Starting phenix.real_space_refine
on Wed Jan 22 19:49:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9chr_45599/01_2025/9chr_45599.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9chr_45599/01_2025/9chr_45599.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9chr_45599/01_2025/9chr_45599.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9chr_45599/01_2025/9chr_45599.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9chr_45599/01_2025/9chr_45599.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9chr_45599/01_2025/9chr_45599.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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
     S      48      5.16       5
     C    6292      2.51       5
     N    1568      2.21       5
     O    1600      1.98       5
     H    9596      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 19104
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4776
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 4776
          Classifications: {'peptide': 293}
          Link IDs: {'PTRANS': 11, 'TRANS': 281}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 4776
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 4776
          Classifications: {'peptide': 293}
          Link IDs: {'PTRANS': 11, 'TRANS': 281}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 4776
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 4776
          Classifications: {'peptide': 293}
          Link IDs: {'PTRANS': 11, 'TRANS': 281}
          Chain breaks: 3
    Chain: "D"
      Number of atoms: 4776
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 4776
          Classifications: {'peptide': 293}
          Link IDs: {'PTRANS': 11, 'TRANS': 281}
          Chain breaks: 3
  Time building chain proxies: 9.81, per 1000 atoms: 0.51
  Number of scatterers: 19104
  At special positions: 0
  Unit cell: (123.9, 122.85, 96.6, 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      48     16.00
     O    1600      8.00
     N    1568      7.00
     C    6292      6.00
     H    9596      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: 4.71
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2208

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 1 sheets defined
      81.1% alpha, 0.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 404 through 432
      removed outlier: 3.688A  pdb=" N   LEU A 416 " --> pdb=" O   TRP A 412 " (cutoff:3.500A)
      Proline residue:  A 426  - end of helix
      removed outlier: 3.607A  pdb=" N   LEU A 432 " --> pdb=" O   SER A 428 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 471
      removed outlier: 3.546A  pdb=" N   LEU A 457 " --> pdb=" O   ALA A 453 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ILE A 467 " --> pdb=" O   PHE A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 495
      removed outlier: 3.632A  pdb=" N   HIS A 492 " --> pdb=" O   ARG A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 504
    Processing helix  chain 'A' and resid 507 through 512
      removed outlier: 4.339A  pdb=" N   ILE A 512 " --> pdb=" O   PHE A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 525
      removed outlier: 3.726A  pdb=" N   LYS A 525 " --> pdb=" O   ILE A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 526 through 531
    Processing helix  chain 'A' and resid 532 through 537
    Processing helix  chain 'A' and resid 538 through 543
    Processing helix  chain 'A' and resid 545 through 575
      removed outlier: 3.548A  pdb=" N   GLU A 575 " --> pdb=" O   ILE A 571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 584 through 593
      removed outlier: 3.660A  pdb=" N   ASN A 588 " --> pdb=" O   GLY A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 623
    Processing helix  chain 'A' and resid 634 through 667
      removed outlier: 3.823A  pdb=" N   PHE A 656 " --> pdb=" O   TYR A 652 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   GLY A 657 " --> pdb=" O   ALA A 653 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   SER A 660 " --> pdb=" O   PHE A 656 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 667 through 687
    Processing helix  chain 'A' and resid 690 through 709
