Starting phenix.real_space_refine
on Tue Mar  3 15:11:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rsb_24668/03_2026/7rsb_24668.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rsb_24668/03_2026/7rsb_24668.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rsb_24668/03_2026/7rsb_24668.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rsb_24668/03_2026/7rsb_24668.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rsb_24668/03_2026/7rsb_24668.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rsb_24668/03_2026/7rsb_24668.cif"
  }
  resolution = 3.68
  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=   0.003 sd=   0.033
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      40      5.16       5
     C    4362      2.51       5
     N    1104      2.21       5
     O    1124      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 50 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: 6630
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3315
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 443, 3315
          Classifications: {'peptide': 443}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 423}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 3315
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 443, 3315
          Classifications: {'peptide': 443}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 423}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
  Time building chain proxies: 1.53, per 1000 atoms: 0.23
  Number of scatterers: 6630
  At special positions: 0
  Unit cell: (72.312, 96.416, 114.232, 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      40     16.00
     O    1124      8.00
     N    1104      7.00
     C    4362      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.53
  Conformation dependent library (CDL) restraints added in 232.3 milliseconds
  

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1544

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 0 sheets defined
      76.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 29
      removed outlier: 4.405A  pdb=" N   GLU A  27 " --> pdb=" O   ARG A  23 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ARG A  28 " --> pdb=" O   GLN A  24 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ASP A  29 " --> pdb=" O   LEU A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 29 through 46
      removed outlier: 3.637A  pdb=" N   LEU A  33 " --> pdb=" O   ASP A  29 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ALA A  34 " --> pdb=" O   LYS A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 59
    Processing helix  chain 'A' and resid 61 through 71
      removed outlier: 3.984A  pdb=" N   THR A  71 " --> pdb=" O   ALA A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 85
      removed outlier: 3.686A  pdb=" N   VAL A  81 " --> pdb=" O   LEU A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 99
      removed outlier: 3.554A  pdb=" N   PHE A  95 " --> pdb=" O   MET A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 116
    Processing helix  chain 'A' and resid 123 through 140
      Proline residue:  A 129  - end of helix
      removed outlier: 3.600A  pdb=" N   PHE A 132 " --> pdb=" O   LEU A 128 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   PHE A 133 " --> pdb=" O   PRO A 129 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   GLY A 137 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 167
      removed outlier: 4.453A  pdb=" N   ILE A 154 " --> pdb=" O   PRO A 150 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   LEU A 163 " --> pdb=" O   GLY A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 191
      removed outlier: 3.724A  pdb=" N   HIS A 175 " --> pdb=" O   ASP A 171 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ALA A 179 " --> pdb=" O   HIS A 175 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   PHE A 190 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 198
      removed outlier: 4.090A  pdb=" N   ILE A 197 " --> pdb=" O   PRO A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 224
      removed outlier: 3.637A  pdb=" N   ILE A 215 " --> pdb=" O   THR A 211 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   LYS A 216 " --> pdb=" O   LEU A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 231
    Processing helix  chain 'A' and resid 251 through 266
      removed outlier: 3.844A  pdb=" N   TYR A 255 " --> pdb=" O   THR A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 285
      removed outlier: 3.816A  pdb=" N   ASP A 278 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   HIS A 284 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 309
      removed outlier: 3.589A  pdb=" N   ALA A 297 " --> pdb=" O   LEU A 293 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   GLY A 306 " --> pdb=" O   CYS A 302 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   PHE A 307 " --> pdb=" O   GLY A 303 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   VAL A 308 " --> pdb=" O   LEU A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 325
    Processing helix  chain 'A' and resid 329 through 349
      removed outlier: 3.678A  pdb=" N   LEU A 346 " --> pdb=" O   ILE A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 379
      removed outlier: 3.523A  pdb=" N   MET A 360 " --> pdb=" O   ILE A 356 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   VAL A 366 " --> pdb=" O   ALA A 362 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   LEU A 367 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   VAL A 374 " --> pdb=" O   ALA A 370 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLU A 377 " --> pdb=" O   MET A 373 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   PHE A 379 " --> pdb=" O   ALA A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 395
      removed outlier: 3.958A  pdb=" N   ILE A 391 " --> pdb=" O   GLY A 387 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ALA A 392 " --> pdb=" O   THR A 388 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   GLY A 395 " --> pdb=" O   ILE A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 415
      removed outlier: 3.709A  pdb=" N   ILE A 410 " --> pdb=" O   LEU A 406 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   LEU A 413 " --> pdb=" O   ILE A 409 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   MET A 415 " --> pdb=" O   LEU A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 439
