Starting phenix.real_space_refine
on Sat Jun  7 15:42:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fuu_50778/06_2025/9fuu_50778.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fuu_50778/06_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fuu_50778/06_2025/9fuu_50778.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fuu_50778/06_2025/9fuu_50778.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fuu_50778/06_2025/9fuu_50778.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fuu_50778/06_2025/9fuu_50778.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.31, per 1000 atoms: 0.72
  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: 2.27
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 1.04
  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: 2.32

  Time building geometry restraints manager: 2.66 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: 0.04
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:             4.170
  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:          0.440
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.750
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.560
-------------------------------------------------------------------------------
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 : 9.05
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.013   0.002   TRP B  66 
 HIS   0.004   0.001   HIS A 214 
 PHE   0.014   0.001   PHE B 429 
 TYR   0.009   0.001   TYR B 439 
 ARG   0.003   0.000   ARG B 102 

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

*********************** 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  : 0.936 
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: 0.2030
  time to fit residues: 40.3917
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  : 0.988 
-------------------------------------------------------------------------------
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 94 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 28 optimal weight:    0.2980
   chunk 57 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 87 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 53 optimal weight:    9.9990
   chunk 65 optimal weight:    0.5980
   chunk 101 optimal weight:    1.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 576 HIS
B 405 HIS
B 435 ASN
** 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 = 0.3996 r_free = 0.3996 target = 0.174089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.124744 restraints weight = 11439.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.119185 restraints weight = 15724.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.121381 restraints weight = 14747.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.1444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8950  Z= 0.163
  Angle     :  0.626   7.046  12092  Z= 0.339
  Chirality :  0.043   0.144   1440
  Planarity :  0.004   0.048   1532
  Dihedral  :  6.282  50.657   1242
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 26.76 %
    Favored  : 69.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.99 (0.24), residues: 1134
  helix: -1.93 (0.19), residues: 720
  sheet: -0.53 (0.70), residues: 50
  loop : -1.92 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  17 
 HIS   0.005   0.001   HIS A 576 
 PHE   0.016   0.002   PHE B 429 
 TYR   0.017   0.001   TYR A 439 
 ARG   0.006   0.000   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04002 (  355)
  hydrogen bonds       : angle       5.64229 ( 1047)
  covalent geometry    : bond        0.00369 ( 8950)
  covalent geometry    : angle       0.62590 (12092)

*********************** 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
  165 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 127
  time to evaluate  : 0.906 
Fit side-chains
REVERT: A  148 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7697 (ttp80)
REVERT: A  319 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8453 (m-80)
REVERT: A  421 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8460 (mp)
REVERT: B  100 MET cc_start: 0.8252 (tmm) cc_final: 0.7839 (ttt)
REVERT: B  255 ILE cc_start: 0.9165 (pt) cc_final: 0.8711 (mp)
REVERT: B  276 MET cc_start: 0.7693 (mpp) cc_final: 0.7234 (mpp)
REVERT: B  280 THR cc_start: 0.7898 (p) cc_final: 0.7635 (p)
REVERT: B  290 SER cc_start: 0.8142 (OUTLIER) cc_final: 0.7881 (p)
  outliers start: 38
  outliers final: 21
  residues processed: 159
  average time/residue: 0.1620
  time to fit residues: 38.4668
Evaluate side-chains
  135 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
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  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  274 SER
Chi-restraints excluded: chain A residue  319 PHE
Chi-restraints excluded: chain A residue  414 SER
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain B residue   19 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  144 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  166 GLN
Chi-restraints excluded: chain B residue  290 SER
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  396 ASP
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 12 optimal weight:    2.9990
   chunk 79 optimal weight:    0.1980
   chunk 62 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 52 optimal weight:    8.9990
   chunk 16 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 82 optimal weight:    2.9990
   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**
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 = 0.4056 r_free = 0.4056 target = 0.179338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.130644 restraints weight = 11641.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.126453 restraints weight = 15003.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.128802 restraints weight = 14187.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.1884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8950  Z= 0.136
  Angle     :  0.582   6.589  12092  Z= 0.311
  Chirality :  0.042   0.142   1440
  Planarity :  0.004   0.054   1532
  Dihedral  :  6.076  55.294   1240
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 27.07 %
    Favored  : 67.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.74 (0.24), residues: 1134
  helix: -1.69 (0.19), residues: 710
  sheet: -0.43 (0.71), residues: 50
  loop : -1.94 (0.29), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  17 
 HIS   0.004   0.001   HIS A 568 
 PHE   0.018   0.001   PHE A 429 
 TYR   0.035   0.001   TYR A 439 
 ARG   0.008   0.000   ARG A 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03376 (  355)
  hydrogen bonds       : angle       5.10997 ( 1047)
  covalent geometry    : bond        0.00308 ( 8950)
  covalent geometry    : angle       0.58166 (12092)