      removed outlier: 4.000A  pdb=" N   ARG A 696 " --> pdb=" O   PRO A 692 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   GLN A 702 " --> pdb=" O   GLU A 698 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 431
      removed outlier: 3.805A  pdb=" N   LEU B 416 " --> pdb=" O   TRP B 412 " (cutoff:3.500A)
      Proline residue:  B 426  - end of helix
    Processing helix  chain 'B' and resid 450 through 471
      removed outlier: 3.622A  pdb=" N   ILE B 467 " --> pdb=" O   PHE B 463 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 485 through 495
      removed outlier: 3.610A  pdb=" N   HIS B 492 " --> pdb=" O   ARG B 488 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 497 through 504
    Processing helix  chain 'B' and resid 507 through 512
    Processing helix  chain 'B' and resid 517 through 525
      removed outlier: 3.971A  pdb=" N   LYS B 525 " --> pdb=" O   ILE B 521 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 526 through 531
    Processing helix  chain 'B' and resid 532 through 537
    Processing helix  chain 'B' and resid 538 through 543
    Processing helix  chain 'B' and resid 545 through 575
      removed outlier: 3.516A  pdb=" N   GLU B 575 " --> pdb=" O   ILE B 571 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 584 through 593
      removed outlier: 3.618A  pdb=" N   ASN B 588 " --> pdb=" O   GLY B 584 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 606 through 623
    Processing helix  chain 'B' and resid 634 through 667
      removed outlier: 4.011A  pdb=" N   PHE B 656 " --> pdb=" O   TYR B 652 " (cutoff:3.500A)
      removed outlier: 4.534A  pdb=" N   GLY B 657 " --> pdb=" O   ALA B 653 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   SER B 660 " --> pdb=" O   PHE B 656 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 667 through 688
    Processing helix  chain 'B' and resid 690 through 709
      removed outlier: 3.926A  pdb=" N   ARG B 696 " --> pdb=" O   PRO B 692 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   GLN B 702 " --> pdb=" O   GLU B 698 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 404 through 432
      removed outlier: 3.645A  pdb=" N   LEU C 416 " --> pdb=" O   TRP C 412 " (cutoff:3.500A)
      Proline residue:  C 426  - end of helix
    Processing helix  chain 'C' and resid 450 through 471
      removed outlier: 4.219A  pdb=" N   ASP C 456 " --> pdb=" O   LEU C 452 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ILE C 467 " --> pdb=" O   PHE C 463 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 485 through 495
      removed outlier: 3.549A  pdb=" N   HIS C 492 " --> pdb=" O   ARG C 488 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 497 through 504
    Processing helix  chain 'C' and resid 507 through 512
      removed outlier: 3.580A  pdb=" N   ILE C 512 " --> pdb=" O   PHE C 508 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 517 through 525
      removed outlier: 3.877A  pdb=" N   LYS C 525 " --> pdb=" O   ILE C 521 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 526 through 531
    Processing helix  chain 'C' and resid 532 through 537
    Processing helix  chain 'C' and resid 538 through 543
    Processing helix  chain 'C' and resid 545 through 575
    Processing helix  chain 'C' and resid 584 through 593
      removed outlier: 3.641A  pdb=" N   ASN C 588 " --> pdb=" O   GLY C 584 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 606 through 623
    Processing helix  chain 'C' and resid 634 through 667
      removed outlier: 4.095A  pdb=" N   PHE C 656 " --> pdb=" O   TYR C 652 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   GLY C 657 " --> pdb=" O   ALA C 653 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 667 through 688
    Processing helix  chain 'C' and resid 690 through 709
      removed outlier: 4.370A  pdb=" N   ARG C 696 " --> pdb=" O   PRO C 692 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 404 through 431
      removed outlier: 3.846A  pdb=" N   LEU D 416 " --> pdb=" O   TRP D 412 " (cutoff:3.500A)
      Proline residue:  D 426  - end of helix
    Processing helix  chain 'D' and resid 450 through 471
