Starting phenix.real_space_refine
on Wed Sep 17 13:13:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fuu_50778/09_2025/9fuu_50778.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fuu_50778/09_2025/9fuu_50778.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fuu_50778/09_2025/9fuu_50778.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fuu_50778/09_2025/9fuu_50778.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fuu_50778/09_2025/9fuu_50778.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fuu_50778/09_2025/9fuu_50778.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.015
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      54      5.16       5
     C    5590      2.51       5
     N    1536      2.21       5
     O    1642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8822
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4411
          Classifications: {'peptide': 569}
          Link IDs: {'PTRANS': 13, 'TRANS': 555}
    Chain: "B"
      Number of atoms: 4411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4411
          Classifications: {'peptide': 569}
          Link IDs: {'PTRANS': 13, 'TRANS': 555}
  Time building chain proxies: 2.20, per 1000 atoms: 0.25
  Number of scatterers: 8822
  At special positions: 0
  Unit cell: (112.88, 104.72, 135.32, 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      54     16.00
     O    1642      8.00
     N    1536      7.00
     C    5590      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: 0.97
  Conformation dependent library (CDL) restraints added in 392.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2128

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 6 sheets defined
      54.1% alpha, 7.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 22
      removed outlier: 4.026A  pdb=" N   ALA A  21 " --> pdb=" O   PRO A  18 " (cutoff:3.500A)
      Proline residue:  A  22  - end of helix
    Processing helix  chain 'A' and resid 23 through 39
      removed outlier: 3.808A  pdb=" N   LEU A  27 " --> pdb=" O   PHE A  23 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LEU A  34 " --> pdb=" O   ALA A  30 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ASN A  37 " --> pdb=" O   ALA A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 46
      removed outlier: 3.511A  pdb=" N   LEU A  45 " --> pdb=" O   ASP A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 54
    Processing helix  chain 'A' and resid 66 through 74
      removed outlier: 3.650A  pdb=" N   VAL A  70 " --> pdb=" O   TRP A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 88
    Processing helix  chain 'A' and resid 100 through 108
    Processing helix  chain 'A' and resid 112 through 117
      removed outlier: 4.256A  pdb=" N   PHE A 116 " --> pdb=" O   PRO A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 145
      removed outlier: 3.779A  pdb=" N   THR A 145 " --> pdb=" O   GLY A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 164
    Processing helix  chain 'A' and resid 164 through 212
      removed outlier: 3.697A  pdb=" N   ILE A 170 " --> pdb=" O   GLN A 166 " (cutoff:3.500A)
      Proline residue:  A 176  - end of helix
      removed outlier: 3.962A  pdb=" N   THR A 199 " --> pdb=" O   ASN A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 220
    Processing helix  chain 'A' and resid 222 through 231
      removed outlier: 3.670A  pdb=" N   THR A 227 " --> pdb=" O   GLN A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 240
      removed outlier: 3.892A  pdb=" N   LEU A 239 " --> pdb=" O   ASN A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 272
      removed outlier: 3.733A  pdb=" N   PHE A 272 " --> pdb=" O   TYR A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 277
      removed outlier: 3.828A  pdb=" N   ASP A 277 " --> pdb=" O   PRO A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 289
    Processing helix  chain 'A' and resid 294 through 303
      removed outlier: 3.591A  pdb=" N   LEU A 298 " --> pdb=" O   LEU A 294 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ASN A 303 " --> pdb=" O   LYS A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 323
      removed outlier: 3.601A  pdb=" N   THR A 317 " --> pdb=" O   ALA A 313 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   LEU A 318 " --> pdb=" O   ALA A 314 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   PHE A 319 " --> pdb=" O   CYS A 315 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ILE A 321 " --> pdb=" O   THR A 317 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ASP A 323 " --> pdb=" O   PHE A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 390
      removed outlier: 3.863A  pdb=" N   ILE A 385 " --> pdb=" O   GLY A 381 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ILE A 389 " --> pdb=" O   ILE A 385 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   THR A 390 " --> pdb=" O   ALA A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 410
      No H-bonds generated for 'chain 'A' and resid 408 through 410'
    Processing helix  chain 'A' and resid 411 through 418
    Processing helix  chain 'A' and resid 446 through 457
    Processing helix  chain 'A' and resid 459 through 466
      removed outlier: 3.900A  pdb=" N   ILE A 463 " --> pdb=" O   ALA A 459 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   MET A 466 " --> pdb=" O   PHE A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 498
      removed outlier: 3.848A  pdb=" N   ARG A 488 " --> pdb=" O   GLY A 484 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ILE A 489 " --> pdb=" O   GLN A 485 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   ALA A 490 " --> pdb=" O   ARG A 486 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ILE A 491 " --> pdb=" O   GLN A 487 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 528
    Processing helix  chain 'A' and resid 538 through 545
    Processing helix  chain 'A' and resid 561 through 568