*********************** 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
  171 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 121
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8801 (tpp) cc_final: 0.8104 (tpt)
REVERT: A  148 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7673 (ttp80)
REVERT: A  319 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8389 (m-80)
REVERT: A  421 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8352 (mp)
REVERT: B   36 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8643 (mp)
REVERT: B  100 MET cc_start: 0.8276 (tmm) cc_final: 0.7889 (ttt)
REVERT: B  255 ILE cc_start: 0.9097 (pt) cc_final: 0.8704 (mp)
REVERT: B  286 VAL cc_start: 0.9393 (p) cc_final: 0.8951 (t)
REVERT: B  290 SER cc_start: 0.8117 (OUTLIER) cc_final: 0.7894 (p)
  outliers start: 50
  outliers final: 28
  residues processed: 160
  average time/residue: 0.1544
  time to fit residues: 37.2661
Evaluate side-chains
  142 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 109
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
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   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  166 GLN
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  402 MET
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  435 ASN
Chi-restraints excluded: chain A residue  488 ARG
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  166 GLN
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain B residue  242 MET
Chi-restraints excluded: chain B residue  290 SER
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  396 ASP
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 87 optimal weight:    0.1980
   chunk 5 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9990
   chunk 39 optimal weight:    9.9990
   chunk 16 optimal weight:    1.9990
   chunk 92 optimal weight:   20.0000
   chunk 99 optimal weight:    0.2980
   chunk 107 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 77 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 430 ASN
A 435 ASN
B 405 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 = 0.4064 r_free = 0.4064 target = 0.180323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.133431 restraints weight = 11604.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.125019 restraints weight = 13703.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.127340 restraints weight = 13643.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.2128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8950  Z= 0.121
  Angle     :  0.567   9.231  12092  Z= 0.300
  Chirality :  0.041   0.196   1440
  Planarity :  0.004   0.055   1532
  Dihedral  :  5.932  58.677   1240
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  5.89 %
    Allowed  : 26.45 %
    Favored  : 67.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.52 (0.24), residues: 1134
  helix: -1.50 (0.19), residues: 710
  sheet: -0.27 (0.71), residues: 50
  loop : -1.88 (0.29), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  17 
 HIS   0.004   0.001   HIS A 568 
 PHE   0.011   0.001   PHE A 462 
 TYR   0.018   0.001   TYR A 439 
 ARG   0.005   0.000   ARG A 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03051 (  355)
  hydrogen bonds       : angle       4.86117 ( 1047)
  covalent geometry    : bond        0.00276 ( 8950)
  covalent geometry    : angle       0.56700 (12092)