      removed outlier: 3.619A  pdb=" N   ILE A 426 " --> pdb=" O   ILE A 422 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   THR A 433 " --> pdb=" O   GLY A 429 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LEU A 435 " --> pdb=" O   GLY A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 460
      removed outlier: 3.674A  pdb=" N   GLN A 460 " --> pdb=" O   GLN A 456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 29
      removed outlier: 3.686A  pdb=" N   GLU B  27 " --> pdb=" O   ARG B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 59
      removed outlier: 3.897A  pdb=" N   ALA B  34 " --> pdb=" O   LYS B  30 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   ILE B  35 " --> pdb=" O   THR B  31 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU B  36 " --> pdb=" O   PRO B  32 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   VAL B  41 " --> pdb=" O   PHE B  37 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   GLY B  47 " --> pdb=" O   GLY B  43 " (cutoff:3.500A)
      removed outlier: 5.852A  pdb=" N   ALA B  50 " --> pdb=" O   VAL B  46 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   VAL B  51 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 66
    Processing helix  chain 'B' and resid 74 through 99
      removed outlier: 3.566A  pdb=" N   VAL B  81 " --> pdb=" O   LEU B  77 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   SER B  86 " --> pdb=" O   ALA B  82 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   LEU B  89 " --> pdb=" O   CYS B  85 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LEU B  96 " --> pdb=" O   PHE B  92 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 114
    Processing helix  chain 'B' and resid 123 through 140
      Proline residue:  B 129  - end of helix
      removed outlier: 3.660A  pdb=" N   PHE B 132 " --> pdb=" O   LEU B 128 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   GLY B 137 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 166
      removed outlier: 3.987A  pdb=" N   THR B 151 " --> pdb=" O   ARG B 147 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   GLN B 153 " --> pdb=" O   GLY B 149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 187
      removed outlier: 4.085A  pdb=" N   ALA B 179 " --> pdb=" O   HIS B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 202
      removed outlier: 3.763A  pdb=" N   ILE B 200 " --> pdb=" O   GLY B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 208
      removed outlier: 3.879A  pdb=" N   GLN B 207 " --> pdb=" O   MET B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 233
      removed outlier: 3.721A  pdb=" N   ALA B 217 " --> pdb=" O   ILE B 213 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ILE B 227 " --> pdb=" O   ILE B 223 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   MET B 228 " --> pdb=" O   MET B 224 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   PHE B 232 " --> pdb=" O   MET B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 269
      Proline residue:  B 267  - end of helix
    Processing helix  chain 'B' and resid 270 through 283
      removed outlier: 3.698A  pdb=" N   ASP B 278 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   HIS B 281 " --> pdb=" O   GLN B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 309
      removed outlier: 4.270A  pdb=" N   MET B 294 " --> pdb=" O   LYS B 290 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   GLY B 306 " --> pdb=" O   CYS B 302 " (cutoff:3.500A)
      removed outlier: 4.996A  pdb=" N   PHE B 307 " --> pdb=" O   GLY B 303 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   VAL B 308 " --> pdb=" O   LEU B 304 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ALA B 309 " --> pdb=" O   LEU B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 324
    Processing helix  chain 'B' and resid 329 through 349
      removed outlier: 4.017A  pdb=" N   ILE B 342 " --> pdb=" O   VAL B 338 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   THR B 343 " --> pdb=" O   ALA B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 379
      removed outlier: 3.562A  pdb=" N   ALA B 362 " --> pdb=" O   ALA B 358 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   GLU B 377 " --> pdb=" O   MET B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 401
      removed outlier: 4.120A  pdb=" N   GLY B 395 " --> pdb=" O   ILE B 391 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   ALA B 396 " --> pdb=" O   ALA B 392 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   LEU B 397 " --> pdb=" O   GLY B 393 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   LEU B 398 " --> pdb=" O   MET B 394 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   ALA B 399 " --> pdb=" O   GLY B 395 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   SER B 401 " --> pdb=" O   LEU B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 417
      removed outlier: 3.638A  pdb=" N   ILE B 410 " --> pdb=" O   LEU B 406 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   VAL B 412 " --> pdb=" O   GLY B 408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 439
      removed outlier: 3.642A  pdb=" N   MET B 425 " --> pdb=" O   LEU B 421 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ILE B 427 " --> pdb=" O   LEU B 423 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ALA B 432 " --> pdb=" O   THR B 428 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 460
      removed outlier: 3.580A  pdb=" N   GLN B 460 " --> pdb=" O   GLN B 456 " (cutoff:3.500A)

    400 hydrogen bonds defined for protein.
    1197 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: 0.88

  Time building geometry restraints manager: 0.70 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2067
        1.34 -     1.46: 1160
        1.46 -     1.57: 3473
        1.57 -     1.69: 0
        1.69 -     1.81: 74
  Bond restraints: 6774
  Sorted by residual:
  bond pdb=" CB  ASN B 270 "
       pdb=" CG  ASN B 270 "
    ideal  model  delta    sigma   weight residual
    1.516  1.570 -0.054 2.50e-02 1.60e+03 4.59e+00
  bond pdb=" CA  ASN B 270 "
       pdb=" CB  ASN B 270 "
    ideal  model  delta    sigma   weight residual
    1.530  1.566 -0.036 1.69e-02 3.50e+03 4.57e+00
  bond pdb=" CA  ASN A 270 "
       pdb=" CB  ASN A 270 "
    ideal  model  delta    sigma   weight residual
    1.530  1.566 -0.036 1.69e-02 3.50e+03 4.57e+00
  bond pdb=" C   THR B  31 "
