Starting phenix.real_space_refine
on Wed Feb 12 01:52:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6npk_0472/02_2025/6npk_0472.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6npk_0472/02_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_0472/02_2025/6npk_0472.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6npk_0472/02_2025/6npk_0472.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6npk_0472/02_2025/6npk_0472.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6npk_0472/02_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-5592/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: 4.37, per 1000 atoms: 0.61
  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: 1.61
  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: 0.80
  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: 1.96

  Time building geometry restraints manager: 1.91 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: 0.03
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:             0.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.800
  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:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.740
-------------------------------------------------------------------------------
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   7306  Z= 0.274
  Angle     :  0.824  11.789   9938  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 

*********************** 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  : 0.774 
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: 0.1918
  time to fit residues: 49.1034
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  : 0.815 
-------------------------------------------------------------------------------
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 = 54)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.123266 restraints weight = 7345.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.125900 restraints weight = 5169.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.127419 restraints weight = 4206.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
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   7306  Z= 0.158
  Angle     :  0.539   6.117   9938  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 

*********************** 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  : 0.717 
Fit side-chains
   revert: symmetry clash
REVERT: A  275 TYR cc_start: 0.8460 (t80) cc_final: 0.7150 (t80)
REVERT: A  318 MET cc_start: 0.7456 (mtm) cc_final: 0.7254 (mtp)
REVERT: A  337 ILE cc_start: 0.8608 (mm) cc_final: 0.8330 (mt)
REVERT: A  441 LYS cc_start: 0.8503 (tttt) cc_final: 0.7814 (mtpp)
REVERT: A  497 ARG cc_start: 0.8108 (mtp-110) cc_final: 0.7774 (ttm170)
REVERT: B  337 ILE cc_start: 0.8702 (mm) cc_final: 0.8419 (mt)
REVERT: B  376 PHE cc_start: 0.8163 (m-10) cc_final: 0.7700 (m-10)
REVERT: B  402 ASP cc_start: 0.7452 (t0) cc_final: 0.7236 (t0)
REVERT: B  436 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7346 (mp10)
REVERT: B  441 LYS cc_start: 0.7865 (tttp) cc_final: 0.7466 (mtpp)
  outliers start: 34
  outliers final: 21
  residues processed: 132
  average time/residue: 0.1777
  time to fit residues: 32.0719
Evaluate side-chains
  112 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 90
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 37 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 43 optimal weight:    0.5980
   chunk 76 optimal weight:   20.0000
   chunk 60 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3683 r_free = 0.3683 target = 0.160447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.121912 restraints weight = 7430.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.124313 restraints weight = 5291.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.126121 restraints weight = 4353.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.2205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7306  Z= 0.162
  Angle     :  0.508   5.618   9938  Z= 0.277
  Chirality :  0.041   0.135   1170
  Planarity :  0.003   0.043   1222
  Dihedral  :  6.489  55.520   1014
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 13.07 %
    Favored  : 83.20 %
  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: -1.54 (0.27), residues: 940
  helix: -0.05 (0.21), residues: 632
  sheet:  None (None), residues: 0
  loop : -3.09 (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   0.007   0.000   ARG A 332 

*********************** 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
  133 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 105
  time to evaluate  : 0.708 
Fit side-chains
REVERT: A  225 MET cc_start: 0.7952 (mmt) cc_final: 0.7608 (mmt)
REVERT: A  275 TYR cc_start: 0.8496 (t80) cc_final: 0.7185 (t80)
REVERT: A  331 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8229 (mt)
REVERT: A  337 ILE cc_start: 0.8686 (mm) cc_final: 0.8386 (mt)
REVERT: A  441 LYS cc_start: 0.8304 (tttt) cc_final: 0.7786 (mtpp)
REVERT: A  497 ARG cc_start: 0.8101 (mtp-110) cc_final: 0.7787 (mtp85)
REVERT: B  337 ILE cc_start: 0.8726 (mm) cc_final: 0.8439 (mt)
REVERT: B  441 LYS cc_start: 0.7824 (tttp) cc_final: 0.7415 (mtpp)
  outliers start: 28
  outliers final: 17
  residues processed: 127
  average time/residue: 0.1680
  time to fit residues: 29.6742
Evaluate side-chains
  107 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
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  346 SER
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:    0.7980
   chunk 47 optimal weight:    6.9990
   chunk 61 optimal weight:    0.8980
   chunk 16 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 22 optimal weight:    9.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    1.5386

