Starting phenix.real_space_refine
on Tue Mar  3 23:14:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7d77_30603/03_2026/7d77_30603.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7d77_30603/03_2026/7d77_30603.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7d77_30603/03_2026/7d77_30603.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7d77_30603/03_2026/7d77_30603.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7d77_30603/03_2026/7d77_30603.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7d77_30603/03_2026/7d77_30603.map"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.014
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      56      5.16       5
     C    5645      2.51       5
     N    1466      2.21       5
     O    1618      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8785
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1711
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1711
          Classifications: {'peptide': 215}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 210}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 429
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "R"
      Number of atoms: 2097
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 265, 2097
          Classifications: {'peptide': 265}
          Link IDs: {'PTRANS': 4, 'TRANS': 260}
    Chain: "S"
      Number of atoms: 1777
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1777
          Classifications: {'peptide': 231}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'PLM': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'PLM:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "R"
      Number of atoms: 154
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 154
          Unusual residues: {'CLR': 2, 'HCY': 1, 'PLM': 2, 'Y01': 1}
          Classifications: {'undetermined': 6, 'water': 1}
          Link IDs: {None: 6}
  Time building chain proxies: 2.43, per 1000 atoms: 0.28
  Number of scatterers: 8785
  At special positions: 0
  Unit cell: (105.456, 126.75, 112.554, 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      56     16.00
     O    1618      8.00
     N    1466      7.00
     C    5645      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 338 " - pdb=" SG  CYS R 420 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.76
  Conformation dependent library (CDL) restraints added in 342.6 milliseconds
  

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2040

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 15 sheets defined
      33.6% alpha, 25.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 30
    Processing helix  chain 'A' and resid 208 through 213
      removed outlier: 3.950A  pdb=" N   TRP A 212 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 217
    Processing helix  chain 'A' and resid 243 through 256
    Processing helix  chain 'A' and resid 271 through 279
      removed outlier: 3.622A  pdb=" N   PHE A 275 " --> pdb=" O   LYS A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 310
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.908A  pdb=" N   ILE A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 26
    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 8 through 24
      removed outlier: 3.765A  pdb=" N   ALA G  12 " --> pdb=" O   SER G   8 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 43
    Processing helix  chain 'R' and resid 264 through 297
      removed outlier: 4.068A  pdb=" N   PHE R 282 " --> pdb=" O   VAL R 278 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 299 through 303
      removed outlier: 3.850A  pdb=" N   GLU R 303 " --> pdb=" O   PHE R 300 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 329
    Processing helix  chain 'R' and resid 334 through 368
      removed outlier: 3.816A  pdb=" N   CYS R 338 " --> pdb=" O   SER R 334 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   ALA R 340 " --> pdb=" O   ALA R 336 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ALA R 360 " --> pdb=" O   MET R 356 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 377 through 400
      Proline residue:  R 390  - end of helix
      removed outlier: 3.723A  pdb=" N   ALA R 400 " --> pdb=" O   GLY R 396 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 428 through 435
      removed outlier: 4.323A  pdb=" N   TYR R 432 " --> pdb=" O   MET R 428 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 435 through 461
    Processing helix  chain 'R' and resid 471 through 495
      removed outlier: 3.673A  pdb=" N   LYS R 475 " --> pdb=" O   LYS R 471 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   LEU R 477 " --> pdb=" O   ARG R 473 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 502 through 525
      removed outlier: 3.549A  pdb=" N   PHE R 506 " --> pdb=" O   THR R 502 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   ILE R 517 " --> pdb=" O   GLN R 513 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 188
      removed outlier: 3.503A  pdb=" N   VAL A 186 " --> pdb=" O   ASP A 201 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 188
      removed outlier: 3.503A  pdb=" N   VAL A 186 " --> pdb=" O   ASP A 201 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   VAL A  34 " --> pdb=" O   ARG A 198 " (cutoff:3.500A)
      removed outlier: 7.679A  pdb=" N   PHE A 200 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 200 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ALA A 221 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   CYS A 225 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   ILE A 222 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   PHE A 268 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 6.063A  pdb=" N   PHE A 224 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   ASN A 270 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
      removed outlier: 6.085A  pdb=" N   VAL A 226 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   ILE A 265 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 8.274A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   LEU A 267 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.449A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.589A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.664A  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: 3.521A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.631A  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: 6.884A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.634A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.029A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.080A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.000A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.860A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.835A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.910A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.434A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.117A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.709A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.049A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.184A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.047A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.513A  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: 6.801A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.451A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'R' and resid 403 through 409
      removed outlier: 3.577A  pdb=" N   LEU R 417 " --> pdb=" O   ILE R 408 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.627A  pdb=" N   VAL S   5 " --> pdb=" O   SER S  23 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.147A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   TYR S  94 " --> pdb=" O   THR S 115 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   VAL S  97 " --> pdb=" O   HIS S  35 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA S  49 " --> pdb=" O   TRP S  36 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.334A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.147A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   TYR S  94 " --> pdb=" O   THR S 115 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136
      removed outlier: 6.440A  pdb=" N   LEU S 162 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 4.660A  pdb=" N   TYR S 178 " --> pdb=" O   LEU S 162 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'S' and resid 143 through 147

    405 hydrogen bonds defined for protein.
