Starting phenix.real_space_refine
on Wed Mar  4 01:23:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7oji_12952/03_2026/7oji_12952_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7oji_12952/03_2026/7oji_12952.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7oji_12952/03_2026/7oji_12952_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7oji_12952/03_2026/7oji_12952_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7oji_12952/03_2026/7oji_12952.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7oji_12952/03_2026/7oji_12952.map"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.040
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       8      5.49       5
     S      58      5.16       5
     C    5997      2.51       5
     N    1483      2.21       5
     O    1649      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9195
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4453
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 572, 4453
          Classifications: {'peptide': 572}
          Link IDs: {'PTRANS': 20, 'TRANS': 551}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 4453
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 572, 4453
          Classifications: {'peptide': 572}
          Link IDs: {'PTRANS': 20, 'TRANS': 551}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 160
          Unusual residues: {'ATP': 1, 'CLR': 2, 'PLC': 1, 'TTC': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "B"
      Number of atoms: 129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 129
          Unusual residues: {'ATP': 1, 'CLR': 2, 'PLC': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 1.94, per 1000 atoms: 0.21
  Number of scatterers: 9195
  At special positions: 0
  Unit cell: (100.98, 91.74, 128.04, 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      58     16.00
     P       8     15.00
     O    1649      8.00
     N    1483      7.00
     C    5997      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 592 " - pdb=" SG  CYS A 608 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 603 " - pdb=" SG  CYS B 603 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 592 " - pdb=" SG  CYS B 608 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.75
  Conformation dependent library (CDL) restraints added in 427.0 milliseconds
  

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2116

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 4 sheets defined
      64.5% alpha, 8.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 85 through 94
    Processing helix  chain 'A' and resid 116 through 119
    Processing helix  chain 'A' and resid 135 through 148
    Processing helix  chain 'A' and resid 153 through 169
    Processing helix  chain 'A' and resid 170 through 174
    Processing helix  chain 'A' and resid 187 through 201
      removed outlier: 3.828A  pdb=" N   GLU A 199 " --> pdb=" O   SER A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 233
    Processing helix  chain 'A' and resid 246 through 253
      removed outlier: 3.607A  pdb=" N   LEU A 252 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   PHE A 253 " --> pdb=" O   ILE A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 281
      removed outlier: 4.398A  pdb=" N   GLY A 275 " --> pdb=" O   GLN A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 299
      removed outlier: 3.577A  pdb=" N   ILE A 298 " --> pdb=" O   PHE A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 338
    Processing helix  chain 'A' and resid 339 through 353
      removed outlier: 3.500A  pdb=" N   LYS A 343 " --> pdb=" O   SER A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 390
      removed outlier: 3.623A  pdb=" N   GLN A 376 " --> pdb=" O   SER A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 395 through 413
    Processing helix  chain 'A' and resid 421 through 440
    Processing helix  chain 'A' and resid 441 through 451
      removed outlier: 3.525A  pdb=" N   PHE A 448 " --> pdb=" O   ALA A 444 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   GLU A 451 " --> pdb=" O   LEU A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 462
    Processing helix  chain 'A' and resid 465 through 477
      removed outlier: 3.510A  pdb=" N   TYR A 469 " --> pdb=" O   ARG A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 498
      removed outlier: 3.612A  pdb=" N   MET A 481 " --> pdb=" O   ASP A 477 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ARG A 482 " --> pdb=" O   LEU A 478 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   MET A 483 " --> pdb=" O   LEU A 479 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LEU A 484 " --> pdb=" O   PRO A 480 " (cutoff:3.500A)
      Proline residue:  A 485  - end of helix
      removed outlier: 4.757A  pdb=" N   PHE A 495 " --> pdb=" O   CYS A 491 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   MET A 496 " --> pdb=" O   ILE A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 529
    Processing helix  chain 'A' and resid 533 through 550
      removed outlier: 3.880A  pdb=" N   ALA A 537 " --> pdb=" O   VAL A 533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 571
      removed outlier: 3.529A  pdb=" N   TYR A 570 " --> pdb=" O   TRP A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 587
      removed outlier: 3.649A  pdb=" N   TYR A 576 " --> pdb=" O   SER A 572 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ASN A 584 " --> pdb=" O   ALA A 580 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   GLU A 585 " --> pdb=" O   LEU A 581 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   LEU A 587 " --> pdb=" O   HIS A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 601
      removed outlier: 3.918A  pdb=" N   ASN A 601 " --> pdb=" O   ALA A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 617
      removed outlier: 3.542A  pdb=" N   TYR A 613 " --> pdb=" O   THR A 609 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 650
      removed outlier: 5.124A  pdb=" N   ASN A 629 " --> pdb=" O   GLY A 625 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   HIS A 630 " --> pdb=" O   LEU A 626 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 94
    Processing helix  chain 'B' and resid 116 through 119
    Processing helix  chain 'B' and resid 135 through 148
    Processing helix  chain 'B' and resid 153 through 169
    Processing helix  chain 'B' and resid 170 through 174
    Processing helix  chain 'B' and resid 187 through 201
      removed outlier: 3.829A  pdb=" N   GLU B 199 " --> pdb=" O   SER B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 233