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.155249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.116206 restraints weight = 7568.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.118561 restraints weight = 5492.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.119959 restraints weight = 4558.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.2431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7306  Z= 0.253
  Angle     :  0.548   5.330   9938  Z= 0.295
  Chirality :  0.043   0.140   1170
  Planarity :  0.003   0.036   1222
  Dihedral  :  6.162  50.961   1008
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 14.27 %
    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: -1.29 (0.27), residues: 940
  helix:  0.13 (0.21), residues: 632
  sheet:  None (None), residues: 0
  loop : -2.94 (0.34), 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   0.021   0.001   PHE B 509 
 TYR   0.013   0.001   TYR B 636 
 ARG   0.005   0.001   ARG A 332 

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

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 111
  time to evaluate  : 0.748 
Fit side-chains
   revert: symmetry clash
REVERT: A  275 TYR cc_start: 0.8663 (t80) cc_final: 0.7426 (t80)
REVERT: A  337 ILE cc_start: 0.8736 (mm) cc_final: 0.8527 (mt)
REVERT: A  380 ASP cc_start: 0.8442 (p0) cc_final: 0.8219 (p0)
REVERT: A  441 LYS cc_start: 0.8306 (tttt) cc_final: 0.7828 (mtpp)
REVERT: A  497 ARG cc_start: 0.8141 (mtp-110) cc_final: 0.7735 (mtp85)
REVERT: A  563 ILE cc_start: 0.7126 (OUTLIER) cc_final: 0.6813 (tp)
REVERT: B  331 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8334 (mt)
REVERT: B  337 ILE cc_start: 0.8790 (mm) cc_final: 0.8585 (mt)
REVERT: B  441 LYS cc_start: 0.7965 (tttp) cc_final: 0.7511 (mtpp)
  outliers start: 25
  outliers final: 19
  residues processed: 130
  average time/residue: 0.1777
  time to fit residues: 31.8405
Evaluate side-chains
  126 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
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  384 LYS
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  496 CYS
Chi-restraints excluded: chain A residue  507 CYS
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  563 ILE
Chi-restraints excluded: chain A residue  646 ILE
Chi-restraints excluded: chain B residue  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:    9.9990
   chunk 69 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0170
   chunk 66 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 63 optimal weight:    6.9990
   chunk 42 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9990
   overall best weight:    1.1624

-------------------------------------------------------------------------------
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 = 0.3645 r_free = 0.3645 target = 0.157118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.118335 restraints weight = 7392.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.120593 restraints weight = 5403.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.122187 restraints weight = 4493.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.2645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7306  Z= 0.205
  Angle     :  0.522   6.672   9938  Z= 0.279
  Chirality :  0.042   0.147   1170
  Planarity :  0.003   0.035   1222
  Dihedral  :  5.843  51.314   1006
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 14.13 %
    Favored  : 81.47 %
  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: -0.99 (0.28), residues: 940
  helix:  0.34 (0.21), residues: 634
  sheet:  None (None), residues: 0
  loop : -2.80 (0.35), 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   0.024   0.001   PHE B 509 
 TYR   0.012   0.001   TYR A 636 
 ARG   0.008   0.000   ARG A 332 

*********************** 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
  131 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 98
  time to evaluate  : 0.694 
Fit side-chains
   revert: symmetry clash
REVERT: A  275 TYR cc_start: 0.8663 (t80) cc_final: 0.7405 (t80)
REVERT: A  331 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8269 (mt)
REVERT: A  337 ILE cc_start: 0.8701 (mm) cc_final: 0.8491 (mt)
REVERT: A  380 ASP cc_start: 0.8509 (p0) cc_final: 0.8251 (p0)
REVERT: A  441 LYS cc_start: 0.8377 (tttt) cc_final: 0.7761 (mtpp)
REVERT: A  497 ARG cc_start: 0.8145 (mtp-110) cc_final: 0.7667 (mtt180)
REVERT: A  563 ILE cc_start: 0.7157 (OUTLIER) cc_final: 0.6531 (tp)
REVERT: B  326 ASP cc_start: 0.8070 (p0) cc_final: 0.7824 (p0)
REVERT: B  331 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8300 (mt)
REVERT: B  441 LYS cc_start: 0.7954 (tttp) cc_final: 0.7466 (mtpp)
  outliers start: 33
  outliers final: 23
  residues processed: 122
  average time/residue: 0.1844
  time to fit residues: 30.7083
Evaluate side-chains
  117 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 91
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  325 ILE
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  496 CYS
Chi-restraints excluded: chain A residue  507 CYS
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  563 ILE
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  646 ILE
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  331 ILE
Chi-restraints excluded: chain B residue  407 THR
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:    0.9990
   chunk 22 optimal weight:    8.9990
   chunk 6 optimal weight:    5.9990
   chunk 62 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0570
   chunk 8 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   overall best weight:    0.7300

