Starting phenix.real_space_refine
on Tue Mar  3 16:20:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6npk_0472/03_2026/6npk_0472.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6npk_0472/03_2026/6npk_0472.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6npk_0472/03_2026/6npk_0472.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6npk_0472/03_2026/6npk_0472.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6npk_0472/03_2026/6npk_0472.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6npk_0472/03_2026/6npk_0472.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     C    4722      2.51       5
     N    1112      2.21       5
     O    1254      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7134
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3567
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 472, 3567
          Classifications: {'peptide': 472}
          Link IDs: {'PTRANS': 13, 'TRANS': 458}
    Chain: "B"
      Number of atoms: 3567
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 472, 3567
          Classifications: {'peptide': 472}
          Link IDs: {'PTRANS': 13, 'TRANS': 458}
  Time building chain proxies: 1.83, per 1000 atoms: 0.26
  Number of scatterers: 7134
  At special positions: 0
  Unit cell: (102.335, 75.96, 92.84, 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      46     16.00
     O    1254      8.00
     N    1112      7.00
     C    4722      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 496 " - pdb=" SG  CYS A 507 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 496 " - pdb=" SG  CYS B 507 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.62
  Conformation dependent library (CDL) restraints added in 299.6 milliseconds
  

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1708

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 1 sheets defined
      70.1% alpha, 0.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 213 through 222
      removed outlier: 3.577A  pdb=" N   TRP A 222 " --> pdb=" O   MET A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 237
    Processing helix  chain 'A' and resid 238 through 265
      removed outlier: 3.619A  pdb=" N   ILE A 244 " --> pdb=" O   ALA A 240 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   THR A 253 " --> pdb=" O   ALA A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 282
      removed outlier: 3.652A  pdb=" N   LEU A 277 " --> pdb=" O   GLY A 273 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ILE A 278 " --> pdb=" O   ALA A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 318
      removed outlier: 3.944A  pdb=" N   ALA A 295 " --> pdb=" O   GLY A 291 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ALA A 299 " --> pdb=" O   ALA A 295 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   ALA A 303 " --> pdb=" O   ALA A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 349
      removed outlier: 3.624A  pdb=" N   ILE A 331 " --> pdb=" O   GLN A 327 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   ARG A 332 " --> pdb=" O   THR A 328 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   THR A 336 " --> pdb=" O   ARG A 332 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   GLY A 344 " --> pdb=" O   ILE A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 377
      removed outlier: 3.633A  pdb=" N   GLU A 353 " --> pdb=" O   GLY A 349 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   ALA A 354 " --> pdb=" O   MET A 350 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   LYS A 355 " --> pdb=" O   GLU A 351 " (cutoff:3.500A)
      removed outlier: 4.803A  pdb=" N   ILE A 358 " --> pdb=" O   ALA A 354 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   PHE A 359 " --> pdb=" O   LYS A 355 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   THR A 366 " --> pdb=" O   VAL A 362 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   ILE A 377 " --> pdb=" O   ILE A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 383
    Processing helix  chain 'A' and resid 391 through 399
    Processing helix  chain 'A' and resid 411 through 416
    Processing helix  chain 'A' and resid 417 through 419
      No H-bonds generated for 'chain 'A' and resid 417 through 419'
    Processing helix  chain 'A' and resid 421 through 425
      removed outlier: 4.273A  pdb=" N   GLY A 425 " --> pdb=" O   ILE A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 463
      removed outlier: 3.884A  pdb=" N   ILE A 439 " --> pdb=" O   PRO A 435 " (cutoff:3.500A)
      Proline residue:  A 440  - end of helix
      removed outlier: 3.999A  pdb=" N   LEU A 445 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   LEU A 448 " --> pdb=" O   LEU A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 522
    Processing helix  chain 'A' and resid 531 through 545
    Processing helix  chain 'A' and resid 546 through 557
      removed outlier: 3.624A  pdb=" N   VAL A 550 " --> pdb=" O   SER A 546 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ASP A 557 " --> pdb=" O   ALA A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 564
      removed outlier: 3.754A  pdb=" N   ILE A 563 " --> pdb=" O   TYR A 560 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   ALA A 564 " --> pdb=" O   PRO A 561 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 560 through 564'
    Processing helix  chain 'A' and resid 577 through 592
      removed outlier: 3.874A  pdb=" N   LEU A 592 " --> pdb=" O   LEU A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 595 through 625
      Proline residue:  A 601  - end of helix
      removed outlier: 3.624A  pdb=" N   ASN A 605 " --> pdb=" O   PRO A 601 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ASN A 615 " --> pdb=" O   TYR A 611 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   PHE A 619 " --> pdb=" O   ASN A 615 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 637 through 656
      removed outlier: 3.663A  pdb=" N   SER A 641 " --> pdb=" O   ASN A 637 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ASN A 656 " --> pdb=" O   MET A 652 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 656 through 676
      removed outlier: 3.536A  pdb=" N   TYR A 676 " --> pdb=" O   ILE A 672 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 222
      removed outlier: 5.302A  pdb=" N   VAL B 215 " --> pdb=" O   LYS B 211 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   ARG B 216 " --> pdb=" O   GLY B 212 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   TRP B 222 " --> pdb=" O   MET B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 237