*********************** 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
  179 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 122
  time to evaluate  : 1.053 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8774 (tpp) cc_final: 0.8159 (tpp)
REVERT: A  148 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7640 (ttp80)
REVERT: A  208 GLU cc_start: 0.7379 (tt0) cc_final: 0.7128 (tt0)
REVERT: A  289 SER cc_start: 0.8741 (p) cc_final: 0.8533 (t)
REVERT: A  319 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.8547 (m-80)
REVERT: A  421 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8354 (mp)
REVERT: A  424 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7292 (tp-100)
REVERT: B  100 MET cc_start: 0.8312 (tmm) cc_final: 0.7933 (ttt)
REVERT: B  255 ILE cc_start: 0.9067 (pt) cc_final: 0.8702 (mp)
REVERT: B  280 THR cc_start: 0.7707 (OUTLIER) cc_final: 0.7489 (p)
REVERT: B  286 VAL cc_start: 0.9396 (p) cc_final: 0.8958 (t)
REVERT: B  290 SER cc_start: 0.8138 (OUTLIER) cc_final: 0.7903 (p)
  outliers start: 57
  outliers final: 36
  residues processed: 162
  average time/residue: 0.1795
  time to fit residues: 44.3308
Evaluate side-chains
  151 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 109
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
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   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  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  390 THR
Chi-restraints excluded: chain A residue  402 MET
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  488 ARG
Chi-restraints excluded: chain A residue  539 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   49 LYS
Chi-restraints excluded: chain B residue   65 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  290 SER
Chi-restraints excluded: chain B residue  294 LEU
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  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 78 optimal weight:    1.9990
   chunk 35 optimal weight:    7.9990
   chunk 89 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0040
   chunk 70 optimal weight:    0.5980
   chunk 65 optimal weight:    0.7980
   chunk 40 optimal weight:   10.0000
   chunk 9 optimal weight:    0.9980
   chunk 60 optimal weight:    0.1980
   chunk 66 optimal weight:    0.4980
   overall best weight:    0.3992

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

Flipped N/Q/H residues before XYZ refinement:
A 430 ASN
A 435 ASN
B 405 HIS
** B 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4080 r_free = 0.4080 target = 0.181711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.132591 restraints weight = 11537.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.128820 restraints weight = 15180.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.131421 restraints weight = 13157.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.2380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8950  Z= 0.105
  Angle     :  0.556   7.677  12092  Z= 0.291
  Chirality :  0.041   0.193   1440
  Planarity :  0.004   0.056   1532
  Dihedral  :  5.764  59.526   1240
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  6.20 %
    Allowed  : 26.45 %
    Favored  : 67.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.32 (0.24), residues: 1134
  helix: -1.32 (0.19), residues: 714
  sheet: -0.20 (0.69), residues: 50
  loop : -1.87 (0.30), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  17 
 HIS   0.004   0.001   HIS A 568 
 PHE   0.010   0.001   PHE A 115 
 TYR   0.013   0.001   TYR A 439 
 ARG   0.003   0.000   ARG A 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02903 (  355)
  hydrogen bonds       : angle       4.65051 ( 1047)
  covalent geometry    : bond        0.00234 ( 8950)
  covalent geometry    : angle       0.55593 (12092)

*********************** 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
  185 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 125
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8812 (tpp) cc_final: 0.8253 (tpp)
REVERT: A  148 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7682 (ttp80)
REVERT: A  208 GLU cc_start: 0.7342 (tt0) cc_final: 0.7070 (tt0)
REVERT: A  289 SER cc_start: 0.8686 (p) cc_final: 0.8435 (t)
REVERT: A  319 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.8459 (m-80)
REVERT: A  421 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8287 (mp)
REVERT: A  424 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7232 (tp-100)
REVERT: A  430 ASN cc_start: 0.7889 (OUTLIER) cc_final: 0.7602 (p0)
REVERT: B   36 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8582 (mp)
REVERT: B  100 MET cc_start: 0.8241 (tmm) cc_final: 0.7879 (ttt)
REVERT: B  255 ILE cc_start: 0.9042 (pt) cc_final: 0.8706 (mp)
REVERT: B  276 MET cc_start: 0.7288 (mpp) cc_final: 0.6998 (mpp)
REVERT: B  280 THR cc_start: 0.7505 (OUTLIER) cc_final: 0.7290 (p)
REVERT: B  286 VAL cc_start: 0.9321 (p) cc_final: 0.8981 (t)
REVERT: B  468 ASN cc_start: 0.7658 (t0) cc_final: 0.7141 (t0)
  outliers start: 60
  outliers final: 37
  residues processed: 167
  average time/residue: 0.1566
  time to fit residues: 39.8801
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  : 0.919 
-------------------------------------------------------------------------------
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   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  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  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  421 LEU
Chi-restraints excluded: chain A residue  424 GLN
Chi-restraints excluded: chain A residue  430 ASN
Chi-restraints excluded: chain A residue  435 ASN
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  539 LEU
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   49 LYS
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   85 SER
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  356 VAL
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  396 ASP
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 63 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0030
   chunk 86 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0870
   chunk 55 optimal weight:    5.9990
   chunk 33 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 101 optimal weight:    1.9990
   chunk 106 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.6970