-------------------------------------------------------------------------------
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 = 0.3668 r_free = 0.3668 target = 0.158791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.119168 restraints weight = 7391.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.121803 restraints weight = 5225.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.123563 restraints weight = 4272.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.2730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7306  Z= 0.158
  Angle     :  0.500   5.471   9938  Z= 0.267
  Chirality :  0.041   0.152   1170
  Planarity :  0.003   0.036   1222
  Dihedral  :  5.732  52.600   1006
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 15.87 %
    Favored  : 80.40 %
  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: -0.66 (0.28), residues: 940
  helix:  0.59 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.70 (0.36), residues: 304

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   0.023   0.001   PHE B 509 
 TYR   0.011   0.001   TYR B 636 
 ARG   0.007   0.000   ARG A 332 

*********************** 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
  128 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 100
  time to evaluate  : 0.674 
Fit side-chains
   revert: symmetry clash
REVERT: A  331 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8269 (mt)
REVERT: A  337 ILE cc_start: 0.8731 (mm) cc_final: 0.8520 (mt)
REVERT: A  350 MET cc_start: 0.7261 (mmp) cc_final: 0.6862 (mtt)
REVERT: A  380 ASP cc_start: 0.8623 (p0) cc_final: 0.8376 (p0)
REVERT: A  441 LYS cc_start: 0.8294 (tttt) cc_final: 0.7761 (mtpp)
REVERT: A  497 ARG cc_start: 0.8108 (mtp-110) cc_final: 0.7662 (mtt180)
REVERT: B  331 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8264 (mt)
REVERT: B  441 LYS cc_start: 0.7898 (tttp) cc_final: 0.7457 (mtpp)
  outliers start: 28
  outliers final: 22
  residues processed: 124
  average time/residue: 0.1850
  time to fit residues: 31.1865
Evaluate side-chains
  117 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  325 ILE
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  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  384 LYS
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 65 optimal weight:    8.9990
   chunk 5 optimal weight:    0.7980
   chunk 17 optimal weight:    9.9990
   chunk 53 optimal weight:    9.9990
   chunk 70 optimal weight:    1.9990
   chunk 22 optimal weight:    7.9990
   chunk 27 optimal weight:    0.0570
   chunk 39 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   chunk 20 optimal weight:    0.4980
   overall best weight:    0.8100

-------------------------------------------------------------------------------
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 = 0.3665 r_free = 0.3665 target = 0.158706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.118909 restraints weight = 7396.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.121518 restraints weight = 5236.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.123232 restraints weight = 4301.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.2824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7306  Z= 0.168
  Angle     :  0.504   6.020   9938  Z= 0.268
  Chirality :  0.041   0.155   1170
  Planarity :  0.003   0.033   1222
  Dihedral  :  5.691  53.104   1006
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 17.73 %
    Favored  : 78.53 %
  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: -0.47 (0.28), residues: 940
  helix:  0.76 (0.20), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.68 (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   0.025   0.001   PHE B 509 
 TYR   0.011   0.001   TYR B 636 
 ARG   0.009   0.000   ARG A 332 

