Starting phenix.real_space_refine
on Thu Jun  5 20:50:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j97_61254/06_2025/9j97_61254.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j97_61254/06_2025/9j97_61254.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j97_61254/06_2025/9j97_61254.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j97_61254/06_2025/9j97_61254.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j97_61254/06_2025/9j97_61254.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j97_61254/06_2025/9j97_61254.cif"
  }
  resolution = 3.3
  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=   0.003 sd=   0.142
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: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      32      5.16       5
     C    4524      2.51       5
     N    1054      2.21       5
     O    1090      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6704
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3272
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 393, 3272
          Classifications: {'peptide': 393}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 14, 'TRANS': 378}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "B"
      Number of atoms: 3272
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 393, 3272
          Classifications: {'peptide': 393}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 14, 'TRANS': 378}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "A"
      Number of atoms: 80
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 80
          Unusual residues: {'8PE': 1, 'CLR': 1, 'PO4': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 80
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 80
          Unusual residues: {'8PE': 1, 'CLR': 1, 'PO4': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 3.92, per 1000 atoms: 0.58
  Number of scatterers: 6704
  At special positions: 0
  Unit cell: (109.787, 94.569, 79.351, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      32     16.00
     P       4     15.00
     O    1090      8.00
     N    1054      7.00
     C    4524      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 415 " - pdb=" SG  CYS A 440 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 415 " - pdb=" SG  CYS B 440 " distance=2.05

  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: 1.55
  Conformation dependent library (CDL) restraints added in 767.7 milliseconds
  

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1492

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 0 sheets defined
      73.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.57
  Creating SS restraints...
    Processing helix  chain 'A' and resid 230 through 257
      removed outlier: 3.768A  pdb=" N   THR A 234 " --> pdb=" O   PRO A 230 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   PHE A 235 " --> pdb=" O   ALA A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 295
      removed outlier: 4.235A  pdb=" N   ILE A 271 " --> pdb=" O   PRO A 267 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   GLY A 275 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   GLY A 286 " --> pdb=" O   LEU A 282 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ARG A 293 " --> pdb=" O   THR A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 303
      removed outlier: 3.686A  pdb=" N   ILE A 302 " --> pdb=" O   ASN A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 337
      removed outlier: 3.655A  pdb=" N   LEU A 316 " --> pdb=" O   SER A 312 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLU A 318 " --> pdb=" O   GLN A 314 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ILE A 319 " --> pdb=" O   HIS A 315 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLY A 321 " --> pdb=" O   PHE A 317 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU A 326 " --> pdb=" O   PHE A 322 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   PHE A 335 " --> pdb=" O   LEU A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 358
      removed outlier: 4.447A  pdb=" N   LEU A 349 " --> pdb=" O   TYR A 345 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   VAL A 356 " --> pdb=" O   TYR A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 376
    Processing helix  chain 'A' and resid 377 through 383
      removed outlier: 3.848A  pdb=" N   PHE A 382 " --> pdb=" O   LEU A 378 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   THR A 383 " --> pdb=" O   PHE A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 387
      removed outlier: 3.883A  pdb=" N   HIS A 387 " --> pdb=" O   ALA A 384 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 384 through 387'
    Processing helix  chain 'A' and resid 390 through 400
    Processing helix  chain 'A' and resid 403 through 420
      removed outlier: 4.272A  pdb=" N   LEU A 407 " --> pdb=" O   LEU A 403 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ILE A 414 " --> pdb=" O   LEU A 410 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   LEU A 419 " --> pdb=" O   CYS A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 453
    Processing helix  chain 'A' and resid 454 through 471
      removed outlier: 3.701A  pdb=" N   LEU A 458 " --> pdb=" O   ILE A 454 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   ARG A 459 " --> pdb=" O   PRO A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 472 through 503
      removed outlier: 4.397A  pdb=" N   HIS A 476 " --> pdb=" O   ARG A 472 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU A 477 " --> pdb=" O   ALA A 473 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   LYS A 482 " --> pdb=" O   VAL A 478 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   TYR A 483 " --> pdb=" O   ASN A 479 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   THR A 485 " --> pdb=" O   GLY A 481 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   VAL A 490 " --> pdb=" O   THR A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 507 through 532
      removed outlier: 3.862A  pdb=" N   PHE A 511 " --> pdb=" O   THR A 507 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LEU A 513 " --> pdb=" O   VAL A 509 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ILE A 515 " --> pdb=" O   PHE A 511 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   THR A 525 " --> pdb=" O   SER A 521 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   LEU A 526 " --> pdb=" O   SER A 522 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ASP A 529 " --> pdb=" O   THR A 525 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LYS A 531 " --> pdb=" O   ILE A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 573
      removed outlier: 3.850A  pdb=" N   VAL A 567 " --> pdb=" O   ILE A 563 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ILE A 568 " --> pdb=" O   ILE A 564 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   ARG A 570 " --> pdb=" O   ASP A 566 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ALA A 572 " --> pdb=" O   ILE A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 580
    Processing helix  chain 'A' and resid 592 through 597
    Processing helix  chain 'A' and resid 598 through 600
      No H-bonds generated for 'chain 'A' and resid 598 through 600'
    Processing helix  chain 'A' and resid 602 through 619
      removed outlier: 4.011A  pdb=" N   PHE A 609 " --> pdb=" O   PHE A 605 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   PHE A 610 " --> pdb=" O   VAL A 606 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   LEU A 612 " --> pdb=" O   ASN A 608 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLU A 613 " --> pdb=" O   PHE A 609 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 257
      removed outlier: 3.769A  pdb=" N   THR B 234 " --> pdb=" O   PRO B 230 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   PHE B 235 " --> pdb=" O   ALA B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 295
      removed outlier: 4.234A  pdb=" N   ILE B 271 " --> pdb=" O   PRO B 267 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   GLY B 275 " --> pdb=" O   ILE B 271 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   GLY B 286 " --> pdb=" O   LEU B 282 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ARG B 293 " --> pdb=" O   THR B 289 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 303
      removed outlier: 3.686A  pdb=" N   ILE B 302 " --> pdb=" O   ASN B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 337
      removed outlier: 3.655A  pdb=" N   LEU B 316 " --> pdb=" O   SER B 312 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLU B 318 " --> pdb=" O   GLN B 314 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ILE B 319 " --> pdb=" O   HIS B 315 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLY B 321 " --> pdb=" O   PHE B 317 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU B 326 " --> pdb=" O   PHE B 322 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   PHE B 335 " --> pdb=" O   LEU B 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 345 through 358
      removed outlier: 4.447A  pdb=" N   LEU B 349 " --> pdb=" O   TYR B 345 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   VAL B 356 " --> pdb=" O   TYR B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 376
    Processing helix  chain 'B' and resid 377 through 383
      removed outlier: 3.847A  pdb=" N   PHE B 382 " --> pdb=" O   LEU B 378 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   THR B 383 " --> pdb=" O   PHE B 379 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 387
      removed outlier: 3.884A  pdb=" N   HIS B 387 " --> pdb=" O   ALA B 384 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 384 through 387'
    Processing helix  chain 'B' and resid 390 through 400
    Processing helix  chain 'B' and resid 403 through 420
      removed outlier: 4.272A  pdb=" N   LEU B 407 " --> pdb=" O   LEU B 403 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ILE B 414 " --> pdb=" O   LEU B 410 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   LEU B 419 " --> pdb=" O   CYS B 415 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 453
      removed outlier: 3.949A  pdb=" N   VAL B 451 " --> pdb=" O   VAL B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 454 through 471
      removed outlier: 3.697A  pdb=" N   LEU B 458 " --> pdb=" O   ILE B 454 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   ARG B 459 " --> pdb=" O   PRO B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 472 through 503
      removed outlier: 4.397A  pdb=" N   HIS B 476 " --> pdb=" O   ARG B 472 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU B 477 " --> pdb=" O   ALA B 473 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   LYS B 482 " --> pdb=" O   VAL B 478 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   TYR B 483 " --> pdb=" O   ASN B 479 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   THR B 485 " --> pdb=" O   GLY B 481 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   VAL B 490 " --> pdb=" O   THR B 486 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 507 through 532
      removed outlier: 3.862A  pdb=" N   PHE B 511 " --> pdb=" O   THR B 507 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LEU B 513 " --> pdb=" O   VAL B 509 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ILE B 515 " --> pdb=" O   PHE B 511 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   THR B 525 " --> pdb=" O   SER B 521 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LEU B 526 " --> pdb=" O   SER B 522 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ASP B 529 " --> pdb=" O   THR B 525 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LYS B 531 " --> pdb=" O   ILE B 527 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 557 through 574
      removed outlier: 3.849A  pdb=" N   VAL B 567 " --> pdb=" O   ILE B 563 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ILE B 568 " --> pdb=" O   ILE B 564 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   ARG B 570 " --> pdb=" O   ASP B 566 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ALA B 572 " --> pdb=" O   ILE B 568 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   THR B 574 " --> pdb=" O   ARG B 570 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 575 through 580
      removed outlier: 3.502A  pdb=" N   THR B 580 " --> pdb=" O   GLN B 576 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 590 through 597
      removed outlier: 3.610A  pdb=" N   VAL B 595 " --> pdb=" O   ILE B 591 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 599 through 619
      removed outlier: 3.597A  pdb=" N   ARG B 603 " --> pdb=" O   LEU B 599 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ARG B 604 " --> pdb=" O   GLU B 600 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   PHE B 605 " --> pdb=" O   VAL B 601 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   PHE B 609 " --> pdb=" O   PHE B 605 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   PHE B 610 " --> pdb=" O   VAL B 606 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LEU B 612 " --> pdb=" O   ASN B 608 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLU B 613 " --> pdb=" O   PHE B 609 " (cutoff:3.500A)