    1152 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.34

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1407
        1.32 -     1.45: 2518
        1.45 -     1.58: 4964
        1.58 -     1.70: 8
        1.70 -     1.83: 80
  Bond restraints: 8977
  Sorted by residual:
  bond pdb=" CAS Y01 R 601 "
       pdb=" CAU Y01 R 601 "
    ideal  model  delta    sigma   weight residual
    1.530  1.304  0.226 2.00e-02 2.50e+03 1.28e+02
  bond pdb=" CBE Y01 R 601 "
       pdb=" CBI Y01 R 601 "
    ideal  model  delta    sigma   weight residual
    1.550  1.375  0.175 2.00e-02 2.50e+03 7.65e+01
  bond pdb=" CAS Y01 R 601 "
       pdb=" CBF Y01 R 601 "
    ideal  model  delta    sigma   weight residual
    1.533  1.363  0.170 2.00e-02 2.50e+03 7.21e+01
  bond pdb=" CBF Y01 R 601 "
       pdb=" CBH Y01 R 601 "
    ideal  model  delta    sigma   weight residual
    1.550  1.689 -0.139 2.00e-02 2.50e+03 4.84e+01
  bond pdb=" CAP Y01 R 601 "
       pdb=" CAQ Y01 R 601 "
    ideal  model  delta    sigma   weight residual
    1.541  1.654 -0.113 2.00e-02 2.50e+03 3.17e+01
  ... (remaining 8972 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.20: 11902
        2.20 -     4.39: 213
        4.39 -     6.59: 34
        6.59 -     8.78: 10
        8.78 -    10.98: 4
  Bond angle restraints: 12163
  Sorted by residual:
  angle pdb=" C   ARG S 179 "
        pdb=" N   MET S 180 "
        pdb=" CA  MET S 180 "
      ideal   model   delta    sigma   weight residual
     121.54  132.52  -10.98 1.91e+00 2.74e-01 3.30e+01
  angle pdb=" N   ARG R 411 "
        pdb=" CA  ARG R 411 "
        pdb=" C   ARG R 411 "
      ideal   model   delta    sigma   weight residual
     112.54  105.87    6.67 1.22e+00 6.72e-01 2.99e+01
  angle pdb=" CBD Y01 R 601 "
        pdb=" CBG Y01 R 601 "
        pdb=" CBI Y01 R 601 "
      ideal   model   delta    sigma   weight residual
     115.11  105.59    9.52 3.00e+00 1.11e-01 1.01e+01
  angle pdb=" N   ASN A 295 "
        pdb=" CA  ASN A 295 "
        pdb=" C   ASN A 295 "
      ideal   model   delta    sigma   weight residual
     108.52  113.97   -5.45 1.74e+00 3.30e-01 9.82e+00
  angle pdb=" CBB Y01 R 601 "
        pdb=" CBE Y01 R 601 "
        pdb=" CBI Y01 R 601 "
      ideal   model   delta    sigma   weight residual
     119.27  110.15    9.12 3.00e+00 1.11e-01 9.24e+00
  ... (remaining 12158 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.33: 5114
       21.33 -    42.66: 323
       42.66 -    63.99: 32
       63.99 -    85.32: 10
       85.32 -   106.65: 2
  Dihedral angle restraints: 5481
    sinusoidal: 2302
      harmonic: 3179
  Sorted by residual:
  dihedral pdb=" CB  CYS R 338 "
           pdb=" SG  CYS R 338 "
           pdb=" SG  CYS R 420 "
           pdb=" CB  CYS R 420 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -33.18  -52.82     1      1.00e+01 1.00e-02 3.80e+01
  dihedral pdb=" CA  GLN A  52 "
           pdb=" C   GLN A  52 "
           pdb=" N   MET A  53 "
           pdb=" CA  MET A  53 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.51  -22.49     0      5.00e+00 4.00e-02 2.02e+01
  dihedral pdb=" CA  THR A 188 "
           pdb=" C   THR A 188 "
           pdb=" N   HIS A 189 "
           pdb=" CA  HIS A 189 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.84  -21.16     0      5.00e+00 4.00e-02 1.79e+01
  ... (remaining 5478 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.109: 1314
       0.109 -    0.217: 53
       0.217 -    0.326: 7
       0.326 -    0.434: 2
       0.434 -    0.543: 1
  Chirality restraints: 1377
  Sorted by residual:
  chirality pdb=" CBG Y01 R 601 "
            pdb=" CAQ Y01 R 601 "
            pdb=" CBD Y01 R 601 "
            pdb=" CBI Y01 R 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.87    0.54 2.00e-01 2.50e+01 7.37e+00
  chirality pdb=" C14 CLR R 606 "
            pdb=" C13 CLR R 606 "
            pdb=" C15 CLR R 606 "
            pdb=" C8  CLR R 606 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.70    0.38 2.00e-01 2.50e+01 3.63e+00
  chirality pdb=" C14 CLR R 605 "
            pdb=" C13 CLR R 605 "
            pdb=" C15 CLR R 605 "
            pdb=" C8  CLR R 605 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.70    0.38 2.00e-01 2.50e+01 3.60e+00
  ... (remaining 1374 not shown)

  Planarity restraints: 1511
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 HCY R 604 "   -0.022 2.00e-02 2.50e+03   7.73e-02 7.46e+01
        pdb=" C3  HCY R 604 "    0.095 2.00e-02 2.50e+03
        pdb=" C4  HCY R 604 "   -0.121 2.00e-02 2.50e+03
        pdb=" C5  HCY R 604 "   -0.023 2.00e-02 2.50e+03
        pdb=" C6  HCY R 604 "    0.071 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 235 "   -0.012 2.00e-02 2.50e+03   2.39e-02 5.73e+00
        pdb=" C   PHE B 235 "    0.041 2.00e-02 2.50e+03
        pdb=" O   PHE B 235 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   PRO B 236 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP R 410 "    0.010 2.00e-02 2.50e+03   2.05e-02 4.20e+00
