Starting phenix.real_space_refine
on Fri Mar  6 01:21:37 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7krj_23004/03_2026/7krj_23004_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7krj_23004/03_2026/7krj_23004.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7krj_23004/03_2026/7krj_23004.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7krj_23004/03_2026/7krj_23004.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7krj_23004/03_2026/7krj_23004_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7krj_23004/03_2026/7krj_23004_trim.cif"
  }
  resolution = 2.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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: 8
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      74      5.16       5
     C    8528      2.51       5
     N    2255      2.21       5
     O    2593      1.98       5
     F       1      1.80       5
     H   13407      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 75 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: 26866
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 10240
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 627, 10240
          Classifications: {'peptide': 627}
          Link IDs: {'CIS': 4, 'PTRANS': 15, 'TRANS': 607}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 10240
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 627, 10240
          Classifications: {'peptide': 627}
          Link IDs: {'CIS': 2, 'PTRANS': 15, 'TRANS': 609}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2122
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 133, 2122
          Classifications: {'peptide': 133}
          Modifications used: {'NH3': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 128}
    Chain: "D"
      Number of atoms: 4172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 4172
          Classifications: {'peptide': 255}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 243}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'DEX': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.08, per 1000 atoms: 0.15
  Number of scatterers: 26866
  At special positions: 0
  Unit cell: (136.105, 114.395, 95.19, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     S      74     16.00
     P       6     15.00
     Mg      2     11.99
     F       1      9.00
     O    2593      8.00
     N    2255      7.00
     C    8528      6.00
     H   13407      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 2.10
  Conformation dependent library (CDL) restraints added in 708.9 milliseconds
  

