Starting phenix.real_space_refine
on Mon Apr 28 05:00:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6npk_0472/04_2025/6npk_0472.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6npk_0472/04_2025/6npk_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6npk_0472/04_2025/6npk_0472.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6npk_0472/04_2025/6npk_0472.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6npk_0472/04_2025/6npk_0472.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6npk_0472/04_2025/6npk_0472.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 4.76, per 1000 atoms: 0.67
  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: 1.77
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.64
  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: 1.77

  Time building geometry restraints manager: 2.10 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.400
  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:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     19.980
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.830
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.016   0.002   TRP A 658 
 HIS   0.001   0.001   HIS A 512 
 PHE   0.029   0.002   PHE A 387 
 TYR   0.019   0.002   TYR B 305 
 ARG   0.044   0.002   ARG B 630 

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

*********************** 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  : 0.714 
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: 0.8113 (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: 0.8446 (mt)
REVERT: B  436 GLN cc_start: 0.8044 (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: 0.1863
  time to fit residues: 47.8882
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  : 0.705 
-------------------------------------------------------------------------------
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 79 optimal weight:    0.0270
   chunk 71 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    0.2980
   chunk 38 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   chunk 44 optimal weight:    0.8980
   chunk 54 optimal weight:    4.9990
   chunk 85 optimal weight:    0.7980
   overall best weight:    0.5838

-------------------------------------------------------------------------------
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 = 0.3691 r_free = 0.3691 target = 0.161421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.123274 restraints weight = 7345.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.125741 restraints weight = 5165.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.127492 restraints weight = 4237.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.1788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7308  Z= 0.117
  Angle     :  0.539   6.117   9942  Z= 0.296
  Chirality :  0.041   0.132   1170
  Planarity :  0.004   0.053   1222
  Dihedral  :  7.066  58.136   1021
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 13.07 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.62 (0.25), residues: 940
  helix: -0.93 (0.19), residues: 624
  sheet:  None (None), residues: 0
  loop : -3.30 (0.30), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 658 
 HIS   0.004   0.001   HIS B 620 
 PHE   0.021   0.001   PHE B 509 
 TYR   0.019   0.001   TYR B 636 
 ARG   0.005   0.000   ARG A 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03851 (  421)
  hydrogen bonds       : angle       4.23059 ( 1248)
  SS BOND              : bond        0.00056 (    2)
  SS BOND              : angle       0.21756 (    4)
  covalent geometry    : bond        0.00242 ( 7306)
  covalent geometry    : angle       0.53908 ( 9938)

*********************** 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
  143 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 109
  time to evaluate  : 0.731 
Fit side-chains
   revert: symmetry clash
REVERT: A  275 TYR cc_start: 0.8459 (t80) cc_final: 0.7154 (t80)
REVERT: A  318 MET cc_start: 0.7450 (mtm) cc_final: 0.7250 (mtp)
REVERT: A  337 ILE cc_start: 0.8613 (mm) cc_final: 0.8335 (mt)
REVERT: A  402 ASP cc_start: 0.7563 (t0) cc_final: 0.7361 (t0)
REVERT: A  441 LYS cc_start: 0.8502 (tttt) cc_final: 0.7819 (mtpp)
REVERT: A  497 ARG cc_start: 0.8088 (mtp-110) cc_final: 0.7769 (ttm170)
REVERT: B  337 ILE cc_start: 0.8707 (mm) cc_final: 0.8423 (mt)
REVERT: B  376 PHE cc_start: 0.8159 (m-10) cc_final: 0.7699 (m-10)
REVERT: B  402 ASP cc_start: 0.7450 (t0) cc_final: 0.7235 (t0)
REVERT: B  436 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7334 (mp10)
REVERT: B  441 LYS cc_start: 0.7865 (tttp) cc_final: 0.7470 (mtpp)
  outliers start: 34
  outliers final: 21
  residues processed: 132
  average time/residue: 0.2569
  time to fit residues: 44.9887
Evaluate side-chains
  114 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
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 10 optimal weight:    0.7980
   chunk 46 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 76 optimal weight:   20.0000
   chunk 60 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3690 r_free = 0.3690 target = 0.161202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.122755 restraints weight = 7421.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.125253 restraints weight = 5273.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.126859 restraints weight = 4342.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7308  Z= 0.111
  Angle     :  0.503   5.567   9942  Z= 0.275
  Chirality :  0.041   0.134   1170
  Planarity :  0.003   0.043   1222
  Dihedral  :  6.488  55.864   1014
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 13.07 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.27), residues: 940
  helix: -0.03 (0.21), residues: 632
  sheet:  None (None), residues: 0
  loop : -3.10 (0.32), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 658 
 HIS   0.002   0.001   HIS B 620 
 PHE   0.020   0.001   PHE A 509 
 TYR   0.014   0.001   TYR B 636 
 ARG   0.008   0.000   ARG A 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03498 (  421)
  hydrogen bonds       : angle       3.80879 ( 1248)
  SS BOND              : bond        0.00103 (    2)
  SS BOND              : angle       0.35176 (    4)
  covalent geometry    : bond        0.00238 ( 7306)
  covalent geometry    : angle       0.50320 ( 9938)