*********************** 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
  124 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 96
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
REVERT: A  331 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8227 (mt)
REVERT: A  337 ILE cc_start: 0.8739 (mm) cc_final: 0.8530 (mt)
REVERT: A  350 MET cc_start: 0.7264 (mmp) cc_final: 0.7019 (mtt)
REVERT: A  441 LYS cc_start: 0.8269 (tttt) cc_final: 0.7747 (mtpp)
REVERT: A  497 ARG cc_start: 0.8122 (mtp-110) cc_final: 0.7682 (mtt180)
REVERT: B  331 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8278 (mt)
REVERT: B  441 LYS cc_start: 0.7877 (tttp) cc_final: 0.7446 (mtpp)
  outliers start: 28
  outliers final: 25
  residues processed: 120
  average time/residue: 0.1829
  time to fit residues: 29.8625
Evaluate side-chains
  124 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 97
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  325 ILE
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  496 CYS
Chi-restraints excluded: chain A residue  507 CYS
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  331 ILE
Chi-restraints excluded: chain B residue  384 LYS
Chi-restraints excluded: chain B residue  407 THR
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   chunk 77 optimal weight:    8.9990
   chunk 91 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0170
   chunk 51 optimal weight:    1.9990
   chunk 61 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   chunk 74 optimal weight:    8.9990
   chunk 46 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    1.2024

-------------------------------------------------------------------------------
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 = 0.3647 r_free = 0.3647 target = 0.157074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.117267 restraints weight = 7416.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.119781 restraints weight = 5306.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.121436 restraints weight = 4366.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.2877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7306  Z= 0.209
  Angle     :  0.522   5.931   9938  Z= 0.277
  Chirality :  0.042   0.158   1170
  Planarity :  0.003   0.035   1222
  Dihedral  :  5.732  52.992   1006
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 17.07 %
    Favored  : 78.53 %
  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: -0.45 (0.28), residues: 940
  helix:  0.79 (0.20), residues: 634
  sheet:  None (None), residues: 0
  loop : -2.69 (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   0.026   0.001   PHE B 509 
 TYR   0.011   0.001   TYR B 636 
 ARG   0.009   0.000   ARG A 332 

*********************** 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
  128 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 95
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
REVERT: A  324 MET cc_start: 0.4194 (tpp) cc_final: 0.3918 (tpp)
REVERT: A  331 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8247 (mt)
REVERT: A  337 ILE cc_start: 0.8757 (mm) cc_final: 0.8555 (mt)
REVERT: A  350 MET cc_start: 0.7217 (mmp) cc_final: 0.6968 (mtt)
REVERT: A  380 ASP cc_start: 0.8517 (p0) cc_final: 0.8295 (p0)
REVERT: A  441 LYS cc_start: 0.8305 (tttt) cc_final: 0.7784 (mtpp)
REVERT: A  497 ARG cc_start: 0.8141 (mtp-110) cc_final: 0.7821 (mtt180)
REVERT: B  331 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8303 (mt)
REVERT: B  441 LYS cc_start: 0.7939 (tttp) cc_final: 0.7486 (mtpp)
  outliers start: 33
  outliers final: 29
  residues processed: 122
  average time/residue: 0.1823
  time to fit residues: 30.4752
Evaluate side-chains
  125 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 94
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
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  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  384 LYS
Chi-restraints excluded: chain B residue  407 THR
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  455 VAL
Chi-restraints excluded: chain B residue  460 SER
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  496 CYS
Chi-restraints excluded: chain B residue  507 CYS
Chi-restraints excluded: chain B residue  646 ILE
Chi-restraints excluded: chain B residue  662 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 56 optimal weight:    4.9990
   chunk 42 optimal weight:    0.0980
   chunk 3 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 18 optimal weight:   10.0000
   chunk 79 optimal weight:    0.0980
   chunk 11 optimal weight:    8.9990
   chunk 69 optimal weight:    7.9990
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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 = 0.3641 r_free = 0.3641 target = 0.156453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.116334 restraints weight = 7467.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.118768 restraints weight = 5352.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.120563 restraints weight = 4415.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7306  Z= 0.211
  Angle     :  0.520   6.351   9938  Z= 0.276
  Chirality :  0.041   0.160   1170
  Planarity :  0.003   0.032   1222
  Dihedral  :  5.754  53.158   1006
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 17.33 %
    Favored  : 78.27 %
  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: -0.42 (0.28), residues: 940
  helix:  0.82 (0.20), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.71 (0.36), residues: 304

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   0.027   0.001   PHE B 509 
 TYR   0.011   0.001   TYR B 636 
 ARG   0.008   0.000   ARG A 332 