    Processing helix  chain 'A' and resid 571 through 580
    Processing helix  chain 'B' and resid 16 through 21
    Processing helix  chain 'B' and resid 23 through 28
      removed outlier: 3.740A  pdb=" N   LEU B  27 " --> pdb=" O   PHE B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 39
    Processing helix  chain 'B' and resid 41 through 46
    Processing helix  chain 'B' and resid 47 through 55
    Processing helix  chain 'B' and resid 62 through 74
      removed outlier: 3.868A  pdb=" N   MET B  67 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
      Proline residue:  B  68  - end of helix
      removed outlier: 3.613A  pdb=" N   ILE B  72 " --> pdb=" O   PRO B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 88
    Processing helix  chain 'B' and resid 100 through 109
    Processing helix  chain 'B' and resid 113 through 119
      removed outlier: 3.538A  pdb=" N   ASP B 117 " --> pdb=" O   VAL B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 130
      removed outlier: 4.088A  pdb=" N   ILE B 128 " --> pdb=" O   LEU B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 164
      removed outlier: 3.576A  pdb=" N   MET B 159 " --> pdb=" O   GLY B 155 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   PHE B 161 " --> pdb=" O   PHE B 157 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 212
      removed outlier: 3.705A  pdb=" N   ILE B 172 " --> pdb=" O   SER B 168 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ALA B 175 " --> pdb=" O   LEU B 171 " (cutoff:3.500A)
      Proline residue:  B 176  - end of helix
      removed outlier: 3.726A  pdb=" N   ILE B 182 " --> pdb=" O   VAL B 178 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   THR B 199 " --> pdb=" O   ASN B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 221
    Processing helix  chain 'B' and resid 224 through 229
    Processing helix  chain 'B' and resid 233 through 242
      removed outlier: 3.580A  pdb=" N   LEU B 239 " --> pdb=" O   ASN B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 272
      removed outlier: 3.687A  pdb=" N   ALA B 259 " --> pdb=" O   ILE B 255 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   PHE B 272 " --> pdb=" O   TYR B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 292
      removed outlier: 3.929A  pdb=" N   SER B 290 " --> pdb=" O   VAL B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 303
      removed outlier: 4.940A  pdb=" N   LEU B 301 " --> pdb=" O   PRO B 297 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ASN B 303 " --> pdb=" O   LYS B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 303 through 309
    Processing helix  chain 'B' and resid 315 through 322
    Processing helix  chain 'B' and resid 382 through 390
      removed outlier: 3.996A  pdb=" N   ALA B 386 " --> pdb=" O   LYS B 382 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   SER B 387 " --> pdb=" O   SER B 383 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LEU B 388 " --> pdb=" O   THR B 384 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ILE B 389 " --> pdb=" O   ILE B 385 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   THR B 390 " --> pdb=" O   ALA B 386 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 382 through 390'
    Processing helix  chain 'B' and resid 408 through 410
      No H-bonds generated for 'chain 'B' and resid 408 through 410'
    Processing helix  chain 'B' and resid 411 through 417
      removed outlier: 3.697A  pdb=" N   ASN B 417 " --> pdb=" O   ALA B 413 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 457
    Processing helix  chain 'B' and resid 459 through 465
      removed outlier: 3.747A  pdb=" N   ILE B 463 " --> pdb=" O   ALA B 459 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LYS B 465 " --> pdb=" O   ASP B 461 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 498
    Processing helix  chain 'B' and resid 515 through 527
    Processing helix  chain 'B' and resid 538 through 544
    Processing helix  chain 'B' and resid 561 through 568
      removed outlier: 3.630A  pdb=" N   GLU B 567 " --> pdb=" O   ASN B 563 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 571 through 580
    Processing sheet with id=AA1, first strand: chain 'A' and resid 357 through 362
      removed outlier: 4.364A  pdb=" N   ASN A 361 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   VAL A 347 " --> pdb=" O   ASN A 361 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 357 through 362
      removed outlier: 4.364A  pdb=" N   ASN A 361 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   VAL A 347 " --> pdb=" O   ASN A 361 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   VAL A 347 " --> pdb=" O   GLU A 397 " (cutoff:3.500A)
      removed outlier: 7.348A  pdb=" N   GLU A 397 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 419 through 422
      removed outlier: 6.682A  pdb=" N   ALA A 420 " --> pdb=" O   ILE A 503 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   ILE A 548 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
      removed outlier: 5.232A  pdb=" N   ARG A 559 " --> pdb=" O   ILE A 548 " (cutoff:3.500A)
      removed outlier: 7.288A  pdb=" N   VAL A 550 " --> pdb=" O   VAL A 557 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 363 through 366
      removed outlier: 5.507A  pdb=" N   PHE B 344 " --> pdb=" O   LEU B 401 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   LEU B 401 " --> pdb=" O   PHE B 344 " (cutoff:3.500A)
      removed outlier: 5.148A  pdb=" N   ASN B 346 " --> pdb=" O   GLU B 399 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   GLU B 399 " --> pdb=" O   ASN B 346 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 533 through 535
      removed outlier: 3.813A  pdb=" N   GLU B 558 " --> pdb=" O   VAL B 550 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 419 through 420

    357 hydrogen bonds defined for protein.