    Processing helix  chain 'B' and resid 238 through 265
      removed outlier: 3.543A  pdb=" N   ILE B 263 " --> pdb=" O   SER B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 282
      removed outlier: 3.816A  pdb=" N   ILE B 278 " --> pdb=" O   ALA B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 320
      removed outlier: 3.752A  pdb=" N   SER B 289 " --> pdb=" O   GLU B 285 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   LEU B 292 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   ALA B 295 " --> pdb=" O   GLY B 291 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ALA B 299 " --> pdb=" O   ALA B 295 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ALA B 303 " --> pdb=" O   ALA B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 349
      removed outlier: 3.602A  pdb=" N   ILE B 331 " --> pdb=" O   GLN B 327 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   ARG B 332 " --> pdb=" O   THR B 328 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   THR B 336 " --> pdb=" O   ARG B 332 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   GLY B 344 " --> pdb=" O   ILE B 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 349 through 377
      removed outlier: 3.629A  pdb=" N   GLU B 353 " --> pdb=" O   GLY B 349 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   ALA B 354 " --> pdb=" O   MET B 350 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   LYS B 355 " --> pdb=" O   GLU B 351 " (cutoff:3.500A)
      removed outlier: 5.139A  pdb=" N   ILE B 358 " --> pdb=" O   ALA B 354 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   PHE B 359 " --> pdb=" O   LYS B 355 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ILE B 377 " --> pdb=" O   ILE B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 391 through 399
    Processing helix  chain 'B' and resid 411 through 416
    Processing helix  chain 'B' and resid 417 through 419
      No H-bonds generated for 'chain 'B' and resid 417 through 419'
    Processing helix  chain 'B' and resid 421 through 425
      removed outlier: 4.200A  pdb=" N   GLY B 425 " --> pdb=" O   ILE B 422 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 434 through 463
      removed outlier: 3.664A  pdb=" N   ILE B 439 " --> pdb=" O   PRO B 435 " (cutoff:3.500A)
      Proline residue:  B 440  - end of helix
      removed outlier: 3.675A  pdb=" N   LEU B 444 " --> pdb=" O   PRO B 440 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   LEU B 445 " --> pdb=" O   LYS B 441 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   LEU B 448 " --> pdb=" O   LEU B 444 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 516 through 522
      removed outlier: 3.972A  pdb=" N   VAL B 520 " --> pdb=" O   GLN B 516 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 530 through 545
      removed outlier: 4.143A  pdb=" N   SER B 534 " --> pdb=" O   ALA B 530 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 546 through 557
      removed outlier: 3.612A  pdb=" N   VAL B 550 " --> pdb=" O   SER B 546 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   ASP B 557 " --> pdb=" O   ALA B 553 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 564
      removed outlier: 3.681A  pdb=" N   ILE B 563 " --> pdb=" O   TYR B 560 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   ALA B 564 " --> pdb=" O   PRO B 561 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 560 through 564'
    Processing helix  chain 'B' and resid 576 through 592
      removed outlier: 3.617A  pdb=" N   PHE B 590 " --> pdb=" O   ILE B 586 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   LEU B 592 " --> pdb=" O   LEU B 588 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 595 through 625
      Proline residue:  B 601  - end of helix
      removed outlier: 3.599A  pdb=" N   ASN B 605 " --> pdb=" O   PRO B 601 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ASN B 615 " --> pdb=" O   TYR B 611 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   PHE B 619 " --> pdb=" O   ASN B 615 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 637 through 656
      removed outlier: 3.813A  pdb=" N   SER B 641 " --> pdb=" O   ASN B 637 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   CYS B 648 " --> pdb=" O   GLY B 644 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   PHE B 653 " --> pdb=" O   CYS B 649 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 656 through 676
      removed outlier: 3.856A  pdb=" N   VAL B 674 " --> pdb=" O   LEU B 670 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 569 through 570

    421 hydrogen bonds defined for protein.
    1248 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.91

  Time building geometry restraints manager: 0.81 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2144
        1.34 -     1.46: 1856
        1.46 -     1.58: 3236
        1.58 -     1.70: 0
        1.70 -     1.82: 70
  Bond restraints: 7306
  Sorted by residual:
  bond pdb=" C   ALA A 600 "
       pdb=" N   PRO A 601 "
    ideal  model  delta    sigma   weight residual
    1.337  1.373 -0.036 9.80e-03 1.04e+04 1.38e+01
  bond pdb=" C   ALA B 600 "
       pdb=" N   PRO B 601 "
    ideal  model  delta    sigma   weight residual
    1.337  1.372 -0.036 9.80e-03 1.04e+04 1.33e+01
  bond pdb=" C   SER B 525 "
       pdb=" N   PRO B 526 "
    ideal  model  delta    sigma   weight residual
    1.337  1.354 -0.017 1.11e-02 8.12e+03 2.46e+00
  bond pdb=" CA  VAL A 234 "
       pdb=" C   VAL A 234 "
    ideal  model  delta    sigma   weight residual
    1.519  1.535 -0.016 1.14e-02 7.69e+03 1.86e+00
  bond pdb=" CA  VAL B 234 "
       pdb=" C   VAL B 234 "
    ideal  model  delta    sigma   weight residual
    1.519  1.533 -0.014 1.14e-02 7.69e+03 1.52e+00
  ... (remaining 7301 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.36: 9743
        2.36 -     4.72: 167
        4.72 -     7.07: 18
        7.07 -     9.43: 6
        9.43 -    11.79: 4
  Bond angle restraints: 9938
  Sorted by residual:
  angle pdb=" C   LYS B 383 "
        pdb=" N   LYS B 384 "
        pdb=" CA  LYS B 384 "
      ideal   model   delta    sigma   weight residual
     121.54  133.33  -11.79 1.91e+00 2.74e-01 3.81e+01
  angle pdb=" C   LYS A 383 "
        pdb=" N   LYS A 384 "
        pdb=" CA  LYS A 384 "
      ideal   model   delta    sigma   weight residual
     121.54  133.29  -11.75 1.91e+00 2.74e-01 3.79e+01
  angle pdb=" N   ILE B 563 "
        pdb=" CA  ILE B 563 "