    Processing helix  chain 'B' and resid 246 through 253
      removed outlier: 3.606A  pdb=" N   LEU B 252 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   PHE B 253 " --> pdb=" O   ILE B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 271 through 281
      removed outlier: 4.399A  pdb=" N   GLY B 275 " --> pdb=" O   GLN B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 299
      removed outlier: 3.576A  pdb=" N   ILE B 298 " --> pdb=" O   PHE B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 338
    Processing helix  chain 'B' and resid 339 through 353
      removed outlier: 3.500A  pdb=" N   LYS B 343 " --> pdb=" O   SER B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 390
      removed outlier: 3.623A  pdb=" N   GLN B 376 " --> pdb=" O   SER B 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 413
    Processing helix  chain 'B' and resid 421 through 440
    Processing helix  chain 'B' and resid 441 through 451
      removed outlier: 3.525A  pdb=" N   PHE B 448 " --> pdb=" O   ALA B 444 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   GLU B 451 " --> pdb=" O   LEU B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 451 through 462
    Processing helix  chain 'B' and resid 465 through 477
      removed outlier: 3.510A  pdb=" N   TYR B 469 " --> pdb=" O   ARG B 465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 477 through 498
      removed outlier: 3.612A  pdb=" N   MET B 481 " --> pdb=" O   ASP B 477 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ARG B 482 " --> pdb=" O   LEU B 478 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   MET B 483 " --> pdb=" O   LEU B 479 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   LEU B 484 " --> pdb=" O   PRO B 480 " (cutoff:3.500A)
      Proline residue:  B 485  - end of helix
      removed outlier: 4.757A  pdb=" N   PHE B 495 " --> pdb=" O   CYS B 491 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   MET B 496 " --> pdb=" O   ILE B 492 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 502 through 529
    Processing helix  chain 'B' and resid 533 through 550
      removed outlier: 3.880A  pdb=" N   ALA B 537 " --> pdb=" O   VAL B 533 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 565 through 571
      removed outlier: 3.528A  pdb=" N   TYR B 570 " --> pdb=" O   TRP B 567 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 572 through 587
      removed outlier: 3.649A  pdb=" N   TYR B 576 " --> pdb=" O   SER B 572 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ASN B 584 " --> pdb=" O   ALA B 580 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLU B 585 " --> pdb=" O   LEU B 581 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   LEU B 587 " --> pdb=" O   HIS B 583 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 594 through 601
      removed outlier: 3.918A  pdb=" N   ASN B 601 " --> pdb=" O   ALA B 597 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 609 through 617
      removed outlier: 3.542A  pdb=" N   TYR B 613 " --> pdb=" O   THR B 609 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 623 through 650
      removed outlier: 5.123A  pdb=" N   ASN B 629 " --> pdb=" O   GLY B 625 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   HIS B 630 " --> pdb=" O   LEU B 626 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 71
      removed outlier: 6.719A  pdb=" N   TYR A  44 " --> pdb=" O   ILE A  63 " (cutoff:3.500A)
      removed outlier: 4.965A  pdb=" N   SER A  65 " --> pdb=" O   ILE A  42 " (cutoff:3.500A)
      removed outlier: 5.429A  pdb=" N   ILE A  42 " --> pdb=" O   SER A  65 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   ILE A  67 " --> pdb=" O   HIS A  40 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   HIS A  40 " --> pdb=" O   ILE A  67 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   GLY A  69 " --> pdb=" O   SER A  38 " (cutoff:3.500A)
      removed outlier: 4.881A  pdb=" N   SER A  38 " --> pdb=" O   GLY A  69 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ASP A 105 " --> pdb=" O   HIS A  40 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 124
      removed outlier: 6.245A  pdb=" N   LEU A 207 " --> pdb=" O   ILE A 239 " (cutoff:3.500A)
      removed outlier: 8.214A  pdb=" N   SER A 241 " --> pdb=" O   LEU A 207 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   LEU A 209 " --> pdb=" O   SER A 241 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   GLY A  74 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
      removed outlier: 8.175A  pdb=" N   PHE A 240 " --> pdb=" O   GLY A  74 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   ASN A  76 " --> pdb=" O   PHE A 240 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   LEU A 256 " --> pdb=" O   HIS A 267 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   HIS A 267 " --> pdb=" O   LEU A 256 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   LEU A 258 " --> pdb=" O   MET A 265 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 71
      removed outlier: 6.719A  pdb=" N   TYR B  44 " --> pdb=" O   ILE B  63 " (cutoff:3.500A)
      removed outlier: 4.966A  pdb=" N   SER B  65 " --> pdb=" O   ILE B  42 " (cutoff:3.500A)
      removed outlier: 5.429A  pdb=" N   ILE B  42 " --> pdb=" O   SER B  65 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   ILE B  67 " --> pdb=" O   HIS B  40 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   HIS B  40 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   GLY B  69 " --> pdb=" O   SER B  38 " (cutoff:3.500A)
      removed outlier: 4.881A  pdb=" N   SER B  38 " --> pdb=" O   GLY B  69 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ASP B 105 " --> pdb=" O   HIS B  40 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 121 through 124
      removed outlier: 6.245A  pdb=" N   LEU B 207 " --> pdb=" O   ILE B 239 " (cutoff:3.500A)
      removed outlier: 8.215A  pdb=" N   SER B 241 " --> pdb=" O   LEU B 207 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   LEU B 209 " --> pdb=" O   SER B 241 " (cutoff:3.500A)
      removed outlier: 5.954A  pdb=" N   GLY B  74 " --> pdb=" O   ILE B 238 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   PHE B 240 " --> pdb=" O   GLY B  74 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   ASN B  76 " --> pdb=" O   PHE B 240 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   LEU B 256 " --> pdb=" O   HIS B 267 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   HIS B 267 " --> pdb=" O   LEU B 256 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   LEU B 258 " --> pdb=" O   MET B 265 " (cutoff:3.500A)

    512 hydrogen bonds defined for protein.