    339 hydrogen bonds defined for protein.
    1017 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: 1.64

  Time building geometry restraints manager: 1.82 seconds

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

  Histogram of bond lengths:
        1.08 -     1.23: 144
        1.23 -     1.38: 2370
        1.38 -     1.52: 3180
        1.52 -     1.67: 1186
        1.67 -     1.81: 44
  Bond restraints: 6924
  Sorted by residual:
  bond pdb=" C   ILE B 454 "
       pdb=" N   PRO B 455 "
    ideal  model  delta    sigma   weight residual
    1.337  1.495 -0.158 1.11e-02 8.12e+03 2.04e+02
  bond pdb=" C   ILE A 454 "
       pdb=" N   PRO A 455 "
    ideal  model  delta    sigma   weight residual
    1.337  1.493 -0.157 1.11e-02 8.12e+03 2.00e+02
  bond pdb=" C   ILE B 454 "
       pdb=" O   ILE B 454 "
    ideal  model  delta    sigma   weight residual
    1.240  1.086  0.154 1.26e-02 6.30e+03 1.49e+02
  bond pdb=" C   ILE A 454 "
       pdb=" O   ILE A 454 "
    ideal  model  delta    sigma   weight residual
    1.240  1.087  0.153 1.26e-02 6.30e+03 1.47e+02
  bond pdb=" C   GLY A 621 "
       pdb=" O   GLY A 621 "
    ideal  model  delta    sigma   weight residual
    1.234  1.098  0.135 1.20e-02 6.94e+03 1.27e+02
  ... (remaining 6919 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.47: 9168
        4.47 -     8.94: 189
        8.94 -    13.41: 37
       13.41 -    17.88: 7
       17.88 -    22.34: 5
  Bond angle restraints: 9406
  Sorted by residual:
  angle pdb=" C   ILE B 454 "
        pdb=" N   PRO B 455 "
        pdb=" CA  PRO B 455 "
      ideal   model   delta    sigma   weight residual
     119.87  136.95  -17.08 1.04e+00 9.25e-01 2.70e+02
  angle pdb=" C   ILE A 454 "
        pdb=" N   PRO A 455 "
        pdb=" CA  PRO A 455 "
      ideal   model   delta    sigma   weight residual
     119.87  136.83  -16.96 1.04e+00 9.25e-01 2.66e+02
  angle pdb=" N   ILE A 575 "
        pdb=" CA  ILE A 575 "
        pdb=" C   ILE A 575 "
      ideal   model   delta    sigma   weight residual
     110.74   98.41   12.33 9.10e-01 1.21e+00 1.84e+02
  angle pdb=" N   ILE B 575 "
        pdb=" CA  ILE B 575 "
        pdb=" C   ILE B 575 "
      ideal   model   delta    sigma   weight residual
     110.74   98.46   12.28 9.10e-01 1.21e+00 1.82e+02
  angle pdb=" CB  ARG B 624 "
        pdb=" CG  ARG B 624 "
        pdb=" CD  ARG B 624 "
      ideal   model   delta    sigma   weight residual
     111.30   88.96   22.34 2.30e+00 1.89e-01 9.44e+01
  ... (remaining 9401 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.85: 3645
       25.85 -    51.69: 346
       51.69 -    77.53: 51
       77.53 -   103.38: 8
      103.38 -   129.22: 2
  Dihedral angle restraints: 4052
    sinusoidal: 1738
      harmonic: 2314
  Sorted by residual:
  dihedral pdb=" C   THR B 580 "
           pdb=" N   THR B 580 "
           pdb=" CA  THR B 580 "
           pdb=" CB  THR B 580 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -154.80   32.80     0      2.50e+00 1.60e-01 1.72e+02
  dihedral pdb=" N   THR B 580 "
           pdb=" C   THR B 580 "
           pdb=" CA  THR B 580 "
           pdb=" CB  THR B 580 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  152.59  -29.19     0      2.50e+00 1.60e-01 1.36e+02
  dihedral pdb=" C   TYR B 518 "
           pdb=" N   TYR B 518 "
           pdb=" CA  TYR B 518 "
           pdb=" CB  TYR B 518 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -143.16   20.56     0      2.50e+00 1.60e-01 6.76e+01
  ... (remaining 4049 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.282: 1001
       0.282 -    0.563: 14
       0.563 -    0.845: 4
       0.845 -    1.127: 0
       1.127 -    1.408: 1
  Chirality restraints: 1020
  Sorted by residual:
  chirality pdb=" CA  THR B 580 "
            pdb=" N   THR B 580 "
            pdb=" C   THR B 580 "
            pdb=" CB  THR B 580 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    1.12    1.41 2.00e-01 2.50e+01 4.96e+01
  chirality pdb=" CA  TYR B 518 "
            pdb=" N   TYR B 518 "
            pdb=" C   TYR B 518 "
            pdb=" CB  TYR B 518 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.77    0.74 2.00e-01 2.50e+01 1.38e+01
  chirality pdb=" CA  TYR A 518 "
            pdb=" N   TYR A 518 "
            pdb=" C   TYR A 518 "
            pdb=" CB  TYR A 518 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.77    0.74 2.00e-01 2.50e+01 1.38e+01
  ... (remaining 1017 not shown)