        pdb=" C   ILE B 563 "
      ideal   model   delta    sigma   weight residual
     113.53  108.82    4.71 9.80e-01 1.04e+00 2.31e+01
  angle pdb=" C   GLY B 490 "
        pdb=" N   TYR B 491 "
        pdb=" CA  TYR B 491 "
      ideal   model   delta    sigma   weight residual
     121.54  129.13   -7.59 1.91e+00 2.74e-01 1.58e+01
  angle pdb=" C   GLY A 490 "
        pdb=" N   TYR A 491 "
        pdb=" CA  TYR A 491 "
      ideal   model   delta    sigma   weight residual
     121.54  128.62   -7.08 1.91e+00 2.74e-01 1.38e+01
  ... (remaining 9933 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.77: 3516
       11.77 -    23.53: 459
       23.53 -    35.30: 135
       35.30 -    47.06: 42
       47.06 -    58.83: 24
  Dihedral angle restraints: 4176
    sinusoidal: 1490
      harmonic: 2686
  Sorted by residual:
  dihedral pdb=" CA  SER B 525 "
           pdb=" C   SER B 525 "
           pdb=" N   PRO B 526 "
           pdb=" CA  PRO B 526 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.75  -29.25     0      5.00e+00 4.00e-02 3.42e+01
  dihedral pdb=" CA  SER A 525 "
           pdb=" C   SER A 525 "
           pdb=" N   PRO A 526 "
           pdb=" CA  PRO A 526 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.09  -27.91     0      5.00e+00 4.00e-02 3.12e+01
  dihedral pdb=" CA  LYS A 488 "
           pdb=" C   LYS A 488 "
           pdb=" N   TYR A 489 "
           pdb=" CA  TYR A 489 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.72   26.28     0      5.00e+00 4.00e-02 2.76e+01
  ... (remaining 4173 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 693
       0.039 -    0.078: 350
       0.078 -    0.117: 93
       0.117 -    0.155: 30
       0.155 -    0.194: 4
  Chirality restraints: 1170
  Sorted by residual:
  chirality pdb=" CA  SER B 525 "
            pdb=" N   SER B 525 "
            pdb=" C   SER B 525 "
            pdb=" CB  SER B 525 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.43e-01
  chirality pdb=" CA  SER A 525 "
            pdb=" N   SER A 525 "
            pdb=" C   SER A 525 "
            pdb=" CB  SER A 525 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.46e-01
  chirality pdb=" CG  LEU B 317 "
            pdb=" CB  LEU B 317 "
            pdb=" CD1 LEU B 317 "
            pdb=" CD2 LEU B 317 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.57e-01
  ... (remaining 1167 not shown)

  Planarity restraints: 1222
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 630 "    0.213 9.50e-02 1.11e+02   9.82e-02 1.19e+01
        pdb=" NE  ARG B 630 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 630 "   -0.046 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 630 "    0.012 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 630 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 416 "    0.051 5.00e-02 4.00e+02   7.68e-02 9.45e+00
        pdb=" N   PRO B 417 "   -0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO B 417 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO B 417 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 416 "    0.050 5.00e-02 4.00e+02   7.52e-02 9.05e+00
        pdb=" N   PRO A 417 "   -0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO A 417 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A 417 "    0.042 5.00e-02 4.00e+02
  ... (remaining 1219 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 2420
        2.84 -     3.35: 6620
        3.35 -     3.87: 11790
        3.87 -     4.38: 13789
        4.38 -     4.90: 23855
  Nonbonded interactions: 58474
  Sorted by model distance:
  nonbonded pdb=" O   THR B 250 "
            pdb=" OG1 THR B 254 "
     model   vdw
     2.320 3.040
  nonbonded pdb=" O   VAL B 362 "
            pdb=" OG1 THR B 366 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" O   TYR A 611 "
            pdb=" ND2 ASN A 615 "
     model   vdw
     2.325 3.120
  nonbonded pdb=" O   LEU B 613 "
            pdb=" OG  SER B 617 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" O   TYR B 611 "
            pdb=" ND2 ASN B 615 "
     model   vdw
     2.329 3.120
  ... (remaining 58469 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.880
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
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      :  0.004   0.051   7308  Z= 0.216
  Angle     :  0.824  11.789   9942  Z= 0.476
  Chirality :  0.050   0.194   1170
  Planarity :  0.008   0.098   1222
  Dihedral  : 13.018  58.825   2462
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  6.13 %
    Allowed  :  8.27 %
    Favored  : 85.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.05 (0.19), residues: 940
  helix: -2.94 (0.14), residues: 620
  sheet:  None (None), residues: 0
  loop : -3.92 (0.26), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.044   0.002   ARG B 630 
 TYR   0.019   0.002   TYR B 305 
 PHE   0.029   0.002   PHE A 387 
 TRP   0.016   0.002   TRP A 658 
 HIS   0.001   0.001   HIS A 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 ( 7306)
  covalent geometry    : angle       0.82369 ( 9938)
  SS BOND              : bond        0.00053 (    2)
  SS BOND              : angle       1.33360 (    4)
  hydrogen bonds       : bond        0.15761 (  421)
  hydrogen bonds       : angle       7.06473 ( 1248)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 161
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8630 (tttm) cc_final: 0.8305 (ttpp)
REVERT: A  318 MET cc_start: 0.7573 (mtm) cc_final: 0.7235 (mtp)
REVERT: A  337 ILE cc_start: 0.8728 (mm) cc_final: 0.8460 (mt)
REVERT: A  436 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7792 (mm-40)
REVERT: A  441 LYS cc_start: 0.8453 (tttt) cc_final: 0.8114 (ttmm)
REVERT: A  497 ARG cc_start: 0.8083 (mtp-110) cc_final: 0.7606 (mtt180)
REVERT: A  634 LYS cc_start: 0.8101 (ttmt) cc_final: 0.7877 (mmmm)
REVERT: A  662 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7394 (tp)
REVERT: B  275 TYR cc_start: 0.7916 (t80) cc_final: 0.7421 (t80)
REVERT: B  337 ILE cc_start: 0.8737 (mm) cc_final: 0.8447 (mt)
REVERT: B  436 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7527 (mp10)
REVERT: B  441 LYS cc_start: 0.7863 (tttp) cc_final: 0.7264 (mtpp)
REVERT: B  489 TYR cc_start: 0.6832 (m-80) cc_final: 0.6622 (m-80)
REVERT: B  516 GLN cc_start: 0.7421 (mm-40) cc_final: 0.7187 (mm110)
REVERT: B  541 LEU cc_start: 0.8207 (tp) cc_final: 0.7981 (mt)
  outliers start: 46
  outliers final: 9
  residues processed: 193
  average time/residue: 0.0821
  time to fit residues: 21.2778
