   1577
  Dihedral  :  4.500  29.342   1314
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.30 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 13.32 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.83 (0.25), residues: 1129
  helix:  3.05 (0.25), residues: 412
  sheet:  0.69 (0.29), residues: 278
  loop : -0.20 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP S  47 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.014   0.001   PHE R 192 
 TYR   0.017   0.001   TYR S 190 
 ARG   0.003   0.000   ARG R 143 

*********************** 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
  151 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 122
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
REVERT: R  376 LEU cc_start: 0.8050 (mm) cc_final: 0.7725 (mm)
REVERT: R  378 MET cc_start: 0.6380 (ttp) cc_final: 0.6176 (tpp)
REVERT: A   24 ARG cc_start: 0.7802 (mtm-85) cc_final: 0.7357 (ttm-80)
REVERT: A  197 LYS cc_start: 0.8984 (mttt) cc_final: 0.8602 (mttp)
REVERT: A  208 ARG cc_start: 0.8149 (ttm110) cc_final: 0.7917 (ttm110)
REVERT: A  231 ASP cc_start: 0.7118 (p0) cc_final: 0.6916 (p0)
REVERT: A  248 LYS cc_start: 0.7902 (mtmm) cc_final: 0.7680 (mtpt)
REVERT: A  306 GLN cc_start: 0.7926 (mm-40) cc_final: 0.7510 (mp10)
REVERT: B   44 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7961 (mt0)
REVERT: B  134 ARG cc_start: 0.8286 (mtm110) cc_final: 0.8011 (ptp90)
REVERT: B  212 ASP cc_start: 0.8189 (t0) cc_final: 0.7864 (t0)
REVERT: B  219 ARG cc_start: 0.8574 (mtp180) cc_final: 0.8183 (mtp85)
REVERT: G   46 LYS cc_start: 0.8380 (mttt) cc_final: 0.7999 (mmtt)
REVERT: S   85 SER cc_start: 0.9003 (m) cc_final: 0.8478 (t)
REVERT: S  183 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8192 (mt0)
  outliers start: 29
  outliers final: 17
  residues processed: 138
  average time/residue: 1.2432
  time to fit residues: 183.1610
Evaluate side-chains
  140 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 121
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   63 SER
Chi-restraints excluded: chain R residue  159 VAL
Chi-restraints excluded: chain R residue  233 LEU
Chi-restraints excluded: chain R residue  392 TYR
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue   23 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  183 GLN
Chi-restraints excluded: chain S residue  245 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 95 optimal weight:    3.9990
   chunk 105 optimal weight:    0.6980
   chunk 94 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 104 optimal weight:    0.8980
   chunk 11 optimal weight:    7.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
S 186 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.174686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.114235 restraints weight = 9614.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 2.05
r_work: 0.3049 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2915 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.2476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   9237  Z= 0.146
  Angle     :  0.486  10.123  12520  Z= 0.256
  Chirality :  0.041   0.159   1408
  Planarity :  0.003   0.040   1577
  Dihedral  :  4.360  30.106   1314
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.13 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 14.86 %
    Favored  : 83.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.92 (0.25), residues: 1129
  helix:  3.15 (0.25), residues: 410
  sheet:  0.73 (0.29), residues: 276
  loop : -0.18 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.018   0.001   PHE R 192 
 TYR   0.015   0.001   TYR S 190 
 ARG   0.003   0.000   ARG R 154 

*********************** 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
  143 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  378 MET cc_start: 0.6440 (ttp) cc_final: 0.6238 (tpp)
REVERT: A   24 ARG cc_start: 0.7875 (mtm-85) cc_final: 0.7521 (ttm-80)
REVERT: A  197 LYS cc_start: 0.8999 (mttt) cc_final: 0.8635 (mttp)
REVERT: A  208 ARG cc_start: 0.8201 (ttm110) cc_final: 0.7997 (ttm110)
REVERT: A  248 LYS cc_start: 0.7966 (mtmm) cc_final: 0.7748 (mtpt)
REVERT: A  306 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7653 (mp10)
REVERT: B   65 THR cc_start: 0.8887 (m) cc_final: 0.8614 (p)
REVERT: B  134 ARG cc_start: 0.8320 (mtm110) cc_final: 0.7551 (ptt-90)
REVERT: B  212 ASP cc_start: 0.8141 (t0) cc_final: 0.7921 (t0)
REVERT: B  219 ARG cc_start: 0.8573 (mtp180) cc_final: 0.7981 (mmm160)
REVERT: G   46 LYS cc_start: 0.8371 (mttt) cc_final: 0.8008 (mmtt)
REVERT: S   85 SER cc_start: 0.9018 (m) cc_final: 0.8515 (t)
REVERT: S  183 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8144 (mt0)
  outliers start: 19
  outliers final: 13
  residues processed: 136
  average time/residue: 1.3152
  time to fit residues: 190.3930
Evaluate side-chains
  133 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   63 SER
Chi-restraints excluded: chain R residue  159 VAL
Chi-restraints excluded: chain R residue  233 LEU
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue   23 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  183 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 110 optimal weight:    0.9980
   chunk 91 optimal weight:    4.9990
   chunk 39 optimal weight:    9.9990
   chunk 27 optimal weight:    0.9980
   chunk 7 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9980
   chunk 86 optimal weight:    4.9990
   chunk 25 optimal weight:    6.9990
   chunk 32 optimal weight:    9.9990
   chunk 102 optimal weight:   20.0000
   overall best weight:    1.7984