    1047 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.46

  Time building geometry restraints manager: 1.28 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1873
        1.33 -     1.45: 1871
        1.45 -     1.57: 5102
        1.57 -     1.69: 0
        1.69 -     1.81: 104
  Bond restraints: 8950
  Sorted by residual:
  bond pdb=" N   MET A  67 "
       pdb=" CA  MET A  67 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.04e-02 9.25e+03 1.17e+01
  bond pdb=" N   MET B  67 "
       pdb=" CA  MET B  67 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.030 1.04e-02 9.25e+03 8.55e+00
  bond pdb=" N   VAL A 113 "
       pdb=" CA  VAL A 113 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.41e-02 5.03e+03 6.52e+00
  bond pdb=" N   TRP B  66 "
       pdb=" CA  TRP B  66 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.29e-02 6.01e+03 6.25e+00
  bond pdb=" N   THR A 384 "
       pdb=" CA  THR A 384 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.030 1.26e-02 6.30e+03 5.80e+00
  ... (remaining 8945 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.23: 11237
        1.23 -     2.46: 701
        2.46 -     3.69: 116
        3.69 -     4.92: 30
        4.92 -     6.15: 8
  Bond angle restraints: 12092
  Sorted by residual:
  angle pdb=" N   VAL B 146 "
        pdb=" CA  VAL B 146 "
        pdb=" C   VAL B 146 "
      ideal   model   delta    sigma   weight residual
     113.53  107.56    5.97 9.80e-01 1.04e+00 3.71e+01
  angle pdb=" N   VAL A 146 "
        pdb=" CA  VAL A 146 "
        pdb=" C   VAL A 146 "
      ideal   model   delta    sigma   weight residual
     113.20  107.78    5.42 9.60e-01 1.09e+00 3.19e+01
  angle pdb=" N   LEU B 298 "
        pdb=" CA  LEU B 298 "
        pdb=" C   LEU B 298 "
      ideal   model   delta    sigma   weight residual
     114.62  108.47    6.15 1.14e+00 7.69e-01 2.91e+01
  angle pdb=" N   ILE A  89 "
        pdb=" CA  ILE A  89 "
        pdb=" C   ILE A  89 "
      ideal   model   delta    sigma   weight residual
     112.90  107.73    5.17 9.60e-01 1.09e+00 2.90e+01
  angle pdb=" N   VAL A  63 "
        pdb=" CA  VAL A  63 "
        pdb=" C   VAL A  63 "
      ideal   model   delta    sigma   weight residual
     113.71  109.12    4.59 9.50e-01 1.11e+00 2.33e+01
  ... (remaining 12087 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 4629
       17.94 -    35.88: 636
       35.88 -    53.82: 149
       53.82 -    71.76: 32
       71.76 -    89.70: 8
  Dihedral angle restraints: 5454
    sinusoidal: 2164
      harmonic: 3290
  Sorted by residual:
  dihedral pdb=" CA  ARG A  14 "
           pdb=" C   ARG A  14 "
           pdb=" N   ARG A  15 "
           pdb=" CA  ARG A  15 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.62   28.38     0      5.00e+00 4.00e-02 3.22e+01
  dihedral pdb=" CA  ARG B  14 "
           pdb=" C   ARG B  14 "
           pdb=" N   ARG B  15 "
           pdb=" CA  ARG B  15 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.72   25.28     0      5.00e+00 4.00e-02 2.56e+01
  dihedral pdb=" CA  ASP B 277 "
           pdb=" C   ASP B 277 "
           pdb=" N   SER B 278 "
           pdb=" CA  SER B 278 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.58   24.42     0      5.00e+00 4.00e-02 2.39e+01
  ... (remaining 5451 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1045
       0.041 -    0.083: 319
       0.083 -    0.124: 69
       0.124 -    0.165: 6
       0.165 -    0.207: 1
  Chirality restraints: 1440
  Sorted by residual:
  chirality pdb=" CA  ASP A 117 "
            pdb=" N   ASP A 117 "
            pdb=" C   ASP A 117 "
            pdb=" CB  ASP A 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CA  VAL A 113 "
            pdb=" N   VAL A 113 "
            pdb=" C   VAL A 113 "
            pdb=" CB  VAL A 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.66e-01
  chirality pdb=" CA  ILE A 548 "
            pdb=" N   ILE A 548 "
            pdb=" C   ILE A 548 "
            pdb=" CB  ILE A 548 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.42e-01
  ... (remaining 1437 not shown)

  Planarity restraints: 1532
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A  65 "   -0.014 2.00e-02 2.50e+03   2.91e-02 8.48e+00
        pdb=" C   VAL A  65 "    0.050 2.00e-02 2.50e+03
        pdb=" O   VAL A  65 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   TRP A  66 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 477 "   -0.007 2.00e-02 2.50e+03   1.48e-02 2.19e+00
        pdb=" C   ASN B 477 "    0.026 2.00e-02 2.50e+03
        pdb=" O   ASN B 477 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   GLY B 478 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A  17 "    0.024 5.00e-02 4.00e+02   3.58e-02 2.06e+00
        pdb=" N   PRO A  18 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO A  18 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A  18 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1529 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 431
        2.71 -     3.26: 9210
        3.26 -     3.81: 14040
        3.81 -     4.35: 18790
        4.35 -     4.90: 30385
  Nonbonded interactions: 72856
  Sorted by model distance:
  nonbonded pdb=" O   ARG A  61 "
            pdb=" OG  SER A  62 "
     model   vdw
     2.163 3.040
  nonbonded pdb=" OD1 ASN A 417 "
            pdb=" NH2 ARG A 441 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" OD1 ASN B 563 "
            pdb=" N   ASP B 564 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" O   THR A 285 "
            pdb=" OG  SER A 289 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" OG1 THR A 348 "
            pdb=" O   LEU A 359 "
     model   vdw
     2.247 3.040
  ... (remaining 72851 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: 0.02
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:             3.750
  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:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     10.620
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8950  Z= 0.235
  Angle     :  0.695   6.151  12092  Z= 0.429
  Chirality :  0.041   0.207   1440
  Planarity :  0.003   0.036   1532
  Dihedral  : 17.551  89.702   3326
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 28.82 %
    Favored  : 70.56 %
  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 aren not related in a simple way.
  whole: -3.08 (0.23), residues: 1134
  helix: -2.02 (0.19), residues: 682
  sheet:  0.27 (0.92), residues: 24
  loop : -1.96 (0.27), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 102 
 TYR   0.009   0.001   TYR B 439 
 PHE   0.014   0.001   PHE B 429 
 TRP   0.013   0.002   TRP B  66 
 HIS   0.004   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 ( 8950)
  covalent geometry    : angle       0.69471 (12092)
  hydrogen bonds       : bond        0.21750 (  355)
  hydrogen bonds       : angle       9.07765 ( 1047)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 138
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 MET cc_start: 0.8127 (ttp) cc_final: 0.7757 (ttp)
REVERT: B  255 ILE cc_start: 0.9180 (pt) cc_final: 0.8734 (mp)
REVERT: B  280 THR cc_start: 0.7456 (p) cc_final: 0.7112 (p)
  outliers start: 6
  outliers final: 2
  residues processed: 141
  average time/residue: 0.0938
  time to fit residues: 18.6437
Evaluate side-chains
  116 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 114
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue  435 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.0970
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:   10.0000
   chunk 106 optimal weight:   20.0000
   overall best weight:    2.8184

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

Flipped N/Q/H residues before XYZ refinement:
** A 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 576 HIS
** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 214 HIS
B 405 HIS
** B 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 435 ASN
** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.167654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.102972 restraints weight = 11756.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.105795 restraints weight = 7714.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.106830 restraints weight = 5212.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.106860 restraints weight = 4689.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.107020 restraints weight = 4804.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.1655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.062   8950  Z= 0.369
  Angle     :  0.783   7.165  12092  Z= 0.413
  Chirality :  0.050   0.164   1440
  Planarity :  0.005   0.048   1532
  Dihedral  :  6.847  48.918   1242
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  5.89 %
    Allowed  : 25.83 %
    Favored  : 68.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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 aren not related in a simple way.