Evaluate side-chains
  111 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  325 ILE
Chi-restraints excluded: chain A residue  436 GLN
Chi-restraints excluded: chain A residue  496 CYS
Chi-restraints excluded: chain A residue  507 CYS
Chi-restraints excluded: chain A residue  557 ASP
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain B residue  436 GLN
Chi-restraints excluded: chain B residue  437 MET
Chi-restraints excluded: chain B residue  496 CYS
Chi-restraints excluded: chain B residue  507 CYS
Chi-restraints excluded: chain B residue  557 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.5980
   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 220 ASN
A 298 ASN
A 327 GLN
B 220 ASN
B 298 ASN
B 327 GLN
** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 552 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.160661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.122368 restraints weight = 7420.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.124802 restraints weight = 5232.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.126518 restraints weight = 4295.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.127429 restraints weight = 3809.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.127429 restraints weight = 3568.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7308  Z= 0.121
  Angle     :  0.541   5.979   9942  Z= 0.297
  Chirality :  0.041   0.131   1170
  Planarity :  0.004   0.052   1222
  Dihedral  :  7.080  57.807   1021
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 12.93 %
    Favored  : 82.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.63 (0.25), residues: 940
  helix: -0.93 (0.19), residues: 630
  sheet:  None (None), residues: 0
  loop : -3.37 (0.30), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 332 
 TYR   0.020   0.001   TYR B 636 
 PHE   0.021   0.001   PHE B 509 
 TRP   0.012   0.001   TRP B 658 
 HIS   0.004   0.001   HIS B 620 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 7306)
  covalent geometry    : angle       0.54124 ( 9938)
  SS BOND              : bond        0.00065 (    2)
  SS BOND              : angle       0.21895 (    4)
  hydrogen bonds       : bond        0.03871 (  421)
  hydrogen bonds       : angle       4.23666 ( 1248)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 110
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A  275 TYR cc_start: 0.8463 (t80) cc_final: 0.7146 (t80)
REVERT: A  337 ILE cc_start: 0.8612 (mm) cc_final: 0.8336 (mt)
REVERT: A  441 LYS cc_start: 0.8459 (tttt) cc_final: 0.7795 (mtpp)
REVERT: A  497 ARG cc_start: 0.8102 (mtp-110) cc_final: 0.7776 (ttm170)
REVERT: B  209 TRP cc_start: 0.8188 (p-90) cc_final: 0.7754 (p-90)
REVERT: B  337 ILE cc_start: 0.8704 (mm) cc_final: 0.8419 (mt)
REVERT: B  376 PHE cc_start: 0.8156 (m-10) cc_final: 0.7688 (m-10)
REVERT: B  402 ASP cc_start: 0.7475 (t0) cc_final: 0.7243 (t0)
REVERT: B  436 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7344 (mp10)
REVERT: B  441 LYS cc_start: 0.7866 (tttp) cc_final: 0.7069 (mtpp)
  outliers start: 34
  outliers final: 21
  residues processed: 133
  average time/residue: 0.0800
  time to fit residues: 14.5188
Evaluate side-chains
  109 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  325 ILE
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  496 CYS
Chi-restraints excluded: chain A residue  507 CYS
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  646 ILE
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  427 ASN
Chi-restraints excluded: chain B residue  436 GLN
Chi-restraints excluded: chain B residue  437 MET
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  460 SER
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  496 CYS
Chi-restraints excluded: chain B residue  507 CYS
Chi-restraints excluded: chain B residue  646 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 82 optimal weight:    6.9990
   chunk 76 optimal weight:   30.0000
   chunk 25 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 47 optimal weight:    6.9990
   chunk 0 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 88 optimal weight:    0.7980
   chunk 35 optimal weight:    6.9990
   chunk 86 optimal weight:    0.6980
   overall best weight:    2.2986

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

Flipped N/Q/H residues before XYZ refinement:
B 357 GLN
B 516 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.150981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.110714 restraints weight = 7574.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.112966 restraints weight = 5485.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.114662 restraints weight = 4593.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.115352 restraints weight = 4133.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.115353 restraints weight = 3912.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   7308  Z= 0.235
  Angle     :  0.613   6.486   9942  Z= 0.332
  Chirality :  0.045   0.146   1170
  Planarity :  0.004   0.042   1222
  Dihedral  :  6.793  51.192   1014
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 13.47 %
    Favored  : 82.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.00 (0.26), residues: 940
  helix: -0.44 (0.20), residues: 632
  sheet:  None (None), residues: 0
  loop : -3.16 (0.32), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 332 
 TYR   0.015   0.002   TYR B 636 
 PHE   0.021   0.002   PHE A 509 
 TRP   0.013   0.002   TRP B 658 
 HIS   0.002   0.001   HIS A 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00561 ( 7306)
  covalent geometry    : angle       0.61310 ( 9938)
  SS BOND              : bond        0.00079 (    2)
  SS BOND              : angle       0.20919 (    4)
  hydrogen bonds       : bond        0.04062 (  421)
  hydrogen bonds       : angle       4.09890 ( 1248)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 117
  time to evaluate  : 0.270 
Fit side-chains
REVERT: A  275 TYR cc_start: 0.8613 (t80) cc_final: 0.7269 (t80)
REVERT: A  326 ASP cc_start: 0.7851 (p0) cc_final: 0.7616 (p0)
REVERT: A  331 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8282 (mt)
REVERT: A  337 ILE cc_start: 0.8716 (mm) cc_final: 0.8500 (mt)
REVERT: A  441 LYS cc_start: 0.8322 (tttt) cc_final: 0.7843 (mtpp)
REVERT: A  497 ARG cc_start: 0.8131 (mtp-110) cc_final: 0.7644 (mtt180)
REVERT: B  337 ILE cc_start: 0.8752 (mm) cc_final: 0.8547 (mt)
REVERT: B  441 LYS cc_start: 0.8004 (tttp) cc_final: 0.7550 (mtpp)
  outliers start: 33