*********************** 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
  132 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 105
  time to evaluate  : 1.158 
Fit side-chains
REVERT: A  225 MET cc_start: 0.7936 (mmt) cc_final: 0.7606 (mmt)
REVERT: A  275 TYR cc_start: 0.8518 (t80) cc_final: 0.7149 (t80)
REVERT: A  331 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8215 (mt)
REVERT: A  337 ILE cc_start: 0.8677 (mm) cc_final: 0.8375 (mt)
REVERT: A  402 ASP cc_start: 0.7734 (t0) cc_final: 0.7465 (t0)
REVERT: A  441 LYS cc_start: 0.8300 (tttt) cc_final: 0.7780 (mtpp)
REVERT: A  497 ARG cc_start: 0.8120 (mtp-110) cc_final: 0.7800 (mtp85)
REVERT: B  337 ILE cc_start: 0.8727 (mm) cc_final: 0.8432 (mt)
REVERT: B  441 LYS cc_start: 0.7816 (tttp) cc_final: 0.7410 (mtpp)
  outliers start: 27
  outliers final: 16
  residues processed: 126
  average time/residue: 0.2505
  time to fit residues: 45.8663
Evaluate side-chains
  109 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
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  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  662 LEU
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  427 ASN
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 80 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 47 optimal weight:    6.9990
   chunk 61 optimal weight:    0.3980
   chunk 16 optimal weight:    6.9990
   chunk 30 optimal weight:    9.9990
   chunk 56 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9980
   chunk 22 optimal weight:    8.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.3679 r_free = 0.3679 target = 0.160434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.121808 restraints weight = 7479.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.124344 restraints weight = 5347.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.126078 restraints weight = 4389.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7308  Z= 0.114
  Angle     :  0.499   5.325   9942  Z= 0.269
  Chirality :  0.041   0.140   1170
  Planarity :  0.003   0.036   1222
  Dihedral  :  6.012  53.356   1008
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 14.40 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.28), residues: 940
  helix:  0.32 (0.21), residues: 634
  sheet:  None (None), residues: 0
  loop : -2.89 (0.34), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 658 
 HIS   0.002   0.001   HIS B 620 
 PHE   0.021   0.001   PHE B 509 
 TYR   0.012   0.001   TYR A 636 
 ARG   0.004   0.000   ARG A 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03414 (  421)
  hydrogen bonds       : angle       3.62534 ( 1248)
  SS BOND              : bond        0.00054 (    2)
  SS BOND              : angle       0.21870 (    4)
  covalent geometry    : bond        0.00251 ( 7306)
  covalent geometry    : angle       0.49866 ( 9938)

*********************** 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
  122 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 2.003 
Fit side-chains
   revert: symmetry clash
REVERT: A  225 MET cc_start: 0.7943 (mmt) cc_final: 0.7664 (mmt)
REVERT: A  275 TYR cc_start: 0.8610 (t80) cc_final: 0.7300 (t80)
REVERT: A  331 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8237 (mp)
REVERT: A  337 ILE cc_start: 0.8683 (mm) cc_final: 0.8463 (mt)
REVERT: A  402 ASP cc_start: 0.7824 (t0) cc_final: 0.7513 (t0)
REVERT: A  441 LYS cc_start: 0.8313 (tttt) cc_final: 0.7783 (mtpp)
REVERT: A  479 ILE cc_start: 0.5028 (OUTLIER) cc_final: 0.4823 (mm)
REVERT: A  497 ARG cc_start: 0.8133 (mtp-110) cc_final: 0.7740 (mtp85)
REVERT: A  563 ILE cc_start: 0.7063 (OUTLIER) cc_final: 0.6777 (tp)
REVERT: B  331 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8288 (mt)
REVERT: B  337 ILE cc_start: 0.8685 (mm) cc_final: 0.8470 (mt)
REVERT: B  441 LYS cc_start: 0.7830 (tttp) cc_final: 0.7409 (mtpp)
  outliers start: 24
  outliers final: 18
  residues processed: 118
  average time/residue: 0.2235
  time to fit residues: 37.2981
Evaluate side-chains
  118 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
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  384 LYS
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  479 ILE
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  662 LEU
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  331 ILE
Chi-restraints excluded: chain B residue  427 ASN
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 69 optimal weight:    0.9990
   chunk 28 optimal weight:    9.9990
   chunk 55 optimal weight:    2.9990
   chunk 64 optimal weight:    9.9990
   chunk 66 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 63 optimal weight:    0.6980
   chunk 42 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9980
   chunk 82 optimal weight:    3.9990
   overall best weight:    1.9386