       pdb=" N   PRO B  32 "
    ideal  model  delta    sigma   weight residual
    1.334  1.377 -0.043 2.34e-02 1.83e+03 3.44e+00
  bond pdb=" CB  ASN A 270 "
       pdb=" CG  ASN A 270 "
    ideal  model  delta    sigma   weight residual
    1.516  1.562 -0.046 2.50e-02 1.60e+03 3.38e+00
  ... (remaining 6769 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.20: 9026
        3.20 -     6.41: 138
        6.41 -     9.61: 30
        9.61 -    12.81: 3
       12.81 -    16.02: 3
  Bond angle restraints: 9200
  Sorted by residual:
  angle pdb=" C   PHE B 269 "
        pdb=" N   ASN B 270 "
        pdb=" CA  ASN B 270 "
      ideal   model   delta    sigma   weight residual
     121.54  131.23   -9.69 1.91e+00 2.74e-01 2.57e+01
  angle pdb=" CA  ASN A 270 "
        pdb=" CB  ASN A 270 "
        pdb=" CG  ASN A 270 "
      ideal   model   delta    sigma   weight residual
     112.60  117.45   -4.85 1.00e+00 1.00e+00 2.35e+01
  angle pdb=" C   ASN B 318 "
        pdb=" N   LEU B 319 "
        pdb=" CA  LEU B 319 "
      ideal   model   delta    sigma   weight residual
     121.54  130.52   -8.98 1.91e+00 2.74e-01 2.21e+01
  angle pdb=" CA  ASN B 270 "
        pdb=" CB  ASN B 270 "
        pdb=" CG  ASN B 270 "
      ideal   model   delta    sigma   weight residual
     112.60  117.21   -4.61 1.00e+00 1.00e+00 2.13e+01
  angle pdb=" CA  LEU A  60 "
        pdb=" CB  LEU A  60 "
        pdb=" CG  LEU A  60 "
      ideal   model   delta    sigma   weight residual
     116.30  132.32  -16.02 3.50e+00 8.16e-02 2.09e+01
  ... (remaining 9195 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 3471
       17.95 -    35.90: 370
       35.90 -    53.86: 67
       53.86 -    71.81: 9
       71.81 -    89.76: 5
  Dihedral angle restraints: 3922
    sinusoidal: 1476
      harmonic: 2446
  Sorted by residual:
  dihedral pdb=" CA  SER A  86 "
           pdb=" C   SER A  86 "
           pdb=" N   ALA A  87 "
           pdb=" CA  ALA A  87 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.48   29.52     0      5.00e+00 4.00e-02 3.49e+01
  dihedral pdb=" CA  GLY A  47 "
           pdb=" C   GLY A  47 "
           pdb=" N   LEU A  48 "
           pdb=" CA  LEU A  48 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.78   28.22     0      5.00e+00 4.00e-02 3.19e+01
  dihedral pdb=" CA  ASN A 270 "
           pdb=" C   ASN A 270 "
           pdb=" N   LYS A 271 "
           pdb=" CA  LYS A 271 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.38   25.62     0      5.00e+00 4.00e-02 2.63e+01
  ... (remaining 3919 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 742
       0.055 -    0.111: 281
       0.111 -    0.166: 52
       0.166 -    0.222: 7
       0.222 -    0.277: 4
  Chirality restraints: 1086
  Sorted by residual:
  chirality pdb=" CB  VAL B 273 "
            pdb=" CA  VAL B 273 "
            pdb=" CG1 VAL B 273 "
            pdb=" CG2 VAL B 273 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 1.92e+00
  chirality pdb=" CB  ILE A 356 "
            pdb=" CA  ILE A 356 "
            pdb=" CG1 ILE A 356 "
            pdb=" CG2 ILE A 356 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.27 2.00e-01 2.50e+01 1.88e+00
  chirality pdb=" CA  THR A  31 "
            pdb=" N   THR A  31 "
            pdb=" C   THR A  31 "
            pdb=" CB  THR A  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.28    0.24 2.00e-01 2.50e+01 1.46e+00
  ... (remaining 1083 not shown)

  Planarity restraints: 1154
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 266 "    0.050 5.00e-02 4.00e+02   7.57e-02 9.18e+00
        pdb=" N   PRO B 267 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO B 267 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO B 267 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 149 "    0.046 5.00e-02 4.00e+02   6.90e-02 7.61e+00
        pdb=" N   PRO B 150 "   -0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO B 150 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B 150 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 270 "   -0.014 2.00e-02 2.50e+03   2.75e-02 7.55e+00
        pdb=" C   ASN B 270 "    0.048 2.00e-02 2.50e+03
        pdb=" O   ASN B 270 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   LYS B 271 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 1151 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1801
        2.80 -     3.32: 6254
        3.32 -     3.85: 11297
        3.85 -     4.37: 13005
        4.37 -     4.90: 22154
  Nonbonded interactions: 54511
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  94 "
            pdb=" OG  SER B 350 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   ARG A 340 "
            pdb=" OG1 THR A 344 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" OH  TYR A  94 "
            pdb=" OG  SER A 350 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" OE2 GLU A 414 "
            pdb=" OH  TYR A 419 "
     model   vdw
     2.335 3.040
  nonbonded pdb=" O   VAL A 412 "
            pdb=" OG1 THR A 416 "
     model   vdw
     2.341 3.040
  ... (remaining 54506 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.470
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.900
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
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      :  0.006   0.084   6774  Z= 0.274
  Angle     :  1.069  16.017   9200  Z= 0.549
  Chirality :  0.059   0.277   1086
  Planarity :  0.008   0.076   1154
  Dihedral  : 15.190  89.760   2378
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  8.86 %
    Favored  : 90.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -5.18 (0.19), residues: 882
  helix: -3.05 (0.14), residues: 648
  sheet:  None (None), residues: 0
  loop : -3.92 (0.30), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 160 
 TYR   0.014   0.002   TYR B 210 
 PHE   0.019   0.002   PHE A 379 
 TRP   0.012   0.002   TRP A 291 
 HIS   0.004   0.001   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00642 ( 6774)
  covalent geometry    : angle       1.06933 ( 9200)
  hydrogen bonds       : bond        0.12003 (  400)
  hydrogen bonds       : angle       6.34538 ( 1197)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 204
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 LEU cc_start: 0.9328 (mp) cc_final: 0.9101 (mm)
REVERT: A   92 PHE cc_start: 0.8744 (t80) cc_final: 0.8525 (t80)
REVERT: A  144 VAL cc_start: 0.8861 (OUTLIER) cc_final: 0.8598 (t)