    1482 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: 1.51

  Time building geometry restraints manager: 0.94 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1414
        1.31 -     1.44: 2486
        1.44 -     1.57: 5370
        1.57 -     1.69: 37
        1.69 -     1.82: 94
  Bond restraints: 9401
  Sorted by residual:
  bond pdb=" C5  ATP A 705 "
       pdb=" N7  ATP A 705 "
    ideal  model  delta    sigma   weight residual
    1.387  1.524 -0.137 1.00e-02 1.00e+04 1.88e+02
  bond pdb=" C5  ATP B 704 "
       pdb=" N7  ATP B 704 "
    ideal  model  delta    sigma   weight residual
    1.387  1.524 -0.137 1.00e-02 1.00e+04 1.86e+02
  bond pdb=" C6  ATP B 704 "
       pdb=" N6  ATP B 704 "
    ideal  model  delta    sigma   weight residual
    1.337  1.451 -0.114 1.10e-02 8.26e+03 1.06e+02
  bond pdb=" C6  ATP A 705 "
       pdb=" N6  ATP A 705 "
    ideal  model  delta    sigma   weight residual
    1.337  1.449 -0.112 1.10e-02 8.26e+03 1.04e+02
  bond pdb=" C4  ATP B 704 "
       pdb=" N9  ATP B 704 "
    ideal  model  delta    sigma   weight residual
    1.374  1.272  0.102 1.00e-02 1.00e+04 1.04e+02
  ... (remaining 9396 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.77: 12590
        3.77 -     7.53: 109
        7.53 -    11.30: 38
       11.30 -    15.07: 9
       15.07 -    18.83: 7
  Bond angle restraints: 12753
  Sorted by residual:
  angle pdb=" PB  ATP B 704 "
        pdb=" O3B ATP B 704 "
        pdb=" PG  ATP B 704 "
      ideal   model   delta    sigma   weight residual
     139.87  121.04   18.83 1.00e+00 1.00e+00 3.55e+02
  angle pdb=" PB  ATP A 705 "
        pdb=" O3B ATP A 705 "
        pdb=" PG  ATP A 705 "
      ideal   model   delta    sigma   weight residual
     139.87  122.31   17.56 1.00e+00 1.00e+00 3.08e+02
  angle pdb=" C4  ATP B 704 "
        pdb=" N9  ATP B 704 "
        pdb=" C8  ATP B 704 "
      ideal   model   delta    sigma   weight residual
     105.72  121.81  -16.09 1.00e+00 1.00e+00 2.59e+02
  angle pdb=" C4  ATP A 705 "
        pdb=" N9  ATP A 705 "
        pdb=" C8  ATP A 705 "
      ideal   model   delta    sigma   weight residual
     105.72  121.70  -15.98 1.00e+00 1.00e+00 2.55e+02
  angle pdb=" PA  ATP B 704 "
        pdb=" O3A ATP B 704 "
        pdb=" PB  ATP B 704 "
      ideal   model   delta    sigma   weight residual
     136.83  121.22   15.61 1.00e+00 1.00e+00 2.44e+02
  ... (remaining 12748 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.49: 5503
       21.49 -    42.97: 274
       42.97 -    64.46: 32
       64.46 -    85.94: 9
       85.94 -   107.43: 4
  Dihedral angle restraints: 5822
    sinusoidal: 2526
      harmonic: 3296
  Sorted by residual:
  dihedral pdb=" CA  HIS B 283 "
           pdb=" C   HIS B 283 "
           pdb=" N   CYS B 284 "
           pdb=" CA  CYS B 284 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -146.86  -33.14     0      5.00e+00 4.00e-02 4.39e+01
  dihedral pdb=" CA  HIS A 283 "
           pdb=" C   HIS A 283 "
           pdb=" N   CYS A 284 "
           pdb=" CA  CYS A 284 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -146.92  -33.08     0      5.00e+00 4.00e-02 4.38e+01
  dihedral pdb=" CA  VAL B 493 "
           pdb=" C   VAL B 493 "
           pdb=" N   TYR B 494 "
           pdb=" CA  TYR B 494 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.59  -20.41     0      5.00e+00 4.00e-02 1.67e+01
  ... (remaining 5819 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.323: 1461
       0.323 -    0.647: 4
       0.647 -    0.970: 0
       0.970 -    1.294: 0
       1.294 -    1.617: 2
  Chirality restraints: 1467
  Sorted by residual:
  chirality pdb=" CG  LEU B 595 "
            pdb=" CB  LEU B 595 "
            pdb=" CD1 LEU B 595 "
            pdb=" CD2 LEU B 595 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.97   -1.62 2.00e-01 2.50e+01 6.54e+01
  chirality pdb=" CG  LEU A 595 "
            pdb=" CB  LEU A 595 "
            pdb=" CD1 LEU A 595 "
            pdb=" CD2 LEU A 595 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.97   -1.62 2.00e-01 2.50e+01 6.52e+01
  chirality pdb=" C21 TTC A 701 "
            pdb=" C16 TTC A 701 "
            pdb=" C20 TTC A 701 "
            pdb=" O24 TTC A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.98    0.47 2.00e-01 2.50e+01 5.63e+00
  ... (remaining 1464 not shown)

  Planarity restraints: 1542
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1  TTC A 701 "    0.009 2.00e-02 2.50e+03   1.08e-02 6.46e+00
        pdb=" C11 TTC A 701 "    0.001 2.00e-02 2.50e+03
        pdb=" C13 TTC A 701 "    0.009 2.00e-02 2.50e+03
        pdb=" C14 TTC A 701 "    0.008 2.00e-02 2.50e+03
        pdb=" C15 TTC A 701 "    0.004 2.00e-02 2.50e+03
        pdb=" C16 TTC A 701 "    0.019 2.00e-02 2.50e+03
        pdb=" C17 TTC A 701 "    0.007 2.00e-02 2.50e+03
        pdb=" C19 TTC A 701 "   -0.007 2.00e-02 2.50e+03
        pdb=" C2  TTC A 701 "    0.004 2.00e-02 2.50e+03
        pdb=" C21 TTC A 701 "   -0.033 2.00e-02 2.50e+03
        pdb=" C27 TTC A 701 "   -0.022 2.00e-02 2.50e+03
        pdb=" C3  TTC A 701 "    0.010 2.00e-02 2.50e+03
        pdb=" C4  TTC A 701 "    0.001 2.00e-02 2.50e+03
        pdb=" C5  TTC A 701 "    0.001 2.00e-02 2.50e+03
        pdb=" C6  TTC A 701 "    0.004 2.00e-02 2.50e+03
        pdb=" C7  TTC A 701 "   -0.005 2.00e-02 2.50e+03
        pdb=" C8  TTC A 701 "    0.001 2.00e-02 2.50e+03
        pdb=" C9  TTC A 701 "   -0.002 2.00e-02 2.50e+03
        pdb=" N10 TTC A 701 "   -0.007 2.00e-02 2.50e+03
        pdb=" N12 TTC A 701 "    0.006 2.00e-02 2.50e+03
        pdb=" O18 TTC A 701 "   -0.001 2.00e-02 2.50e+03
        pdb=" O26 TTC A 701 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 211 "    0.024 5.00e-02 4.00e+02   3.66e-02 2.15e+00
        pdb=" N   PRO A 212 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 212 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 212 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 211 "   -0.024 5.00e-02 4.00e+02   3.65e-02 2.13e+00
        pdb=" N   PRO B 212 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO B 212 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 212 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 1539 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1825