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

Flipped N/Q/H residues before XYZ refinement:
A 430 ASN
A 435 ASN
B 405 HIS
** B 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4071 r_free = 0.4071 target = 0.180967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.133805 restraints weight = 11509.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.130958 restraints weight = 18814.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.132670 restraints weight = 15221.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.2475

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= 0.128
  Angle     :  0.573   7.197  12092  Z= 0.298
  Chirality :  0.042   0.147   1440
  Planarity :  0.004   0.055   1532
  Dihedral  :  5.752  58.628   1240
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.41 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  5.89 %
    Allowed  : 27.07 %
    Favored  : 67.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.26 (0.24), residues: 1134
  helix: -1.30 (0.19), residues: 722
  sheet: -0.13 (0.68), residues: 50
  loop : -1.78 (0.30), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  17 
 HIS   0.004   0.001   HIS A 568 
 PHE   0.011   0.001   PHE A 462 
 TYR   0.015   0.001   TYR A 130 
 ARG   0.003   0.000   ARG A 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02957 (  355)
  hydrogen bonds       : angle       4.59432 ( 1047)
  covalent geometry    : bond        0.00297 ( 8950)
  covalent geometry    : angle       0.57267 (12092)

*********************** 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
  175 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 118
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7956 (t80)
REVERT: A   67 MET cc_start: 0.8833 (tpp) cc_final: 0.8226 (tpp)
REVERT: A  148 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7726 (ttp80)
REVERT: A  319 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.8543 (m-80)
REVERT: A  421 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8291 (mp)
REVERT: A  424 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7264 (tp-100)
REVERT: A  430 ASN cc_start: 0.7935 (OUTLIER) cc_final: 0.7644 (p0)
REVERT: B   12 THR cc_start: 0.6064 (OUTLIER) cc_final: 0.5611 (m)
REVERT: B   36 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8494 (mp)
REVERT: B  100 MET cc_start: 0.8291 (tmm) cc_final: 0.7944 (ttt)
REVERT: B  208 GLU cc_start: 0.7544 (tt0) cc_final: 0.7291 (tt0)
REVERT: B  255 ILE cc_start: 0.9090 (pt) cc_final: 0.8734 (mp)
REVERT: B  280 THR cc_start: 0.7571 (OUTLIER) cc_final: 0.7369 (p)
REVERT: B  286 VAL cc_start: 0.9379 (p) cc_final: 0.9027 (t)
REVERT: B  468 ASN cc_start: 0.7607 (t0) cc_final: 0.7089 (t0)
  outliers start: 57
  outliers final: 41
  residues processed: 159
  average time/residue: 0.1536
  time to fit residues: 37.0816
Evaluate side-chains
  162 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 112
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
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   43 PHE
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   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  339 THR
Chi-restraints excluded: chain A residue  351 TYR
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  424 GLN
Chi-restraints excluded: chain A residue  430 ASN
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  539 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   36 LEU
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   85 SER
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  356 VAL
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  396 ASP
Chi-restraints excluded: chain B residue  472 THR
Chi-restraints excluded: chain B residue  523 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 103 optimal weight:    7.9990
   chunk 100 optimal weight:    8.9990
   chunk 57 optimal weight:    0.4980
   chunk 104 optimal weight:    0.0060
   chunk 40 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   chunk 71 optimal weight:    0.5980
   chunk 59 optimal weight:    0.5980
   chunk 30 optimal weight:    0.5980
   chunk 67 optimal weight:    0.8980
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
A 430 ASN
A 435 ASN
B 405 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 = 0.4082 r_free = 0.4082 target = 0.182074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.133780 restraints weight = 11662.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.130068 restraints weight = 15314.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.132372 restraints weight = 14390.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.2625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8950  Z= 0.109
  Angle     :  0.560   7.728  12092  Z= 0.291
  Chirality :  0.041   0.144   1440
  Planarity :  0.003   0.055   1532
  Dihedral  :  5.615  57.711   1240
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.50 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 27.58 %
    Favored  : 66.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.13 (0.24), residues: 1134
  helix: -1.19 (0.19), residues: 724
  sheet: -0.09 (0.68), residues: 50
  loop : -1.74 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  17 
 HIS   0.004   0.001   HIS A 568 
 PHE   0.008   0.001   PHE A 288 
 TYR   0.013   0.001   TYR A 130 
 ARG   0.003   0.000   ARG A 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02856 (  355)
  hydrogen bonds       : angle       4.50183 ( 1047)
  covalent geometry    : bond        0.00247 ( 8950)
  covalent geometry    : angle       0.56023 (12092)