  whole: -3.28 (0.23), residues: 1134
  helix: -2.16 (0.18), residues: 722
  sheet: -0.67 (0.69), residues: 50
  loop : -2.01 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 488 
 TYR   0.023   0.002   TYR A 439 
 PHE   0.020   0.003   PHE B 429 
 TRP   0.019   0.002   TRP B  17 
 HIS   0.005   0.002   HIS A 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00867 ( 8950)
  covalent geometry    : angle       0.78329 (12092)
  hydrogen bonds       : bond        0.04510 (  355)
  hydrogen bonds       : angle       5.93534 ( 1047)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 123
  time to evaluate  : 0.430 
Fit side-chains
REVERT: A  148 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7833 (ttp80)
REVERT: A  322 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8715 (tt)
REVERT: A  324 SER cc_start: 0.8383 (OUTLIER) cc_final: 0.8104 (t)
REVERT: A  421 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8548 (mp)
REVERT: B   36 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8658 (mp)
REVERT: B  100 MET cc_start: 0.8432 (tmm) cc_final: 0.7958 (ttt)
REVERT: B  276 MET cc_start: 0.7791 (mpp) cc_final: 0.7535 (mpp)
REVERT: B  280 THR cc_start: 0.8300 (p) cc_final: 0.8022 (p)
REVERT: B  423 SER cc_start: 0.9279 (OUTLIER) cc_final: 0.8964 (t)
REVERT: B  460 MET cc_start: 0.8649 (tpt) cc_final: 0.8449 (tpt)
  outliers start: 57
  outliers final: 36
  residues processed: 169
  average time/residue: 0.0763
  time to fit residues: 19.5327
Evaluate side-chains
  147 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 105
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue   80 ILE
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  120 SER
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  148 ARG
Chi-restraints excluded: chain A residue  166 GLN
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  312 MET
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  414 SER
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  532 SER
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain B residue   19 THR
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  114 SER
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  166 GLN
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  396 ASP
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  423 SER
Chi-restraints excluded: chain B residue  472 THR
Chi-restraints excluded: chain B residue  562 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 51 optimal weight:    7.9990
   chunk 32 optimal weight:    7.9990
   chunk 17 optimal weight:    0.8980
   chunk 83 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 39 optimal weight:    0.3980
   chunk 55 optimal weight:   20.0000
   chunk 38 optimal weight:    0.9980
   chunk 96 optimal weight:    5.9990
   chunk 79 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 435 ASN
B 405 HIS
** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.176123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.128305 restraints weight = 11524.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.122800 restraints weight = 15724.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.125676 restraints weight = 13690.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.127096 restraints weight = 7528.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.127538 restraints weight = 6891.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8950  Z= 0.131
  Angle     :  0.591   6.232  12092  Z= 0.320
  Chirality :  0.043   0.175   1440
  Planarity :  0.004   0.054   1532
  Dihedral  :  6.352  53.309   1240
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 27.89 %
    Favored  : 66.84 %
  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 aren not related in a simple way.
  whole: -2.79 (0.24), residues: 1134
  helix: -1.75 (0.19), residues: 712
  sheet: -0.44 (0.71), residues: 50
  loop : -1.88 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 488 
 TYR   0.034   0.001   TYR A 439 
 PHE   0.020   0.001   PHE A 429 
 TRP   0.018   0.002   TRP B  17 
 HIS   0.003   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 8950)
  covalent geometry    : angle       0.59124 (12092)
  hydrogen bonds       : bond        0.03392 (  355)
  hydrogen bonds       : angle       5.23692 ( 1047)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 128
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
REVERT: A  148 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7632 (ttp80)
REVERT: A  319 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8548 (m-80)
REVERT: A  421 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8406 (mp)
REVERT: B  100 MET cc_start: 0.8338 (tmm) cc_final: 0.7902 (ttt)
REVERT: B  255 ILE cc_start: 0.9187 (pt) cc_final: 0.8708 (mp)
REVERT: B  280 THR cc_start: 0.7931 (p) cc_final: 0.7707 (p)
REVERT: B  286 VAL cc_start: 0.9375 (p) cc_final: 0.8935 (t)
REVERT: B  322 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8293 (tt)
  outliers start: 51
  outliers final: 28
  residues processed: 168
  average time/residue: 0.0896
  time to fit residues: 22.1290
Evaluate side-chains
  142 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 110
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue   80 ILE
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  148 ARG
Chi-restraints excluded: chain A residue  166 GLN
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  319 PHE
Chi-restraints excluded: chain A residue  351 TYR
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  435 ASN
Chi-restraints excluded: chain A residue  466 MET
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  488 ARG
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain B residue   19 THR
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  166 GLN
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  396 ASP
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  562 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 89 optimal weight:    0.8980
   chunk 28 optimal weight:    0.4980
   chunk 12 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0970
   chunk 36 optimal weight:    9.9990
   chunk 81 optimal weight:    0.9980
   chunk 53 optimal weight:    6.9990
   chunk 85 optimal weight:    2.9990
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
A 435 ASN
B 405 HIS
B 427 HIS
** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.179074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.131704 restraints weight = 11716.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.123458 restraints weight = 14253.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.126232 restraints weight = 12974.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.127377 restraints weight = 7651.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.127780 restraints weight = 6681.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8950  Z= 0.128
  Angle     :  0.581   6.773  12092  Z= 0.310
  Chirality :  0.042   0.143   1440
  Planarity :  0.004   0.057   1532
  Dihedral  :  6.174  56.887   1240
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 27.48 %
    Favored  : 66.53 %
  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 aren not related in a simple way.