  outliers final: 19
  residues processed: 141
  average time/residue: 0.0752
  time to fit residues: 14.8654
Evaluate side-chains
  122 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  346 SER
Chi-restraints excluded: chain A residue  384 LYS
Chi-restraints excluded: chain A residue  407 THR
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  496 CYS
Chi-restraints excluded: chain A residue  507 CYS
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  646 ILE
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  407 THR
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  460 SER
Chi-restraints excluded: chain B residue  496 CYS
Chi-restraints excluded: chain B residue  507 CYS
Chi-restraints excluded: chain B residue  646 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 76 optimal weight:    8.9990
   chunk 66 optimal weight:    3.9990
   chunk 78 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 29 optimal weight:    6.9990
   chunk 62 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 329 ASN
** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.154098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.114162 restraints weight = 7577.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.116846 restraints weight = 5339.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.118473 restraints weight = 4362.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.119667 restraints weight = 3895.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.119667 restraints weight = 3622.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.2545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7308  Z= 0.140
  Angle     :  0.540   6.879   9942  Z= 0.291
  Chirality :  0.042   0.136   1170
  Planarity :  0.003   0.034   1222
  Dihedral  :  5.921  50.996   1004
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 13.87 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.44 (0.27), residues: 940
  helix:  0.02 (0.21), residues: 632
  sheet:  None (None), residues: 0
  loop : -3.03 (0.33), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 332 
 TYR   0.013   0.001   TYR A 636 
 PHE   0.023   0.001   PHE A 509 
 TRP   0.010   0.001   TRP B 658 
 HIS   0.003   0.001   HIS B 620 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 7306)
  covalent geometry    : angle       0.54010 ( 9938)
  SS BOND              : bond        0.00009 (    2)
  SS BOND              : angle       0.16898 (    4)
  hydrogen bonds       : bond        0.03651 (  421)
  hydrogen bonds       : angle       3.86419 ( 1248)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
REVERT: A  275 TYR cc_start: 0.8636 (t80) cc_final: 0.7275 (t80)
REVERT: A  331 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8294 (mt)
REVERT: A  337 ILE cc_start: 0.8738 (mm) cc_final: 0.8526 (mt)
REVERT: A  441 LYS cc_start: 0.8307 (tttt) cc_final: 0.7797 (mtpp)
REVERT: A  497 ARG cc_start: 0.8082 (mtp-110) cc_final: 0.7655 (mtt180)
REVERT: A  563 ILE cc_start: 0.7142 (OUTLIER) cc_final: 0.6811 (tp)
REVERT: B  331 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8309 (mt)
REVERT: B  337 ILE cc_start: 0.8801 (mm) cc_final: 0.8599 (mt)
REVERT: B  413 SER cc_start: 0.9028 (m) cc_final: 0.8795 (t)
REVERT: B  441 LYS cc_start: 0.7919 (tttp) cc_final: 0.7478 (mtpp)
REVERT: B  563 ILE cc_start: 0.7520 (tp) cc_final: 0.7252 (tt)
  outliers start: 28
  outliers final: 19
  residues processed: 131
  average time/residue: 0.0741
  time to fit residues: 13.6677
Evaluate side-chains
  124 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  369 PHE
Chi-restraints excluded: chain A residue  384 LYS
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  496 CYS
Chi-restraints excluded: chain A residue  507 CYS
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  563 ILE
Chi-restraints excluded: chain A residue  646 ILE
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  331 ILE
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  460 SER
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  496 CYS
Chi-restraints excluded: chain B residue  507 CYS
Chi-restraints excluded: chain B residue  646 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 6 optimal weight:    8.9990
   chunk 92 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 76 optimal weight:    8.9990
   chunk 34 optimal weight:    0.5980
   chunk 57 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 89 optimal weight:    0.7980
   chunk 93 optimal weight:    0.6980
   chunk 27 optimal weight:   30.0000
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.157121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.117767 restraints weight = 7507.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.120335 restraints weight = 5323.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.121857 restraints weight = 4359.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.123038 restraints weight = 3909.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.123038 restraints weight = 3632.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.2721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7308  Z= 0.115
  Angle     :  0.506   5.464   9942  Z= 0.272
  Chirality :  0.041   0.146   1170
  Planarity :  0.003   0.034   1222
  Dihedral  :  5.730  51.880   1004
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 15.33 %
    Favored  : 80.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.97 (0.28), residues: 940
  helix:  0.36 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.83 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 332 
 TYR   0.011   0.001   TYR B 636 
 PHE   0.024   0.001   PHE B 509 
 TRP   0.009   0.001   TRP B 658 
 HIS   0.002   0.001   HIS B 620 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 7306)
  covalent geometry    : angle       0.50559 ( 9938)
  SS BOND              : bond        0.00054 (    2)
  SS BOND              : angle       0.24823 (    4)
  hydrogen bonds       : bond        0.03431 (  421)
  hydrogen bonds       : angle       3.68435 ( 1248)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 101
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
REVERT: A  225 MET cc_start: 0.7973 (mmt) cc_final: 0.7730 (mmt)
REVERT: A  331 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8244 (mt)
REVERT: A  337 ILE cc_start: 0.8714 (mm) cc_final: 0.8504 (mt)
REVERT: A  441 LYS cc_start: 0.8304 (tttt) cc_final: 0.7774 (mtpp)
REVERT: A  497 ARG cc_start: 0.8084 (mtp-110) cc_final: 0.7640 (mtt180)