        pdb=" C   ASP R 410 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   ASP R 410 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ARG R 411 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1508 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 154
        2.67 -     3.22: 8050
        3.22 -     3.78: 12843
        3.78 -     4.34: 18190
        4.34 -     4.90: 31345
  Nonbonded interactions: 70582
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.107 3.040
  nonbonded pdb=" NZ  LYS A 210 "
            pdb=" OD2 ASP B 228 "
     model   vdw
     2.132 3.120
  nonbonded pdb=" O   THR R 397 "
            pdb=" OG  SER R 402 "
     model   vdw
     2.135 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.136 3.040
  nonbonded pdb=" OG  SER S 149 "
            pdb=" O   LYS S 151 "
     model   vdw
     2.157 3.040
  ... (remaining 70577 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:             0.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.910
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:9.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
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      :  0.008   0.226   8980  Z= 0.382
  Angle     :  0.779  10.977  12167  Z= 0.404
  Chirality :  0.056   0.543   1377
  Planarity :  0.004   0.077   1511
  Dihedral  : 13.717 106.650   3435
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  4.83 %
    Favored  : 94.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.58 (0.22), residues: 1091
  helix: -0.32 (0.25), residues: 352
  sheet: -1.90 (0.28), residues: 274
  loop : -2.64 (0.24), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  49 
 TYR   0.015   0.002   TYR S 178 
 PHE   0.016   0.002   PHE A 190 
 TRP   0.014   0.002   TRP R 339 
 HIS   0.008   0.001   HIS R 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00830 ( 8977)
  covalent geometry    : angle       0.77824 (12163)
  SS BOND              : bond        0.00865 (    2)
  SS BOND              : angle       2.35053 (    4)
  hydrogen bonds       : bond        0.16814 (  401)
  hydrogen bonds       : angle       6.29731 ( 1152)
  Misc. bond           : bond        0.00050 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 138
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 ARG cc_start: 0.7982 (ttp-110) cc_final: 0.7774 (ttp80)
REVERT: B  124 TYR cc_start: 0.8913 (m-80) cc_final: 0.8592 (m-80)
REVERT: B  130 GLU cc_start: 0.7681 (mp0) cc_final: 0.7465 (mp0)
REVERT: B  138 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8475 (mt-10)
REVERT: B  153 ASP cc_start: 0.7626 (m-30) cc_final: 0.7394 (m-30)
REVERT: R  447 MET cc_start: 0.6609 (mmt) cc_final: 0.6388 (mpt)
REVERT: S  168 ARG cc_start: 0.7769 (mtt90) cc_final: 0.7522 (mtt90)
REVERT: S  174 GLN cc_start: 0.8810 (pt0) cc_final: 0.8591 (pt0)
REVERT: S  194 SER cc_start: 0.8264 (t) cc_final: 0.8025 (p)
  outliers start: 2
  outliers final: 1
  residues processed: 140
  average time/residue: 0.7395
  time to fit residues: 108.9502
Evaluate side-chains
  97 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 96
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  234 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    0.0980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.3980
   chunk 106 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
R 362 HIS
S 171 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.166532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.116783 restraints weight = 9797.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 2.74
r_work: 0.3146 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.1375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8980  Z= 0.111
  Angle     :  0.531   7.883  12167  Z= 0.277
  Chirality :  0.041   0.148   1377
  Planarity :  0.003   0.038   1511
  Dihedral  :  7.261  58.857   1508
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 11.17 %
    Favored  : 87.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.08 (0.24), residues: 1091
  helix:  1.48 (0.28), residues: 355
  sheet: -1.39 (0.28), residues: 269
  loop : -2.05 (0.25), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 197 
 TYR   0.017   0.001   TYR S 178 
 PHE   0.023   0.001   PHE R 285 
 TRP   0.021   0.001   TRP B 169 
 HIS   0.005   0.001   HIS R 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 8977)
  covalent geometry    : angle       0.53073 (12163)
  SS BOND              : bond        0.00680 (    2)
  SS BOND              : angle       1.29175 (    4)
  hydrogen bonds       : bond        0.03724 (  401)
  hydrogen bonds       : angle       4.30932 ( 1152)
  Misc. bond           : bond        0.00006 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 123
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.7568 (t0) cc_final: 0.7199 (t0)