  whole: -2.59 (0.24), residues: 1134
  helix: -1.59 (0.19), residues: 712
  sheet: -0.32 (0.72), residues: 50
  loop : -1.84 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 530 
 TYR   0.017   0.001   TYR A 439 
 PHE   0.011   0.001   PHE A 462 
 TRP   0.017   0.002   TRP B  17 
 HIS   0.004   0.001   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 8950)
  covalent geometry    : angle       0.58105 (12092)
  hydrogen bonds       : bond        0.03163 (  355)
  hydrogen bonds       : angle       4.99839 ( 1047)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 125
  time to evaluate  : 0.354 
Fit side-chains
REVERT: A   67 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7797 (ttp)
REVERT: A  148 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7618 (ttp80)
REVERT: A  289 SER cc_start: 0.8823 (p) cc_final: 0.8609 (t)
REVERT: A  319 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8527 (m-80)
REVERT: A  421 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8378 (mp)
REVERT: A  424 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7223 (tp-100)
REVERT: B   12 THR cc_start: 0.5897 (OUTLIER) cc_final: 0.5654 (m)
REVERT: B   89 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8162 (tt)
REVERT: B  100 MET cc_start: 0.8342 (tmm) cc_final: 0.7939 (ttt)
REVERT: B  255 ILE cc_start: 0.9147 (pt) cc_final: 0.8700 (mp)
REVERT: B  280 THR cc_start: 0.7847 (OUTLIER) cc_final: 0.7613 (p)
REVERT: B  286 VAL cc_start: 0.9382 (p) cc_final: 0.9017 (t)
REVERT: B  322 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8164 (tt)
REVERT: B  423 SER cc_start: 0.9223 (m) cc_final: 0.8994 (t)
  outliers start: 58
  outliers final: 35
  residues processed: 169
  average time/residue: 0.0746
  time to fit residues: 19.4990
Evaluate side-chains
  160 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 116
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue   67 MET
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  148 ARG
Chi-restraints excluded: chain A residue  166 GLN
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  319 PHE
Chi-restraints excluded: chain A residue  351 TYR
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  424 GLN
Chi-restraints excluded: chain A residue  435 ASN
Chi-restraints excluded: chain A residue  466 MET
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue   19 THR
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  166 GLN
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  396 ASP
Chi-restraints excluded: chain B residue  412 LEU
Chi-restraints excluded: chain B residue  472 THR
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  562 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 111 optimal weight:    3.9990
   chunk 44 optimal weight:   10.0000
   chunk 83 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 81 optimal weight:    0.8980
   chunk 72 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 99 optimal weight:    6.9990
   chunk 49 optimal weight:   10.0000
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 405 HIS
** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 485 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.171757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.108485 restraints weight = 11689.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.110199 restraints weight = 7621.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.110722 restraints weight = 5554.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.110864 restraints weight = 5339.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.111285 restraints weight = 5060.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8950  Z= 0.219
  Angle     :  0.627   6.680  12092  Z= 0.332
  Chirality :  0.045   0.146   1440
  Planarity :  0.004   0.057   1532
  Dihedral  :  6.384  58.638   1240
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  7.02 %
    Allowed  : 27.27 %
    Favored  : 65.70 %
  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 aren not related in a simple way.
  whole: -2.60 (0.24), residues: 1134
  helix: -1.56 (0.19), residues: 706
  sheet: -0.23 (0.71), residues: 50
  loop : -1.95 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 530 
 TYR   0.018   0.001   TYR A 439 
 PHE   0.013   0.002   PHE B  43 
 TRP   0.018   0.002   TRP B  17 
 HIS   0.005   0.001   HIS B 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00515 ( 8950)
  covalent geometry    : angle       0.62718 (12092)
  hydrogen bonds       : bond        0.03437 (  355)
  hydrogen bonds       : angle       4.98935 ( 1047)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 118
  time to evaluate  : 0.402 
Fit side-chains
REVERT: A   67 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7870 (ttp)
REVERT: A  148 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7701 (ttp80)
REVERT: A  319 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8734 (m-80)
REVERT: A  421 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8437 (mp)
REVERT: A  424 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7093 (tp-100)
REVERT: B   36 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8636 (mp)
REVERT: B   89 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8200 (tt)
REVERT: B  100 MET cc_start: 0.8509 (tmm) cc_final: 0.8105 (ttt)
REVERT: B  255 ILE cc_start: 0.9202 (pt) cc_final: 0.8653 (mp)
REVERT: B  280 THR cc_start: 0.8097 (OUTLIER) cc_final: 0.7839 (p)
REVERT: B  289 SER cc_start: 0.9100 (p) cc_final: 0.8734 (t)
REVERT: B  305 ASN cc_start: 0.8601 (OUTLIER) cc_final: 0.8390 (t0)
REVERT: B  322 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8294 (tt)
REVERT: B  491 ILE cc_start: 0.9350 (mp) cc_final: 0.9124 (mp)
  outliers start: 68
  outliers final: 46
  residues processed: 173
  average time/residue: 0.0685
  time to fit residues: 18.4610
Evaluate side-chains
  164 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 108
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue   67 MET
Chi-restraints excluded: chain A residue   80 ILE
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  148 ARG
Chi-restraints excluded: chain A residue  166 GLN
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  319 PHE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  351 TYR
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  414 SER
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  424 GLN
Chi-restraints excluded: chain A residue  435 ASN
Chi-restraints excluded: chain A residue  466 MET
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain B residue   19 THR
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  114 SER
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  166 GLN
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  291 MET
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  305 ASN
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  372 VAL
Chi-restraints excluded: chain B residue  396 ASP
Chi-restraints excluded: chain B residue  412 LEU
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  435 ASN
Chi-restraints excluded: chain B residue  472 THR
Chi-restraints excluded: chain B residue  523 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 109 optimal weight:    5.9990
   chunk 95 optimal weight:    9.9990
   chunk 7 optimal weight:    0.7980
   chunk 108 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 53 optimal weight:    0.5980
   chunk 14 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 107 HIS
B 405 HIS
B 430 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.178429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.130422 restraints weight = 11674.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.127411 restraints weight = 17721.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.129467 restraints weight = 15551.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.129572 restraints weight = 8964.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.130123 restraints weight = 8311.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.2450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8950  Z= 0.139
  Angle     :  0.585   8.620  12092  Z= 0.310
  Chirality :  0.042   0.170   1440
  Planarity :  0.004   0.056   1532
  Dihedral  :  6.162  55.793   1240
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.94 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  6.82 %
    Allowed  : 27.79 %
    Favored  : 65.39 %
  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 aren not related in a simple way.