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

Flipped N/Q/H residues before XYZ refinement:
S 186 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.172664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.111758 restraints weight = 9460.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 2.03
r_work: 0.3067 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.2397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9237  Z= 0.232
  Angle     :  0.538  10.338  12520  Z= 0.283
  Chirality :  0.043   0.177   1408
  Planarity :  0.004   0.039   1577
  Dihedral  :  4.546  29.687   1314
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.21 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 15.06 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.82 (0.25), residues: 1129
  helix:  3.05 (0.25), residues: 411
  sheet:  0.70 (0.29), residues: 276
  loop : -0.23 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP S  47 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.014   0.002   PHE R 192 
 TYR   0.018   0.002   TYR S 190 
 ARG   0.002   0.000   ARG B 314 

*********************** 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
  139 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 117
  time to evaluate  : 1.085 
Fit side-chains
   revert: symmetry clash
REVERT: A  197 LYS cc_start: 0.8996 (mttt) cc_final: 0.8648 (mttp)
REVERT: A  208 ARG cc_start: 0.8244 (ttm110) cc_final: 0.8033 (ttm110)
REVERT: A  248 LYS cc_start: 0.8013 (mtmm) cc_final: 0.7787 (mtpt)
REVERT: A  306 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7668 (mp10)
REVERT: B   65 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8666 (p)
REVERT: B  134 ARG cc_start: 0.8339 (mtm110) cc_final: 0.8064 (ptp90)
REVERT: B  212 ASP cc_start: 0.8209 (t0) cc_final: 0.7920 (t0)
REVERT: B  219 ARG cc_start: 0.8670 (mtp180) cc_final: 0.8073 (mmm160)
REVERT: G   46 LYS cc_start: 0.8408 (mttt) cc_final: 0.8033 (mmtt)
REVERT: S   85 SER cc_start: 0.9040 (m) cc_final: 0.8532 (t)
REVERT: S  183 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8241 (mt0)
  outliers start: 22
  outliers final: 14
  residues processed: 130
  average time/residue: 1.3425
  time to fit residues: 185.4297
Evaluate side-chains
  131 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   63 SER
Chi-restraints excluded: chain R residue  159 VAL
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue   23 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  183 GLN
Chi-restraints excluded: chain S residue  245 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 44 optimal weight:    0.6980
   chunk 101 optimal weight:   20.0000
   chunk 21 optimal weight:    8.9990
   chunk 97 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 76 optimal weight:    0.3980
   chunk 89 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 79 optimal weight:    0.6980
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
S 186 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.173207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.112694 restraints weight = 9521.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.3206 rms_B_bonded: 2.02
r_work: 0.3069 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2937 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.2460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9237  Z= 0.191
  Angle     :  0.520  10.425  12520  Z= 0.274
  Chirality :  0.042   0.161   1408
  Planarity :  0.004   0.039   1577
  Dihedral  :  4.515  30.016   1314
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.30 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 15.98 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.85 (0.25), residues: 1129
  helix:  3.11 (0.25), residues: 411
  sheet:  0.70 (0.29), residues: 276
  loop : -0.24 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.019   0.001   PHE R 192 
 TYR   0.018   0.001   TYR S 190 
 ARG   0.010   0.000   ARG A 313 

********************** 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
  135 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 1.082 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 ARG cc_start: 0.7903 (ttm-80) cc_final: 0.7548 (ttm-80)
REVERT: A  197 LYS cc_start: 0.8969 (mttt) cc_final: 0.8587 (mttm)
REVERT: A  208 ARG cc_start: 0.8179 (ttm110) cc_final: 0.7975 (ttm110)
REVERT: A  248 LYS cc_start: 0.7965 (mtmm) cc_final: 0.7744 (mtpt)
REVERT: A  277 LYS cc_start: 0.8509 (ttpt) cc_final: 0.8210 (ttpt)
REVERT: A  306 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7598 (mp10)
REVERT: B   65 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8625 (p)
REVERT: B  134 ARG cc_start: 0.8326 (mtm110) cc_final: 0.7495 (ptt-90)
REVERT: B  212 ASP cc_start: 0.8171 (t0) cc_final: 0.7915 (t0)
REVERT: B  219 ARG cc_start: 0.8599 (mtp180) cc_final: 0.7995 (mmm160)
REVERT: G   46 LYS cc_start: 0.8395 (mttt) cc_final: 0.8010 (mmtt)
REVERT: S   85 SER cc_start: 0.9014 (m) cc_final: 0.8536 (t)
REVERT: S  183 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8202 (mt0)
  outliers start: 18
  outliers final: 14
  residues processed: 127
  average time/residue: 1.4045
  time to fit residues: 190.0795
Evaluate side-chains
  133 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   63 SER
Chi-restraints excluded: chain R residue  159 VAL
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue   23 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  183 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 11 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 38 optimal weight:    9.9990
   chunk 24 optimal weight:    3.9990
   chunk 89 optimal weight:    0.9990
   chunk 53 optimal weight:    0.2980
   chunk 16 optimal weight:    2.9990
   chunk 48 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0970
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
S 186 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.174134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.113984 restraints weight = 9530.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 2.01
r_work: 0.2989 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2851 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.2534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9237  Z= 0.165
  Angle     :  0.503  10.491  12520  Z= 0.265
  Chirality :  0.041   0.157   1408
  Planarity :  0.004   0.040   1577
  Dihedral  :  4.428  30.756   1314
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 16.19 %
    Favored  : 82.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  1.90 (0.25), residues: 1129
  helix:  3.16 (0.25), residues: 409
  sheet:  0.74 (0.29), residues: 276
  loop : -0.22 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.019   0.001   PHE R 192 
 TYR   0.016   0.001   TYR S 190 
 ARG   0.010   0.000   ARG A 313 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9228.75 seconds
wall clock time: 159 minutes 58.34 seconds (9598.34 seconds total)