  Planarity restraints: 1124
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 575 "    0.028 2.00e-02 2.50e+03   5.79e-02 3.35e+01
        pdb=" C   ILE B 575 "   -0.100 2.00e-02 2.50e+03
        pdb=" O   ILE B 575 "    0.038 2.00e-02 2.50e+03
        pdb=" N   GLN B 576 "    0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 575 "    0.028 2.00e-02 2.50e+03   5.78e-02 3.34e+01
        pdb=" C   ILE A 575 "   -0.100 2.00e-02 2.50e+03
        pdb=" O   ILE A 575 "    0.038 2.00e-02 2.50e+03
        pdb=" N   GLN A 576 "    0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 621 "   -0.023 2.00e-02 2.50e+03   5.14e-02 2.64e+01
        pdb=" C   GLY A 621 "    0.089 2.00e-02 2.50e+03
        pdb=" O   GLY A 621 "   -0.036 2.00e-02 2.50e+03
        pdb=" N   GLU A 622 "   -0.030 2.00e-02 2.50e+03
  ... (remaining 1121 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 392
        2.70 -     3.25: 6588
        3.25 -     3.80: 10038
        3.80 -     4.35: 13244
        4.35 -     4.90: 22471
  Nonbonded interactions: 52733
  Sorted by model distance:
  nonbonded pdb=" CE  MET B 489 "
            pdb=" OG1 THR B 574 "
     model   vdw
     2.155 3.460
  nonbonded pdb=" NH2 ARG A 548 "
            pdb=" OE2 GLU A 613 "
     model   vdw
     2.155 3.120
  nonbonded pdb=" NH2 ARG B 548 "
            pdb=" OE2 GLU B 613 "
     model   vdw
     2.155 3.120
  nonbonded pdb=" NE2 GLN B 576 "
            pdb=" OE1 GLU B 600 "
     model   vdw
     2.187 3.120
  nonbonded pdb=" CE  MET A 489 "
            pdb=" OG1 THR A 574 "
     model   vdw
     2.200 3.460
  ... (remaining 52728 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 individual isotropic
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:             0.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     17.480
  Find NCS groups from input model:        0.100
  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:2.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
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      :  0.014   0.158   6926  Z= 0.872
  Angle     :  1.856  55.797   9410  Z= 1.083
  Chirality :  0.092   1.408   1020
  Planarity :  0.008   0.058   1124
  Dihedral  : 19.356 129.222   2554
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  :  6.85 %
    Favored  : 92.25 %
  Rotamer:
    Outliers : 12.25 %
    Allowed  : 13.69 %
    Favored  : 74.06 %
  Cbeta Deviations :  2.01 %
  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: -4.11 (0.25), residues: 774
  helix: -2.29 (0.18), residues: 550
  sheet:  None (None), residues: 0
  loop : -3.43 (0.37), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 573 
 HIS   0.008   0.001   HIS B 441 
 PHE   0.044   0.002   PHE B 571 
 TYR   0.026   0.003   TYR A 443 
 ARG   0.014   0.001   ARG B 624 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20428 (  339)
  hydrogen bonds       : angle       7.90704 ( 1017)
  SS BOND              : bond        0.01832 (    2)
  SS BOND              : angle      45.54622 (    4)
  covalent geometry    : bond        0.01371 ( 6924)
  covalent geometry    : angle       1.60137 ( 9406)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 85
    poor density    : 78
  time to evaluate  : 0.699 
Fit side-chains
REVERT: A  272 TYR cc_start: 0.9079 (m-80) cc_final: 0.8852 (m-80)
REVERT: A  342 ILE cc_start: 0.6785 (OUTLIER) cc_final: 0.6474 (tt)
REVERT: A  420 GLU cc_start: 0.7454 (tt0) cc_final: 0.7247 (mt-10)
REVERT: A  452 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.7620 (tm-30)
REVERT: A  464 LEU cc_start: 0.8434 (mt) cc_final: 0.8180 (mt)
REVERT: A  468 ARG cc_start: 0.6783 (ttm170) cc_final: 0.6356 (ttm170)
REVERT: A  482 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.6664 (ptmm)
REVERT: A  496 TYR cc_start: 0.8072 (t80) cc_final: 0.7796 (t80)
REVERT: A  500 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7389 (ttpp)
REVERT: A  508 MET cc_start: 0.7484 (tpp) cc_final: 0.7234 (tpt)
REVERT: A  532 MET cc_start: 0.8451 (mmm) cc_final: 0.8133 (mmp)
REVERT: B  272 TYR cc_start: 0.9074 (m-80) cc_final: 0.8857 (m-80)
REVERT: B  342 ILE cc_start: 0.6785 (OUTLIER) cc_final: 0.6465 (tt)
REVERT: B  355 MET cc_start: 0.8869 (mtt) cc_final: 0.8464 (mtm)
REVERT: B  452 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.7610 (tm-30)
REVERT: B  464 LEU cc_start: 0.8454 (mt) cc_final: 0.8181 (mt)
REVERT: B  468 ARG cc_start: 0.6865 (ttm170) cc_final: 0.6439 (ttm170)
REVERT: B  482 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.6724 (ptmm)
REVERT: B  496 TYR cc_start: 0.8105 (t80) cc_final: 0.7829 (t80)
REVERT: B  500 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7419 (ttpp)
REVERT: B  508 MET cc_start: 0.7286 (tpp) cc_final: 0.6983 (tpt)
REVERT: B  532 MET cc_start: 0.8444 (mmm) cc_final: 0.8113 (mmp)
REVERT: B  559 TYR cc_start: 0.8675 (m-80) cc_final: 0.7990 (m-80)
  outliers start: 85
  outliers final: 64
  residues processed: 153
  average time/residue: 0.1794
  time to fit residues: 36.3308
Evaluate side-chains
  146 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 74
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  364 LYS
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  399 GLN
Chi-restraints excluded: chain A residue  418 SER
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  439 ILE
Chi-restraints excluded: chain A residue  440 CYS
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  444 THR
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  452 GLN
Chi-restraints excluded: chain A residue  454 ILE
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  482 LYS
Chi-restraints excluded: chain A residue  500 LYS
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  518 TYR
Chi-restraints excluded: chain A residue  519 ILE
Chi-restraints excluded: chain A residue  521 SER
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  543 GLU
Chi-restraints excluded: chain A residue  574 THR
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain A residue  577 ILE
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  587 HIS
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  310 ASN
Chi-restraints excluded: chain B residue  342 ILE
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  364 LYS
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  399 GLN
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  439 ILE
Chi-restraints excluded: chain B residue  440 CYS
Chi-restraints excluded: chain B residue  442 LYS
Chi-restraints excluded: chain B residue  444 THR
Chi-restraints excluded: chain B residue  445 TYR
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain B residue  452 GLN
Chi-restraints excluded: chain B residue  454 ILE
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain B residue  482 LYS
Chi-restraints excluded: chain B residue  500 LYS
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  518 TYR
Chi-restraints excluded: chain B residue  519 ILE
Chi-restraints excluded: chain B residue  521 SER
Chi-restraints excluded: chain B residue  522 SER
Chi-restraints excluded: chain B residue  543 GLU
Chi-restraints excluded: chain B residue  574 THR
Chi-restraints excluded: chain B residue  575 ILE
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  580 THR
Chi-restraints excluded: chain B residue  587 HIS
Chi-restraints excluded: chain B residue  617 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 59 optimal weight:    0.0570
   chunk 32 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 39 optimal weight:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   chunk 45 optimal weight:    0.7980
   chunk 70 optimal weight:    0.3980
   overall best weight:    0.4698