  whole: -2.40 (0.24), residues: 1134
  helix: -1.42 (0.19), residues: 722
  sheet: -0.27 (0.70), residues: 50
  loop : -1.79 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 530 
 TYR   0.014   0.001   TYR B 445 
 PHE   0.015   0.001   PHE B  43 
 TRP   0.017   0.002   TRP B  17 
 HIS   0.004   0.001   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8950)
  covalent geometry    : angle       0.58534 (12092)
  hydrogen bonds       : bond        0.03103 (  355)
  hydrogen bonds       : angle       4.78954 ( 1047)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 119
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7743 (ttp)
REVERT: A  148 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7684 (ttp80)
REVERT: A  319 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.8617 (m-80)
REVERT: A  421 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8392 (mp)
REVERT: A  424 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.7146 (tp-100)
REVERT: B   89 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8211 (tt)
REVERT: B  100 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.7932 (ttt)
REVERT: B  208 GLU cc_start: 0.7550 (tt0) cc_final: 0.7315 (tt0)
REVERT: B  255 ILE cc_start: 0.9167 (pt) cc_final: 0.8722 (mp)
REVERT: B  280 THR cc_start: 0.7920 (OUTLIER) cc_final: 0.7710 (p)
REVERT: B  286 VAL cc_start: 0.9354 (p) cc_final: 0.9044 (t)
REVERT: B  322 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8091 (tt)
  outliers start: 66
  outliers final: 46
  residues processed: 165
  average time/residue: 0.0730
  time to fit residues: 18.4582
Evaluate side-chains
  162 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 107
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue   67 MET
Chi-restraints excluded: chain A residue   80 ILE
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  148 ARG
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  166 GLN
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  312 MET
Chi-restraints excluded: chain A residue  319 PHE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  351 TYR
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  424 GLN
Chi-restraints excluded: chain A residue  435 ASN
Chi-restraints excluded: chain A residue  466 MET
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain B residue   19 THR
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  100 MET
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  166 GLN
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  291 MET
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  372 VAL
Chi-restraints excluded: chain B residue  396 ASP
Chi-restraints excluded: chain B residue  412 LEU
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  435 ASN
Chi-restraints excluded: chain B residue  472 THR
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  561 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0980
   chunk 57 optimal weight:    0.0980
   chunk 104 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 88 optimal weight:    4.9990
   chunk 65 optimal weight:    0.5980
   chunk 109 optimal weight:   10.0000
   chunk 36 optimal weight:    8.9990
   chunk 93 optimal weight:    0.8980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 405 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.180569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.131419 restraints weight = 11650.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.126873 restraints weight = 15872.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.129804 restraints weight = 13461.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.129829 restraints weight = 7793.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.130398 restraints weight = 7414.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.2688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8950  Z= 0.114
  Angle     :  0.576   8.477  12092  Z= 0.303
  Chirality :  0.042   0.185   1440
  Planarity :  0.004   0.056   1532
  Dihedral  :  5.912  52.556   1240
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.11 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 29.75 %
    Favored  : 64.88 %
  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 aren not related in a simple way.
  whole: -2.24 (0.25), residues: 1134
  helix: -1.29 (0.19), residues: 714
  sheet: -0.03 (0.63), residues: 72
  loop : -1.87 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 530 
 TYR   0.015   0.001   TYR B 445 
 PHE   0.011   0.001   PHE B  43 
 TRP   0.017   0.002   TRP B  17 
 HIS   0.004   0.001   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 8950)
  covalent geometry    : angle       0.57581 (12092)
  hydrogen bonds       : bond        0.02947 (  355)
  hydrogen bonds       : angle       4.63284 ( 1047)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 120
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7823 (ttp)
REVERT: A  148 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7732 (ttp80)
REVERT: A  208 GLU cc_start: 0.7616 (tt0) cc_final: 0.7372 (tt0)
REVERT: A  319 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8517 (m-80)
REVERT: A  421 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8393 (mp)
REVERT: A  424 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.7139 (tp-100)
REVERT: B   36 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8679 (mp)
REVERT: B   89 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8183 (tt)
REVERT: B  100 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7930 (ttt)
REVERT: B  208 GLU cc_start: 0.7547 (tt0) cc_final: 0.7283 (tt0)
REVERT: B  255 ILE cc_start: 0.9078 (pt) cc_final: 0.8701 (mp)
REVERT: B  280 THR cc_start: 0.7775 (OUTLIER) cc_final: 0.7561 (p)
REVERT: B  286 VAL cc_start: 0.9334 (p) cc_final: 0.9027 (t)
REVERT: B  322 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8064 (tt)
  outliers start: 52
  outliers final: 35
  residues processed: 159
  average time/residue: 0.0742
  time to fit residues: 17.9104
Evaluate side-chains
  156 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 111
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue   67 MET
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  148 ARG
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  319 PHE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  351 TYR
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  424 GLN
Chi-restraints excluded: chain A residue  435 ASN
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain B residue   19 THR
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   49 LYS
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  100 MET
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  166 GLN
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  291 MET
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  372 VAL
Chi-restraints excluded: chain B residue  396 ASP
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  472 THR
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  561 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 53 optimal weight:    6.9990
   chunk 88 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 37 optimal weight:    8.9990
   chunk 21 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 99 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 28 optimal weight:    0.4980
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 326 GLN
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 405 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.178451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.129094 restraints weight = 11641.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.124850 restraints weight = 16816.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.127750 restraints weight = 13827.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.127896 restraints weight = 8063.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.128508 restraints weight = 7724.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.2694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   8950  Z= 0.161
  Angle     :  0.611   8.266  12092  Z= 0.318
  Chirality :  0.043   0.178   1440
  Planarity :  0.004   0.055   1532
  Dihedral  :  5.996  50.003   1240
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.11 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  : 29.03 %
    Favored  : 64.67 %
  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 aren not related in a simple way.