-------------------------------------------------------------------------------
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 = 0.3646 r_free = 0.3646 target = 0.156552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.114347 restraints weight = 7525.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.117096 restraints weight = 5259.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.119099 restraints weight = 4315.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.2531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   7308  Z= 0.199
  Angle     :  0.570   7.947   9942  Z= 0.303
  Chirality :  0.044   0.149   1170
  Planarity :  0.003   0.035   1222
  Dihedral  :  6.160  51.318   1008
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 14.13 %
    Favored  : 81.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.28), residues: 940
  helix:  0.24 (0.21), residues: 632
  sheet:  None (None), residues: 0
  loop : -2.84 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 658 
 HIS   0.003   0.001   HIS B 620 
 PHE   0.024   0.002   PHE B 509 
 TYR   0.013   0.001   TYR B 636 
 ARG   0.005   0.001   ARG A 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03752 (  421)
  hydrogen bonds       : angle       3.80657 ( 1248)
  SS BOND              : bond        0.00076 (    2)
  SS BOND              : angle       0.23912 (    4)
  covalent geometry    : bond        0.00468 ( 7306)
  covalent geometry    : angle       0.56986 ( 9938)

*********************** 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
  147 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 115
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
REVERT: A  275 TYR cc_start: 0.8688 (t80) cc_final: 0.7398 (t80)
REVERT: A  331 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8268 (mt)
REVERT: A  337 ILE cc_start: 0.8724 (mm) cc_final: 0.8513 (mt)
REVERT: A  380 ASP cc_start: 0.8498 (p0) cc_final: 0.8292 (p0)
REVERT: A  441 LYS cc_start: 0.8305 (tttt) cc_final: 0.7822 (mtpp)
REVERT: A  497 ARG cc_start: 0.8163 (mtp-110) cc_final: 0.7744 (mtp85)
REVERT: A  563 ILE cc_start: 0.7148 (OUTLIER) cc_final: 0.6553 (tp)
REVERT: B  326 ASP cc_start: 0.8216 (p0) cc_final: 0.7881 (p0)
REVERT: B  331 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8347 (mt)
REVERT: B  441 LYS cc_start: 0.7963 (tttp) cc_final: 0.7495 (mtpp)
  outliers start: 32
  outliers final: 24
  residues processed: 139
  average time/residue: 0.1625
  time to fit residues: 31.4797
Evaluate side-chains
  138 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 111
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
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  331 ILE
Chi-restraints excluded: chain A residue  346 SER
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  384 LYS
Chi-restraints excluded: chain A residue  413 SER
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  307 VAL
Chi-restraints excluded: chain B residue  331 ILE
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  413 SER
Chi-restraints excluded: chain B residue  427 ASN
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 22 optimal weight:    0.3980
   chunk 6 optimal weight:    9.9990
   chunk 62 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9980
   chunk 90 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 70 optimal weight:    4.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3654 r_free = 0.3654 target = 0.157700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.117728 restraints weight = 7419.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.120340 restraints weight = 5272.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.121834 restraints weight = 4327.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.2718

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= 0.121
  Angle     :  0.516   7.360   9942  Z= 0.276
  Chirality :  0.041   0.159   1170
  Planarity :  0.003   0.033   1222
  Dihedral  :  5.832  52.038   1006
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 15.33 %
    Favored  : 81.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.28), residues: 940
  helix:  0.51 (0.21), residues: 634
  sheet:  None (None), residues: 0
  loop : -2.74 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 658 
 HIS   0.002   0.001   HIS B 620 
 PHE   0.025   0.001   PHE B 509 
 TYR   0.012   0.001   TYR B 636 
 ARG   0.003   0.000   ARG A 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03452 (  421)
  hydrogen bonds       : angle       3.65997 ( 1248)
  SS BOND              : bond        0.00027 (    2)
  SS BOND              : angle       0.17110 (    4)
  covalent geometry    : bond        0.00268 ( 7306)
  covalent geometry    : angle       0.51564 ( 9938)