REVERT: A  248 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6994 (tt)
REVERT: A  341 ASP cc_start: 0.8132 (t70) cc_final: 0.7892 (t0)
REVERT: B  138 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8564 (mt-10)
REVERT: B  155 ASN cc_start: 0.7988 (t0) cc_final: 0.7717 (t0)
REVERT: B  175 GLN cc_start: 0.8281 (mm110) cc_final: 0.7836 (mm110)
REVERT: R  459 THR cc_start: 0.8104 (t) cc_final: 0.7827 (p)
  outliers start: 16
  outliers final: 8
  residues processed: 133
  average time/residue: 0.5960
  time to fit residues: 84.4281
Evaluate side-chains
  113 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  254 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain R residue  264 THR
Chi-restraints excluded: chain S residue   82 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 22 optimal weight:    6.9990
   chunk 5 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 77 optimal weight:    0.6980
   chunk 46 optimal weight:    6.9990
   chunk 67 optimal weight:    0.5980
   chunk 59 optimal weight:    8.9990
   chunk 107 optimal weight:    1.9990
   chunk 55 optimal weight:    8.9990
   chunk 102 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.159710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.120015 restraints weight = 10000.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 2.39
r_work: 0.3106 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2965 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.1626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8980  Z= 0.108
  Angle     :  0.507   7.020  12167  Z= 0.264
  Chirality :  0.041   0.138   1377
  Planarity :  0.003   0.036   1511
  Dihedral  :  6.915  59.025   1508
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 14.93 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.25), residues: 1091
  helix:  2.09 (0.28), residues: 353
  sheet: -1.10 (0.28), residues: 275
  loop : -1.82 (0.26), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 197 
 TYR   0.015   0.001   TYR B 105 
 PHE   0.022   0.001   PHE R 292 
 TRP   0.016   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 8977)
  covalent geometry    : angle       0.50691 (12163)
  SS BOND              : bond        0.00480 (    2)
  SS BOND              : angle       1.28837 (    4)
  hydrogen bonds       : bond        0.03476 (  401)
  hydrogen bonds       : angle       4.01083 ( 1152)
  Misc. bond           : bond        0.00022 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.7506 (t0) cc_final: 0.7119 (t0)
REVERT: A  341 ASP cc_start: 0.8198 (t70) cc_final: 0.7941 (t0)
REVERT: B  138 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8546 (mt-10)
REVERT: B  155 ASN cc_start: 0.7865 (t0) cc_final: 0.7496 (t0)
REVERT: B  175 GLN cc_start: 0.8113 (mm110) cc_final: 0.7625 (mm110)
REVERT: B  197 ARG cc_start: 0.8045 (ttm110) cc_final: 0.7816 (ttm110)
REVERT: R  447 MET cc_start: 0.6869 (mmt) cc_final: 0.6623 (mpt)
REVERT: R  459 THR cc_start: 0.7925 (t) cc_final: 0.7558 (p)
REVERT: S  211 ASP cc_start: 0.8501 (m-30) cc_final: 0.8265 (m-30)
  outliers start: 15
  outliers final: 7
  residues processed: 122
  average time/residue: 0.6097
  time to fit residues: 79.0267
Evaluate side-chains
  118 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 111
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  264 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 14 optimal weight:    9.9990
   chunk 64 optimal weight:    0.7980
   chunk 63 optimal weight:    0.6980
   chunk 35 optimal weight:    8.9990
   chunk 70 optimal weight:    0.9990
   chunk 100 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 78 optimal weight:    0.7980
   chunk 83 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.161186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.122476 restraints weight = 10053.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 2.38
r_work: 0.3135 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.1811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8980  Z= 0.104
  Angle     :  0.493   7.915  12167  Z= 0.257
  Chirality :  0.040   0.139   1377
  Planarity :  0.003   0.042   1511
  Dihedral  :  6.633  58.747   1508
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 15.15 %
    Favored  : 83.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.14 (0.25), residues: 1091
  helix:  2.29 (0.28), residues: 358
  sheet: -0.72 (0.29), residues: 266
  loop : -1.66 (0.26), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  19 
 TYR   0.014   0.001   TYR S 178 
 PHE   0.025   0.001   PHE R 285 
 TRP   0.015   0.001   TRP B 169 
 HIS   0.003   0.001   HIS R 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 8977)
  covalent geometry    : angle       0.49275 (12163)
  SS BOND              : bond        0.00402 (    2)
  SS BOND              : angle       1.24914 (    4)
  hydrogen bonds       : bond        0.03294 (  401)