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

Flipped N/Q/H residues before XYZ refinement:
A 614 ASN
B 614 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.157454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.113670 restraints weight = 7257.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 2.25
r_work: 0.2969 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.1365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   6926  Z= 0.154
  Angle     :  0.663   6.919   9410  Z= 0.341
  Chirality :  0.041   0.156   1020
  Planarity :  0.005   0.030   1124
  Dihedral  : 16.455 120.631   1229
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  8.36 %
    Allowed  : 16.28 %
    Favored  : 75.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.75 (0.28), residues: 774
  helix: -1.02 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop : -3.76 (0.33), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 457 
 HIS   0.002   0.001   HIS B 313 
 PHE   0.019   0.001   PHE A 546 
 TYR   0.012   0.001   TYR A 553 
 ARG   0.008   0.001   ARG B 624 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06485 (  339)
  hydrogen bonds       : angle       5.10134 ( 1017)
  SS BOND              : bond        0.00202 (    2)
  SS BOND              : angle       3.29602 (    4)
  covalent geometry    : bond        0.00343 ( 6924)
  covalent geometry    : angle       0.65971 ( 9406)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 83
  time to evaluate  : 0.798 
Fit side-chains
REVERT: A  268 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7878 (tp)
REVERT: A  272 TYR cc_start: 0.8770 (m-80) cc_final: 0.8344 (m-80)
REVERT: A  468 ARG cc_start: 0.6538 (ttm170) cc_final: 0.6214 (ttm170)
REVERT: A  519 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7557 (pt)
REVERT: A  532 MET cc_start: 0.9146 (mmm) cc_final: 0.8800 (mmp)
REVERT: B  272 TYR cc_start: 0.8851 (m-80) cc_final: 0.8459 (m-80)
REVERT: B  447 VAL cc_start: 0.8677 (OUTLIER) cc_final: 0.8477 (p)
REVERT: B  468 ARG cc_start: 0.6541 (ttm170) cc_final: 0.6220 (ttm170)
REVERT: B  519 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7569 (pt)
REVERT: B  532 MET cc_start: 0.9146 (mmm) cc_final: 0.8796 (mmp)
  outliers start: 58
  outliers final: 36
  residues processed: 134
  average time/residue: 0.1566
  time to fit residues: 29.6098
Evaluate side-chains
  120 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 80
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  364 LYS
Chi-restraints excluded: chain A residue  399 GLN
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  439 ILE
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  519 ILE
Chi-restraints excluded: chain A residue  521 SER
Chi-restraints excluded: chain A residue  543 GLU
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  574 THR
Chi-restraints excluded: chain A residue  577 ILE
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain A residue  587 HIS
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  364 LYS
Chi-restraints excluded: chain B residue  399 GLN
Chi-restraints excluded: chain B residue  418 SER
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  439 ILE
Chi-restraints excluded: chain B residue  444 THR
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  519 ILE
Chi-restraints excluded: chain B residue  521 SER
Chi-restraints excluded: chain B residue  543 GLU
Chi-restraints excluded: chain B residue  552 VAL
Chi-restraints excluded: chain B residue  567 VAL
Chi-restraints excluded: chain B residue  574 THR
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  580 THR
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain B residue  587 HIS
Chi-restraints excluded: chain B residue  626 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 51 optimal weight:    0.0970
   chunk 0 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 48 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
A 576 GLN
B 576 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.158755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.114394 restraints weight = 7304.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 2.31
r_work: 0.2959 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.1752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6926  Z= 0.149
  Angle     :  0.631   7.078   9410  Z= 0.323
  Chirality :  0.040   0.213   1020
  Planarity :  0.004   0.032   1124
  Dihedral  : 14.093 113.061   1141
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  7.06 %
    Allowed  : 18.16 %
    Favored  : 74.78 %
  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: -2.04 (0.28), residues: 774
  helix: -0.45 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -3.56 (0.33), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 607 
 HIS   0.003   0.001   HIS B 441 
 PHE   0.020   0.001   PHE B 546 
 TYR   0.013   0.001   TYR A 553 
 ARG   0.003   0.000   ARG A 448 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05890 (  339)
  hydrogen bonds       : angle       4.73017 ( 1017)
  SS BOND              : bond        0.00431 (    2)
  SS BOND              : angle       3.69625 (    4)
  covalent geometry    : bond        0.00336 ( 6924)
  covalent geometry    : angle       0.62698 ( 9406)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 87
  time to evaluate  : 0.766 
Fit side-chains
REVERT: A  272 TYR cc_start: 0.8804 (m-80) cc_final: 0.8263 (m-80)
REVERT: A  532 MET cc_start: 0.9140 (mmm) cc_final: 0.8747 (mmp)
REVERT: A  543 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7637 (pm20)
REVERT: B  272 TYR cc_start: 0.8773 (m-80) cc_final: 0.8256 (m-80)
REVERT: B  415 CYS cc_start: 0.6890 (OUTLIER) cc_final: 0.6238 (t)
REVERT: B  532 MET cc_start: 0.9150 (mmm) cc_final: 0.8763 (mmp)
REVERT: B  543 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7651 (pm20)
  outliers start: 49
  outliers final: 33
  residues processed: 129
  average time/residue: 0.1767
  time to fit residues: 31.3671
Evaluate side-chains
  119 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 83
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  364 LYS
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  399 GLN
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  454 ILE
Chi-restraints excluded: chain A residue  498 THR
Chi-restraints excluded: chain A residue  543 GLU
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  574 THR
Chi-restraints excluded: chain A residue  577 ILE
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  587 HIS
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  364 LYS
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  399 GLN
Chi-restraints excluded: chain B residue  415 CYS
Chi-restraints excluded: chain B residue  418 SER
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  439 ILE
Chi-restraints excluded: chain B residue  454 ILE
Chi-restraints excluded: chain B residue  543 GLU
Chi-restraints excluded: chain B residue  552 VAL
Chi-restraints excluded: chain B residue  567 VAL
Chi-restraints excluded: chain B residue  574 THR
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  580 THR
Chi-restraints excluded: chain B residue  587 HIS
Chi-restraints excluded: chain B residue  592 ILE
Chi-restraints excluded: chain B residue  626 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   chunk 41 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 27 optimal weight:    8.9990
   chunk 47 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 576 GLN
B 576 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.158849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.114022 restraints weight = 7297.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 2.33
r_work: 0.2954 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.1947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6926  Z= 0.157
  Angle     :  0.615   7.175   9410  Z= 0.312
  Chirality :  0.040   0.174   1020
  Planarity :  0.004   0.034   1124
  Dihedral  : 12.817 109.828   1126
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  7.78 %
    Allowed  : 17.72 %
    Favored  : 74.50 %
  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: -1.52 (0.29), residues: 774
  helix: -0.12 (0.22), residues: 552
  sheet:  None (None), residues: 0
  loop : -3.22 (0.35), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 607 
 HIS   0.004   0.001   HIS A 441 
 PHE   0.018   0.001   PHE B 546 
 TYR   0.015   0.002   TYR A 553 
 ARG   0.003   0.000   ARG A 448 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05835 (  339)
  hydrogen bonds       : angle       4.60375 ( 1017)
  SS BOND              : bond        0.00618 (    2)
  SS BOND              : angle       3.41946 (    4)
  covalent geometry    : bond        0.00361 ( 6924)
  covalent geometry    : angle       0.61153 ( 9406)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 83
  time to evaluate  : 0.713 
Fit side-chains
REVERT: A  272 TYR cc_start: 0.8793 (m-80) cc_final: 0.8339 (m-80)
REVERT: A  439 ILE cc_start: 0.8153 (mp) cc_final: 0.7950 (mp)
REVERT: A  442 LYS cc_start: 0.6050 (OUTLIER) cc_final: 0.5162 (pttt)
REVERT: A  532 MET cc_start: 0.9146 (mmm) cc_final: 0.8624 (mmp)
REVERT: A  543 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7771 (pm20)
REVERT: B  272 TYR cc_start: 0.8795 (m-80) cc_final: 0.8284 (m-80)
REVERT: B  415 CYS cc_start: 0.6318 (OUTLIER) cc_final: 0.5990 (t)
REVERT: B  532 MET cc_start: 0.9179 (mmm) cc_final: 0.8679 (mmp)
REVERT: B  543 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7774 (pm20)
  outliers start: 54
  outliers final: 34
  residues processed: 134
  average time/residue: 0.1603
  time to fit residues: 29.8221
Evaluate side-chains
  120 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 82
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  364 LYS
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  399 GLN
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  454 ILE
Chi-restraints excluded: chain A residue  498 THR
Chi-restraints excluded: chain A residue  543 GLU
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  574 THR
Chi-restraints excluded: chain A residue  577 ILE
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  587 HIS
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  364 LYS
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  399 GLN
Chi-restraints excluded: chain B residue  415 CYS
Chi-restraints excluded: chain B residue  418 SER
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  439 ILE
Chi-restraints excluded: chain B residue  454 ILE
Chi-restraints excluded: chain B residue  498 THR
Chi-restraints excluded: chain B residue  543 GLU
Chi-restraints excluded: chain B residue  567 VAL
Chi-restraints excluded: chain B residue  574 THR
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  587 HIS
Chi-restraints excluded: chain B residue  592 ILE
Chi-restraints excluded: chain B residue  626 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 36 optimal weight:    0.0870
   chunk 53 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 4 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0070
   chunk 58 optimal weight:    0.6980
   chunk 42 optimal weight:    5.9990
   overall best weight:    0.4776