REVERT: A  281 HIS cc_start: 0.7925 (t-90) cc_final: 0.7710 (t-90)
REVERT: A  336 ILE cc_start: 0.9010 (mt) cc_final: 0.8730 (mt)
REVERT: A  360 MET cc_start: 0.8408 (mtt) cc_final: 0.8163 (mtt)
REVERT: B   45 LEU cc_start: 0.8735 (mm) cc_final: 0.8305 (mm)
REVERT: B   55 LYS cc_start: 0.8880 (tttt) cc_final: 0.8657 (tttt)
REVERT: B  330 MET cc_start: 0.7701 (tpp) cc_final: 0.7112 (ptm)
REVERT: B  332 MET cc_start: 0.7835 (tpt) cc_final: 0.7490 (tpp)
REVERT: B  455 LYS cc_start: 0.8815 (tmtt) cc_final: 0.8504 (ttpp)
  outliers start: 5
  outliers final: 2
  residues processed: 206
  average time/residue: 0.0846
  time to fit residues: 22.7654
Evaluate side-chains
  159 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 156
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain B residue  144 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:   20.0000
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.0060
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.6998

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

Flipped N/Q/H residues before XYZ refinement:
A 119 GLN
A 153 GLN
A 157 ASN
A 460 GLN
B 119 GLN
B 157 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.137476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.104771 restraints weight = 10022.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.107827 restraints weight = 6212.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.109631 restraints weight = 4699.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.111043 restraints weight = 4004.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.111289 restraints weight = 3610.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.1730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6774  Z= 0.138
  Angle     :  0.691  10.311   9200  Z= 0.337
  Chirality :  0.043   0.139   1086
  Planarity :  0.006   0.057   1154
  Dihedral  :  5.923  43.238    944
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 17.57 %
    Favored  : 79.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.16 (0.24), residues: 882
  helix: -1.41 (0.18), residues: 642
  sheet:  None (None), residues: 0
  loop : -3.72 (0.30), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 282 
 TYR   0.015   0.001   TYR A 100 
 PHE   0.014   0.001   PHE B  92 
 TRP   0.019   0.001   TRP A 291 
 HIS   0.005   0.001   HIS A  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6774)
  covalent geometry    : angle       0.69124 ( 9200)
  hydrogen bonds       : bond        0.03480 (  400)
  hydrogen bonds       : angle       4.48950 ( 1197)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 163
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.8400 (m-30) cc_final: 0.8061 (m-30)
REVERT: A  144 VAL cc_start: 0.8868 (OUTLIER) cc_final: 0.8633 (t)
REVERT: A  227 ILE cc_start: 0.9168 (mm) cc_final: 0.8746 (mt)
REVERT: A  228 MET cc_start: 0.8194 (mmm) cc_final: 0.7960 (mmm)
REVERT: A  243 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7142 (mtpp)
REVERT: A  264 ILE cc_start: 0.8613 (pt) cc_final: 0.8362 (pt)
REVERT: A  332 MET cc_start: 0.7450 (tpp) cc_final: 0.6619 (tpp)
REVERT: A  336 ILE cc_start: 0.9002 (mt) cc_final: 0.8487 (mt)
REVERT: B   45 LEU cc_start: 0.8746 (mm) cc_final: 0.8279 (mm)
REVERT: B   55 LYS cc_start: 0.8849 (tttt) cc_final: 0.8202 (mtpt)
REVERT: B   99 LYS cc_start: 0.7625 (tptt) cc_final: 0.7327 (tptt)
REVERT: B  330 MET cc_start: 0.7074 (tpp) cc_final: 0.6598 (ptm)
REVERT: B  332 MET cc_start: 0.7624 (tpt) cc_final: 0.7302 (tpp)
  outliers start: 22
  outliers final: 11
  residues processed: 178
  average time/residue: 0.0768
  time to fit residues: 18.4272
Evaluate side-chains
  157 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 144
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   70 HIS
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  243 LYS
Chi-restraints excluded: chain A residue  385 GLU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  460 GLN
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  365 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 84 optimal weight:    0.5980
   chunk 5 optimal weight:    6.9990
   chunk 28 optimal weight:    0.0870
   chunk 56 optimal weight:    0.4980
   chunk 80 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9980
   chunk 52 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 70 optimal weight:    5.9990
   chunk 69 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.138932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.106663 restraints weight = 9980.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.109797 restraints weight = 6213.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.111848 restraints weight = 4682.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.112854 restraints weight = 3952.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.113709 restraints weight = 3593.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.2207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6774  Z= 0.132
  Angle     :  0.666  10.777   9200  Z= 0.323
  Chirality :  0.042   0.199   1086
  Planarity :  0.005   0.050   1154
  Dihedral  :  5.490  46.699    943
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 19.82 %
    Favored  : 76.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.27 (0.27), residues: 882
  helix: -0.71 (0.20), residues: 646
  sheet:  None (None), residues: 0
  loop : -3.56 (0.31), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  98 
 TYR   0.014   0.001   TYR A 210 
 PHE   0.016   0.001   PHE A  92 
 TRP   0.021   0.001   TRP B  59 
 HIS   0.013   0.002   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 6774)
  covalent geometry    : angle       0.66624 ( 9200)
  hydrogen bonds       : bond        0.03284 (  400)
  hydrogen bonds       : angle       4.26728 ( 1197)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 151
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 MET cc_start: 0.7772 (mtp) cc_final: 0.7315 (mtp)
REVERT: A  144 VAL cc_start: 0.8839 (OUTLIER) cc_final: 0.8590 (t)
REVERT: A  227 ILE cc_start: 0.9132 (mm) cc_final: 0.8703 (mt)
REVERT: A  243 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7143 (mtpp)
REVERT: A  281 HIS cc_start: 0.8101 (t70) cc_final: 0.7884 (t70)
REVERT: A  332 MET cc_start: 0.7128 (tpp) cc_final: 0.6579 (tpp)
REVERT: A  336 ILE cc_start: 0.8980 (mt) cc_final: 0.8211 (mt)
REVERT: A  360 MET cc_start: 0.8243 (mtt) cc_final: 0.8016 (mtt)