  hydrogen bonds       : angle       3.82298 ( 1152)
  Misc. bond           : bond        0.00017 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 122
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.7531 (t0) cc_final: 0.7164 (t0)
REVERT: A  341 ASP cc_start: 0.8231 (t70) cc_final: 0.7989 (t0)
REVERT: B  138 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8500 (mt-10)
REVERT: B  155 ASN cc_start: 0.7867 (t0) cc_final: 0.7481 (t0)
REVERT: B  175 GLN cc_start: 0.8157 (mm110) cc_final: 0.7693 (mm110)
REVERT: B  197 ARG cc_start: 0.8056 (ttm110) cc_final: 0.7852 (ttm110)
REVERT: S   84 THR cc_start: 0.8701 (m) cc_final: 0.8444 (p)
REVERT: S  211 ASP cc_start: 0.8376 (m-30) cc_final: 0.7921 (m-30)
  outliers start: 16
  outliers final: 11
  residues processed: 133
  average time/residue: 0.6736
  time to fit residues: 94.8310
Evaluate side-chains
  126 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 115
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  264 THR
Chi-restraints excluded: chain R residue  356 MET
Chi-restraints excluded: chain R residue  366 LEU
Chi-restraints excluded: chain R residue  407 THR
Chi-restraints excluded: chain S residue   82 GLN
Chi-restraints excluded: chain S residue   91 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 67 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 54 optimal weight:    8.9990
   chunk 4 optimal weight:    7.9990
   chunk 105 optimal weight:    9.9990
   chunk 62 optimal weight:    5.9990
   chunk 63 optimal weight:    0.6980
   chunk 81 optimal weight:    1.9990
   chunk 90 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B 156 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.156628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.117498 restraints weight = 10082.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 2.37
r_work: 0.3105 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2966 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.1810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8980  Z= 0.142
  Angle     :  0.532   8.610  12167  Z= 0.275
  Chirality :  0.042   0.208   1377
  Planarity :  0.003   0.046   1511
  Dihedral  :  6.747  58.969   1508
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 16.65 %
    Favored  : 81.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.25), residues: 1091
  helix:  2.33 (0.28), residues: 358
  sheet: -0.63 (0.30), residues: 265
  loop : -1.59 (0.26), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG S 148 
 TYR   0.015   0.001   TYR S 178 
 PHE   0.025   0.001   PHE R 292 
 TRP   0.014   0.001   TRP B 169 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 8977)
  covalent geometry    : angle       0.53104 (12163)
  SS BOND              : bond        0.00759 (    2)
  SS BOND              : angle       1.35114 (    4)
  hydrogen bonds       : bond        0.03611 (  401)
  hydrogen bonds       : angle       3.85364 ( 1152)
  Misc. bond           : bond        0.00009 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.283 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.7606 (t0) cc_final: 0.7284 (t0)
REVERT: A  341 ASP cc_start: 0.8260 (t70) cc_final: 0.8003 (t0)
REVERT: B  138 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8468 (mt-10)
REVERT: B  155 ASN cc_start: 0.7794 (t0) cc_final: 0.7395 (t0)
REVERT: B  175 GLN cc_start: 0.8246 (mm110) cc_final: 0.7792 (mm110)
REVERT: B  197 ARG cc_start: 0.8101 (ttm110) cc_final: 0.7849 (ttm110)
REVERT: S   84 THR cc_start: 0.8707 (m) cc_final: 0.8328 (p)
  outliers start: 18
  outliers final: 15
  residues processed: 122
  average time/residue: 0.6111
  time to fit residues: 79.3494
Evaluate side-chains
  116 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain R residue  264 THR
Chi-restraints excluded: chain R residue  356 MET
Chi-restraints excluded: chain R residue  366 LEU
Chi-restraints excluded: chain R residue  407 THR
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   91 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 75 optimal weight:    7.9990
   chunk 104 optimal weight:    5.9990
   chunk 54 optimal weight:    9.9990
   chunk 90 optimal weight:    0.8980
   chunk 66 optimal weight:    9.9990
   chunk 17 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 51 optimal weight:    8.9990
   chunk 105 optimal weight:    0.0050
   chunk 59 optimal weight:    2.9990
   overall best weight:    1.5800

-------------------------------------------------------------------------------
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 = 0.3825 r_free = 0.3825 target = 0.158277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.119038 restraints weight = 10008.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 2.37
r_work: 0.3098 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8980  Z= 0.152
  Angle     :  0.536   8.874  12167  Z= 0.277
  Chirality :  0.042   0.196   1377