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

Flipped N/Q/H residues before XYZ refinement:
A 576 GLN
B 576 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.163828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.122204 restraints weight = 7439.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 2.40
r_work: 0.3007 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.2294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6926  Z= 0.122
  Angle     :  0.575   8.738   9410  Z= 0.287
  Chirality :  0.039   0.150   1020
  Planarity :  0.004   0.033   1124
  Dihedral  : 11.895 102.309   1125
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  6.34 %
    Allowed  : 19.02 %
    Favored  : 74.64 %
  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: -0.86 (0.30), residues: 774
  helix:  0.37 (0.22), residues: 550
  sheet:  None (None), residues: 0
  loop : -2.93 (0.37), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 607 
 HIS   0.002   0.001   HIS B 313 
 PHE   0.023   0.001   PHE A 546 
 TYR   0.012   0.001   TYR B 553 
 ARG   0.002   0.000   ARG A 448 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05026 (  339)
  hydrogen bonds       : angle       4.38191 ( 1017)
  SS BOND              : bond        0.00343 (    2)
  SS BOND              : angle       2.71294 (    4)
  covalent geometry    : bond        0.00265 ( 6924)
  covalent geometry    : angle       0.57258 ( 9406)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 94
  time to evaluate  : 0.707 
Fit side-chains
REVERT: A  272 TYR cc_start: 0.8783 (m-80) cc_final: 0.8020 (m-80)
REVERT: A  364 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7806 (mmmt)
REVERT: A  442 LYS cc_start: 0.6015 (OUTLIER) cc_final: 0.5330 (pttt)
REVERT: A  504 HIS cc_start: 0.6481 (OUTLIER) cc_final: 0.6092 (m-70)
REVERT: A  508 MET cc_start: 0.6074 (mmm) cc_final: 0.5718 (mmp)
REVERT: A  532 MET cc_start: 0.9242 (mmm) cc_final: 0.8821 (mmp)
REVERT: B  272 TYR cc_start: 0.8773 (m-80) cc_final: 0.8019 (m-80)
REVERT: B  415 CYS cc_start: 0.6479 (OUTLIER) cc_final: 0.6208 (t)
REVERT: B  442 LYS cc_start: 0.6076 (OUTLIER) cc_final: 0.5279 (pttt)
REVERT: B  504 HIS cc_start: 0.6459 (OUTLIER) cc_final: 0.6067 (m-70)
REVERT: B  508 MET cc_start: 0.6404 (mmm) cc_final: 0.5948 (mmp)
REVERT: B  532 MET cc_start: 0.9202 (mmm) cc_final: 0.8777 (mmp)
  outliers start: 44
  outliers final: 28
  residues processed: 136
  average time/residue: 0.1637
  time to fit residues: 30.7841
Evaluate side-chains
  124 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 90
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  364 LYS
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  399 GLN
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  454 ILE
Chi-restraints excluded: chain A residue  504 HIS
Chi-restraints excluded: chain A residue  521 SER
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  574 THR
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  587 HIS
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  399 GLN
Chi-restraints excluded: chain B residue  415 CYS
Chi-restraints excluded: chain B residue  418 SER
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  439 ILE
Chi-restraints excluded: chain B residue  442 LYS
Chi-restraints excluded: chain B residue  454 ILE
Chi-restraints excluded: chain B residue  504 HIS
Chi-restraints excluded: chain B residue  567 VAL
Chi-restraints excluded: chain B residue  574 THR
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  580 THR
Chi-restraints excluded: chain B residue  587 HIS
Chi-restraints excluded: chain B residue  592 ILE
Chi-restraints excluded: chain B residue  626 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 56 optimal weight:    0.0670
   chunk 37 optimal weight:    0.9990
   chunk 59 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 1 optimal weight:    0.5980
   chunk 55 optimal weight:    0.5980
   chunk 74 optimal weight:    0.3980
   overall best weight:    0.5320