        2.77 -     3.30: 9201
        3.30 -     3.83: 14441
        3.83 -     4.37: 17140
        4.37 -     4.90: 30112
  Nonbonded interactions: 72719
  Sorted by model distance:
  nonbonded pdb=" O   GLY B 594 "
            pdb=" OG1 THR B 598 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" O   GLY A 594 "
            pdb=" OG1 THR A 598 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OD1 ASP B  91 "
            pdb=" OH  TYR B 123 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" OD1 ASP A  91 "
            pdb=" OH  TYR A 123 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" O   TYR B 336 "
            pdb=" OG  SER B 339 "
     model   vdw
     2.312 3.040
  ... (remaining 72714 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 34 through 654 or resid 702 through 703))
  selection = (chain 'B' and (resid 34 through 654 or resid 702 through 703))
}

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=0.00 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:             6.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.090
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  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:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
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      :  0.012   0.195   9404  Z= 0.656
  Angle     :  1.079  18.833  12759  Z= 0.646
  Chirality :  0.080   1.617   1467
  Planarity :  0.004   0.037   1542
  Dihedral  : 12.846 107.428   3697
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.79 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  2.46 %
    Favored  : 97.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.15 (0.24), residues: 1128
  helix:  1.03 (0.19), residues: 672
  sheet: -1.28 (0.50), residues: 82
  loop : -1.91 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  45 
 TYR   0.014   0.002   TYR B 282 
 PHE   0.014   0.001   PHE A 448 
 TRP   0.011   0.002   TRP A 379 
 HIS   0.004   0.001   HIS B 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.01242 ( 9401)
  covalent geometry    : angle       1.07856 (12753)
  SS BOND              : bond        0.00857 (    3)
  SS BOND              : angle       2.14928 (    6)
  hydrogen bonds       : bond        0.15782 (  512)
  hydrogen bonds       : angle       5.82729 ( 1482)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 178
  time to evaluate  : 0.299 
Fit side-chains
REVERT: B  231 MET cc_start: 0.8750 (ttm) cc_final: 0.8520 (ttm)
  outliers start: 4
  outliers final: 3
  residues processed: 182
  average time/residue: 0.1097
  time to fit residues: 26.7732
Evaluate side-chains
  92 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 89
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  489 PHE
Chi-restraints excluded: chain B residue   68 ASN
Chi-restraints excluded: chain B residue  489 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    0.0980
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    7.9990
   chunk 100 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 181 GLN
A 351 GLN
A 436 ASN
B 436 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.117502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.101652 restraints weight = 16195.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 1.90
r_work: 0.3278 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3157 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3161
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3154 r_free = 0.3154    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3154
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.2173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9404  Z= 0.136
  Angle     :  0.573  10.854  12759  Z= 0.294
  Chirality :  0.041   0.176   1467
  Planarity :  0.003   0.032   1542
  Dihedral  : 10.672  89.952   1649
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  8.61 %
    Favored  : 89.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.00 (0.26), residues: 1128
  helix:  1.98 (0.20), residues: 694
  sheet: -0.88 (0.51), residues: 76
  loop : -1.69 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  45 
 TYR   0.013   0.001   TYR A 282 
 PHE   0.015   0.001   PHE B 591 
 TRP   0.012   0.002   TRP B 379 
 HIS   0.006   0.001   HIS A 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 9401)
  covalent geometry    : angle       0.57107 (12753)
  SS BOND              : bond        0.01870 (    3)
  SS BOND              : angle       2.32259 (    6)
  hydrogen bonds       : bond        0.05086 (  512)
  hydrogen bonds       : angle       3.94008 ( 1482)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.380 
Fit side-chains
REVERT: A  131 MET cc_start: 0.8100 (tpp) cc_final: 0.7803 (tpp)
REVERT: A  446 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7932 (mt-10)
REVERT: B  102 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.8003 (mt)
REVERT: B  595 LEU cc_start: 0.5812 (OUTLIER) cc_final: 0.5486 (tt)
  outliers start: 17
  outliers final: 7
  residues processed: 108
  average time/residue: 0.0847
  time to fit residues: 13.5618
Evaluate side-chains
  85 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  257 THR
Chi-restraints excluded: chain B residue  489 PHE
Chi-restraints excluded: chain B residue  592 CYS
Chi-restraints excluded: chain B residue  595 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 67 optimal weight:    7.9990
   chunk 97 optimal weight:    1.9990
   chunk 79 optimal weight:    8.9990
   chunk 54 optimal weight:    2.9990
   chunk 72 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9990
   chunk 63 optimal weight:    9.9990
   chunk 19 optimal weight:    3.9990
   chunk 52 optimal weight:    6.9990
   chunk 78 optimal weight:    1.9990
   chunk 106 optimal weight:    3.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
B  66 ASN
B 271 GLN
B 375 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.109445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.092794 restraints weight = 16583.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 1.94
r_work: 0.3147 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3024
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3024