*********************** 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
  137 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 104
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8178 (mt)
REVERT: A  337 ILE cc_start: 0.8789 (mm) cc_final: 0.8587 (mt)
REVERT: A  441 LYS cc_start: 0.8311 (tttt) cc_final: 0.7775 (mtpp)
REVERT: A  497 ARG cc_start: 0.8144 (mtp-110) cc_final: 0.7825 (mtt180)
REVERT: B  331 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8203 (mp)
REVERT: B  441 LYS cc_start: 0.7924 (tttp) cc_final: 0.7471 (mtpp)
  outliers start: 33
  outliers final: 31
  residues processed: 132
  average time/residue: 0.1654
  time to fit residues: 30.2683
Evaluate side-chains
  137 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 104
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
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  347 VAL
Chi-restraints excluded: chain B residue  384 LYS
Chi-restraints excluded: chain B residue  407 THR
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  455 VAL
Chi-restraints excluded: chain B residue  460 SER
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  496 CYS
Chi-restraints excluded: chain B residue  507 CYS
Chi-restraints excluded: chain B residue  646 ILE
Chi-restraints excluded: chain B residue  662 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 6 optimal weight:    9.9990
   chunk 86 optimal weight:    0.6980
   chunk 42 optimal weight:    0.4980
   chunk 3 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 93 optimal weight:    0.0980
   chunk 48 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   overall best weight:    0.6582

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.157291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.116601 restraints weight = 7529.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.119467 restraints weight = 5172.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.121438 restraints weight = 4177.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.3030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7306  Z= 0.156
  Angle     :  0.507   6.546   9938  Z= 0.271
  Chirality :  0.041   0.162   1170
  Planarity :  0.003   0.034   1222
  Dihedral  :  5.680  54.134   1006
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 18.93 %
    Favored  : 77.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.18 (0.28), residues: 940
  helix:  1.04 (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   0.009   0.001   TRP B 658 
 HIS   0.002   0.001   HIS B 620 
 PHE   0.026   0.001   PHE B 509 
 TYR   0.010   0.001   TYR B 636 
 ARG   0.007   0.000   ARG A 332 

********************** 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
  129 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 101
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
REVERT: A  331 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8115 (mp)
REVERT: A  337 ILE cc_start: 0.8771 (mm) cc_final: 0.8563 (mt)
REVERT: A  350 MET cc_start: 0.7279 (mmp) cc_final: 0.6975 (mtt)
REVERT: A  380 ASP cc_start: 0.8458 (p0) cc_final: 0.8245 (p0)
REVERT: A  441 LYS cc_start: 0.8344 (tttt) cc_final: 0.7748 (mtpp)
REVERT: A  497 ARG cc_start: 0.8164 (mtp-110) cc_final: 0.7811 (mtt180)
REVERT: B  331 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8091 (mp)
REVERT: B  441 LYS cc_start: 0.7889 (tttp) cc_final: 0.7439 (mtpp)
  outliers start: 28
  outliers final: 22
  residues processed: 126
  average time/residue: 0.1843
  time to fit residues: 32.2367
Evaluate side-chains
  129 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 105
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  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  347 VAL
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:    7.9990
   chunk 59 optimal weight:    0.2980
   chunk 65 optimal weight:    8.9990
   chunk 31 optimal weight:    0.8980
   chunk 64 optimal weight:    3.9990
   chunk 52 optimal weight:    0.8980
   chunk 79 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    1.2184

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.154958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.114125 restraints weight = 7487.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.116923 restraints weight = 5231.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.118379 restraints weight = 4287.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.3049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7306  Z= 0.217
  Angle     :  0.532   6.231   9938  Z= 0.283
  Chirality :  0.042   0.156   1170
  Planarity :  0.003   0.033   1222
  Dihedral  :  5.616  54.489   1004
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 19.07 %
    Favored  : 77.20 %
  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: -0.25 (0.28), residues: 940
  helix:  0.98 (0.20), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.74 (0.36), residues: 304

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   0.026   0.001   PHE B 509 
 TYR   0.010   0.001   TYR B 636 
 ARG   0.008   0.000   ARG A 332 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2157.57 seconds
wall clock time: 39 minutes 44.37 seconds (2384.37 seconds total)