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

Flipped N/Q/H residues before XYZ refinement:
A 576 GLN
B 576 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.163934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.122796 restraints weight = 7336.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 2.18
r_work: 0.3030 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.2464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6926  Z= 0.126
  Angle     :  0.567   7.598   9410  Z= 0.285
  Chirality :  0.039   0.146   1020
  Planarity :  0.004   0.032   1124
  Dihedral  : 10.955  98.726   1111
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 20.03 %
    Favored  : 74.35 %
  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: -0.51 (0.30), residues: 774
  helix:  0.59 (0.22), residues: 550
  sheet:  None (None), residues: 0
  loop : -2.70 (0.38), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 457 
 HIS   0.003   0.001   HIS A 313 
 PHE   0.019   0.001   PHE A 546 
 TYR   0.013   0.001   TYR A 553 
 ARG   0.003   0.000   ARG A 448 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04962 (  339)
  hydrogen bonds       : angle       4.29234 ( 1017)
  SS BOND              : bond        0.00325 (    2)
  SS BOND              : angle       2.20491 (    4)
  covalent geometry    : bond        0.00280 ( 6924)
  covalent geometry    : angle       0.56536 ( 9406)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 92
  time to evaluate  : 0.698 
Fit side-chains
REVERT: A  272 TYR cc_start: 0.8831 (m-80) cc_final: 0.7951 (m-80)
REVERT: A  305 LEU cc_start: 0.7970 (mt) cc_final: 0.7755 (mt)
REVERT: A  442 LYS cc_start: 0.6089 (OUTLIER) cc_final: 0.5509 (pttt)
REVERT: A  452 GLN cc_start: 0.8576 (tp-100) cc_final: 0.8367 (tp40)
REVERT: A  504 HIS cc_start: 0.6429 (OUTLIER) cc_final: 0.6090 (m-70)
REVERT: A  508 MET cc_start: 0.6155 (mmm) cc_final: 0.5820 (mmp)
REVERT: B  272 TYR cc_start: 0.8809 (m-80) cc_final: 0.7952 (m-80)
REVERT: B  305 LEU cc_start: 0.7959 (mt) cc_final: 0.7738 (mt)
REVERT: B  331 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8291 (tp)
REVERT: B  415 CYS cc_start: 0.6570 (OUTLIER) cc_final: 0.6297 (t)
REVERT: B  442 LYS cc_start: 0.6055 (OUTLIER) cc_final: 0.5317 (pttt)
REVERT: B  504 HIS cc_start: 0.6356 (OUTLIER) cc_final: 0.6028 (m-70)
  outliers start: 39
  outliers final: 27
  residues processed: 129
  average time/residue: 0.1571
  time to fit residues: 28.2273
Evaluate side-chains
  125 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 92
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  399 GLN
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  504 HIS
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  574 THR
Chi-restraints excluded: chain A residue  587 HIS
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  399 GLN
Chi-restraints excluded: chain B residue  415 CYS
Chi-restraints excluded: chain B residue  418 SER
Chi-restraints excluded: chain B residue  439 ILE
Chi-restraints excluded: chain B residue  442 LYS
Chi-restraints excluded: chain B residue  454 ILE
Chi-restraints excluded: chain B residue  504 HIS
Chi-restraints excluded: chain B residue  565 GLU
Chi-restraints excluded: chain B residue  567 VAL
Chi-restraints excluded: chain B residue  574 THR
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  580 THR
Chi-restraints excluded: chain B residue  587 HIS
Chi-restraints excluded: chain B residue  592 ILE
Chi-restraints excluded: chain B residue  626 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 75 optimal weight:    0.0000
   chunk 38 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9980
   chunk 59 optimal weight:    9.9990
   chunk 76 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.7184

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
A 576 GLN
B 576 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.163647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.120967 restraints weight = 7292.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 2.56
r_work: 0.3000 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.2511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6926  Z= 0.139
  Angle     :  0.574   7.613   9410  Z= 0.287
  Chirality :  0.039   0.139   1020
  Planarity :  0.004   0.032   1124
  Dihedral  : 10.463  96.283   1104
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  6.20 %
    Allowed  : 19.60 %
    Favored  : 74.21 %
  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: -0.35 (0.30), residues: 774
  helix:  0.71 (0.22), residues: 550
  sheet:  None (None), residues: 0
  loop : -2.62 (0.39), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 457 
 HIS   0.003   0.001   HIS B 313 
 PHE   0.023   0.001   PHE A 546 
 TYR   0.014   0.001   TYR B 553 
 ARG   0.002   0.000   ARG B 448 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05178 (  339)
  hydrogen bonds       : angle       4.29681 ( 1017)
  SS BOND              : bond        0.00397 (    2)
  SS BOND              : angle       2.06527 (    4)
  covalent geometry    : bond        0.00317 ( 6924)
  covalent geometry    : angle       0.57260 ( 9406)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 91
  time to evaluate  : 0.736 
Fit side-chains
REVERT: A  272 TYR cc_start: 0.8792 (m-80) cc_final: 0.7993 (m-80)
REVERT: A  305 LEU cc_start: 0.7917 (mt) cc_final: 0.7703 (mt)
REVERT: A  331 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8264 (tp)
REVERT: A  442 LYS cc_start: 0.6119 (OUTLIER) cc_final: 0.5549 (pttt)
REVERT: A  452 GLN cc_start: 0.8517 (tp-100) cc_final: 0.8310 (tp40)
REVERT: A  504 HIS cc_start: 0.6318 (OUTLIER) cc_final: 0.6036 (m-70)
REVERT: A  508 MET cc_start: 0.6153 (mmm) cc_final: 0.5819 (mmp)
REVERT: B  272 TYR cc_start: 0.8786 (m-80) cc_final: 0.7988 (m-80)
REVERT: B  305 LEU cc_start: 0.7898 (mt) cc_final: 0.7694 (mt)
REVERT: B  331 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8209 (tp)
REVERT: B  415 CYS cc_start: 0.6487 (OUTLIER) cc_final: 0.6218 (t)
REVERT: B  442 LYS cc_start: 0.6045 (OUTLIER) cc_final: 0.5372 (pttt)
REVERT: B  504 HIS cc_start: 0.6303 (OUTLIER) cc_final: 0.6020 (m-70)
REVERT: B  508 MET cc_start: 0.6308 (mmm) cc_final: 0.5876 (mmp)
  outliers start: 43
  outliers final: 31
  residues processed: 132
  average time/residue: 0.1611
  time to fit residues: 29.9042
Evaluate side-chains
  126 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 88
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  399 GLN
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  504 HIS
Chi-restraints excluded: chain A residue  565 GLU
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  574 THR
Chi-restraints excluded: chain A residue  587 HIS
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  399 GLN
Chi-restraints excluded: chain B residue  415 CYS
Chi-restraints excluded: chain B residue  418 SER
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  439 ILE
Chi-restraints excluded: chain B residue  442 LYS
Chi-restraints excluded: chain B residue  454 ILE
Chi-restraints excluded: chain B residue  504 HIS
Chi-restraints excluded: chain B residue  565 GLU
Chi-restraints excluded: chain B residue  567 VAL
Chi-restraints excluded: chain B residue  574 THR
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  580 THR
Chi-restraints excluded: chain B residue  587 HIS
Chi-restraints excluded: chain B residue  592 ILE
Chi-restraints excluded: chain B residue  626 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 72 optimal weight:    0.6980
   chunk 19 optimal weight:    4.9990
   chunk 3 optimal weight:    0.7980
   chunk 39 optimal weight:    0.0670
   chunk 14 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0570
   chunk 9 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.4636