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3138

  Finding SS restraints...
    Secondary structure from input PDB file:
      67 helices and 13 sheets defined
      46.9% alpha, 15.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 36
    Processing helix  chain 'A' and resid 42 through 63
      removed outlier: 3.712A  pdb=" N   ARG A  46 " --> pdb=" O   GLU A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 65
      No H-bonds generated for 'chain 'A' and resid 64 through 65'
    Processing helix  chain 'A' and resid 66 through 71
    Processing helix  chain 'A' and resid 99 through 108
    Processing helix  chain 'A' and resid 113 through 121
    Processing helix  chain 'A' and resid 136 through 144
    Processing helix  chain 'A' and resid 194 through 198
    Processing helix  chain 'A' and resid 199 through 212
      removed outlier: 3.940A  pdb=" N   GLN A 212 " --> pdb=" O   LYS A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 304
    Processing helix  chain 'A' and resid 305 through 318
    Processing helix  chain 'A' and resid 379 through 383
    Processing helix  chain 'A' and resid 407 through 431
      removed outlier: 3.927A  pdb=" N   VAL A 411 " --> pdb=" O   LYS A 407 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ASP A 430 " --> pdb=" O   GLU A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 452
      removed outlier: 6.459A  pdb=" N   LYS A 443 " --> pdb=" O   GLU A 439 " (cutoff:3.500A)
      removed outlier: 6.056A  pdb=" N   ASN A 444 " --> pdb=" O   GLN A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 461
      removed outlier: 3.733A  pdb=" N   GLU A 461 " --> pdb=" O   LYS A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 483
    Processing helix  chain 'A' and resid 498 through 504
    Processing helix  chain 'A' and resid 505 through 507
      No H-bonds generated for 'chain 'A' and resid 505 through 507'
    Processing helix  chain 'A' and resid 508 through 514
    Processing helix  chain 'A' and resid 525 through 530
    Processing helix  chain 'A' and resid 554 through 568
    Processing helix  chain 'A' and resid 568 through 579
    Processing helix  chain 'A' and resid 607 through 615
    Processing helix  chain 'A' and resid 621 through 625
    Processing helix  chain 'A' and resid 640 through 653
    Processing helix  chain 'A' and resid 656 through 674
      removed outlier: 3.511A  pdb=" N   LEU A 672 " --> pdb=" O   GLU A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 696
      removed outlier: 4.057A  pdb=" N   HIS A 684 " --> pdb=" O   ASP A 680 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 37
      removed outlier: 3.802A  pdb=" N   PHE B  37 " --> pdb=" O   ILE B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 42
      No H-bonds generated for 'chain 'B' and resid 40 through 42'
    Processing helix  chain 'B' and resid 43 through 63
    Processing helix  chain 'B' and resid 64 through 65
      No H-bonds generated for 'chain 'B' and resid 64 through 65'
    Processing helix  chain 'B' and resid 66 through 71
    Processing helix  chain 'B' and resid 99 through 108
      removed outlier: 3.564A  pdb=" N   GLY B 108 " --> pdb=" O   ILE B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 122
    Processing helix  chain 'B' and resid 137 through 143
    Processing helix  chain 'B' and resid 195 through 198
    Processing helix  chain 'B' and resid 199 through 212
      removed outlier: 4.191A  pdb=" N   GLN B 212 " --> pdb=" O   LYS B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 300 through 304
    Processing helix  chain 'B' and resid 305 through 318
    Processing helix  chain 'B' and resid 379 through 383
    Processing helix  chain 'B' and resid 406 through 428
      removed outlier: 3.583A  pdb=" N   LYS B 410 " --> pdb=" O   SER B 406 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   VAL B 411 " --> pdb=" O   LYS B 407 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 430 through 452
      removed outlier: 3.619A  pdb=" N   GLN B 440 " --> pdb=" O   LYS B 436 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   LYS B 443 " --> pdb=" O   GLU B 439 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   ASN B 444 " --> pdb=" O   GLN B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 460
    Processing helix  chain 'B' and resid 461 through 463
      No H-bonds generated for 'chain 'B' and resid 461 through 463'
    Processing helix  chain 'B' and resid 476 through 483
      removed outlier: 3.633A  pdb=" N   ARG B 483 " --> pdb=" O   ASP B 479 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 498 through 504
    Processing helix  chain 'B' and resid 505 through 507
      No H-bonds generated for 'chain 'B' and resid 505 through 507'
    Processing helix  chain 'B' and resid 508 through 514
    Processing helix  chain 'B' and resid 525 through 531
      removed outlier: 3.834A  pdb=" N   GLN B 531 " --> pdb=" O   GLU B 527 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 554 through 568
    Processing helix  chain 'B' and resid 568 through 580
    Processing helix  chain 'B' and resid 607 through 615
    Processing helix  chain 'B' and resid 621 through 625
    Processing helix  chain 'B' and resid 640 through 653
    Processing helix  chain 'B' and resid 656 through 674
    Processing helix  chain 'B' and resid 680 through 696
      removed outlier: 3.673A  pdb=" N   HIS B 684 " --> pdb=" O   ASP B 680 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 103 through 106
    Processing helix  chain 'C' and resid 119 through 131
    Processing helix  chain 'D' and resid 531 through 540
    Processing helix  chain 'D' and resid 555 through 581
      removed outlier: 3.524A  pdb=" N   ALA D 580 " --> pdb=" O   LYS D 576 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ILE D 581 " --> pdb=" O   TRP D 577 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 583 through 587
    Processing helix  chain 'D' and resid 588 through 614
      removed outlier: 5.205A  pdb=" N   MET D 601 " --> pdb=" O   GLN D 597 " (cutoff:3.500A)
      removed outlier: 5.780A  pdb=" N   SER D 602 " --> pdb=" O   TYR D 598 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 642 through 656
    Processing helix  chain 'D' and resid 659 through 672
      removed outlier: 3.748A  pdb=" N   LEU D 672 " --> pdb=" O   THR D 668 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 682 through 703
    Processing helix  chain 'D' and resid 707 through 742
      removed outlier: 4.173A  pdb=" N   HIS D 726 " --> pdb=" O   LEU D 722 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   GLU D 727 " --> pdb=" O   ASP D 723 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 750 through 765
      Proline residue:  D 762  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 21
      removed outlier: 6.008A  pdb=" N   GLU B 223 " --> pdb=" O   PRO B  82 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 284 through 289
      removed outlier: 6.313A  pdb=" N   GLU A 223 " --> pdb=" O   PRO A  82 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 110
    Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 331
      removed outlier: 6.014A  pdb=" N   VAL A 365 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 5.277A  pdb=" N   PHE A 369 " --> pdb=" O   VAL A 365 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 466 through 467
      removed outlier: 4.222A  pdb=" N   TYR A 466 " --> pdb=" O   TYR A 520 " (cutoff:3.500A)
      removed outlier: 6.062A  pdb=" N   ILE A 491 " --> pdb=" O   VAL A 542 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 586 through 588
      removed outlier: 7.034A  pdb=" N   VAL A 587 " --> pdb=" O   ILE A 636 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 323 through 331
      removed outlier: 6.598A  pdb=" N   VAL B 343 " --> pdb=" O   LEU B 324 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   VAL B 326 " --> pdb=" O   LEU B 341 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   LEU B 341 " --> pdb=" O   VAL B 326 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   HIS B 328 " --> pdb=" O   ALA B 339 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   ALA B 339 " --> pdb=" O   HIS B 328 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   SER B 330 " --> pdb=" O   PHE B 337 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   PHE B 337 " --> pdb=" O   SER B 330 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   LEU B 363 " --> pdb=" O   ILE B 370 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 466 through 467
      removed outlier: 4.212A  pdb=" N   TYR B 466 " --> pdb=" O   TYR B 520 " (cutoff:3.500A)
      removed outlier: 6.180A  pdb=" N   ILE B 491 " --> pdb=" O   VAL B 542 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 585 through 588
      removed outlier: 4.266A  pdb=" N   LYS B 585 " --> pdb=" O   LYS B 632 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 68
      removed outlier: 6.847A  pdb=" N   ASP C  63 " --> pdb=" O   ARG C  78 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   ARG C  78 " --> pdb=" O   ASP C  63 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 24 through 32
      removed outlier: 4.552A  pdb=" N   VAL C  27 " --> pdb=" O   SER C  39 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   SER C  39 " --> pdb=" O   VAL C  27 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   VAL C  29 " --> pdb=" O   THR C  37 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   THR C  37 " --> pdb=" O   VAL C  29 " (cutoff:3.500A)
      removed outlier: 4.883A  pdb=" N   PHE C  31 " --> pdb=" O   LYS C  35 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   LYS C  35 " --> pdb=" O   PHE C  31 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 621 through 622
    Processing sheet with id=AB4, first strand: chain 'D' and resid 674 through 676