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.3051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   9404  Z= 0.215
  Angle     :  0.600   8.078  12759  Z= 0.308
  Chirality :  0.043   0.131   1467
  Planarity :  0.004   0.038   1542
  Dihedral  : 10.410  89.306   1645
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 10.14 %
    Favored  : 87.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.26), residues: 1128
  helix:  1.95 (0.19), residues: 694
  sheet: -0.73 (0.51), residues: 76
  loop : -1.71 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 246 
 TYR   0.013   0.002   TYR A 282 
 PHE   0.012   0.002   PHE B 506 
 TRP   0.017   0.002   TRP B 379 
 HIS   0.005   0.002   HIS B 630 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 ( 9401)
  covalent geometry    : angle       0.59763 (12753)
  SS BOND              : bond        0.01192 (    3)
  SS BOND              : angle       2.54183 (    6)
  hydrogen bonds       : bond        0.05535 (  512)
  hydrogen bonds       : angle       3.76213 ( 1482)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.291 
Fit side-chains
REVERT: A  131 MET cc_start: 0.8357 (tpp) cc_final: 0.8009 (tpp)
REVERT: A  226 LEU cc_start: 0.8551 (pp) cc_final: 0.8270 (pp)
REVERT: A  446 GLU cc_start: 0.8269 (mt-10) cc_final: 0.8048 (mt-10)
REVERT: B  125 VAL cc_start: 0.9201 (OUTLIER) cc_final: 0.9000 (p)
REVERT: B  233 LYS cc_start: 0.8712 (tptm) cc_final: 0.8490 (ttmt)
REVERT: B  614 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8917 (mp)
  outliers start: 20
  outliers final: 9
  residues processed: 104
  average time/residue: 0.0746
  time to fit residues: 11.7555
Evaluate side-chains
  89 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  257 THR
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  489 PHE
Chi-restraints excluded: chain B residue  614 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 109 optimal weight:    0.9980
   chunk 54 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   chunk 88 optimal weight:    5.9990
   chunk 43 optimal weight:    0.8980
   chunk 15 optimal weight:    5.9990
   chunk 110 optimal weight:    0.0470
   chunk 86 optimal weight:    2.9990
   overall best weight:    1.1480

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

Flipped N/Q/H residues before XYZ refinement:
A 283 HIS
B 457 HIS
B 617 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.111844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.095208 restraints weight = 16571.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 1.95
r_work: 0.3175 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3052 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3066
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3066 r_free = 0.3066    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3066 r_free = 0.3066    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3066
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8560
moved from start:          0.3317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9404  Z= 0.127
  Angle     :  0.510  10.318  12759  Z= 0.261
  Chirality :  0.039   0.146   1467
  Planarity :  0.003   0.033   1542
  Dihedral  : 10.103  88.638   1645
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 10.76 %
    Favored  : 86.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.29 (0.26), residues: 1128
  helix:  2.15 (0.20), residues: 696
  sheet: -0.47 (0.54), residues: 76
  loop : -1.53 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  45 
 TYR   0.011   0.001   TYR B 336 
 PHE   0.013   0.001   PHE A 385 
 TRP   0.012   0.001   TRP B 379 
 HIS   0.006   0.001   HIS A 457 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9401)
  covalent geometry    : angle       0.50826 (12753)
  SS BOND              : bond        0.00620 (    3)
  SS BOND              : angle       2.00468 (    6)
  hydrogen bonds       : bond        0.04355 (  512)
  hydrogen bonds       : angle       3.45096 ( 1482)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 86
  time to evaluate  : 0.325 
Fit side-chains
REVERT: A  127 ASP cc_start: 0.7658 (p0) cc_final: 0.7322 (p0)
REVERT: A  131 MET cc_start: 0.8284 (tpp) cc_final: 0.7954 (tpp)
REVERT: A  226 LEU cc_start: 0.8519 (pp) cc_final: 0.8240 (pp)
REVERT: A  386 LYS cc_start: 0.8678 (mttm) cc_final: 0.8444 (mttt)
REVERT: B  525 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8689 (mp)
  outliers start: 25
  outliers final: 10
  residues processed: 100
  average time/residue: 0.0808
  time to fit residues: 12.0844
Evaluate side-chains
  91 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  489 PHE
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  257 THR
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  451 GLU
Chi-restraints excluded: chain B residue  489 PHE
Chi-restraints excluded: chain B residue  525 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 76 optimal weight:    2.9990
   chunk 24 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 19 optimal weight:    6.9990
   chunk 98 optimal weight:    3.9990
   chunk 59 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   chunk 57 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 155 HIS
A 283 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.105528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.088965 restraints weight = 16940.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 1.92
r_work: 0.3057 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2931 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2941
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2941
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8658
moved from start:          0.3669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   9404  Z= 0.234
  Angle     :  0.618   8.523  12759  Z= 0.313
  Chirality :  0.043   0.179   1467
  Planarity :  0.004   0.035   1542
  Dihedral  : 10.286  88.429   1645
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 10.76 %
    Favored  : 86.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.26), residues: 1128
  helix:  2.04 (0.20), residues: 694
  sheet: -0.47 (0.56), residues: 76
  loop : -1.64 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 191 