  Planarity :  0.003   0.036   1511
  Dihedral  :  6.720  59.225   1508
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 17.08 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.25), residues: 1091
  helix:  2.34 (0.28), residues: 358
  sheet: -0.57 (0.30), residues: 268
  loop : -1.50 (0.27), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG S 148 
 TYR   0.015   0.001   TYR S 178 
 PHE   0.024   0.001   PHE R 285 
 TRP   0.013   0.001   TRP B 169 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 8977)
  covalent geometry    : angle       0.53551 (12163)
  SS BOND              : bond        0.00528 (    2)
  SS BOND              : angle       1.39997 (    4)
  hydrogen bonds       : bond        0.03666 (  401)
  hydrogen bonds       : angle       3.86574 ( 1152)
  Misc. bond           : bond        0.00012 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.7743 (t0) cc_final: 0.7402 (t0)
REVERT: A  341 ASP cc_start: 0.8230 (t70) cc_final: 0.7955 (t0)
REVERT: B  138 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8446 (mt-10)
REVERT: B  155 ASN cc_start: 0.7742 (t0) cc_final: 0.7309 (t0)
REVERT: B  175 GLN cc_start: 0.8205 (mm110) cc_final: 0.7737 (mm110)
REVERT: B  197 ARG cc_start: 0.8079 (ttm110) cc_final: 0.7796 (ttm110)
REVERT: S   84 THR cc_start: 0.8651 (m) cc_final: 0.8258 (p)
  outliers start: 23
  outliers final: 18
  residues processed: 124
  average time/residue: 0.5979
  time to fit residues: 79.2205
Evaluate side-chains
  126 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain R residue  264 THR
Chi-restraints excluded: chain R residue  356 MET
Chi-restraints excluded: chain R residue  366 LEU
Chi-restraints excluded: chain R residue  407 THR
Chi-restraints excluded: chain R residue  447 MET
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   91 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 93 optimal weight:    8.9990
   chunk 96 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 37 optimal weight:    0.3980
   chunk 21 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0270
   chunk 48 optimal weight:    0.9990
   chunk 70 optimal weight:    4.9990
   overall best weight:    0.6642

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
G  59 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.161509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.122851 restraints weight = 9939.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 2.33
r_work: 0.3157 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3018 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7428
moved from start:          0.2111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8980  Z= 0.098
  Angle     :  0.496   8.859  12167  Z= 0.257
  Chirality :  0.041   0.189   1377
  Planarity :  0.003   0.044   1511
  Dihedral  :  6.334  58.943   1508
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 18.15 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.25 (0.25), residues: 1091
  helix:  2.51 (0.28), residues: 358
  sheet: -0.40 (0.30), residues: 264
  loop : -1.40 (0.26), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG S 148 
 TYR   0.014   0.001   TYR S 178 
 PHE   0.031   0.001   PHE R 292 
 TRP   0.017   0.001   TRP B 169 
 HIS   0.002   0.001   HIS R 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 8977)
  covalent geometry    : angle       0.49597 (12163)
  SS BOND              : bond        0.00487 (    2)
  SS BOND              : angle       1.21082 (    4)
  hydrogen bonds       : bond        0.03078 (  401)
  hydrogen bonds       : angle       3.68266 ( 1152)
  Misc. bond           : bond        0.00006 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 118
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.7717 (t0) cc_final: 0.7361 (t0)
REVERT: A  341 ASP cc_start: 0.8172 (t70) cc_final: 0.7876 (t0)
REVERT: B  138 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8500 (mt-10)
REVERT: B  155 ASN cc_start: 0.7643 (t0) cc_final: 0.7150 (t0)
REVERT: B  175 GLN cc_start: 0.8055 (mm110) cc_final: 0.7802 (mm110)
REVERT: B  197 ARG cc_start: 0.8035 (ttm110) cc_final: 0.7774 (ttm110)
REVERT: R  525 TYR cc_start: 0.8052 (m-80) cc_final: 0.7742 (m-80)
  outliers start: 20
  outliers final: 10
  residues processed: 131
  average time/residue: 0.5495
  time to fit residues: 77.0313
Evaluate side-chains
  133 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 123
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain R residue  366 LEU
Chi-restraints excluded: chain R residue  407 THR
Chi-restraints excluded: chain R residue  447 MET
Chi-restraints excluded: chain S residue   91 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 87 optimal weight:    6.9990
   chunk 38 optimal weight:    0.7980
   chunk 94 optimal weight:    1.9990
   chunk 80 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   chunk 41 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 106 optimal weight:    5.9990