*********************** 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
  125 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 99
  time to evaluate  : 0.710 
Fit side-chains
   revert: symmetry clash
REVERT: A  331 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8266 (mt)
REVERT: A  337 ILE cc_start: 0.8716 (mm) cc_final: 0.8508 (mt)
REVERT: A  350 MET cc_start: 0.7319 (mmp) cc_final: 0.6858 (mtt)
REVERT: A  380 ASP cc_start: 0.8529 (p0) cc_final: 0.8258 (p0)
REVERT: A  441 LYS cc_start: 0.8381 (tttt) cc_final: 0.7780 (mtpp)
REVERT: A  497 ARG cc_start: 0.8134 (mtp-110) cc_final: 0.7736 (mtp85)
REVERT: A  563 ILE cc_start: 0.6804 (OUTLIER) cc_final: 0.6503 (tp)
REVERT: B  331 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8287 (mt)
REVERT: B  441 LYS cc_start: 0.7898 (tttp) cc_final: 0.7453 (mtpp)
  outliers start: 26
  outliers final: 22
  residues processed: 121
  average time/residue: 0.1721
  time to fit residues: 28.8088
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  : 0.706 
-------------------------------------------------------------------------------
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  413 SER
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  662 LEU
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  331 ILE
Chi-restraints excluded: chain B residue  413 SER
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 65 optimal weight:    8.9990
   chunk 5 optimal weight:    0.9980
   chunk 17 optimal weight:    9.9990
   chunk 53 optimal weight:    9.9990
   chunk 70 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   chunk 52 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 329 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.158253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.118522 restraints weight = 7429.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.121102 restraints weight = 5259.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.122856 restraints weight = 4310.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.2820

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     :  0.513   6.326   9942  Z= 0.273
  Chirality :  0.041   0.152   1170
  Planarity :  0.003   0.035   1222
  Dihedral  :  5.756  53.021   1006
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 15.20 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.28), residues: 940
  helix:  0.75 (0.21), residues: 634
  sheet:  None (None), residues: 0
  loop : -2.75 (0.36), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 658 
 HIS   0.002   0.001   HIS B 620 
 PHE   0.025   0.001   PHE B 509 
 TYR   0.012   0.001   TYR B 636 
 ARG   0.003   0.000   ARG A 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03373 (  421)
  hydrogen bonds       : angle       3.60433 ( 1248)
  SS BOND              : bond        0.00022 (    2)
  SS BOND              : angle       0.21660 (    4)
  covalent geometry    : bond        0.00269 ( 7306)
  covalent geometry    : angle       0.51314 ( 9938)

*********************** 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
  130 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 98
  time to evaluate  : 0.801 
Fit side-chains
   revert: symmetry clash
REVERT: A  331 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8231 (mt)
REVERT: A  337 ILE cc_start: 0.8728 (mm) cc_final: 0.8514 (mt)
REVERT: A  350 MET cc_start: 0.7267 (mmp) cc_final: 0.7012 (mtt)
REVERT: A  380 ASP cc_start: 0.8633 (p0) cc_final: 0.8381 (p0)
REVERT: A  441 LYS cc_start: 0.8287 (tttt) cc_final: 0.7749 (mtpp)
REVERT: A  497 ARG cc_start: 0.8135 (mtp-110) cc_final: 0.7748 (mtp85)
REVERT: B  331 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8344 (mt)
REVERT: B  441 LYS cc_start: 0.7905 (tttp) cc_final: 0.7449 (mtpp)
  outliers start: 32
  outliers final: 27
  residues processed: 124
  average time/residue: 0.1803
  time to fit residues: 30.9281
Evaluate side-chains
  133 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 104
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
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  384 LYS
Chi-restraints excluded: chain A residue  413 SER
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  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  413 SER
Chi-restraints excluded: chain B residue  427 ASN
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 87 optimal weight:    0.8980
   chunk 77 optimal weight:    6.9990
   chunk 91 optimal weight:    0.5980
   chunk 32 optimal weight:    0.0770
   chunk 51 optimal weight:    2.9990
   chunk 61 optimal weight:    7.9990
   chunk 6 optimal weight:    9.9990
   chunk 74 optimal weight:    7.9990
   chunk 46 optimal weight:    0.6980
   chunk 62 optimal weight:    0.5980
   overall best weight:    0.5738