    667 hydrogen bonds defined for protein.
    1833 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: 5.74

  Time building geometry restraints manager: 3.01 seconds

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

  Histogram of bond lengths:
        0.95 -     1.13: 13383
        1.13 -     1.30: 2456
        1.30 -     1.48: 5699
        1.48 -     1.65: 5445
        1.65 -     1.83: 125
  Bond restraints: 27108
  Sorted by residual:
  bond pdb=" NE1 TRP C 109 "
       pdb=" HE1 TRP C 109 "
    ideal  model  delta    sigma   weight residual
    0.860  1.057 -0.197 2.00e-02 2.50e+03 9.72e+01
  bond pdb=" C4  ATP A 801 "
       pdb=" C5  ATP A 801 "
    ideal  model  delta    sigma   weight residual
    1.388  1.486 -0.098 1.00e-02 1.00e+04 9.69e+01
  bond pdb=" C4  ATP B 801 "
       pdb=" C5  ATP B 801 "
    ideal  model  delta    sigma   weight residual
    1.388  1.486 -0.098 1.00e-02 1.00e+04 9.58e+01
  bond pdb=" C5  ATP B 801 "
       pdb=" C6  ATP B 801 "
    ideal  model  delta    sigma   weight residual
    1.409  1.503 -0.094 1.00e-02 1.00e+04 8.87e+01
  bond pdb=" NE2 GLN D 683 "
       pdb="HE22 GLN D 683 "
    ideal  model  delta    sigma   weight residual
    0.860  1.047 -0.187 2.00e-02 2.50e+03 8.72e+01
  ... (remaining 27103 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    10.15: 49020
       10.15 -    20.30: 40
       20.30 -    30.45: 5
       30.45 -    40.61: 7
       40.61 -    50.76: 6
  Bond angle restraints: 49078
  Sorted by residual:
  angle pdb=" C   ARG B 366 "
        pdb=" N   ARG B 367 "
        pdb=" CA  ARG B 367 "
      ideal   model   delta    sigma   weight residual
     123.47  154.85  -31.38 1.53e+00 4.27e-01 4.21e+02
  angle pdb=" C   VAL B 365 "
        pdb=" N   ARG B 366 "
        pdb=" CA  ARG B 366 "
      ideal   model   delta    sigma   weight residual
     122.07  148.10  -26.03 1.43e+00 4.89e-01 3.31e+02
  angle pdb=" C   VAL A 365 "
        pdb=" N   ARG A 366 "
        pdb=" CA  ARG A 366 "
      ideal   model   delta    sigma   weight residual
     122.36  147.84  -25.48 1.42e+00 4.96e-01 3.22e+02
  angle pdb=" C   LEU B 107 "
        pdb=" N   GLY B 108 "
        pdb=" CA  GLY B 108 "
      ideal   model   delta    sigma   weight residual
     120.79  150.63  -29.84 1.75e+00 3.27e-01 2.91e+02
  angle pdb=" C   VAL B 365 "
        pdb=" N   ARG B 366 "
        pdb=" H   ARG B 366 "
      ideal   model   delta    sigma   weight residual
     124.11   73.36   50.76 3.00e+00 1.11e-01 2.86e+02
  ... (remaining 49073 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.14: 12130
       17.14 -    34.27: 363
       34.27 -    51.41: 148
       51.41 -    68.55: 65
       68.55 -    85.69: 15
  Dihedral angle restraints: 12721
    sinusoidal: 7083
      harmonic: 5638
  Sorted by residual:
  dihedral pdb=" CA  PRO B 348 "
           pdb=" C   PRO B 348 "
           pdb=" N   PHE B 349 "
           pdb=" CA  PHE B 349 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.56  -26.44     0      5.00e+00 4.00e-02 2.80e+01
  dihedral pdb=" CA  PHE A 352 "
           pdb=" C   PHE A 352 "
           pdb=" N   GLU A 353 "
           pdb=" CA  GLU A 353 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.53  -23.47     0      5.00e+00 4.00e-02 2.20e+01
  dihedral pdb=" N   GLU A  25 "
           pdb=" C   GLU A  25 "
           pdb=" CA  GLU A  25 "
           pdb=" CB  GLU A  25 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  132.87  -10.07     0      2.50e+00 1.60e-01 1.62e+01
  ... (remaining 12718 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.146: 1731
       0.146 -    0.291: 297
       0.291 -    0.437: 13
       0.437 -    0.583: 2
       0.583 -    0.728: 1
  Chirality restraints: 2044
  Sorted by residual:
  chirality pdb=" C8  DEX D 801 "
            pdb=" C14 DEX D 801 "
            pdb=" C7  DEX D 801 "
            pdb=" C9  DEX D 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.68    1.95    0.73 2.00e-01 2.50e+01 1.33e+01
  chirality pdb=" CB  ILE B 378 "
            pdb=" CA  ILE B 378 "
            pdb=" CG1 ILE B 378 "
            pdb=" CG2 ILE B 378 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.08    0.56 2.00e-01 2.50e+01 7.95e+00
  chirality pdb=" CA  GLU A  25 "
            pdb=" N   GLU A  25 "
            pdb=" C   GLU A  25 "
            pdb=" CB  GLU A  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.00    0.51 2.00e-01 2.50e+01 6.54e+00
  ... (remaining 2041 not shown)