  whole: -2.20 (0.24), residues: 1134
  helix: -1.31 (0.19), residues: 714
  sheet:  0.05 (0.62), residues: 72
  loop : -1.76 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 530 
 TYR   0.028   0.001   TYR A 439 
 PHE   0.010   0.001   PHE A 429 
 TRP   0.018   0.002   TRP B  17 
 HIS   0.004   0.001   HIS B 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 8950)
  covalent geometry    : angle       0.61058 (12092)
  hydrogen bonds       : bond        0.03146 (  355)
  hydrogen bonds       : angle       4.68603 ( 1047)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 117
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7733 (ttt)
REVERT: A  148 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7666 (ttp80)
REVERT: A  208 GLU cc_start: 0.7732 (tt0) cc_final: 0.7455 (tt0)
REVERT: A  209 GLN cc_start: 0.8271 (tm-30) cc_final: 0.8052 (tm-30)
REVERT: A  319 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8665 (m-80)
REVERT: A  421 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8479 (mp)
REVERT: A  424 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7100 (tp-100)
REVERT: B   36 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8636 (mp)
REVERT: B   89 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8212 (tt)
REVERT: B  100 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8028 (ttt)
REVERT: B  208 GLU cc_start: 0.7591 (tt0) cc_final: 0.7342 (tt0)
REVERT: B  255 ILE cc_start: 0.9186 (pt) cc_final: 0.8725 (mp)
REVERT: B  280 THR cc_start: 0.7873 (OUTLIER) cc_final: 0.7659 (p)
REVERT: B  286 VAL cc_start: 0.9360 (p) cc_final: 0.9045 (t)
REVERT: B  322 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8115 (tt)
  outliers start: 61
  outliers final: 47
  residues processed: 163
  average time/residue: 0.0712
  time to fit residues: 17.7781
Evaluate side-chains
  166 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 109
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue   67 MET
Chi-restraints excluded: chain A residue   80 ILE
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  148 ARG
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  312 MET
Chi-restraints excluded: chain A residue  319 PHE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  351 TYR
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  424 GLN
Chi-restraints excluded: chain A residue  435 ASN
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain B residue   19 THR
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  100 MET
Chi-restraints excluded: chain B residue  114 SER
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  166 GLN
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  291 MET
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  372 VAL
Chi-restraints excluded: chain B residue  396 ASP
Chi-restraints excluded: chain B residue  412 LEU
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  472 THR
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  561 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 109 optimal weight:    9.9990
   chunk 26 optimal weight:    0.2980
   chunk 1 optimal weight:    0.0570
   chunk 105 optimal weight:    7.9990
   chunk 9 optimal weight:    0.9980
   chunk 57 optimal weight:    0.4980
   chunk 33 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   chunk 83 optimal weight:    0.7980
   chunk 89 optimal weight:    2.9990
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
A 326 GLN
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 405 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.181790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.133981 restraints weight = 11568.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.131348 restraints weight = 17256.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.132789 restraints weight = 15868.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.135883 restraints weight = 9683.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.135403 restraints weight = 6821.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.2877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8950  Z= 0.117
  Angle     :  0.586   8.503  12092  Z= 0.304
  Chirality :  0.042   0.182   1440
  Planarity :  0.004   0.057   1532
  Dihedral  :  5.820  48.882   1240
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.67 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 29.65 %
    Favored  : 64.77 %
  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 aren not related in a simple way.