 TYR   0.012   0.001   TYR B 459 
 PHE   0.015   0.002   PHE B 495 
 TRP   0.012   0.001   TRP B 379 
 HIS   0.008   0.002   HIS A 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00558 ( 9401)
  covalent geometry    : angle       0.61580 (12753)
  SS BOND              : bond        0.00475 (    3)
  SS BOND              : angle       2.33342 (    6)
  hydrogen bonds       : bond        0.05593 (  512)
  hydrogen bonds       : angle       3.65304 ( 1482)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 85
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A  131 MET cc_start: 0.8532 (tpp) cc_final: 0.8138 (tpp)
REVERT: A  226 LEU cc_start: 0.8606 (pp) cc_final: 0.8083 (mm)
REVERT: B  125 VAL cc_start: 0.9156 (OUTLIER) cc_final: 0.8899 (p)
REVERT: B  243 HIS cc_start: 0.8245 (OUTLIER) cc_final: 0.8044 (t-90)
REVERT: B  525 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8628 (mp)
REVERT: B  604 ASN cc_start: 0.6635 (OUTLIER) cc_final: 0.5537 (t0)
REVERT: B  614 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8864 (mp)
  outliers start: 26
  outliers final: 13
  residues processed: 103
  average time/residue: 0.0839
  time to fit residues: 12.6963
Evaluate side-chains
  95 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 77
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  283 HIS
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  489 PHE
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  620 ASP
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  257 THR
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  451 GLU
Chi-restraints excluded: chain B residue  489 PHE
Chi-restraints excluded: chain B residue  525 LEU
Chi-restraints excluded: chain B residue  604 ASN
Chi-restraints excluded: chain B residue  614 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 58 optimal weight:    8.9990
   chunk 48 optimal weight:    0.9980
   chunk 1 optimal weight:    8.9990
   chunk 15 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   chunk 95 optimal weight:    0.6980
   chunk 14 optimal weight:    3.9990
   chunk 34 optimal weight:    0.7980
   chunk 37 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 155 HIS
A 283 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.109349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.092742 restraints weight = 16804.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 1.95
r_work: 0.3131 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3008 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3013
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3013 r_free = 0.3013    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3013 r_free = 0.3013    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3013
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.3787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9404  Z= 0.133
  Angle     :  0.511   9.492  12759  Z= 0.263
  Chirality :  0.039   0.139   1467
  Planarity :  0.003   0.032   1542
  Dihedral  :  9.861  87.915   1645
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 11.48 %
    Favored  : 85.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.44 (0.26), residues: 1128
  helix:  2.24 (0.20), residues: 696
  sheet: -0.25 (0.57), residues: 76
  loop : -1.47 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 163 
 TYR   0.011   0.001   TYR A 336 
 PHE   0.009   0.001   PHE A 432 
 TRP   0.013   0.001   TRP B 379 
 HIS   0.010   0.001   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 9401)
  covalent geometry    : angle       0.51017 (12753)
  SS BOND              : bond        0.00790 (    3)
  SS BOND              : angle       1.67786 (    6)
  hydrogen bonds       : bond        0.04496 (  512)
  hydrogen bonds       : angle       3.39525 ( 1482)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 84
  time to evaluate  : 0.351 
Fit side-chains
REVERT: A  131 MET cc_start: 0.8401 (tpp) cc_final: 0.7993 (tpp)
REVERT: A  226 LEU cc_start: 0.8566 (pp) cc_final: 0.8039 (mm)
REVERT: B  125 VAL cc_start: 0.9120 (OUTLIER) cc_final: 0.8881 (p)
REVERT: B  525 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8702 (mp)
  outliers start: 25
  outliers final: 14
  residues processed: 101
  average time/residue: 0.0718
  time to fit residues: 11.1474
Evaluate side-chains
  94 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  489 PHE
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  620 ASP
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  257 THR
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  451 GLU
Chi-restraints excluded: chain B residue  489 PHE
Chi-restraints excluded: chain B residue  525 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 104 optimal weight:    5.9990
   chunk 92 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 94 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 4 optimal weight:    8.9990
   chunk 28 optimal weight:    5.9990
   chunk 108 optimal weight:    6.9990
   chunk 64 optimal weight:    0.8980
   chunk 57 optimal weight:    7.9990
   overall best weight:    2.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 155 HIS
A 283 HIS
B 243 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.107522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.090804 restraints weight = 16877.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 1.95
r_work: 0.3098 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2975 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2981
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2981 r_free = 0.2981    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2981 r_free = 0.2981    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2981
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8646
moved from start:          0.3952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9404  Z= 0.188
  Angle     :  0.559  10.187  12759  Z= 0.284
  Chirality :  0.041   0.151   1467
  Planarity :  0.003   0.032   1542
  Dihedral  :  9.820  88.165   1645
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 12.60 %
    Favored  : 84.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.41 (0.26), residues: 1128
  helix:  2.23 (0.20), residues: 694