-------------------------------------------------------------------------------
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 = 0.3683 r_free = 0.3683 target = 0.160285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.121057 restraints weight = 7399.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.123690 restraints weight = 5176.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.125587 restraints weight = 4212.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.2926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7308  Z= 0.107
  Angle     :  0.498   6.447   9942  Z= 0.266
  Chirality :  0.040   0.154   1170
  Planarity :  0.003   0.034   1222
  Dihedral  :  5.688  53.611   1006
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 16.53 %
    Favored  : 79.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.28), residues: 940
  helix:  0.94 (0.21), residues: 634
  sheet:  None (None), residues: 0
  loop : -2.72 (0.36), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 658 
 HIS   0.002   0.001   HIS B 620 
 PHE   0.024   0.001   PHE B 509 
 TYR   0.011   0.001   TYR B 636 
 ARG   0.004   0.000   ARG A 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03290 (  421)
  hydrogen bonds       : angle       3.55779 ( 1248)
  SS BOND              : bond        0.00045 (    2)
  SS BOND              : angle       0.19882 (    4)
  covalent geometry    : bond        0.00229 ( 7306)
  covalent geometry    : angle       0.49774 ( 9938)

*********************** 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
  136 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 109
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
REVERT: A  331 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8264 (mp)
REVERT: A  337 ILE cc_start: 0.8743 (mm) cc_final: 0.8538 (mt)
REVERT: A  350 MET cc_start: 0.7213 (mmp) cc_final: 0.6885 (mtt)
REVERT: A  380 ASP cc_start: 0.8436 (p0) cc_final: 0.8208 (p0)
REVERT: A  441 LYS cc_start: 0.8281 (tttt) cc_final: 0.7757 (mtpp)
REVERT: A  497 ARG cc_start: 0.8098 (mtp-110) cc_final: 0.7726 (mtp85)
REVERT: B  331 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8257 (mt)
REVERT: B  402 ASP cc_start: 0.7790 (t0) cc_final: 0.7517 (t0)
REVERT: B  441 LYS cc_start: 0.7904 (tttp) cc_final: 0.7450 (mtpp)
  outliers start: 27
  outliers final: 24
  residues processed: 132
  average time/residue: 0.1758
  time to fit residues: 32.3576
Evaluate side-chains
  133 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 107
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
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  376 PHE
Chi-restraints excluded: chain A residue  384 LYS
Chi-restraints excluded: chain A residue  413 SER
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  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  413 SER
Chi-restraints excluded: chain B residue  427 ASN
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 56 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0270
   chunk 3 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 18 optimal weight:   10.0000
   chunk 79 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0870
   chunk 69 optimal weight:    7.9990
   overall best weight:    0.7620

-------------------------------------------------------------------------------
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 = 0.3677 r_free = 0.3677 target = 0.160074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.120654 restraints weight = 7451.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.123088 restraints weight = 5246.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.124997 restraints weight = 4322.765|
|-----------------------------------------------------------------------------|
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.2972

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= 0.115
  Angle     :  0.512   6.389   9942  Z= 0.271
  Chirality :  0.041   0.156   1170
  Planarity :  0.003   0.034   1222
  Dihedral  :  5.536  53.816   1004
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 16.93 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.28), residues: 940
  helix:  1.04 (0.21), residues: 634
  sheet:  None (None), residues: 0
  loop : -2.74 (0.36), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 222 
 HIS   0.002   0.001   HIS B 620 
 PHE   0.024   0.001   PHE B 509 
 TYR   0.010   0.001   TYR B 636 
 ARG   0.003   0.000   ARG A 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03316 (  421)
  hydrogen bonds       : angle       3.59008 ( 1248)
  SS BOND              : bond        0.00012 (    2)
  SS BOND              : angle       0.18425 (    4)
  covalent geometry    : bond        0.00254 ( 7306)
  covalent geometry    : angle       0.51168 ( 9938)