  whole: -2.12 (0.24), residues: 1134
  helix: -1.23 (0.19), residues: 732
  sheet:  0.11 (0.62), residues: 72
  loop : -1.77 (0.33), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 530 
 TYR   0.013   0.001   TYR A 130 
 PHE   0.011   0.001   PHE A 429 
 TRP   0.016   0.002   TRP B  17 
 HIS   0.007   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 8950)
  covalent geometry    : angle       0.58563 (12092)
  hydrogen bonds       : bond        0.02942 (  355)
  hydrogen bonds       : angle       4.56981 ( 1047)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 118
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7622 (ttt)
REVERT: A  208 GLU cc_start: 0.7619 (tt0) cc_final: 0.7275 (tt0)
REVERT: A  209 GLN cc_start: 0.8284 (tm-30) cc_final: 0.8055 (tm-30)
REVERT: A  421 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8408 (mp)
REVERT: A  424 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.7074 (tp-100)
REVERT: B   36 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8649 (mp)
REVERT: B   89 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8202 (tt)
REVERT: B  100 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7987 (ttt)
REVERT: B  208 GLU cc_start: 0.7514 (tt0) cc_final: 0.7259 (tt0)
REVERT: B  209 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7875 (tm-30)
REVERT: B  255 ILE cc_start: 0.9077 (pt) cc_final: 0.8710 (mp)
REVERT: B  280 THR cc_start: 0.7726 (OUTLIER) cc_final: 0.7517 (p)
REVERT: B  286 VAL cc_start: 0.9361 (p) cc_final: 0.9048 (t)
REVERT: B  322 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8144 (tt)
  outliers start: 54
  outliers final: 38
  residues processed: 158
  average time/residue: 0.0707
  time to fit residues: 17.1765
Evaluate side-chains
  157 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 111
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue   67 MET
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  351 TYR
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  424 GLN
Chi-restraints excluded: chain A residue  435 ASN
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain B residue   19 THR
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  100 MET
Chi-restraints excluded: chain B residue  114 SER
Chi-restraints excluded: chain B residue  140 SER
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  166 GLN
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  291 MET
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  396 ASP
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  472 THR
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  561 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 81 optimal weight:    0.5980
   chunk 82 optimal weight:    0.8980
   chunk 3 optimal weight:    0.3980
   chunk 76 optimal weight:    0.8980
   chunk 61 optimal weight:    0.8980
   chunk 92 optimal weight:    9.9990
   chunk 108 optimal weight:    1.9990
   chunk 44 optimal weight:   10.0000
   chunk 109 optimal weight:    8.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 405 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.181049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.133017 restraints weight = 11624.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.129113 restraints weight = 18201.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.131618 restraints weight = 15609.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.132032 restraints weight = 8703.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.132612 restraints weight = 8300.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.2957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8950  Z= 0.133
  Angle     :  0.591   8.304  12092  Z= 0.306
  Chirality :  0.043   0.179   1440
  Planarity :  0.004   0.057   1532
  Dihedral  :  5.819  52.041   1240
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.03 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 30.06 %
    Favored  : 64.77 %
  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 aren not related in a simple way.
  whole: -2.06 (0.24), residues: 1134
  helix: -1.18 (0.19), residues: 730
  sheet:  0.11 (0.62), residues: 72
  loop : -1.76 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 530 
 TYR   0.023   0.001   TYR A 439 
 PHE   0.018   0.001   PHE A 429 
 TRP   0.017   0.002   TRP B  17 
 HIS   0.003   0.001   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 8950)
  covalent geometry    : angle       0.59113 (12092)
  hydrogen bonds       : bond        0.02989 (  355)
  hydrogen bonds       : angle       4.54484 ( 1047)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 116
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7687 (ttt)
REVERT: A  208 GLU cc_start: 0.7610 (tt0) cc_final: 0.7332 (tt0)
REVERT: A  209 GLN cc_start: 0.8329 (tm-30) cc_final: 0.8106 (tm-30)
REVERT: A  421 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8483 (mp)
REVERT: A  424 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7120 (tp-100)
REVERT: B   36 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8652 (mp)
REVERT: B   89 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8233 (tt)
REVERT: B  100 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7996 (ttt)
REVERT: B  208 GLU cc_start: 0.7606 (tt0) cc_final: 0.7360 (tt0)
REVERT: B  255 ILE cc_start: 0.9096 (pt) cc_final: 0.8704 (mp)
REVERT: B  280 THR cc_start: 0.7731 (OUTLIER) cc_final: 0.7520 (p)
REVERT: B  286 VAL cc_start: 0.9359 (p) cc_final: 0.9028 (t)
REVERT: B  322 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8138 (tt)
  outliers start: 50
  outliers final: 42
  residues processed: 155
  average time/residue: 0.0703
  time to fit residues: 16.6463
Evaluate side-chains
  160 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 110
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 PHE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue   67 MET
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  274 SER
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  351 TYR
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  424 GLN
Chi-restraints excluded: chain A residue  435 ASN
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  568 HIS
Chi-restraints excluded: chain B residue   19 THR
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   49 LYS
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  100 MET
Chi-restraints excluded: chain B residue  140 SER
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  166 GLN
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  291 MET
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  396 ASP
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  435 ASN
Chi-restraints excluded: chain B residue  472 THR
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  561 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 80 optimal weight:    0.5980
   chunk 104 optimal weight:    0.2980
   chunk 84 optimal weight:    2.9990
   chunk 49 optimal weight:    7.9990
   chunk 29 optimal weight:    0.0770
   chunk 50 optimal weight:    5.9990
   chunk 59 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0270
   chunk 65 optimal weight:    0.9990
   chunk 94 optimal weight:    0.0060
   chunk 30 optimal weight:    0.1980
   overall best weight:    0.1212

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

Flipped N/Q/H residues before XYZ refinement:
A 430 ASN
** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 405 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.186073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.137253 restraints weight = 11379.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.133714 restraints weight = 14300.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.136314 restraints weight = 11855.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.136003 restraints weight = 7595.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.136477 restraints weight = 8220.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.3341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   8950  Z= 0.100
  Angle     :  0.570   8.379  12092  Z= 0.294
  Chirality :  0.041   0.180   1440
  Planarity :  0.004   0.058   1532
  Dihedral  :  5.482  51.642   1240
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.50 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 30.99 %
    Favored  : 64.67 %
  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 aren not related in a simple way.
  whole: -1.85 (0.25), residues: 1134
  helix: -0.91 (0.20), residues: 718
  sheet:  0.16 (0.62), residues: 72
  loop : -1.92 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 530 
 TYR   0.012   0.001   TYR A 439 
 PHE   0.013   0.001   PHE A 462 
 TRP   0.015   0.001   TRP B  66 
 HIS   0.003   0.001   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 ( 8950)
  covalent geometry    : angle       0.56978 (12092)
  hydrogen bonds       : bond        0.02757 (  355)
  hydrogen bonds       : angle       4.35171 ( 1047)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1915.51 seconds
wall clock time: 33 minutes 44.07 seconds (2024.07 seconds total)