      removed outlier: 4.046A  pdb=" N   ASP D 456 " --> pdb=" O   LEU D 452 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ILE D 467 " --> pdb=" O   PHE D 463 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 485 through 496
      removed outlier: 3.745A  pdb=" N   HIS D 492 " --> pdb=" O   ARG D 488 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 497 through 504
    Processing helix  chain 'D' and resid 507 through 512
      removed outlier: 3.849A  pdb=" N   ILE D 512 " --> pdb=" O   PHE D 508 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 517 through 525
      removed outlier: 3.801A  pdb=" N   LYS D 525 " --> pdb=" O   ILE D 521 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 526 through 531
    Processing helix  chain 'D' and resid 532 through 537
      removed outlier: 3.536A  pdb=" N   ALA D 536 " --> pdb=" O   LEU D 532 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 538 through 543
    Processing helix  chain 'D' and resid 545 through 575
      removed outlier: 3.537A  pdb=" N   PHE D 551 " --> pdb=" O   ALA D 547 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLU D 575 " --> pdb=" O   ILE D 571 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 584 through 593
      removed outlier: 3.667A  pdb=" N   ASN D 588 " --> pdb=" O   GLY D 584 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 606 through 623
    Processing helix  chain 'D' and resid 634 through 653
    Processing helix  chain 'D' and resid 654 through 667
      removed outlier: 3.560A  pdb=" N   SER D 660 " --> pdb=" O   PHE D 656 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 667 through 688
    Processing helix  chain 'D' and resid 690 through 709
      removed outlier: 4.501A  pdb=" N   ARG D 696 " --> pdb=" O   PRO D 692 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLN D 702 " --> pdb=" O   GLU D 698 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 597 through 598
      removed outlier: 3.751A  pdb=" N   LEU C 602 " --> pdb=" O   ASN C 598 " (cutoff:3.500A)

    651 hydrogen bonds defined for protein.
    1917 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: 6.85

  Time building geometry restraints manager: 5.70 seconds

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

  Histogram of bond lengths:
        0.96 -     1.13: 9580
        1.13 -     1.30: 1520
        1.30 -     1.48: 4059
        1.48 -     1.65: 4133
        1.65 -     1.82: 80
  Bond restraints: 19372
  Sorted by residual:
  bond pdb=" CD1 PHE B 551 "
       pdb=" HD1 PHE B 551 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" N   ASP B 509 "
       pdb=" H   ASP B 509 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" NE2 GLN A 592 "
       pdb="HE21 GLN A 592 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" N   ALA A 653 "
       pdb=" H   ALA A 653 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" NH2 ARG B 672 "
       pdb="HH21 ARG B 672 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  ... (remaining 19367 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.51: 29601
        2.51 -     5.02: 4093
        5.02 -     7.52: 1148
        7.52 -    10.03: 54
       10.03 -    12.54: 16
  Bond angle restraints: 34912
  Sorted by residual:
  angle pdb=" C   GLY C 604 "
        pdb=" N   PRO C 605 "
        pdb=" CA  PRO C 605 "
      ideal   model   delta    sigma   weight residual
     119.76  125.05   -5.29 1.03e+00 9.43e-01 2.64e+01
  angle pdb=" CB  HIS D 587 "
        pdb=" CG  HIS D 587 "
        pdb=" CD2 HIS D 587 "
      ideal   model   delta    sigma   weight residual
     131.20  124.66    6.54 1.30e+00 5.92e-01 2.53e+01
  angle pdb=" CB  HIS C 587 "
        pdb=" CG  HIS C 587 "
        pdb=" CD2 HIS C 587 "
      ideal   model   delta    sigma   weight residual
     131.20  124.72    6.48 1.30e+00 5.92e-01 2.48e+01
  angle pdb=" C   GLY B 604 "
        pdb=" N   PRO B 605 "
        pdb=" CA  PRO B 605 "
      ideal   model   delta    sigma   weight residual
     119.78  124.79   -5.01 1.03e+00 9.43e-01 2.37e+01
  angle pdb=" CB  HIS A 587 "
        pdb=" CG  HIS A 587 "
        pdb=" CD2 HIS A 587 "
      ideal   model   delta    sigma   weight residual
     131.20  124.91    6.29 1.30e+00 5.92e-01 2.34e+01
  ... (remaining 34907 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.53: 8479