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

Flipped N/Q/H residues before XYZ refinement:
A 576 GLN
B 387 HIS
B 576 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.164548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.119447 restraints weight = 7184.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 2.31
r_work: 0.3063 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.2741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6926  Z= 0.117
  Angle     :  0.551   8.116   9410  Z= 0.276
  Chirality :  0.037   0.123   1020
  Planarity :  0.004   0.032   1124
  Dihedral  :  9.998  84.962   1104
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 20.46 %
    Favored  : 73.92 %
  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:  0.03 (0.31), residues: 774
  helix:  0.96 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -2.45 (0.40), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 607 
 HIS   0.002   0.001   HIS A 313 
 PHE   0.023   0.001   PHE A 546 
 TYR   0.010   0.001   TYR B 352 
 ARG   0.003   0.000   ARG A 448 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04676 (  339)
  hydrogen bonds       : angle       4.22315 ( 1017)
  SS BOND              : bond        0.00309 (    2)
  SS BOND              : angle       1.84311 (    4)
  covalent geometry    : bond        0.00255 ( 6924)
  covalent geometry    : angle       0.54952 ( 9406)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 88
  time to evaluate  : 0.809 
Fit side-chains
REVERT: A  272 TYR cc_start: 0.8672 (m-80) cc_final: 0.7572 (m-80)
REVERT: A  305 LEU cc_start: 0.7806 (mt) cc_final: 0.7595 (mt)
REVERT: A  331 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8090 (tp)
REVERT: A  442 LYS cc_start: 0.6086 (OUTLIER) cc_final: 0.5775 (pttt)
REVERT: A  452 GLN cc_start: 0.8431 (tp-100) cc_final: 0.8217 (tp40)
REVERT: A  472 ARG cc_start: 0.7834 (ttm110) cc_final: 0.7566 (ttp-110)
REVERT: A  489 MET cc_start: 0.6288 (tpt) cc_final: 0.6052 (tpt)
REVERT: A  504 HIS cc_start: 0.6223 (OUTLIER) cc_final: 0.5992 (m-70)
REVERT: A  508 MET cc_start: 0.6008 (mmm) cc_final: 0.5696 (mmp)
REVERT: B  272 TYR cc_start: 0.8670 (m-80) cc_final: 0.7573 (m-80)
REVERT: B  305 LEU cc_start: 0.7812 (mt) cc_final: 0.7598 (mt)
REVERT: B  331 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8039 (tp)
REVERT: B  415 CYS cc_start: 0.6527 (OUTLIER) cc_final: 0.6182 (t)
REVERT: B  439 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7180 (mm)
REVERT: B  442 LYS cc_start: 0.6033 (OUTLIER) cc_final: 0.5431 (pttt)
REVERT: B  472 ARG cc_start: 0.7867 (ttm110) cc_final: 0.7605 (ttp-110)
REVERT: B  504 HIS cc_start: 0.6201 (OUTLIER) cc_final: 0.5976 (m-70)
REVERT: B  508 MET cc_start: 0.6138 (mmm) cc_final: 0.5776 (mmp)
REVERT: B  545 THR cc_start: 0.7876 (p) cc_final: 0.7664 (p)
  outliers start: 39
  outliers final: 27
  residues processed: 127
  average time/residue: 0.1607
  time to fit residues: 28.7087
Evaluate side-chains
  121 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 86
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  399 GLN
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  504 HIS
Chi-restraints excluded: chain A residue  565 GLU
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  587 HIS
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  399 GLN
Chi-restraints excluded: chain B residue  415 CYS
Chi-restraints excluded: chain B residue  418 SER
Chi-restraints excluded: chain B residue  439 ILE
Chi-restraints excluded: chain B residue  442 LYS
Chi-restraints excluded: chain B residue  454 ILE
Chi-restraints excluded: chain B residue  504 HIS
Chi-restraints excluded: chain B residue  565 GLU
Chi-restraints excluded: chain B residue  567 VAL
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  580 THR
Chi-restraints excluded: chain B residue  587 HIS
Chi-restraints excluded: chain B residue  592 ILE
Chi-restraints excluded: chain B residue  626 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   chunk 21 optimal weight:    4.9990
   chunk 69 optimal weight:    1.9990
   chunk 58 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 64 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 576 GLN
B 576 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.161205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.117828 restraints weight = 7302.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 2.42
r_work: 0.3001 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6926  Z= 0.133
  Angle     :  0.578   8.459   9410  Z= 0.286
  Chirality :  0.038   0.132   1020
  Planarity :  0.004   0.032   1124
  Dihedral  :  9.918  76.902   1102
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 20.46 %
    Favored  : 74.06 %
  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:  0.07 (0.30), residues: 774
  helix:  0.99 (0.22), residues: 552
  sheet:  None (None), residues: 0
  loop : -2.40 (0.39), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 457 
 HIS   0.003   0.001   HIS B 313 
 PHE   0.023   0.001   PHE A 546 
 TYR   0.015   0.001   TYR B 352 
 ARG   0.002   0.000   ARG A 448 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04989 (  339)
  hydrogen bonds       : angle       4.24533 ( 1017)
  SS BOND              : bond        0.00323 (    2)
  SS BOND              : angle       1.89999 (    4)
  covalent geometry    : bond        0.00302 ( 6924)
  covalent geometry    : angle       0.57636 ( 9406)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 88
  time to evaluate  : 0.777 
Fit side-chains
REVERT: A  272 TYR cc_start: 0.8791 (m-80) cc_final: 0.7833 (m-80)
REVERT: A  305 LEU cc_start: 0.7875 (mt) cc_final: 0.7674 (mt)
REVERT: A  331 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8165 (tp)
REVERT: A  442 LYS cc_start: 0.5931 (OUTLIER) cc_final: 0.5706 (pttt)
REVERT: A  452 GLN cc_start: 0.8438 (tp-100) cc_final: 0.8196 (tp40)
REVERT: A  472 ARG cc_start: 0.7862 (ttm110) cc_final: 0.7592 (ttp-110)
REVERT: A  504 HIS cc_start: 0.6232 (OUTLIER) cc_final: 0.6021 (m-70)
REVERT: A  508 MET cc_start: 0.6042 (mmm) cc_final: 0.5741 (mmp)
REVERT: B  272 TYR cc_start: 0.8799 (m-80) cc_final: 0.7821 (m-80)
REVERT: B  305 LEU cc_start: 0.7876 (mt) cc_final: 0.7676 (mt)
REVERT: B  331 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8138 (tp)
REVERT: B  415 CYS cc_start: 0.6651 (OUTLIER) cc_final: 0.6296 (t)
REVERT: B  439 ILE cc_start: 0.7495 (OUTLIER) cc_final: 0.7110 (mm)
REVERT: B  442 LYS cc_start: 0.6192 (OUTLIER) cc_final: 0.5468 (pttt)
REVERT: B  472 ARG cc_start: 0.7885 (ttm110) cc_final: 0.7620 (ttp-110)
REVERT: B  504 HIS cc_start: 0.6201 (OUTLIER) cc_final: 0.5988 (m-70)
REVERT: B  508 MET cc_start: 0.6272 (mmm) cc_final: 0.5894 (mmp)
  outliers start: 38
  outliers final: 25
  residues processed: 126
  average time/residue: 0.1615
  time to fit residues: 28.5093
Evaluate side-chains
  121 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 88
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  399 GLN
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  504 HIS
Chi-restraints excluded: chain A residue  565 GLU
Chi-restraints excluded: chain A residue  577 ILE
Chi-restraints excluded: chain A residue  587 HIS
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  399 GLN
Chi-restraints excluded: chain B residue  415 CYS
Chi-restraints excluded: chain B residue  418 SER
Chi-restraints excluded: chain B residue  439 ILE
Chi-restraints excluded: chain B residue  442 LYS
Chi-restraints excluded: chain B residue  504 HIS
Chi-restraints excluded: chain B residue  565 GLU
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  580 THR
Chi-restraints excluded: chain B residue  587 HIS
Chi-restraints excluded: chain B residue  592 ILE
Chi-restraints excluded: chain B residue  626 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 38 optimal weight:    0.0970
   chunk 1 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0050
   chunk 63 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   chunk 75 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 53 optimal weight:    0.0050
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.2806