REVERT: A  397 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8644 (tt)
REVERT: A  455 LYS cc_start: 0.8744 (ttpp) cc_final: 0.7999 (mtmm)
REVERT: B   45 LEU cc_start: 0.8724 (mm) cc_final: 0.8262 (mm)
REVERT: B   55 LYS cc_start: 0.8880 (tttt) cc_final: 0.8223 (mtpt)
REVERT: B  330 MET cc_start: 0.7037 (tpp) cc_final: 0.6501 (ptm)
REVERT: B  332 MET cc_start: 0.7367 (tpt) cc_final: 0.7125 (tpp)
REVERT: B  419 TYR cc_start: 0.6688 (m-80) cc_final: 0.6449 (m-80)
  outliers start: 22
  outliers final: 16
  residues processed: 165
  average time/residue: 0.0591
  time to fit residues: 13.7284
Evaluate side-chains
  158 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   70 HIS
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  243 LYS
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  385 GLU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  407 THR
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  410 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 13 optimal weight:    0.3980
   chunk 43 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 81 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 11 optimal weight:    0.8980
   chunk 83 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 175 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.144460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.114922 restraints weight = 9840.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.117866 restraints weight = 6192.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.119784 restraints weight = 4679.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.120667 restraints weight = 3928.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.121682 restraints weight = 3577.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.2417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6774  Z= 0.132
  Angle     :  0.649  10.620   9200  Z= 0.313
  Chirality :  0.042   0.155   1086
  Planarity :  0.004   0.047   1154
  Dihedral  :  5.253  46.020    943
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 21.62 %
    Favored  : 74.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.75 (0.27), residues: 882
  helix: -0.31 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -3.30 (0.31), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 282 
 TYR   0.013   0.001   TYR B 100 
 PHE   0.026   0.001   PHE B  92 
 TRP   0.022   0.001   TRP B  59 
 HIS   0.013   0.001   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6774)
  covalent geometry    : angle       0.64930 ( 9200)
  hydrogen bonds       : bond        0.03199 (  400)
  hydrogen bonds       : angle       4.16467 ( 1197)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 155
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8601 (t)
REVERT: A  210 TYR cc_start: 0.7821 (t80) cc_final: 0.7579 (t80)
REVERT: A  227 ILE cc_start: 0.9161 (mm) cc_final: 0.8787 (mt)
REVERT: A  332 MET cc_start: 0.7213 (tpp) cc_final: 0.6703 (tpp)
REVERT: A  336 ILE cc_start: 0.9045 (mt) cc_final: 0.8275 (mt)
REVERT: A  397 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8622 (tt)
REVERT: A  455 LYS cc_start: 0.8700 (ttpp) cc_final: 0.7993 (mtmm)
REVERT: B   45 LEU cc_start: 0.8714 (mm) cc_final: 0.8222 (mm)
REVERT: B   55 LYS cc_start: 0.8822 (tttt) cc_final: 0.8225 (mtpt)
REVERT: B  290 LYS cc_start: 0.8353 (mttm) cc_final: 0.7748 (mmtt)
REVERT: B  330 MET cc_start: 0.6992 (tpp) cc_final: 0.6377 (ptm)
REVERT: B  332 MET cc_start: 0.7492 (tpt) cc_final: 0.7201 (tpp)
  outliers start: 24
  outliers final: 17
  residues processed: 171
  average time/residue: 0.0716
  time to fit residues: 16.8345
Evaluate side-chains
  164 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 145
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   70 HIS
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  385 GLU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  407 THR
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  220 ILE
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  410 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 175 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.142750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.113572 restraints weight = 9991.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.116130 restraints weight = 7268.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.116894 restraints weight = 5268.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.117414 restraints weight = 4549.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.117560 restraints weight = 4228.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.2559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6774  Z= 0.156
  Angle     :  0.672  10.622   9200  Z= 0.322
  Chirality :  0.043   0.210   1086
  Planarity :  0.004   0.058   1154
  Dihedral  :  5.238  47.783    943
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 22.07 %
    Favored  : 73.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.44 (0.28), residues: 882
  helix: -0.14 (0.21), residues: 646
  sheet:  None (None), residues: 0
  loop : -3.14 (0.33), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 282 
 TYR   0.016   0.002   TYR B 100 
 PHE   0.012   0.001   PHE A  92 
 TRP   0.020   0.001   TRP B  59 
 HIS   0.014   0.001   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 6774)
  covalent geometry    : angle       0.67218 ( 9200)
  hydrogen bonds       : bond        0.03229 (  400)
  hydrogen bonds       : angle       4.12036 ( 1197)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 151
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 VAL cc_start: 0.8918 (OUTLIER) cc_final: 0.8626 (t)
REVERT: A  153 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8716 (tt0)
REVERT: A  210 TYR cc_start: 0.7872 (t80) cc_final: 0.7661 (t80)
REVERT: A  227 ILE cc_start: 0.9231 (mm) cc_final: 0.8832 (mt)
REVERT: A  332 MET cc_start: 0.7351 (tpp) cc_final: 0.6796 (tpp)
REVERT: A  336 ILE cc_start: 0.9050 (mt) cc_final: 0.8287 (mt)
REVERT: A  397 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8631 (tt)
REVERT: A  455 LYS cc_start: 0.8650 (ttpp) cc_final: 0.7921 (mtmm)
REVERT: B   45 LEU cc_start: 0.8753 (mm) cc_final: 0.8237 (mm)
REVERT: B   55 LYS cc_start: 0.8876 (tttt) cc_final: 0.8220 (mtpt)
REVERT: B   92 PHE cc_start: 0.8869 (t80) cc_final: 0.8615 (t80)
REVERT: B   99 LYS cc_start: 0.7889 (tppp) cc_final: 0.7583 (tptt)