       16.53 -    33.06: 419
       33.06 -    49.58: 137
       49.58 -    66.11: 84
       66.11 -    82.64: 5
  Dihedral angle restraints: 9124
    sinusoidal: 4760
      harmonic: 4364
  Sorted by residual:
  dihedral pdb=" CA  HIS A 578 "
           pdb=" C   HIS A 578 "
           pdb=" N   MET A 579 "
           pdb=" CA  MET A 579 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.71  -29.29     0      5.00e+00 4.00e-02 3.43e+01
  dihedral pdb=" CA  HIS B 578 "
           pdb=" C   HIS B 578 "
           pdb=" N   MET B 579 "
           pdb=" CA  MET B 579 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.05  -28.95     0      5.00e+00 4.00e-02 3.35e+01
  dihedral pdb=" CA  HIS C 578 "
           pdb=" C   HIS C 578 "
           pdb=" N   MET C 579 "
           pdb=" CA  MET C 579 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.16  -28.84     0      5.00e+00 4.00e-02 3.33e+01
  ... (remaining 9121 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.083: 971
       0.083 -    0.166: 447
       0.166 -    0.249: 55
       0.249 -    0.332: 18
       0.332 -    0.415: 5
  Chirality restraints: 1496
  Sorted by residual:
  chirality pdb=" CA  SER C 624 "
            pdb=" N   SER C 624 "
            pdb=" C   SER C 624 "
            pdb=" CB  SER C 624 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.42 2.00e-01 2.50e+01 4.31e+00
  chirality pdb=" CA  SER D 624 "
            pdb=" N   SER D 624 "
            pdb=" C   SER D 624 "
            pdb=" CB  SER D 624 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 3.99e+00
  chirality pdb=" CA  SER B 624 "
            pdb=" N   SER B 624 "
            pdb=" C   SER B 624 "
            pdb=" CB  SER B 624 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.71e+00
  ... (remaining 1493 not shown)

  Planarity restraints: 2732
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 652 "   -0.213 2.00e-02 2.50e+03   8.80e-02 2.32e+02
        pdb=" CG  TYR B 652 "    0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 652 "    0.069 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 652 "    0.061 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 652 "    0.032 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 652 "    0.053 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 652 "   -0.012 2.00e-02 2.50e+03
        pdb=" OH  TYR B 652 "   -0.164 2.00e-02 2.50e+03
        pdb=" HD1 TYR B 652 "    0.070 2.00e-02 2.50e+03
        pdb=" HD2 TYR B 652 "    0.037 2.00e-02 2.50e+03
        pdb=" HE1 TYR B 652 "    0.006 2.00e-02 2.50e+03
        pdb=" HE2 TYR B 652 "    0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 652 "   -0.209 2.00e-02 2.50e+03   8.53e-02 2.18e+02
        pdb=" CG  TYR C 652 "    0.029 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 652 "    0.068 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 652 "    0.060 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 652 "    0.028 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 652 "    0.051 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 652 "   -0.012 2.00e-02 2.50e+03
        pdb=" OH  TYR C 652 "   -0.154 2.00e-02 2.50e+03
        pdb=" HD1 TYR C 652 "    0.072 2.00e-02 2.50e+03
        pdb=" HD2 TYR C 652 "    0.035 2.00e-02 2.50e+03
        pdb=" HE1 TYR C 652 "    0.001 2.00e-02 2.50e+03
        pdb=" HE2 TYR C 652 "    0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D 652 "   -0.192 2.00e-02 2.50e+03   7.97e-02 1.91e+02
        pdb=" CG  TYR D 652 "    0.025 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 652 "    0.063 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 652 "    0.054 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 652 "    0.029 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 652 "    0.050 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 652 "   -0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR D 652 "   -0.150 2.00e-02 2.50e+03
        pdb=" HD1 TYR D 652 "    0.065 2.00e-02 2.50e+03
        pdb=" HD2 TYR D 652 "    0.030 2.00e-02 2.50e+03
        pdb=" HE1 TYR D 652 "    0.002 2.00e-02 2.50e+03
        pdb=" HE2 TYR D 652 "    0.032 2.00e-02 2.50e+03