   chunk 78 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
S 174 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.160837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.121680 restraints weight = 10007.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 2.36
r_work: 0.3143 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3004 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.2192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8980  Z= 0.108
  Angle     :  0.519   9.280  12167  Z= 0.270
  Chirality :  0.042   0.267   1377
  Planarity :  0.003   0.049   1511
  Dihedral  :  6.282  58.440   1508
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 18.69 %
    Favored  : 79.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.26), residues: 1091
  helix:  2.55 (0.28), residues: 358
  sheet: -0.33 (0.30), residues: 265
  loop : -1.30 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG S 148 
 TYR   0.013   0.001   TYR S 178 
 PHE   0.027   0.001   PHE R 516 
 TRP   0.015   0.001   TRP B 169 
 HIS   0.002   0.001   HIS R 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 8977)
  covalent geometry    : angle       0.51134 (12163)
  SS BOND              : bond        0.00959 (    2)
  SS BOND              : angle       5.04303 (    4)
  hydrogen bonds       : bond        0.03140 (  401)
  hydrogen bonds       : angle       3.71556 ( 1152)
  Misc. bond           : bond        0.00005 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.333 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.7719 (t0) cc_final: 0.7388 (t0)
REVERT: A  341 ASP cc_start: 0.8187 (t70) cc_final: 0.7923 (t0)
REVERT: B  138 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8384 (mt-10)
REVERT: B  155 ASN cc_start: 0.7659 (t0) cc_final: 0.7147 (t0)
REVERT: B  175 GLN cc_start: 0.8042 (mm110) cc_final: 0.7782 (mm110)
REVERT: B  197 ARG cc_start: 0.8032 (ttm110) cc_final: 0.7748 (ttm110)
REVERT: B  219 ARG cc_start: 0.7931 (mtm180) cc_final: 0.7346 (mtt-85)
REVERT: R  525 TYR cc_start: 0.8054 (m-80) cc_final: 0.7745 (m-80)
REVERT: S   93 MET cc_start: 0.8035 (ttm) cc_final: 0.7764 (ttt)
  outliers start: 17
  outliers final: 13
  residues processed: 128
  average time/residue: 0.6168
  time to fit residues: 84.1898
Evaluate side-chains
  119 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain R residue  264 THR
Chi-restraints excluded: chain R residue  366 LEU
Chi-restraints excluded: chain R residue  407 THR
Chi-restraints excluded: chain R residue  447 MET
Chi-restraints excluded: chain S residue   91 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 81 optimal weight:   10.0000
   chunk 91 optimal weight:    0.6980
   chunk 42 optimal weight:   10.0000
   chunk 78 optimal weight:    0.9980
   chunk 52 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   chunk 59 optimal weight:   10.0000
   chunk 16 optimal weight:    0.8980
   chunk 50 optimal weight:    0.7980
   chunk 24 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    1.6782

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
S 174 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.158601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.119494 restraints weight = 9933.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 2.36
r_work: 0.3098 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.2037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8980  Z= 0.161
  Angle     :  0.561   9.363  12167  Z= 0.289
  Chirality :  0.043   0.275   1377
  Planarity :  0.003   0.046   1511
  Dihedral  :  6.514  58.932   1508
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 18.90 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.25), residues: 1091
  helix:  2.44 (0.28), residues: 358
  sheet: -0.40 (0.30), residues: 268
  loop : -1.29 (0.27), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG S 148 
 TYR   0.014   0.001   TYR S 178 
 PHE   0.033   0.001   PHE R 292 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 8977)
  covalent geometry    : angle       0.55520 (12163)
  SS BOND              : bond        0.00884 (    2)
  SS BOND              : angle       4.40298 (    4)
  hydrogen bonds       : bond        0.03618 (  401)
  hydrogen bonds       : angle       3.85002 ( 1152)
  Misc. bond           : bond        0.00003 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.335 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.7785 (t0) cc_final: 0.7458 (t0)
REVERT: A  341 ASP cc_start: 0.8229 (t70) cc_final: 0.7951 (t0)
REVERT: B  138 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8357 (mt-10)
REVERT: B  155 ASN cc_start: 0.7738 (t0) cc_final: 0.7243 (t0)
REVERT: B  175 GLN cc_start: 0.8087 (mm110) cc_final: 0.7798 (mm110)
REVERT: B  197 ARG cc_start: 0.8064 (ttm110) cc_final: 0.7752 (ttm110)
  outliers start: 19
  outliers final: 16
  residues processed: 117