  Planarity restraints: 3934
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 350 "   -0.085 2.00e-02 2.50e+03   1.62e-01 2.61e+02
        pdb=" N   LEU B 351 "    0.278 2.00e-02 2.50e+03
        pdb=" CA  LEU B 351 "   -0.073 2.00e-02 2.50e+03
        pdb=" H   LEU B 351 "   -0.120 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 380 "   -0.086 2.00e-02 2.50e+03   1.59e-01 2.53e+02
        pdb=" N   TYR A 381 "    0.275 2.00e-02 2.50e+03
        pdb=" CA  TYR A 381 "   -0.076 2.00e-02 2.50e+03
        pdb=" H   TYR A 381 "   -0.113 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 351 "    0.086 2.00e-02 2.50e+03   1.54e-01 2.37e+02
        pdb=" N   PHE B 352 "   -0.266 2.00e-02 2.50e+03
        pdb=" CA  PHE B 352 "    0.079 2.00e-02 2.50e+03
        pdb=" H   PHE B 352 "    0.101 2.00e-02 2.50e+03
  ... (remaining 3931 not shown)

  Histogram of nonbonded interaction distances:
        1.14 -     1.83: 150
        1.83 -     2.53: 23050
        2.53 -     3.22: 84067
        3.22 -     3.91: 108107
        3.91 -     4.60: 171788
  Nonbonded interactions: 387162
  Sorted by model distance:
  nonbonded pdb=" H   PHE B 349 "
            pdb=" H   ASP B 350 "
     model   vdw
     1.143 2.100
  nonbonded pdb=" H   TYR A 381 "
            pdb=" H   LEU A 382 "
     model   vdw
     1.211 2.100
  nonbonded pdb=" H   TRP B 320 "
            pdb=" H   GLU B 321 "
     model   vdw
     1.224 2.100
  nonbonded pdb=" H   GLU A 353 "
            pdb=" H   ASN A 354 "
     model   vdw
     1.261 2.100
  nonbonded pdb=" H   ARG D 611 "
            pdb=" H   SER D 612 "
     model   vdw
     1.283 2.100
  ... (remaining 387157 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'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.640
  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:             0.150
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.080
  Set scattering table:                    0.070
  Process input model:                     23.650
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.040
  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:6.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8798
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      :  0.026   0.169  13701  Z= 1.444
  Angle     :  1.839  31.381  18463  Z= 1.234
  Chirality :  0.107   0.728   2044
  Planarity :  0.012   0.145   2341
  Dihedral  : 11.322  85.686   5372
  Min Nonbonded Distance : 1.787

Molprobity Statistics.
  All-atom Clashscore : 0.78
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  1.90 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.27 %
    Favored  : 99.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.50 %
    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:  0.71 (0.20), residues: 1630
  helix:  0.12 (0.17), residues: 688
  sheet:  1.41 (0.30), residues: 285
  loop :  0.68 (0.24), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 591 
 TYR   0.057   0.009   TYR D 613 
 PHE   0.036   0.005   PHE D 606 
 TRP   0.047   0.009   TRP B 297 
 HIS   0.008   0.002   HIS D 775 

Details of bonding type rmsd
  covalent geometry    : bond        0.02633 (13701)
  covalent geometry    : angle       1.83890 (18463)
  hydrogen bonds       : bond        0.16252 (  667)
  hydrogen bonds       : angle       6.83547 ( 1833)

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 204
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 MET cc_start: 0.9064 (mtm) cc_final: 0.8844 (mtm)
REVERT: A  628 MET cc_start: 0.7791 (mmm) cc_final: 0.7367 (mmt)
REVERT: B  357 LYS cc_start: 0.7706 (tptt) cc_final: 0.7410 (tttp)
REVERT: D  606 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.8267 (m-10)
  outliers start: 1
  outliers final: 1
  residues processed: 205
  average time/residue: 1.7468
  time to fit residues: 382.7459
Evaluate side-chains
  109 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 107
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  472 ASP
Chi-restraints excluded: chain D residue  606 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    0.8980
   chunk 149 optimal weight:    0.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
D 707 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.082316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.063304 restraints weight = 91888.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 2.64
r_work: 0.3019 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2904 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8828
moved from start:          0.2480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  13701  Z= 0.176
  Angle     :  0.767  20.156  18463  Z= 0.439
  Chirality :  0.044   0.191   2044
  Planarity :  0.004   0.044   2341
  Dihedral  :  8.589 103.562   1926
  Min Nonbonded Distance : 1.864

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  6.96 %
    Favored  : 92.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.50 %
    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:  1.08 (0.20), residues: 1630
  helix:  1.03 (0.19), residues: 702
  sheet:  0.91 (0.30), residues: 290
  loop :  0.46 (0.25), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 714 
 TYR   0.023   0.002   TYR D 735 
 PHE   0.021   0.002   PHE C 120 
 TRP   0.012   0.001   TRP B 162 
 HIS   0.007   0.001   HIS D 726 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (13701)
  covalent geometry    : angle       0.76669 (18463)
  hydrogen bonds       : bond        0.06963 (  667)
  hydrogen bonds       : angle       5.21606 ( 1833)