  ... (remaining 2729 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 953
        2.20 -     2.80: 34043
        2.80 -     3.40: 52130
        3.40 -     4.00: 68372
        4.00 -     4.60: 97650
  Nonbonded interactions: 253148
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU D 575 "
            pdb=" HG  SER D 636 "
     model   vdw
     1.602 2.450
  nonbonded pdb=" OE2 GLU C 575 "
            pdb=" HG  SER C 636 "
     model   vdw
     1.602 2.450
  nonbonded pdb=" OE2 GLU B 575 "
            pdb=" HG  SER B 636 "
     model   vdw
     1.604 2.450
  nonbonded pdb=" OE2 GLU A 575 "
            pdb=" HG  SER A 636 "
     model   vdw
     1.608 2.450
  nonbonded pdb=" HH  TYR C 420 "
            pdb=" OD1 ASP C 456 "
     model   vdw
     1.620 2.450
  ... (remaining 253143 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.870
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.300
  Extract box with map and model:          0.630
  Check model and map are aligned:         0.140
  Set scattering table:                    0.160
  Process input model:                     41.910
  Find NCS groups from input model:        0.470
  Set up NCS constraints:                  0.060
  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:             0.010
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
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      :  0.013   0.045   9776  Z= 0.827
  Angle     :  1.699   8.247  13288  Z= 1.177
  Chirality :  0.091   0.415   1496
  Planarity :  0.016   0.169   1620
  Dihedral  : 11.424  82.638   3420
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.23), residues: 1140
  helix: -0.72 (0.15), residues: 868
  sheet:  None (None), residues: 0
  loop :  0.63 (0.45), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.122   0.016   TRP B 705 
 HIS   0.013   0.003   HIS A 587 
 PHE   0.086   0.012   PHE D 701 
 TYR   0.184   0.022   TYR B 652 
 ARG   0.008   0.001   ARG D 531 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 254
  time to evaluate  : 1.483 
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: A  461 ILE cc_start: 0.7911 (mm) cc_final: 0.7649 (mt)
REVERT: A  688 GLN cc_start: 0.8191 (mt0) cc_final: 0.7960 (tm-30)
REVERT: A  707 TYR cc_start: 0.7726 (t80) cc_final: 0.7475 (t80)
REVERT: B  398 TRP cc_start: 0.6067 (m-90) cc_final: 0.5723 (m100)
REVERT: B  468 LEU cc_start: 0.7761 (mt) cc_final: 0.7556 (mt)
REVERT: B  472 ARG cc_start: 0.6638 (mmt180) cc_final: 0.6425 (mmm160)
REVERT: B  578 HIS cc_start: 0.5045 (t-170) cc_final: 0.3686 (m170)
REVERT: B  583 ILE cc_start: 0.8712 (mm) cc_final: 0.8478 (mt)
REVERT: C  574 MET cc_start: 0.7535 (mtt) cc_final: 0.7331 (mtp)
REVERT: C  591 ASP cc_start: 0.7814 (m-30) cc_final: 0.7215 (m-30)
REVERT: C  677 MET cc_start: 0.8348 (tpp) cc_final: 0.8115 (tpt)
REVERT: D  578 HIS cc_start: 0.6452 (t-170) cc_final: 0.5725 (t70)
REVERT: D  673 TYR cc_start: 0.8452 (t80) cc_final: 0.8168 (t80)
REVERT: D  682 GLU cc_start: 0.8304 (tt0) cc_final: 0.7913 (tt0)
REVERT: D  696 ARG cc_start: 0.8301 (mtp180) cc_final: 0.8059 (mtm-85)
REVERT: D  702 GLN cc_start: 0.7913 (mt0) cc_final: 0.7703 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 254
  average time/residue: 0.6468
  time to fit residues: 209.9239
Evaluate side-chains
  177 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 1.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 87 optimal weight:    0.8980
   chunk 48 optimal weight:    0.6980
   chunk 30 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 90 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 105 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 450 GLN
A 576 GLN
B 674 HIS
C 470 ASN
C 578 HIS
C 674 HIS
C 702 GLN
D 703 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.156714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.106489 restraints weight = 31304.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.109483 restraints weight = 21669.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.111685 restraints weight = 17679.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.3213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   9776  Z= 0.199
  Angle     :  0.554   4.695  13288  Z= 0.310