REVERT: A  563 ILE cc_start: 0.7146 (OUTLIER) cc_final: 0.6830 (tp)
REVERT: B  326 ASP cc_start: 0.8156 (p0) cc_final: 0.7863 (p0)
REVERT: B  331 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8274 (mt)
REVERT: B  441 LYS cc_start: 0.7889 (tttp) cc_final: 0.7474 (mtpp)
REVERT: B  563 ILE cc_start: 0.7475 (tp) cc_final: 0.7168 (tt)
  outliers start: 31
  outliers final: 22
  residues processed: 126
  average time/residue: 0.0790
  time to fit residues: 13.9075
Evaluate side-chains
  119 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 94
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  384 LYS
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  496 CYS
Chi-restraints excluded: chain A residue  507 CYS
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  563 ILE
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  331 ILE
Chi-restraints excluded: chain B residue  384 LYS
Chi-restraints excluded: chain B residue  437 MET
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  460 SER
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  496 CYS
Chi-restraints excluded: chain B residue  507 CYS
Chi-restraints excluded: chain B residue  646 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 72 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 79 optimal weight:    0.0970
   chunk 85 optimal weight:    0.2980
   chunk 55 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 71 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.4978

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.160177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.120871 restraints weight = 7379.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.123543 restraints weight = 5229.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.125326 restraints weight = 4265.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.126436 restraints weight = 3785.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.126797 restraints weight = 3521.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.2834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7308  Z= 0.103
  Angle     :  0.502   7.071   9942  Z= 0.267
  Chirality :  0.041   0.151   1170
  Planarity :  0.003   0.034   1222
  Dihedral  :  5.627  53.124   1004
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 17.60 %
    Favored  : 79.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.58 (0.28), residues: 940
  helix:  0.69 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.76 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 332 
 TYR   0.011   0.001   TYR B 636 
 PHE   0.024   0.001   PHE B 509 
 TRP   0.008   0.001   TRP B 209 
 HIS   0.002   0.001   HIS B 620 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 7306)
  covalent geometry    : angle       0.50211 ( 9938)
  SS BOND              : bond        0.00066 (    2)
  SS BOND              : angle       0.23307 (    4)
  hydrogen bonds       : bond        0.03307 (  421)
  hydrogen bonds       : angle       3.58012 ( 1248)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
REVERT: A  225 MET cc_start: 0.7860 (mmt) cc_final: 0.7637 (mmt)
REVERT: A  331 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8191 (mp)
REVERT: A  337 ILE cc_start: 0.8732 (mm) cc_final: 0.8526 (mt)
REVERT: A  441 LYS cc_start: 0.8219 (tttt) cc_final: 0.7754 (mtpp)
REVERT: A  497 ARG cc_start: 0.8060 (mtp-110) cc_final: 0.7688 (mtp85)
REVERT: B  331 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8266 (mp)
REVERT: B  441 LYS cc_start: 0.7878 (tttp) cc_final: 0.7555 (mtpp)
REVERT: B  563 ILE cc_start: 0.7451 (tp) cc_final: 0.7147 (tt)
  outliers start: 24
  outliers final: 19
  residues processed: 119
  average time/residue: 0.0810
  time to fit residues: 13.3959
Evaluate side-chains
  115 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  325 ILE
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  369 PHE
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  496 CYS
Chi-restraints excluded: chain A residue  507 CYS
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain B residue  331 ILE
Chi-restraints excluded: chain B residue  437 MET
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  460 SER
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  496 CYS
Chi-restraints excluded: chain B residue  507 CYS
Chi-restraints excluded: chain B residue  662 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 54 optimal weight:    4.9990
   chunk 83 optimal weight:    8.9990
   chunk 42 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 87 optimal weight:    0.2980
   chunk 46 optimal weight:    1.9990
   chunk 50 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   overall best weight:    0.9782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.157811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.118189 restraints weight = 7425.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.120820 restraints weight = 5255.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.122503 restraints weight = 4301.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.123046 restraints weight = 3837.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.124033 restraints weight = 3664.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7308  Z= 0.129
  Angle     :  0.515   6.175   9942  Z= 0.275
  Chirality :  0.041   0.155   1170
  Planarity :  0.003   0.033   1222
  Dihedral  :  5.623  53.070   1004
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 18.27 %
    Favored  : 77.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.52 (0.28), residues: 940
  helix:  0.76 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.81 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 332 
 TYR   0.011   0.001   TYR B 636 
 PHE   0.023   0.001   PHE B 509 
 TRP   0.008   0.001   TRP B 658 
 HIS   0.002   0.001   HIS B 620 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 7306)
  covalent geometry    : angle       0.51481 ( 9938)
  SS BOND              : bond        0.00012 (    2)
  SS BOND              : angle       0.16968 (    4)
  hydrogen bonds       : bond        0.03387 (  421)
  hydrogen bonds       : angle       3.63874 ( 1248)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 105
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
REVERT: A  331 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8224 (mt)
REVERT: A  337 ILE cc_start: 0.8766 (mm) cc_final: 0.8560 (mt)
REVERT: A  441 LYS cc_start: 0.8277 (tttt) cc_final: 0.7743 (mtpp)
REVERT: A  497 ARG cc_start: 0.8075 (mtp-110) cc_final: 0.7709 (mtp85)