  sheet: -0.12 (0.59), residues: 76
  loop : -1.53 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 163 
 TYR   0.011   0.001   TYR B 459 
 PHE   0.011   0.001   PHE B 373 
 TRP   0.012   0.001   TRP B 379 
 HIS   0.007   0.001   HIS A 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 9401)
  covalent geometry    : angle       0.55727 (12753)
  SS BOND              : bond        0.00681 (    3)
  SS BOND              : angle       2.01030 (    6)
  hydrogen bonds       : bond        0.04909 (  512)
  hydrogen bonds       : angle       3.45203 ( 1482)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 83
  time to evaluate  : 0.378 
Fit side-chains
REVERT: A  131 MET cc_start: 0.8484 (tpp) cc_final: 0.8067 (tpp)
REVERT: A  226 LEU cc_start: 0.8573 (pp) cc_final: 0.8050 (mm)
REVERT: B  125 VAL cc_start: 0.9139 (OUTLIER) cc_final: 0.8896 (p)
REVERT: B  525 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8690 (mp)
REVERT: B  604 ASN cc_start: 0.6759 (p0) cc_final: 0.5712 (t0)
  outliers start: 25
  outliers final: 16
  residues processed: 98
  average time/residue: 0.0702
  time to fit residues: 10.4479
Evaluate side-chains
  96 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  489 PHE
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  257 THR
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  451 GLU
Chi-restraints excluded: chain B residue  489 PHE
Chi-restraints excluded: chain B residue  525 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 96 optimal weight:    0.0870
   chunk 12 optimal weight:    0.8980
   chunk 4 optimal weight:    6.9990
   chunk 35 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 27 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
A 155 HIS
A 283 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.111136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.093913 restraints weight = 16652.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 2.05
r_work: 0.3135 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3009 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3011
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3011 r_free = 0.3011    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3011 r_free = 0.3011    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3011
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8605
moved from start:          0.4024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9404  Z= 0.105
  Angle     :  0.504  10.638  12759  Z= 0.255
  Chirality :  0.038   0.138   1467
  Planarity :  0.003   0.030   1542
  Dihedral  :  9.530  87.509   1645
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 13.01 %
    Favored  : 84.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.64 (0.26), residues: 1128
  helix:  2.38 (0.20), residues: 696
  sheet:  0.12 (0.60), residues: 76
  loop : -1.42 (0.35), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 163 
 TYR   0.011   0.001   TYR A 336 
 PHE   0.009   0.001   PHE A 591 
 TRP   0.013   0.001   TRP A 379 
 HIS   0.012   0.001   HIS B 243 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 9401)
  covalent geometry    : angle       0.50301 (12753)
  SS BOND              : bond        0.00516 (    3)
  SS BOND              : angle       1.62640 (    6)
  hydrogen bonds       : bond        0.04044 (  512)
  hydrogen bonds       : angle       3.29516 ( 1482)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 82
  time to evaluate  : 0.378 
Fit side-chains
REVERT: A  226 LEU cc_start: 0.8553 (pp) cc_final: 0.8035 (mm)
REVERT: A  287 TYR cc_start: 0.7482 (m-80) cc_final: 0.7111 (m-80)
REVERT: B  525 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8686 (mp)
REVERT: B  604 ASN cc_start: 0.6764 (p0) cc_final: 0.5725 (t0)
  outliers start: 21
  outliers final: 14
  residues processed: 94
  average time/residue: 0.0780
  time to fit residues: 11.2919
Evaluate side-chains
  94 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  489 PHE
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  620 ASP
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  446 GLU
Chi-restraints excluded: chain B residue  451 GLU
Chi-restraints excluded: chain B residue  489 PHE
Chi-restraints excluded: chain B residue  525 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 95 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0370
   chunk 72 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 13 optimal weight:    9.9990
   chunk 50 optimal weight:    0.6980
   chunk 93 optimal weight:    0.8980
   chunk 58 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 108 optimal weight:    6.9990
   overall best weight:    1.1262

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

Flipped N/Q/H residues before XYZ refinement:
A 283 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.108511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.092204 restraints weight = 16712.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 1.92
r_work: 0.3114 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2994
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2994 r_free = 0.2994    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2994 r_free = 0.2994    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2994
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8595
moved from start:          0.4132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9404  Z= 0.122
  Angle     :  0.508  11.104  12759  Z= 0.254
  Chirality :  0.038   0.137   1467
  Planarity :  0.003   0.030   1542
  Dihedral  :  9.323  86.541   1645
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.42 %
    Favored  : 84.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.80 (0.26), residues: 1128
  helix:  2.47 (0.20), residues: 696
  sheet:  0.07 (0.71), residues: 50
  loop : -1.16 (0.34), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 163 
 TYR   0.010   0.001   TYR B 459 
 PHE   0.011   0.001   PHE B 432 
 TRP   0.012   0.001   TRP B 379 
 HIS   0.005   0.001   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 9401)
  covalent geometry    : angle       0.50673 (12753)
  SS BOND              : bond        0.00763 (    3)
  SS BOND              : angle       1.71733 (    6)