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 128
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  180 MET cc_start: 0.8796 (mtp) cc_final: 0.8525 (mtp)
REVERT: B  357 LYS cc_start: 0.7723 (tptt) cc_final: 0.7328 (tttp)
REVERT: C   78 ARG cc_start: 0.8923 (tpt-90) cc_final: 0.8673 (tpt170)
  outliers start: 13
  outliers final: 5
  residues processed: 137
  average time/residue: 1.5178
  time to fit residues: 224.6850
Evaluate side-chains
  108 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 103
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  378 ILE
Chi-restraints excluded: chain B residue  472 ASP
Chi-restraints excluded: chain B residue  660 LYS
Chi-restraints excluded: chain D residue  606 PHE
Chi-restraints excluded: chain D residue  626 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 160 optimal weight:    5.9990
   chunk 81 optimal weight:    0.0870
   chunk 147 optimal weight:    0.9990
   chunk 161 optimal weight:    3.9990
   chunk 96 optimal weight:    1.9990
   chunk 102 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 110 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   overall best weight:    1.8166

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

Flipped N/Q/H residues before XYZ refinement:
A 531 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.081294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.062228 restraints weight = 91605.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3107 rms_B_bonded: 2.63
r_work: 0.2991 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2882 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8858
moved from start:          0.2949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  13701  Z= 0.183
  Angle     :  0.668  19.912  18463  Z= 0.381
  Chirality :  0.041   0.168   2044
  Planarity :  0.003   0.039   2341
  Dihedral  :  7.968  87.550   1926
  Min Nonbonded Distance : 1.878

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  8.70 %
    Favored  : 90.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.50 %
    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:  1.10 (0.21), residues: 1630
  helix:  1.32 (0.19), residues: 706
  sheet:  0.55 (0.30), residues: 293
  loop :  0.29 (0.25), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 612 
 TYR   0.022   0.002   TYR D 735 
 PHE   0.016   0.001   PHE C  47 
 TRP   0.014   0.001   TRP B 162 
 HIS   0.005   0.001   HIS D 726 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 (13701)
  covalent geometry    : angle       0.66771 (18463)
  hydrogen bonds       : bond        0.05724 (  667)
  hydrogen bonds       : angle       4.72626 ( 1833)

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.707 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  461 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8731 (mt-10)
REVERT: B  357 LYS cc_start: 0.7888 (tptt) cc_final: 0.7551 (tttp)
REVERT: C   18 GLU cc_start: 0.8866 (tt0) cc_final: 0.8488 (tm-30)
REVERT: C   78 ARG cc_start: 0.8981 (tpt-90) cc_final: 0.8781 (tpt170)
REVERT: D  554 ASP cc_start: 0.7382 (p0) cc_final: 0.6771 (p0)
  outliers start: 11
  outliers final: 7
  residues processed: 114
  average time/residue: 1.5654
  time to fit residues: 192.8202
Evaluate side-chains
  111 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 103
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  322 ASP
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  461 GLU
Chi-restraints excluded: chain B residue  378 ILE
Chi-restraints excluded: chain B residue  472 ASP
Chi-restraints excluded: chain B residue  627 TYR
Chi-restraints excluded: chain B residue  660 LYS
Chi-restraints excluded: chain D residue  678 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 156 optimal weight:    5.9990
   chunk 108 optimal weight:    3.9990
   chunk 115 optimal weight:    0.0670
   chunk 69 optimal weight:    4.9990
   chunk 152 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 149 optimal weight:    0.9980
   chunk 71 optimal weight:    0.2980
   chunk 63 optimal weight:    1.9990
   chunk 133 optimal weight:    0.7980
   overall best weight:    0.8320

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 707 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.082148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.063211 restraints weight = 90716.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 2.64
r_work: 0.3014 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2901 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8838
moved from start:          0.3243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  13701  Z= 0.120
  Angle     :  0.604  19.934  18463  Z= 0.342
  Chirality :  0.040   0.163   2044
  Planarity :  0.003   0.033   2341
  Dihedral  :  7.141  80.558   1924
  Min Nonbonded Distance : 1.888

Molprobity Statistics.
  All-atom Clashscore : 2.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  8.90 %
    Favored  : 90.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.50 %
    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:  1.22 (0.21), residues: 1630
  helix:  1.58 (0.20), residues: 705
  sheet:  0.55 (0.30), residues: 277
  loop :  0.20 (0.25), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 714 
 TYR   0.018   0.001   TYR D 735 
 PHE   0.009   0.001   PHE D 774 
 TRP   0.012   0.001   TRP B 162 
 HIS   0.003   0.001   HIS B 684 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (13701)
  covalent geometry    : angle       0.60376 (18463)
  hydrogen bonds       : bond        0.04785 (  667)
  hydrogen bonds       : angle       4.38941 ( 1833)