*********************** 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
  134 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 106
  time to evaluate  : 0.772 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8253 (mt)
REVERT: A  380 ASP cc_start: 0.8543 (p0) cc_final: 0.8288 (p0)
REVERT: A  441 LYS cc_start: 0.8247 (tttt) cc_final: 0.7773 (mtpp)
REVERT: A  497 ARG cc_start: 0.8129 (mtp-110) cc_final: 0.7497 (mtt180)
REVERT: B  331 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8196 (mp)
REVERT: B  441 LYS cc_start: 0.7915 (tttp) cc_final: 0.7471 (mtpp)
  outliers start: 28
  outliers final: 25
  residues processed: 130
  average time/residue: 0.1715
  time to fit residues: 30.9500
Evaluate side-chains
  127 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 100
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
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  413 SER
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  251 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  331 ILE
Chi-restraints excluded: chain B residue  413 SER
Chi-restraints excluded: chain B residue  427 ASN
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 62 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 6 optimal weight:    8.9990
   chunk 86 optimal weight:    0.7980
   chunk 42 optimal weight:    0.0570
   chunk 3 optimal weight:    5.9990
   chunk 35 optimal weight:    0.5980
   chunk 93 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 12 optimal weight:    0.1980
   overall best weight:    0.4698

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.163322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.124032 restraints weight = 7439.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.126724 restraints weight = 5155.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.128621 restraints weight = 4176.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.3126

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= 0.101
  Angle     :  0.502   7.689   9942  Z= 0.266
  Chirality :  0.041   0.160   1170
  Planarity :  0.003   0.033   1222
  Dihedral  :  5.447  54.547   1004
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.29), residues: 940
  helix:  1.29 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.72 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 222 
 HIS   0.002   0.001   HIS B 620 
 PHE   0.021   0.001   PHE B 509 
 TYR   0.010   0.001   TYR B 636 
 ARG   0.004   0.000   ARG A 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03176 (  421)
  hydrogen bonds       : angle       3.52804 ( 1248)
  SS BOND              : bond        0.00066 (    2)
  SS BOND              : angle       0.24430 (    4)
  covalent geometry    : bond        0.00211 ( 7306)
  covalent geometry    : angle       0.50172 ( 9938)

********************** 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
  125 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 101
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
REVERT: A  225 MET cc_start: 0.7646 (mmt) cc_final: 0.7406 (mmt)
REVERT: A  331 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8119 (mp)
REVERT: A  350 MET cc_start: 0.7116 (mmp) cc_final: 0.6898 (mtt)
REVERT: A  380 ASP cc_start: 0.8264 (p0) cc_final: 0.8057 (p0)
REVERT: A  441 LYS cc_start: 0.8248 (tttt) cc_final: 0.7834 (mtpp)
REVERT: A  497 ARG cc_start: 0.8130 (mtp-110) cc_final: 0.7647 (mtt180)
REVERT: B  331 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8135 (mp)
REVERT: B  402 ASP cc_start: 0.7704 (t0) cc_final: 0.7470 (t0)
REVERT: B  441 LYS cc_start: 0.7871 (tttp) cc_final: 0.7437 (mtpp)
  outliers start: 24
  outliers final: 22
  residues processed: 122
  average time/residue: 0.1750
  time to fit residues: 29.7899
Evaluate side-chains
  128 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 104
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
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  331 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  413 SER
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  638 MET
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain B residue  331 ILE
Chi-restraints excluded: chain B residue  413 SER
Chi-restraints excluded: chain B residue  427 ASN
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 18 optimal weight:    9.9990
   chunk 59 optimal weight:    0.8980
   chunk 65 optimal weight:    8.9990
   chunk 31 optimal weight:    5.9990
   chunk 64 optimal weight:    5.9990
   chunk 52 optimal weight:    0.6980
   chunk 79 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3701 r_free = 0.3701 target = 0.162437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.123967 restraints weight = 7367.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.126547 restraints weight = 5289.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.127981 restraints weight = 4368.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.3131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7308  Z= 0.116
  Angle     :  0.514   7.972   9942  Z= 0.271
  Chirality :  0.041   0.154   1170
  Planarity :  0.003   0.032   1222
  Dihedral  :  5.500  54.709   1004
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 18.13 %
    Favored  : 78.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.28), residues: 940
  helix:  1.32 (0.21), residues: 634
  sheet:  None (None), residues: 0
  loop : -2.74 (0.36), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 222 
 HIS   0.002   0.001   HIS B 620 
 PHE   0.022   0.001   PHE A 509 
 TYR   0.010   0.001   TYR B 636 
 ARG   0.003   0.000   ARG A 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03283 (  421)
  hydrogen bonds       : angle       3.60886 ( 1248)
  SS BOND              : bond        0.00010 (    2)
  SS BOND              : angle       0.19188 (    4)
  covalent geometry    : bond        0.00260 ( 7306)
  covalent geometry    : angle       0.51368 ( 9938)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2705.59 seconds
wall clock time: 49 minutes 30.50 seconds (2970.50 seconds total)