REVERT: B  290 LYS cc_start: 0.8476 (mttm) cc_final: 0.7879 (mmtt)
REVERT: B  330 MET cc_start: 0.7060 (tpp) cc_final: 0.6378 (ptm)
REVERT: B  332 MET cc_start: 0.7648 (tpt) cc_final: 0.7330 (tpp)
REVERT: B  419 TYR cc_start: 0.6857 (m-80) cc_final: 0.6590 (m-80)
  outliers start: 28
  outliers final: 18
  residues processed: 172
  average time/residue: 0.0743
  time to fit residues: 17.4633
Evaluate side-chains
  164 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 143
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   70 HIS
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  153 GLN
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  385 GLU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  407 THR
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  410 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 5 optimal weight:    0.1980
   chunk 44 optimal weight:    5.9990
   chunk 27 optimal weight:    6.9990
   chunk 83 optimal weight:    0.6980
   chunk 45 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 437 GLN
** A 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 175 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.142580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.111468 restraints weight = 9991.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.114418 restraints weight = 6396.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.116373 restraints weight = 4881.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.117309 restraints weight = 4160.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.118136 restraints weight = 3788.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.2717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6774  Z= 0.130
  Angle     :  0.649  10.617   9200  Z= 0.310
  Chirality :  0.042   0.174   1086
  Planarity :  0.004   0.053   1154
  Dihedral  :  5.096  45.106    943
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 23.87 %
    Favored  : 71.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.14 (0.28), residues: 882
  helix:  0.15 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -3.15 (0.32), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 282 
 TYR   0.015   0.001   TYR B 100 
 PHE   0.026   0.001   PHE A  92 
 TRP   0.021   0.001   TRP B  59 
 HIS   0.011   0.001   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6774)
  covalent geometry    : angle       0.64925 ( 9200)
  hydrogen bonds       : bond        0.03088 (  400)
  hydrogen bonds       : angle       4.05168 ( 1197)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 153
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 VAL cc_start: 0.8939 (OUTLIER) cc_final: 0.8594 (t)
REVERT: A  153 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8715 (tt0)
REVERT: A  227 ILE cc_start: 0.9187 (mm) cc_final: 0.8783 (mt)
REVERT: A  332 MET cc_start: 0.7266 (tpp) cc_final: 0.6790 (tpp)
REVERT: A  336 ILE cc_start: 0.9034 (mt) cc_final: 0.8284 (mt)
REVERT: A  360 MET cc_start: 0.8247 (mtt) cc_final: 0.7946 (mtt)
REVERT: A  397 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8536 (tt)
REVERT: A  455 LYS cc_start: 0.8697 (ttpp) cc_final: 0.7980 (mtmm)
REVERT: B   45 LEU cc_start: 0.8731 (mm) cc_final: 0.8232 (mm)
REVERT: B   55 LYS cc_start: 0.8834 (tttt) cc_final: 0.8190 (mtpt)
REVERT: B   78 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8624 (pp)
REVERT: B  330 MET cc_start: 0.7002 (tpp) cc_final: 0.6401 (ptm)
REVERT: B  332 MET cc_start: 0.7622 (tpt) cc_final: 0.7324 (tpp)
  outliers start: 28
  outliers final: 15
  residues processed: 174
  average time/residue: 0.0664
  time to fit residues: 16.0468
Evaluate side-chains
  164 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 145
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   70 HIS
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  153 GLN
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  385 GLU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  410 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 57 optimal weight:    0.5980
   chunk 37 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 70 optimal weight:    6.9990
   chunk 71 optimal weight:    4.9990
   chunk 48 optimal weight:    7.9990
   chunk 3 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
A 460 GLN
B 175 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.134993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.103843 restraints weight = 9930.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.106410 restraints weight = 6413.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.108392 restraints weight = 4959.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.109152 restraints weight = 4213.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.110013 restraints weight = 3883.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.2760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.077   6774  Z= 0.228
  Angle     :  0.747  10.619   9200  Z= 0.354
  Chirality :  0.046   0.177   1086
  Planarity :  0.005   0.056   1154
  Dihedral  :  5.309  47.554    943
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 24.47 %
    Favored  : 71.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.19 (0.28), residues: 882
  helix:  0.12 (0.21), residues: 640
  sheet:  None (None), residues: 0
  loop : -3.21 (0.32), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  98 
 TYR   0.016   0.002   TYR B 419 
 PHE   0.026   0.002   PHE A 357 
 TRP   0.022   0.001   TRP B  59 
 HIS   0.015   0.002   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00555 ( 6774)
  covalent geometry    : angle       0.74669 ( 9200)
  hydrogen bonds       : bond        0.03483 (  400)
  hydrogen bonds       : angle       4.21320 ( 1197)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 138
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
REVERT: A  210 TYR cc_start: 0.7981 (t80) cc_final: 0.7672 (t80)
REVERT: A  332 MET cc_start: 0.7292 (tpp) cc_final: 0.6664 (tpp)
REVERT: A  336 ILE cc_start: 0.9088 (mt) cc_final: 0.8320 (mt)
REVERT: A  397 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8692 (tt)
REVERT: A  455 LYS cc_start: 0.8664 (ttpp) cc_final: 0.7970 (mtmm)
REVERT: B   45 LEU cc_start: 0.8776 (mm) cc_final: 0.8263 (mm)
REVERT: B   55 LYS cc_start: 0.8905 (tttt) cc_final: 0.8250 (mtpt)
REVERT: B   99 LYS cc_start: 0.7855 (tppp) cc_final: 0.7560 (tptt)
REVERT: B  330 MET cc_start: 0.7289 (tpp) cc_final: 0.6623 (ptt)