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 110
  time to evaluate  : 0.677 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  133 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8515 (pt0)
REVERT: B  180 MET cc_start: 0.8791 (mtp) cc_final: 0.8446 (mtp)
REVERT: B  357 LYS cc_start: 0.7858 (tptt) cc_final: 0.7413 (tttp)
REVERT: C   18 GLU cc_start: 0.8891 (tt0) cc_final: 0.8517 (tm-30)
REVERT: D  557 TRP cc_start: 0.7758 (p-90) cc_final: 0.7506 (p-90)
  outliers start: 9
  outliers final: 8
  residues processed: 113
  average time/residue: 1.5549
  time to fit residues: 189.3579
Evaluate side-chains
  106 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain B residue   93 ASP
Chi-restraints excluded: chain B residue  133 GLN
Chi-restraints excluded: chain B residue  378 ILE
Chi-restraints excluded: chain B residue  472 ASP
Chi-restraints excluded: chain B residue  627 TYR
Chi-restraints excluded: chain B residue  660 LYS
Chi-restraints excluded: chain C residue   47 PHE
Chi-restraints excluded: chain C residue  117 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 125 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   chunk 120 optimal weight:    6.9990
   chunk 79 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 127 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 123 optimal weight:    0.5980
   chunk 137 optimal weight:    4.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 707 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.081800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.062848 restraints weight = 90821.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 2.63
r_work: 0.3010 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2897 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8844
moved from start:          0.3436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13701  Z= 0.124
  Angle     :  0.588  19.805  18463  Z= 0.333
  Chirality :  0.039   0.161   2044
  Planarity :  0.003   0.034   2341
  Dihedral  :  6.938  86.053   1924
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 2.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  8.43 %
    Favored  : 90.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.50 %
    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:  1.25 (0.21), residues: 1630
  helix:  1.72 (0.20), residues: 706
  sheet:  0.41 (0.30), residues: 279
  loop :  0.14 (0.25), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 346 
 TYR   0.017   0.001   TYR D 735 
 PHE   0.008   0.001   PHE A 221 
 TRP   0.011   0.001   TRP B 162 
 HIS   0.004   0.001   HIS A 323 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (13701)
  covalent geometry    : angle       0.58836 (18463)
  hydrogen bonds       : bond        0.04504 (  667)
  hydrogen bonds       : angle       4.27071 ( 1833)

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  133 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8514 (pt0)
REVERT: B  222 VAL cc_start: 0.9147 (t) cc_final: 0.8893 (m)
REVERT: B  357 LYS cc_start: 0.7838 (tptt) cc_final: 0.7459 (tttp)
REVERT: B  393 ASP cc_start: 0.8593 (t0) cc_final: 0.8393 (t0)
REVERT: C   18 GLU cc_start: 0.8905 (tt0) cc_final: 0.8465 (tm-30)
REVERT: C  130 MET cc_start: 0.5347 (mmp) cc_final: 0.4629 (mmt)
REVERT: D  557 TRP cc_start: 0.7785 (p-90) cc_final: 0.7548 (p-90)
  outliers start: 13
  outliers final: 7
  residues processed: 109
  average time/residue: 1.5992
  time to fit residues: 187.6851
Evaluate side-chains
  103 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain B residue  133 GLN
Chi-restraints excluded: chain B residue  378 ILE
Chi-restraints excluded: chain B residue  627 TYR
Chi-restraints excluded: chain B residue  660 LYS
Chi-restraints excluded: chain C residue   47 PHE
Chi-restraints excluded: chain C residue  117 MET
Chi-restraints excluded: chain C residue  123 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 116 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 134 optimal weight:    2.9990
   chunk 123 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   chunk 57 optimal weight:    6.9990
   chunk 55 optimal weight:    9.9990
   chunk 22 optimal weight:    0.5980
   chunk 76 optimal weight:    6.9990
   overall best weight:    2.5188

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

Flipped N/Q/H residues before XYZ refinement:
** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.079403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.060557 restraints weight = 91360.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 2.61
r_work: 0.2953 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2838 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8902
moved from start:          0.3588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070  13701  Z= 0.216
  Angle     :  0.633  19.783  18463  Z= 0.358
  Chirality :  0.041   0.186   2044
  Planarity :  0.004   0.041   2341
  Dihedral  :  7.204  85.321   1922
  Min Nonbonded Distance : 1.871

Molprobity Statistics.
  All-atom Clashscore : 2.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  9.17 %
    Favored  : 89.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.50 %
    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:  1.09 (0.21), residues: 1630
  helix:  1.67 (0.20), residues: 706
  sheet:  0.35 (0.30), residues: 279
  loop : -0.08 (0.24), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 346 
 TYR   0.019   0.002   TYR D 735 
 PHE   0.011   0.001   PHE D 740 
 TRP   0.012   0.001   TRP A 162 
 HIS   0.007   0.001   HIS B 633 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 (13701)
  covalent geometry    : angle       0.63335 (18463)
  hydrogen bonds       : bond        0.05035 (  667)
  hydrogen bonds       : angle       4.38609 ( 1833)