*********************** 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
  178 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 122
  time to evaluate  : 1.051 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8835 (tpp) cc_final: 0.8231 (tpp)
REVERT: A  148 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7695 (ttp80)
REVERT: A  319 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8473 (m-80)
REVERT: A  421 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8287 (mp)
REVERT: A  424 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7237 (tp-100)
REVERT: B   12 THR cc_start: 0.6031 (OUTLIER) cc_final: 0.5583 (m)
REVERT: B   36 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8636 (mp)
REVERT: B   89 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8134 (tt)
REVERT: B  100 MET cc_start: 0.8275 (tmm) cc_final: 0.7927 (ttt)
REVERT: B  208 GLU cc_start: 0.7515 (tt0) cc_final: 0.7256 (tt0)
REVERT: B  255 ILE cc_start: 0.9042 (pt) cc_final: 0.8723 (mp)
REVERT: B  286 VAL cc_start: 0.9304 (p) cc_final: 0.8987 (t)
REVERT: B  468 ASN cc_start: 0.7670 (t0) cc_final: 0.7107 (t0)
  outliers start: 56
  outliers final: 40
  residues processed: 166
  average time/residue: 0.1553
  time to fit residues: 39.4674
Evaluate side-chains
  158 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 111
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
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   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  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  359 LEU
Chi-restraints excluded: chain A residue  390 THR
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  539 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   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  166 GLN
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain B residue  242 MET
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  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  472 THR
Chi-restraints excluded: chain B residue  523 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 96 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 85 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 102 optimal weight:    0.5980
   chunk 99 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 41 optimal weight:    0.8980
   chunk 49 optimal weight:    6.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 ** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.180538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.132899 restraints weight = 11751.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.131375 restraints weight = 20937.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.133246 restraints weight = 14621.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.2676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8950  Z= 0.136
  Angle     :  0.595  12.780  12092  Z= 0.303
  Chirality :  0.043   0.283   1440
  Planarity :  0.004   0.055   1532
  Dihedral  :  5.676  53.954   1240
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.67 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 28.10 %
    Favored  : 66.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.12 (0.24), residues: 1134
  helix: -1.16 (0.19), residues: 722
  sheet: -0.02 (0.69), residues: 50
  loop : -1.81 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  17 
 HIS   0.003   0.001   HIS A 568 
 PHE   0.009   0.001   PHE A 189 
 TYR   0.027   0.001   TYR A 439 
 ARG   0.003   0.000   ARG A 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02934 (  355)
  hydrogen bonds       : angle       4.51499 ( 1047)
  covalent geometry    : bond        0.00317 ( 8950)
  covalent geometry    : angle       0.59533 (12092)