REVERT: B  332 MET cc_start: 0.7653 (tpt) cc_final: 0.7351 (tpp)
REVERT: B  419 TYR cc_start: 0.7052 (m-80) cc_final: 0.6753 (m-80)
  outliers start: 28
  outliers final: 21
  residues processed: 158
  average time/residue: 0.0770
  time to fit residues: 16.4747
Evaluate side-chains
  153 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 131
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   70 HIS
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  260 ILE
Chi-restraints excluded: chain A residue  363 LEU
Chi-restraints excluded: chain A residue  385 GLU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  407 THR
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  374 VAL
Chi-restraints excluded: chain B residue  435 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 76 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 77 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 85 optimal weight:    2.9990
   chunk 45 optimal weight:    0.1980
   chunk 31 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 460 GLN
B 175 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.143869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.112933 restraints weight = 9871.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.115789 restraints weight = 6424.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.117582 restraints weight = 4964.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.118918 restraints weight = 4234.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.119322 restraints weight = 3826.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.2888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6774  Z= 0.137
  Angle     :  0.684  10.673   9200  Z= 0.322
  Chirality :  0.044   0.223   1086
  Planarity :  0.004   0.052   1154
  Dihedral  :  5.066  44.946    942
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 25.68 %
    Favored  : 70.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.87 (0.28), residues: 882
  helix:  0.33 (0.21), residues: 642
  sheet:  None (None), residues: 0
  loop : -3.05 (0.33), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 205 
 TYR   0.015   0.002   TYR B 100 
 PHE   0.018   0.001   PHE A 379 
 TRP   0.028   0.001   TRP B  59 
 HIS   0.014   0.001   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 6774)
  covalent geometry    : angle       0.68448 ( 9200)
  hydrogen bonds       : bond        0.03146 (  400)
  hydrogen bonds       : angle       4.06870 ( 1197)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 154
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8650 (tt0)
REVERT: A  227 ILE cc_start: 0.9259 (mm) cc_final: 0.8863 (mt)
REVERT: A  332 MET cc_start: 0.7154 (tpp) cc_final: 0.6717 (tpp)
REVERT: A  336 ILE cc_start: 0.9022 (mt) cc_final: 0.8280 (mt)
REVERT: A  397 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8514 (tt)
REVERT: A  455 LYS cc_start: 0.8716 (ttpp) cc_final: 0.8019 (mtmm)
REVERT: B   45 LEU cc_start: 0.8731 (mm) cc_final: 0.8344 (mm)
REVERT: B   55 LYS cc_start: 0.8872 (tttt) cc_final: 0.8221 (mtpt)
REVERT: B   99 LYS cc_start: 0.7841 (tppp) cc_final: 0.7488 (tptt)
REVERT: B  330 MET cc_start: 0.7034 (tpp) cc_final: 0.6382 (ptm)
REVERT: B  332 MET cc_start: 0.7625 (tpt) cc_final: 0.7317 (tpp)
REVERT: B  419 TYR cc_start: 0.7036 (m-80) cc_final: 0.6712 (m-80)
  outliers start: 23
  outliers final: 15
  residues processed: 169
  average time/residue: 0.0656
  time to fit residues: 15.3761
Evaluate side-chains
  159 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 142
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   70 HIS
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  153 GLN
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  385 GLU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain A residue  460 GLN
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  365 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 66 optimal weight:    5.9990
   chunk 59 optimal weight:    0.0770
   chunk 51 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 65 optimal weight:    0.8980
   chunk 86 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 57 optimal weight:    0.2980
   chunk 2 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
B 175 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.149147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.118479 restraints weight = 9789.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.121476 restraints weight = 6325.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.123175 restraints weight = 4807.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.124706 restraints weight = 4109.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.125386 restraints weight = 3686.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.3056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6774  Z= 0.133
  Angle     :  0.713  10.662   9200  Z= 0.333
  Chirality :  0.044   0.204   1086
  Planarity :  0.004   0.046   1154
  Dihedral  :  4.970  43.561    942
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 26.43 %
    Favored  : 70.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.77 (0.28), residues: 882
  helix:  0.47 (0.21), residues: 634
  sheet:  None (None), residues: 0
  loop : -3.08 (0.32), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 205 
 TYR   0.015   0.002   TYR B 419 
 PHE   0.039   0.001   PHE A  92 
 TRP   0.029   0.001   TRP B  59 
 HIS   0.012   0.001   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 6774)
  covalent geometry    : angle       0.71263 ( 9200)
  hydrogen bonds       : bond        0.03118 (  400)
  hydrogen bonds       : angle       4.07134 ( 1197)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 156
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
REVERT: A  144 VAL cc_start: 0.9034 (OUTLIER) cc_final: 0.8776 (t)
REVERT: A  153 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8619 (tt0)
REVERT: A  210 TYR cc_start: 0.7604 (t80) cc_final: 0.6633 (t80)
REVERT: A  227 ILE cc_start: 0.9242 (mm) cc_final: 0.8842 (mt)
REVERT: A  332 MET cc_start: 0.7072 (tpp) cc_final: 0.6675 (tpp)
REVERT: A  336 ILE cc_start: 0.9019 (mt) cc_final: 0.8273 (mt)
REVERT: A  397 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8485 (tt)
REVERT: A  455 LYS cc_start: 0.8660 (ttpp) cc_final: 0.7942 (mtmm)
REVERT: B   45 LEU cc_start: 0.8713 (mm) cc_final: 0.8239 (mm)