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

Flipped N/Q/H residues before XYZ refinement:
A 576 GLN
B 576 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.168444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.126372 restraints weight = 7369.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 2.21
r_work: 0.3067 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.2940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   6926  Z= 0.114
  Angle     :  0.543   8.364   9410  Z= 0.271
  Chirality :  0.037   0.130   1020
  Planarity :  0.004   0.031   1124
  Dihedral  :  9.504  61.557   1102
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 20.89 %
    Favored  : 74.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.31), residues: 774
  helix:  1.20 (0.23), residues: 544
  sheet:  None (None), residues: 0
  loop : -2.27 (0.39), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 607 
 HIS   0.002   0.001   HIS A 441 
 PHE   0.022   0.001   PHE A 546 
 TYR   0.013   0.001   TYR B 352 
 ARG   0.003   0.000   ARG A 448 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04413 (  339)
  hydrogen bonds       : angle       4.17168 ( 1017)
  SS BOND              : bond        0.00289 (    2)
  SS BOND              : angle       1.81249 (    4)
  covalent geometry    : bond        0.00240 ( 6924)
  covalent geometry    : angle       0.54136 ( 9406)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 90
  time to evaluate  : 0.712 
Fit side-chains
REVERT: A  272 TYR cc_start: 0.8765 (m-80) cc_final: 0.7359 (m-80)
REVERT: A  331 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8271 (tp)
REVERT: A  442 LYS cc_start: 0.6239 (OUTLIER) cc_final: 0.5768 (pttt)
REVERT: A  452 GLN cc_start: 0.8484 (tp-100) cc_final: 0.8257 (tp40)
REVERT: A  472 ARG cc_start: 0.7915 (ttm110) cc_final: 0.7652 (ttp-110)
REVERT: A  504 HIS cc_start: 0.6325 (OUTLIER) cc_final: 0.6114 (m-70)
REVERT: A  508 MET cc_start: 0.6069 (mmm) cc_final: 0.5805 (mmp)
REVERT: B  272 TYR cc_start: 0.8750 (m-80) cc_final: 0.7341 (m-80)
REVERT: B  331 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8233 (tp)
REVERT: B  415 CYS cc_start: 0.6750 (OUTLIER) cc_final: 0.6412 (t)
REVERT: B  442 LYS cc_start: 0.6254 (OUTLIER) cc_final: 0.5599 (pttp)
REVERT: B  452 GLN cc_start: 0.8663 (tp-100) cc_final: 0.8152 (tp-100)
REVERT: B  472 ARG cc_start: 0.7919 (ttm110) cc_final: 0.7656 (ttp-110)
REVERT: B  504 HIS cc_start: 0.6317 (OUTLIER) cc_final: 0.6101 (m-70)
REVERT: B  508 MET cc_start: 0.6068 (mmm) cc_final: 0.5697 (mmp)
  outliers start: 34
  outliers final: 22
  residues processed: 124
  average time/residue: 0.1779
  time to fit residues: 30.4821
Evaluate side-chains
  117 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 88
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  399 GLN
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  504 HIS
Chi-restraints excluded: chain A residue  577 ILE
Chi-restraints excluded: chain A residue  587 HIS
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  399 GLN
Chi-restraints excluded: chain B residue  415 CYS
Chi-restraints excluded: chain B residue  418 SER
Chi-restraints excluded: chain B residue  442 LYS
Chi-restraints excluded: chain B residue  504 HIS
Chi-restraints excluded: chain B residue  565 GLU
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  580 THR
Chi-restraints excluded: chain B residue  587 HIS
Chi-restraints excluded: chain B residue  592 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 73 optimal weight:    0.5980
   chunk 47 optimal weight:    2.9990
   chunk 74 optimal weight:    0.4980
   chunk 55 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 39 optimal weight:    0.3980
   chunk 13 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 71 optimal weight:    0.2980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 576 GLN
B 576 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.167555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.122185 restraints weight = 7253.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 2.29
r_work: 0.3093 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.2917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6926  Z= 0.121
  Angle     :  0.552   8.096   9410  Z= 0.276
  Chirality :  0.038   0.132   1020
  Planarity :  0.004   0.031   1124
  Dihedral  :  9.351  53.005   1100
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 21.04 %
    Favored  : 74.06 %
  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:  0.34 (0.31), residues: 774
  helix:  1.23 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -2.23 (0.38), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 573 
 HIS   0.002   0.001   HIS A 313 
 PHE   0.022   0.001   PHE A 546 
 TYR   0.013   0.001   TYR B 352 
 ARG   0.002   0.000   ARG A 448 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04683 (  339)
  hydrogen bonds       : angle       4.13665 ( 1017)
  SS BOND              : bond        0.00378 (    2)
  SS BOND              : angle       1.85422 (    4)
  covalent geometry    : bond        0.00266 ( 6924)
  covalent geometry    : angle       0.55092 ( 9406)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3335.82 seconds
wall clock time: 58 minutes 12.51 seconds (3492.51 seconds total)