  hydrogen bonds       : bond        0.03983 (  512)
  hydrogen bonds       : angle       3.26198 ( 1482)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 81
  time to evaluate  : 0.381 
Fit side-chains
REVERT: A  226 LEU cc_start: 0.8577 (pp) cc_final: 0.8036 (mm)
REVERT: A  287 TYR cc_start: 0.7503 (m-80) cc_final: 0.7183 (m-80)
REVERT: A  652 LYS cc_start: 0.8690 (mmtm) cc_final: 0.8273 (mptt)
REVERT: B  125 VAL cc_start: 0.9077 (OUTLIER) cc_final: 0.8864 (p)
REVERT: B  243 HIS cc_start: 0.8269 (OUTLIER) cc_final: 0.7525 (t-90)
REVERT: B  525 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8629 (mp)
REVERT: B  604 ASN cc_start: 0.6763 (p0) cc_final: 0.5846 (t0)
  outliers start: 19
  outliers final: 13
  residues processed: 93
  average time/residue: 0.0759
  time to fit residues: 10.7313
Evaluate side-chains
  95 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  489 PHE
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  620 ASP
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  451 GLU
Chi-restraints excluded: chain B residue  489 PHE
Chi-restraints excluded: chain B residue  525 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 55 optimal weight:    0.7980
   chunk 111 optimal weight:    2.9990
   chunk 17 optimal weight:    9.9990
   chunk 16 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   chunk 76 optimal weight:    0.7980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A 155 HIS
A 283 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.109812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.093165 restraints weight = 16721.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 1.97
r_work: 0.3115 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3006
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3006 r_free = 0.3006    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3006 r_free = 0.3006    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3006
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.4180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9404  Z= 0.119
  Angle     :  0.508  11.580  12759  Z= 0.254
  Chirality :  0.038   0.141   1467
  Planarity :  0.003   0.030   1542
  Dihedral  :  9.199  85.964   1645
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.63 %
    Favored  : 84.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.83 (0.26), residues: 1128
  helix:  2.51 (0.20), residues: 696
  sheet:  0.24 (0.71), residues: 50
  loop : -1.21 (0.34), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 191 
 TYR   0.010   0.001   TYR A 336 
 PHE   0.011   0.001   PHE B 432 
 TRP   0.012   0.001   TRP B 379 
 HIS   0.008   0.001   HIS A 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 9401)
  covalent geometry    : angle       0.50725 (12753)
  SS BOND              : bond        0.00532 (    3)
  SS BOND              : angle       1.65976 (    6)
  hydrogen bonds       : bond        0.03883 (  512)
  hydrogen bonds       : angle       3.25005 ( 1482)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 80
  time to evaluate  : 0.331 
Fit side-chains
REVERT: A  226 LEU cc_start: 0.8578 (pp) cc_final: 0.8034 (mm)
REVERT: A  287 TYR cc_start: 0.7504 (m-80) cc_final: 0.7186 (m-80)
REVERT: A  652 LYS cc_start: 0.8682 (mmtm) cc_final: 0.8266 (mptt)
REVERT: B  125 VAL cc_start: 0.9074 (OUTLIER) cc_final: 0.8860 (p)
REVERT: B  243 HIS cc_start: 0.8266 (OUTLIER) cc_final: 0.7569 (t-90)
REVERT: B  525 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8631 (mp)
REVERT: B  604 ASN cc_start: 0.6791 (p0) cc_final: 0.5880 (t0)
  outliers start: 19
  outliers final: 13
  residues processed: 92
  average time/residue: 0.0779
  time to fit residues: 10.9783
Evaluate side-chains
  94 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  243 HIS
Chi-restraints excluded: chain A residue  489 PHE
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  620 ASP
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  451 GLU
Chi-restraints excluded: chain B residue  489 PHE
Chi-restraints excluded: chain B residue  525 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 20 optimal weight:    0.0870
   chunk 7 optimal weight:    0.6980
   chunk 92 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 74 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 69 optimal weight:    7.9990
   chunk 27 optimal weight:    3.9990
   chunk 94 optimal weight:    3.9990
   overall best weight:    1.9564

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

Flipped N/Q/H residues before XYZ refinement:
A 283 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.107352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.090606 restraints weight = 16769.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 1.97
r_work: 0.3076 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2956
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2956 r_free = 0.2956    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2956 r_free = 0.2956    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2956
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8640
moved from start:          0.4217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9404  Z= 0.175
  Angle     :  0.555  11.601  12759  Z= 0.279
  Chirality :  0.040   0.143   1467
  Planarity :  0.003   0.029   1542
  Dihedral  :  9.298  85.462   1645
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.73 %
    Favored  : 84.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.68 (0.26), residues: 1128
  helix:  2.42 (0.19), residues: 694
  sheet:  0.18 (0.70), residues: 50
  loop : -1.30 (0.34), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 163 
 TYR   0.011   0.001   TYR A 336 
 PHE   0.013   0.001   PHE B 432 
 TRP   0.010   0.001   TRP B 379 
 HIS   0.005   0.001   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 9401)
  covalent geometry    : angle       0.55314 (12753)
  SS BOND              : bond        0.00785 (    3)
  SS BOND              : angle       1.88836 (    6)
  hydrogen bonds       : bond        0.04588 (  512)
  hydrogen bonds       : angle       3.36467 ( 1482)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2335.02 seconds
wall clock time: 40 minutes 39.51 seconds (2439.51 seconds total)