REVERT: B   55 LYS cc_start: 0.8826 (tttt) cc_final: 0.8213 (mtpt)
REVERT: B   99 LYS cc_start: 0.7810 (tppp) cc_final: 0.7451 (tptt)
REVERT: B  205 ARG cc_start: 0.7312 (ttp80) cc_final: 0.7011 (ttp-110)
REVERT: B  228 MET cc_start: 0.8031 (mmt) cc_final: 0.7739 (mmm)
REVERT: B  330 MET cc_start: 0.7010 (tpp) cc_final: 0.6386 (ptm)
REVERT: B  332 MET cc_start: 0.7623 (tpt) cc_final: 0.7296 (tpp)
REVERT: B  338 VAL cc_start: 0.9259 (t) cc_final: 0.9028 (m)
REVERT: B  414 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7750 (mp0)
REVERT: B  419 TYR cc_start: 0.6977 (m-80) cc_final: 0.6568 (m-80)
  outliers start: 21
  outliers final: 17
  residues processed: 170
  average time/residue: 0.0746
  time to fit residues: 17.1136
Evaluate side-chains
  168 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  153 GLN
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  385 GLU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  407 THR
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  435 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 64 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 14 optimal weight:    4.9990
   chunk 40 optimal weight:    0.3980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 119 GLN
A 460 GLN
B 175 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.147058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.116782 restraints weight = 9839.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.119638 restraints weight = 6241.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.121429 restraints weight = 4769.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.122800 restraints weight = 4064.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.123464 restraints weight = 3657.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.3057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6774  Z= 0.158
  Angle     :  0.745  12.390   9200  Z= 0.346
  Chirality :  0.044   0.211   1086
  Planarity :  0.004   0.044   1154
  Dihedral  :  4.955  41.411    942
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 26.58 %
    Favored  : 70.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.74 (0.28), residues: 882
  helix:  0.43 (0.21), residues: 642
  sheet:  None (None), residues: 0
  loop : -3.01 (0.33), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 205 
 TYR   0.017   0.002   TYR A 210 
 PHE   0.019   0.001   PHE A 379 
 TRP   0.031   0.001   TRP B  59 
 HIS   0.013   0.001   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 6774)
  covalent geometry    : angle       0.74522 ( 9200)
  hydrogen bonds       : bond        0.03173 (  400)
  hydrogen bonds       : angle       4.11093 ( 1197)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 147
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
REVERT: A  144 VAL cc_start: 0.9048 (OUTLIER) cc_final: 0.8764 (t)
REVERT: A  153 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8653 (tt0)
REVERT: A  210 TYR cc_start: 0.7802 (t80) cc_final: 0.7324 (t80)
REVERT: A  227 ILE cc_start: 0.9264 (mm) cc_final: 0.8863 (mt)
REVERT: A  332 MET cc_start: 0.7073 (tpp) cc_final: 0.6668 (tpp)
REVERT: A  336 ILE cc_start: 0.9016 (mt) cc_final: 0.8277 (mt)
REVERT: A  455 LYS cc_start: 0.8677 (ttpp) cc_final: 0.7968 (mtmm)
REVERT: B   45 LEU cc_start: 0.8724 (mm) cc_final: 0.8229 (mm)
REVERT: B   55 LYS cc_start: 0.8879 (tttt) cc_final: 0.8252 (mtpt)
REVERT: B   99 LYS cc_start: 0.7826 (tppp) cc_final: 0.7469 (tptt)
REVERT: B  208 PHE cc_start: 0.7872 (t80) cc_final: 0.7568 (t80)
REVERT: B  216 LYS cc_start: 0.8631 (mtmm) cc_final: 0.8415 (mtmm)
REVERT: B  228 MET cc_start: 0.8015 (mmt) cc_final: 0.7698 (mmm)
REVERT: B  290 LYS cc_start: 0.8245 (mmtt) cc_final: 0.7914 (mmtp)
REVERT: B  330 MET cc_start: 0.7100 (tpp) cc_final: 0.6494 (ptt)
REVERT: B  332 MET cc_start: 0.7608 (tpt) cc_final: 0.7306 (tpp)
REVERT: B  414 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7757 (mp0)
REVERT: B  419 TYR cc_start: 0.7018 (m-80) cc_final: 0.6614 (m-80)
  outliers start: 22
  outliers final: 18
  residues processed: 162
  average time/residue: 0.0745
  time to fit residues: 16.4079
Evaluate side-chains
  166 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 146
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ILE
Chi-restraints excluded: chain A residue   70 HIS
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  153 GLN
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  385 GLU
Chi-restraints excluded: chain A residue  407 THR
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain A residue  460 GLN
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  435 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 84 optimal weight:    0.7980
   chunk 69 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 77 optimal weight:    9.9990
   chunk 57 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 460 GLN
B 175 HIS
** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.142447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.110884 restraints weight = 9899.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.113774 restraints weight = 6464.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.115580 restraints weight = 4987.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.116468 restraints weight = 4280.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.117515 restraints weight = 3922.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.3145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6774  Z= 0.150
  Angle     :  0.756  10.625   9200  Z= 0.350
  Chirality :  0.044   0.207   1086
  Planarity :  0.005   0.068   1154
  Dihedral  :  4.941  40.972    942
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 27.63 %
    Favored  : 69.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.73 (0.28), residues: 882
  helix:  0.44 (0.21), residues: 642
  sheet:  None (None), residues: 0
  loop : -3.00 (0.33), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 205 
 TYR   0.017   0.002   TYR A 210 
 PHE   0.036   0.001   PHE B  92 
 TRP   0.033   0.001   TRP B  59 
 HIS   0.013   0.001   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 6774)
  covalent geometry    : angle       0.75565 ( 9200)
  hydrogen bonds       : bond        0.03173 (  400)
  hydrogen bonds       : angle       4.13193 ( 1197)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1126.09 seconds
wall clock time: 20 minutes 2.88 seconds (1202.88 seconds total)