*********************** 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
  167 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 116
  time to evaluate  : 0.984 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8751 (tpp) cc_final: 0.8151 (tpp)
REVERT: A  148 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7723 (ttp80)
REVERT: A  319 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.8575 (m-80)
REVERT: A  421 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8330 (mp)
REVERT: A  424 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.7197 (tp-100)
REVERT: B   12 THR cc_start: 0.6095 (OUTLIER) cc_final: 0.5833 (m)
REVERT: B   36 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8673 (mp)
REVERT: B   89 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8096 (tt)
REVERT: B  100 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.8025 (ttt)
REVERT: B  208 GLU cc_start: 0.7559 (tt0) cc_final: 0.7314 (tt0)
REVERT: B  255 ILE cc_start: 0.9096 (pt) cc_final: 0.8734 (mp)
REVERT: B  286 VAL cc_start: 0.9369 (p) cc_final: 0.9028 (t)
REVERT: B  468 ASN cc_start: 0.7556 (t0) cc_final: 0.6973 (t0)
  outliers start: 51
  outliers final: 42
  residues processed: 156
  average time/residue: 0.1603
  time to fit residues: 38.2133
Evaluate side-chains
  162 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 112
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   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  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  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  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   12 THR
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  114 SER
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  291 MET
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  301 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  435 ASN
Chi-restraints excluded: chain B residue  472 THR
Chi-restraints excluded: chain B residue  523 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 78 optimal weight:    0.0570
   chunk 6 optimal weight:    0.6980
   chunk 79 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 87 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 49 optimal weight:   10.0000
   chunk 32 optimal weight:   10.0000
   overall best weight:    0.6098

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4072 r_free = 0.4072 target = 0.181402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.133423 restraints weight = 11605.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.130947 restraints weight = 16763.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.133050 restraints weight = 16380.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.2764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8950  Z= 0.121
  Angle     :  0.595  13.311  12092  Z= 0.301
  Chirality :  0.042   0.301   1440
  Planarity :  0.003   0.055   1532
  Dihedral  :  5.630  52.157   1240
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.67 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 28.31 %
    Favored  : 66.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.07 (0.24), residues: 1134
  helix: -1.12 (0.19), residues: 724
  sheet: -0.01 (0.69), residues: 50
  loop : -1.79 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  17 
 HIS   0.003   0.001   HIS A 568 
 PHE   0.009   0.001   PHE A 115 
 TYR   0.023   0.001   TYR A 439 
 ARG   0.003   0.000   ARG A 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02872 (  355)
  hydrogen bonds       : angle       4.45807 ( 1047)
  covalent geometry    : bond        0.00279 ( 8950)
  covalent geometry    : angle       0.59550 (12092)

*********************** 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
  171 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 117
  time to evaluate  : 0.923 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8816 (tpp) cc_final: 0.8188 (tpp)
REVERT: A  148 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7782 (ttp80)
REVERT: A  319 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8531 (m-80)
REVERT: A  421 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8327 (mp)
REVERT: A  424 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.7199 (tp-100)
REVERT: B   12 THR cc_start: 0.6004 (OUTLIER) cc_final: 0.5604 (m)
REVERT: B   36 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8500 (mp)
REVERT: B   89 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8110 (tt)
REVERT: B  100 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.8018 (ttt)
REVERT: B  208 GLU cc_start: 0.7580 (tt0) cc_final: 0.7329 (tt0)
REVERT: B  255 ILE cc_start: 0.9068 (pt) cc_final: 0.8713 (mp)
REVERT: B  286 VAL cc_start: 0.9319 (p) cc_final: 0.8986 (t)
REVERT: B  468 ASN cc_start: 0.7596 (t0) cc_final: 0.7042 (t0)
REVERT: B  566 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6508 (pp)
  outliers start: 54
  outliers final: 44
  residues processed: 159
  average time/residue: 0.1540
  time to fit residues: 37.3669
Evaluate side-chains
  166 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 113
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   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  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  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  539 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   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  114 SER
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  291 MET
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  301 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  472 THR
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  561 THR
Chi-restraints excluded: chain B residue  566 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 24 optimal weight:    0.3980
   chunk 95 optimal weight:    7.9990
   chunk 72 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 73 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 88 optimal weight:    6.9990
   chunk 100 optimal weight:   10.0000
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 435 ASN
B 405 HIS
** B 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4070 r_free = 0.4070 target = 0.181095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.132869 restraints weight = 11621.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.129910 restraints weight = 16561.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.131915 restraints weight = 15292.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.2846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8950  Z= 0.129
  Angle     :  0.602  14.167  12092  Z= 0.303
  Chirality :  0.042   0.315   1440
  Planarity :  0.003   0.055   1532
  Dihedral  :  5.607  50.860   1240
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.76 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 28.62 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.99 (0.24), residues: 1134
  helix: -1.05 (0.19), residues: 722
  sheet:  0.01 (0.69), residues: 50
  loop : -1.78 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  17 
 HIS   0.003   0.001   HIS A 568 
 PHE   0.009   0.001   PHE B 429 
 TYR   0.023   0.001   TYR A 439 
 ARG   0.003   0.000   ARG A 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02904 (  355)
  hydrogen bonds       : angle       4.44809 ( 1047)
  covalent geometry    : bond        0.00301 ( 8950)
  covalent geometry    : angle       0.60156 (12092)