  average time/residue: 0.5296
  time to fit residues: 66.3310
Evaluate side-chains
  125 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain R residue  264 THR
Chi-restraints excluded: chain R residue  356 MET
Chi-restraints excluded: chain R residue  366 LEU
Chi-restraints excluded: chain R residue  407 THR
Chi-restraints excluded: chain R residue  447 MET
Chi-restraints excluded: chain S residue   91 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 13 optimal weight:   10.0000
   chunk 50 optimal weight:    0.5980
   chunk 21 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 99 optimal weight:   10.0000
   chunk 46 optimal weight:    0.8980
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
S 174 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.160371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.121264 restraints weight = 9981.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 2.36
r_work: 0.3136 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8980  Z= 0.109
  Angle     :  0.524   9.829  12167  Z= 0.270
  Chirality :  0.042   0.282   1377
  Planarity :  0.003   0.046   1511
  Dihedral  :  6.294  58.910   1508
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 19.55 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.41 (0.26), residues: 1091
  helix:  2.49 (0.28), residues: 360
  sheet: -0.23 (0.30), residues: 265
  loop : -1.25 (0.27), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG S 148 
 TYR   0.014   0.001   TYR S 178 
 PHE   0.027   0.001   PHE R 516 
 TRP   0.015   0.001   TRP B 169 
 HIS   0.002   0.001   HIS R 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 8977)
  covalent geometry    : angle       0.51902 (12163)
  SS BOND              : bond        0.00747 (    2)
  SS BOND              : angle       4.10104 (    4)
  hydrogen bonds       : bond        0.03177 (  401)
  hydrogen bonds       : angle       3.73920 ( 1152)
  Misc. bond           : bond        0.00005 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.7785 (t0) cc_final: 0.7458 (t0)
REVERT: A  341 ASP cc_start: 0.8199 (t70) cc_final: 0.7923 (t0)
REVERT: B   46 ARG cc_start: 0.7821 (mtm-85) cc_final: 0.7399 (mtm-85)
REVERT: B  138 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8447 (mt-10)
REVERT: B  155 ASN cc_start: 0.7645 (t0) cc_final: 0.7154 (t0)
REVERT: B  175 GLN cc_start: 0.8072 (mm110) cc_final: 0.7805 (mm110)
REVERT: B  197 ARG cc_start: 0.8043 (ttm110) cc_final: 0.7744 (ttm110)
REVERT: R  525 TYR cc_start: 0.8081 (m-80) cc_final: 0.7779 (m-80)
  outliers start: 14
  outliers final: 14
  residues processed: 124
  average time/residue: 0.5550
  time to fit residues: 73.5351
Evaluate side-chains
  121 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  254 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain R residue  264 THR
Chi-restraints excluded: chain R residue  366 LEU
Chi-restraints excluded: chain R residue  407 THR
Chi-restraints excluded: chain R residue  447 MET
Chi-restraints excluded: chain S residue   91 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 107 optimal weight:    6.9990
   chunk 64 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 72 optimal weight:    7.9990
   chunk 106 optimal weight:    1.9990
   chunk 101 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9980
   chunk 74 optimal weight:    0.3980
   chunk 46 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 174 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.160720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.121706 restraints weight = 9827.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 2.35
r_work: 0.3147 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3008 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.2257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8980  Z= 0.106
  Angle     :  0.521   9.766  12167  Z= 0.268
  Chirality :  0.042   0.289   1377
  Planarity :  0.003   0.047   1511
  Dihedral  :  6.239  58.757   1508
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 19.76 %
    Favored  : 78.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.46 (0.26), residues: 1091
  helix:  2.58 (0.28), residues: 358
  sheet: -0.18 (0.30), residues: 265
  loop : -1.24 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG S 148 
 TYR   0.013   0.001   TYR S 178 
 PHE   0.036   0.001   PHE R 292 
 TRP   0.015   0.001   TRP B 169 
 HIS   0.002   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 8977)
  covalent geometry    : angle       0.51660 (12163)
  SS BOND              : bond        0.00688 (    2)
  SS BOND              : angle       3.76841 (    4)
  hydrogen bonds       : bond        0.03131 (  401)
  hydrogen bonds       : angle       3.71040 ( 1152)
  Misc. bond           : bond        0.00008 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3580.76 seconds
wall clock time: 61 minutes 39.66 seconds (3699.66 seconds total)