  Chirality :  0.040   0.147   1496
  Planarity :  0.005   0.061   1620
  Dihedral  :  5.011  25.624   1280
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 1.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  4.22 %
    Favored  : 94.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.25), residues: 1140
  helix:  0.77 (0.16), residues: 888
  sheet:  None (None), residues: 0
  loop :  1.28 (0.49), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 585 
 HIS   0.014   0.002   HIS C 578 
 PHE   0.018   0.002   PHE B 701 
 TYR   0.015   0.002   TYR D 700 
 ARG   0.008   0.001   ARG C 528 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 179
  time to evaluate  : 1.445 
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  673 TYR cc_start: 0.8250 (t80) cc_final: 0.8023 (t80)
REVERT: B  681 ARG cc_start: 0.7866 (ttp-170) cc_final: 0.7601 (mtm-85)
REVERT: D  578 HIS cc_start: 0.6178 (t-170) cc_final: 0.5342 (t70)
REVERT: D  673 TYR cc_start: 0.8324 (t80) cc_final: 0.8024 (t80)
  outliers start: 11
  outliers final: 8
  residues processed: 185
  average time/residue: 0.4786
  time to fit residues: 122.0777
Evaluate side-chains
  160 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 152
  time to evaluate  : 1.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  682 GLU
Chi-restraints excluded: chain B residue  506 ILE
Chi-restraints excluded: chain C residue  678 LEU
Chi-restraints excluded: chain D residue  464 ILE
Chi-restraints excluded: chain D residue  662 ILE
Chi-restraints excluded: chain D residue  698 GLU
Chi-restraints excluded: chain D residue  703 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 93 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 100 optimal weight:    3.9990
   chunk 108 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 113 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 450 GLN
A 587 HIS
A 635 ASN
B 687 HIS
D 702 GLN
D 703 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.152963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.103904 restraints weight = 31942.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.106605 restraints weight = 22039.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.107000 restraints weight = 18113.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.3809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   9776  Z= 0.310
  Angle     :  0.551   5.021  13288  Z= 0.308
  Chirality :  0.040   0.158   1496
  Planarity :  0.005   0.054   1620
  Dihedral  :  4.691  25.159   1280
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 2.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  :  5.20 %
    Favored  : 93.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.25), residues: 1140
  helix:  0.96 (0.17), residues: 884
  sheet:  None (None), residues: 0
  loop :  1.45 (0.48), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 585 
 HIS   0.016   0.001   HIS D 703 
 PHE   0.016   0.002   PHE B 701 
 TYR   0.016   0.002   TYR D 700 
 ARG   0.006   0.000   ARG B 679 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 163
  time to evaluate  : 1.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  578 HIS cc_start: 0.5072 (t-170) cc_final: 0.3367 (m90)
REVERT: B  673 TYR cc_start: 0.8311 (t80) cc_final: 0.7970 (t80)
REVERT: B  681 ARG cc_start: 0.7938 (ttp-170) cc_final: 0.7660 (mtm-85)
REVERT: C  677 MET cc_start: 0.8761 (tpp) cc_final: 0.8325 (tpt)
REVERT: D  578 HIS cc_start: 0.6440 (t-170) cc_final: 0.5457 (t70)
REVERT: D  673 TYR cc_start: 0.8419 (t80) cc_final: 0.8080 (t80)
REVERT: D  688 GLN cc_start: 0.8839 (mt0) cc_final: 0.8413 (mm-40)
REVERT: D  699 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7918 (mt-10)
  outliers start: 14
  outliers final: 11
  residues processed: 170
  average time/residue: 0.4281
  time to fit residues: 104.7823
Evaluate side-chains
  169 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 158
  time to evaluate  : 1.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain A residue  682 GLU
Chi-restraints excluded: chain B residue  506 ILE
Chi-restraints excluded: chain B residue  649 SER
Chi-restraints excluded: chain C residue  464 ILE
Chi-restraints excluded: chain D residue  464 ILE