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.714 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  222 VAL cc_start: 0.9131 (t) cc_final: 0.8873 (m)
REVERT: B  357 LYS cc_start: 0.7802 (tptt) cc_final: 0.7384 (tttp)
REVERT: C   18 GLU cc_start: 0.8963 (tt0) cc_final: 0.8474 (tm-30)
REVERT: C  130 MET cc_start: 0.5389 (mmp) cc_final: 0.4617 (mmt)
REVERT: D  557 TRP cc_start: 0.7867 (p-90) cc_final: 0.7654 (p-90)
  outliers start: 14
  outliers final: 6
  residues processed: 104
  average time/residue: 1.4703
  time to fit residues: 166.5560
Evaluate side-chains
  95 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain B residue  378 ILE
Chi-restraints excluded: chain B residue  627 TYR
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  117 MET
Chi-restraints excluded: chain C residue  123 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 99 optimal weight:    2.9990
   chunk 154 optimal weight:    2.9990
   chunk 124 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 125 optimal weight:    2.9990
   chunk 106 optimal weight:    3.9990
   chunk 149 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 120 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.080141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.061173 restraints weight = 91134.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.3083 rms_B_bonded: 2.61
r_work: 0.2969 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2855 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8886
moved from start:          0.3730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13701  Z= 0.155
  Angle     :  0.601  19.730  18463  Z= 0.339
  Chirality :  0.040   0.173   2044
  Planarity :  0.003   0.036   2341
  Dihedral  :  6.791  88.797   1922
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  9.84 %
    Favored  : 89.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.50 %
    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:  1.09 (0.21), residues: 1630
  helix:  1.76 (0.20), residues: 706
  sheet:  0.22 (0.29), residues: 283
  loop : -0.11 (0.24), residues: 641

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 346 
 TYR   0.018   0.001   TYR D 735 
 PHE   0.008   0.001   PHE D 774 
 TRP   0.009   0.001   TRP A 162 
 HIS   0.005   0.001   HIS B 633 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (13701)
  covalent geometry    : angle       0.60105 (18463)
  hydrogen bonds       : bond        0.04641 (  667)
  hydrogen bonds       : angle       4.27557 ( 1833)

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.740 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  413 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.7946 (ttt90)
REVERT: B  222 VAL cc_start: 0.9133 (t) cc_final: 0.8880 (m)
REVERT: B  357 LYS cc_start: 0.7841 (tptt) cc_final: 0.7360 (tttp)
REVERT: C   18 GLU cc_start: 0.8936 (tt0) cc_final: 0.8461 (tm-30)
REVERT: C  130 MET cc_start: 0.5302 (mmp) cc_final: 0.4683 (mmt)
REVERT: D  557 TRP cc_start: 0.7816 (p-90) cc_final: 0.7607 (p-90)
  outliers start: 12
  outliers final: 6
  residues processed: 101
  average time/residue: 1.4055
  time to fit residues: 154.8210
Evaluate side-chains
  97 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  413 ARG
Chi-restraints excluded: chain B residue  378 ILE
Chi-restraints excluded: chain B residue  627 TYR
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  117 MET
Chi-restraints excluded: chain C residue  123 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 117 optimal weight:    7.9990
   chunk 136 optimal weight:    4.9990
   chunk 139 optimal weight:    8.9990
   chunk 43 optimal weight:    3.9990
   chunk 140 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 89 optimal weight:    2.9990
   chunk 135 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.079528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.060527 restraints weight = 91763.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3069 rms_B_bonded: 2.63
r_work: 0.2953 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2842 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8900
moved from start:          0.3834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  13701  Z= 0.189
  Angle     :  0.618  19.744  18463  Z= 0.348
  Chirality :  0.040   0.172   2044
  Planarity :  0.003   0.065   2341
  Dihedral  :  6.815  85.657   1922
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 2.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 10.31 %
    Favored  : 89.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.50 %
    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:  1.04 (0.21), residues: 1630
  helix:  1.75 (0.20), residues: 703
  sheet:  0.18 (0.29), residues: 283
  loop : -0.16 (0.24), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 201 
 TYR   0.019   0.002   TYR D 735 
 PHE   0.009   0.001   PHE D 740 
 TRP   0.010   0.001   TRP A 162 
 HIS   0.006   0.001   HIS B 633 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 (13701)
  covalent geometry    : angle       0.61759 (18463)
  hydrogen bonds       : bond        0.04736 (  667)
  hydrogen bonds       : angle       4.30809 ( 1833)