REVERT: A  563 ILE cc_start: 0.6806 (OUTLIER) cc_final: 0.6523 (tp)
REVERT: B  331 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8346 (mt)
REVERT: B  441 LYS cc_start: 0.7916 (tttp) cc_final: 0.7469 (mtpp)
  outliers start: 30
  outliers final: 23
  residues processed: 129
  average time/residue: 0.0754
  time to fit residues: 13.5208
Evaluate side-chains
  126 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 100
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  325 ILE
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  496 CYS
Chi-restraints excluded: chain A residue  507 CYS
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  563 ILE
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  331 ILE
Chi-restraints excluded: chain B residue  437 MET
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  455 VAL
Chi-restraints excluded: chain B residue  460 SER
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  496 CYS
Chi-restraints excluded: chain B residue  507 CYS
Chi-restraints excluded: chain B residue  646 ILE
Chi-restraints excluded: chain B residue  662 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    5.9990
   chunk 89 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 91 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 65 optimal weight:    8.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
B 558 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.159540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.117579 restraints weight = 7601.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.120518 restraints weight = 5319.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.121928 restraints weight = 4366.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.123469 restraints weight = 3925.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.123935 restraints weight = 3658.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.2936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7308  Z= 0.146
  Angle     :  0.537   6.747   9942  Z= 0.285
  Chirality :  0.042   0.157   1170
  Planarity :  0.003   0.034   1222
  Dihedral  :  5.673  53.001   1004
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 18.27 %
    Favored  : 77.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.28), residues: 940
  helix:  0.79 (0.21), residues: 634
  sheet:  None (None), residues: 0
  loop : -2.83 (0.34), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 332 
 TYR   0.011   0.001   TYR B 636 
 PHE   0.024   0.001   PHE B 509 
 TRP   0.012   0.001   TRP B 222 
 HIS   0.002   0.001   HIS B 620 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 7306)
  covalent geometry    : angle       0.53716 ( 9938)
  SS BOND              : bond        0.00053 (    2)
  SS BOND              : angle       0.12980 (    4)
  hydrogen bonds       : bond        0.03488 (  421)
  hydrogen bonds       : angle       3.68822 ( 1248)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 102
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
REVERT: A  331 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8240 (mt)
REVERT: A  337 ILE cc_start: 0.8774 (mm) cc_final: 0.8573 (mt)
REVERT: A  350 MET cc_start: 0.6851 (mmp) cc_final: 0.6451 (mmm)
REVERT: A  441 LYS cc_start: 0.8318 (tttt) cc_final: 0.7800 (mtpp)
REVERT: A  497 ARG cc_start: 0.8150 (mtp-110) cc_final: 0.7767 (mtt180)
REVERT: A  563 ILE cc_start: 0.6768 (OUTLIER) cc_final: 0.6512 (tp)
REVERT: B  331 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8218 (mp)
REVERT: B  441 LYS cc_start: 0.7951 (tttp) cc_final: 0.7482 (mtpp)
  outliers start: 33
  outliers final: 25
  residues processed: 128
  average time/residue: 0.0733
  time to fit residues: 13.2928
Evaluate side-chains
  124 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 96
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  325 ILE
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  496 CYS
Chi-restraints excluded: chain A residue  507 CYS
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  563 ILE
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  646 ILE
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  331 ILE
Chi-restraints excluded: chain B residue  437 MET
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  455 VAL
Chi-restraints excluded: chain B residue  460 SER
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  496 CYS
Chi-restraints excluded: chain B residue  507 CYS
Chi-restraints excluded: chain B residue  646 ILE
Chi-restraints excluded: chain B residue  662 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 65 optimal weight:    8.9990
   chunk 73 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 37 optimal weight:    6.9990
   chunk 71 optimal weight:    2.9990
   chunk 74 optimal weight:    5.9990
   chunk 64 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 69 optimal weight:    8.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 558 ASN
B 558 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.150539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.109459 restraints weight = 7661.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.111672 restraints weight = 5526.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.113357 restraints weight = 4608.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.114187 restraints weight = 4155.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.114486 restraints weight = 3907.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.3019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   7308  Z= 0.204
  Angle     :  0.589   8.610   9942  Z= 0.313
  Chirality :  0.044   0.165   1170
  Planarity :  0.003   0.035   1222
  Dihedral  :  5.875  52.476   1004
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 18.40 %
    Favored  : 77.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.75 (0.28), residues: 940
  helix:  0.58 (0.20), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.88 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 332 
 TYR   0.012   0.001   TYR B 636 
 PHE   0.026   0.002   PHE B 509 
 TRP   0.008   0.002   TRP A 658 
 HIS   0.002   0.001   HIS B 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 ( 7306)
  covalent geometry    : angle       0.58876 ( 9938)
  SS BOND              : bond        0.00156 (    2)
  SS BOND              : angle       0.09614 (    4)
  hydrogen bonds       : bond        0.03786 (  421)
  hydrogen bonds       : angle       3.94989 ( 1248)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 112