********************** 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
  170 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 115
  time to evaluate  : 1.002 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8816 (tpp) cc_final: 0.8200 (tpp)
REVERT: A  319 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.8566 (m-80)
REVERT: A  421 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8342 (mp)
REVERT: A  424 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.7184 (tp-100)
REVERT: B   12 THR cc_start: 0.5998 (OUTLIER) cc_final: 0.5610 (m)
REVERT: B   36 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8539 (mp)
REVERT: B   89 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8155 (tt)
REVERT: B  100 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.8038 (ttt)
REVERT: B  208 GLU cc_start: 0.7591 (tt0) cc_final: 0.7343 (tt0)
REVERT: B  255 ILE cc_start: 0.9086 (pt) cc_final: 0.8723 (mp)
REVERT: B  286 VAL cc_start: 0.9292 (p) cc_final: 0.8968 (t)
REVERT: B  468 ASN cc_start: 0.7572 (t0) cc_final: 0.7036 (t0)
REVERT: B  566 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6548 (pp)
  outliers start: 55
  outliers final: 45
  residues processed: 157
  average time/residue: 0.1584
  time to fit residues: 37.7565
Evaluate side-chains
  166 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 113
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   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  279 LEU
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  390 THR
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  539 LEU
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   12 THR
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  114 SER
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  291 MET
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  301 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  472 THR
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  561 THR
Chi-restraints excluded: chain B residue  566 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 78 optimal weight:    0.8980
   chunk 37 optimal weight:    0.0170
   chunk 12 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 86 optimal weight:    0.6980
   chunk 54 optimal weight:    0.4980
   chunk 111 optimal weight:   20.0000
   chunk 102 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9990
   chunk 87 optimal weight:    0.7980
   overall best weight:    0.5818

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4074 r_free = 0.4074 target = 0.181663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.134295 restraints weight = 11655.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.132930 restraints weight = 14831.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.133985 restraints weight = 13191.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.2929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8950  Z= 0.119
  Angle     :  0.593  13.611  12092  Z= 0.299
  Chirality :  0.042   0.305   1440
  Planarity :  0.003   0.055   1532
  Dihedral  :  5.585  53.840   1240
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.59 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 29.03 %
    Favored  : 65.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.95 (0.24), residues: 1134
  helix: -0.99 (0.19), residues: 726
  sheet:  0.04 (0.69), residues: 50
  loop : -1.82 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  17 
 HIS   0.003   0.001   HIS A 568 
 PHE   0.013   0.001   PHE A 462 
 TYR   0.021   0.001   TYR A 439 
 ARG   0.003   0.000   ARG A 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02851 (  355)
  hydrogen bonds       : angle       4.41892 ( 1047)
  covalent geometry    : bond        0.00273 ( 8950)
  covalent geometry    : angle       0.59280 (12092)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3592.00 seconds
wall clock time: 63 minutes 2.03 seconds (3782.03 seconds total)