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  413 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.7968 (ttt90)
REVERT: B  222 VAL cc_start: 0.9136 (t) cc_final: 0.8881 (m)
REVERT: C   18 GLU cc_start: 0.8955 (tt0) cc_final: 0.8467 (tm-30)
  outliers start: 10
  outliers final: 6
  residues processed: 98
  average time/residue: 1.4008
  time to fit residues: 150.4166
Evaluate side-chains
  98 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  413 ARG
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain B residue  378 ILE
Chi-restraints excluded: chain B residue  627 TYR
Chi-restraints excluded: chain C residue  117 MET
Chi-restraints excluded: chain C residue  123 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 160 optimal weight:    0.8980
   chunk 120 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 131 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 101 optimal weight:    2.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.079634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.060631 restraints weight = 91115.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.3072 rms_B_bonded: 2.63
r_work: 0.2957 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2843 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8898
moved from start:          0.3942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  13701  Z= 0.173
  Angle     :  0.614  19.660  18463  Z= 0.345
  Chirality :  0.040   0.169   2044
  Planarity :  0.003   0.047   2341
  Dihedral  :  6.657  82.561   1922
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 10.64 %
    Favored  : 88.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.50 %
    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:  1.06 (0.21), residues: 1630
  helix:  1.79 (0.20), residues: 703
  sheet:  0.15 (0.29), residues: 283
  loop : -0.18 (0.24), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 201 
 TYR   0.019   0.002   TYR D 735 
 PHE   0.008   0.001   PHE C 120 
 TRP   0.020   0.001   TRP D 557 
 HIS   0.005   0.001   HIS B 633 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 (13701)
  covalent geometry    : angle       0.61426 (18463)
  hydrogen bonds       : bond        0.04625 (  667)
  hydrogen bonds       : angle       4.27117 ( 1833)

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.567 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  413 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.7948 (ttt90)
REVERT: B  222 VAL cc_start: 0.9132 (t) cc_final: 0.8875 (m)
REVERT: C   18 GLU cc_start: 0.8950 (tt0) cc_final: 0.8470 (tm-30)
REVERT: C  130 MET cc_start: 0.5532 (mmp) cc_final: 0.4693 (mmm)
  outliers start: 12
  outliers final: 6
  residues processed: 100
  average time/residue: 1.3528
  time to fit residues: 148.3588
Evaluate side-chains
  98 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  413 ARG
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain B residue  378 ILE
Chi-restraints excluded: chain B residue  627 TYR
Chi-restraints excluded: chain C residue  117 MET
Chi-restraints excluded: chain C residue  123 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 107 optimal weight:    0.4980
   chunk 0 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 142 optimal weight:    0.9990
   chunk 88 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    2.0988

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

Flipped N/Q/H residues before XYZ refinement:
** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.079386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.060381 restraints weight = 91878.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 2.63
r_work: 0.2954 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2842 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8898
moved from start:          0.4004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  13701  Z= 0.183
  Angle     :  0.617  19.672  18463  Z= 0.346
  Chirality :  0.040   0.167   2044
  Planarity :  0.003   0.049   2341
  Dihedral  :  6.669  80.776   1922
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 10.84 %
    Favored  : 88.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.50 %
    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:  1.11 (0.21), residues: 1630
  helix:  1.90 (0.20), residues: 691
  sheet:  0.15 (0.29), residues: 283
  loop : -0.18 (0.24), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 346 
 TYR   0.019   0.002   TYR D 735 
 PHE   0.007   0.001   PHE C 120 
 TRP   0.027   0.001   TRP D 557 
 HIS   0.006   0.001   HIS B 633 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (13701)
  covalent geometry    : angle       0.61731 (18463)
  hydrogen bonds       : bond        0.04650 (  667)
  hydrogen bonds       : angle       4.27822 ( 1833)

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

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

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3260 Ramachandran restraints generated.
    1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  413 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.7943 (ttt90)
REVERT: B  222 VAL cc_start: 0.9131 (t) cc_final: 0.8879 (m)
REVERT: C   18 GLU cc_start: 0.8955 (tt0) cc_final: 0.8467 (tm-30)
REVERT: C  130 MET cc_start: 0.5501 (mmp) cc_final: 0.4687 (mmm)
  outliers start: 9
  outliers final: 5
  residues processed: 97
  average time/residue: 1.3158
  time to fit residues: 140.3900
Evaluate side-chains
  97 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 GLU
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  413 ARG
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain B residue  627 TYR
Chi-restraints excluded: chain C residue  123 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 122 optimal weight:    3.9990
   chunk 81 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 135 optimal weight:    9.9990
   chunk 103 optimal weight:    5.9990
   chunk 98 optimal weight:    1.9990
   chunk 105 optimal weight:    0.9980
   chunk 62 optimal weight:    3.9990
   chunk 152 optimal weight:    3.9990
   chunk 102 optimal weight:    2.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.079253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.060308 restraints weight = 91585.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3066 rms_B_bonded: 2.60
r_work: 0.2953 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2841 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8900
moved from start:          0.4038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  13701  Z= 0.190
  Angle     :  0.623  19.625  18463  Z= 0.349
  Chirality :  0.041   0.167   2044
  Planarity :  0.003   0.050   2341
  Dihedral  :  6.681  79.499   1922
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 10.84 %
    Favored  : 88.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.50 %
    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:  1.10 (0.21), residues: 1630
  helix:  1.90 (0.20), residues: 691
  sheet:  0.18 (0.29), residues: 281
  loop : -0.22 (0.24), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 346 
 TYR   0.020   0.002   TYR D 735 
 PHE   0.008   0.001   PHE D 740 
 TRP   0.037   0.002   TRP D 557 
 HIS   0.006   0.001   HIS B 633 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 (13701)
  covalent geometry    : angle       0.62342 (18463)
  hydrogen bonds       : bond        0.04674 (  667)
  hydrogen bonds       : angle       4.28690 ( 1833)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9744.64 seconds
wall clock time: 164 minutes 56.28 seconds (9896.28 seconds total)