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8263 (mt)
REVERT: A  441 LYS cc_start: 0.8341 (tttt) cc_final: 0.7835 (mtpp)
REVERT: A  497 ARG cc_start: 0.8173 (mtp-110) cc_final: 0.7846 (mtt180)
REVERT: A  563 ILE cc_start: 0.6808 (OUTLIER) cc_final: 0.6547 (tp)
REVERT: B  331 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8341 (mt)
REVERT: B  350 MET cc_start: 0.6805 (ttt) cc_final: 0.6560 (ttm)
REVERT: B  441 LYS cc_start: 0.8007 (tttp) cc_final: 0.7491 (mtpp)
  outliers start: 32
  outliers final: 22
  residues processed: 137
  average time/residue: 0.0751
  time to fit residues: 14.1774
Evaluate side-chains
  134 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 109
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  496 CYS
Chi-restraints excluded: chain A residue  507 CYS
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  563 ILE
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  646 ILE
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  331 ILE
Chi-restraints excluded: chain B residue  384 LYS
Chi-restraints excluded: chain B residue  437 MET
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  460 SER
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  496 CYS
Chi-restraints excluded: chain B residue  507 CYS
Chi-restraints excluded: chain B residue  646 ILE
Chi-restraints excluded: chain B residue  662 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 20 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 61 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 34 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   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 558 ASN
B 558 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.155447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.114877 restraints weight = 7547.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.117681 restraints weight = 5277.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.119321 restraints weight = 4318.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.120474 restraints weight = 3844.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.120474 restraints weight = 3581.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.3094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7308  Z= 0.120
  Angle     :  0.542   8.793   9942  Z= 0.289
  Chirality :  0.042   0.159   1170
  Planarity :  0.003   0.035   1222
  Dihedral  :  5.683  53.140   1004
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 19.60 %
    Favored  : 76.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.28), residues: 940
  helix:  0.84 (0.21), residues: 640
  sheet:  None (None), residues: 0
  loop : -2.79 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 467 
 TYR   0.010   0.001   TYR B 636 
 PHE   0.021   0.001   PHE A 509 
 TRP   0.010   0.001   TRP B 222 
 HIS   0.002   0.001   HIS B 620 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 7306)
  covalent geometry    : angle       0.54224 ( 9938)
  SS BOND              : bond        0.00019 (    2)
  SS BOND              : angle       0.08428 (    4)
  hydrogen bonds       : bond        0.03454 (  421)
  hydrogen bonds       : angle       3.78179 ( 1248)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 90
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
REVERT: A  331 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8254 (mt)
REVERT: A  350 MET cc_start: 0.7080 (mmp) cc_final: 0.6580 (mmm)
REVERT: A  441 LYS cc_start: 0.8316 (tttt) cc_final: 0.7807 (mtpp)
REVERT: A  497 ARG cc_start: 0.8142 (mtp-110) cc_final: 0.7820 (mtt180)
REVERT: A  563 ILE cc_start: 0.6898 (OUTLIER) cc_final: 0.6628 (tp)
REVERT: B  331 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8181 (mp)
REVERT: B  441 LYS cc_start: 0.7934 (tttp) cc_final: 0.7573 (mtpp)
  outliers start: 26
  outliers final: 20
  residues processed: 112
  average time/residue: 0.0773
  time to fit residues: 12.0681
Evaluate side-chains
  115 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 92
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  496 CYS
Chi-restraints excluded: chain A residue  507 CYS
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  563 ILE
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  331 ILE
Chi-restraints excluded: chain B residue  384 LYS
Chi-restraints excluded: chain B residue  437 MET
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  460 SER
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  496 CYS
Chi-restraints excluded: chain B residue  507 CYS
Chi-restraints excluded: chain B residue  662 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 53 optimal weight:    0.4980
   chunk 46 optimal weight:    2.9990
   chunk 22 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 50 optimal weight:    6.9990
   chunk 87 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 558 ASN
B 558 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.156170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.116250 restraints weight = 7459.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.118995 restraints weight = 5208.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.120779 restraints weight = 4225.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.121690 restraints weight = 3786.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.122052 restraints weight = 3550.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.3149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7308  Z= 0.128
  Angle     :  0.543   8.506   9942  Z= 0.289
  Chirality :  0.042   0.156   1170
  Planarity :  0.003   0.035   1222
  Dihedral  :  5.691  54.055   1004
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 19.47 %
    Favored  : 77.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.28), residues: 940
  helix:  1.01 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.79 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 332 
 TYR   0.010   0.001   TYR B 636 
 PHE   0.042   0.001   PHE B 509 
 TRP   0.008   0.001   TRP B 222 
 HIS   0.003   0.001   HIS B 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 7306)
  covalent geometry    : angle       0.54360 ( 9938)
  SS BOND              : bond        0.00037 (    2)
  SS BOND              : angle       0.15166 (    4)
  hydrogen bonds       : bond        0.03433 (  421)
  hydrogen bonds       : angle       3.76344 ( 1248)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1147.05 seconds
wall clock time: 20 minutes 32.88 seconds (1232.88 seconds total)