Chi-restraints excluded: chain D residue  662 ILE
Chi-restraints excluded: chain D residue  702 GLN
Chi-restraints excluded: chain D residue  703 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 18 optimal weight:    0.0570
   chunk 84 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 49 optimal weight:    0.5980
   chunk 1 optimal weight:    2.9990
   chunk 108 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.6900

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

Flipped N/Q/H residues before XYZ refinement:
A 635 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.156627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.106509 restraints weight = 31542.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.109664 restraints weight = 21731.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.111818 restraints weight = 17585.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7478
moved from start:          0.4144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   9776  Z= 0.152
  Angle     :  0.466   6.504  13288  Z= 0.254
  Chirality :  0.037   0.151   1496
  Planarity :  0.004   0.048   1620
  Dihedral  :  4.324  23.566   1280
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 1.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  6.47 %
    Favored  : 92.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.98 (0.26), residues: 1140
  helix:  1.31 (0.17), residues: 884
  sheet:  None (None), residues: 0
  loop :  1.76 (0.49), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 585 
 HIS   0.008   0.001   HIS C 578 
 PHE   0.016   0.001   PHE D 701 
 TYR   0.012   0.001   TYR B 616 
 ARG   0.004   0.000   ARG C 528 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 157
  time to evaluate  : 1.398 
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  578 HIS cc_start: 0.5080 (t-170) cc_final: 0.3368 (m90)
REVERT: B  673 TYR cc_start: 0.8195 (t80) cc_final: 0.7829 (t80)
REVERT: B  681 ARG cc_start: 0.7908 (ttp-170) cc_final: 0.7654 (mtm-85)
REVERT: B  688 GLN cc_start: 0.8645 (mt0) cc_final: 0.8387 (mt0)
REVERT: C  677 MET cc_start: 0.8714 (tpp) cc_final: 0.8236 (tpt)
REVERT: C  699 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7143 (mt-10)
REVERT: D  578 HIS cc_start: 0.6424 (t-170) cc_final: 0.5432 (t70)
REVERT: D  579 MET cc_start: 0.6355 (ttm) cc_final: 0.6076 (mtp)
REVERT: D  673 TYR cc_start: 0.8455 (t80) cc_final: 0.8078 (t80)
REVERT: D  688 GLN cc_start: 0.8723 (mt0) cc_final: 0.8354 (mm-40)
  outliers start: 7
  outliers final: 4
  residues processed: 159
  average time/residue: 0.4086
  time to fit residues: 94.9464
Evaluate side-chains
  158 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 154
  time to evaluate  : 1.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain A residue  682 GLU
Chi-restraints excluded: chain C residue  464 ILE
Chi-restraints excluded: chain D residue  703 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 94 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
A 450 GLN
A 635 ASN
C 578 HIS
D 703 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.154660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.104653 restraints weight = 31855.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.107578 restraints weight = 22065.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.109504 restraints weight = 18054.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.4258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   9776  Z= 0.225
  Angle     :  0.482   4.978  13288  Z= 0.264
  Chirality :  0.038   0.155   1496
  Planarity :  0.004   0.047   1620
  Dihedral  :  4.229  21.327   1280
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  7.35 %
    Favored  : 91.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.26), residues: 1140
  helix:  1.39 (0.17), residues: 880
  sheet:  None (None), residues: 0
  loop :  1.50 (0.48), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 568 
 HIS   0.009   0.001   HIS D 703 
 PHE   0.011   0.001   PHE C 656 
 TYR   0.015   0.002   TYR B 616 
 ARG   0.002   0.000   ARG B 534 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 158
  time to evaluate  : 1.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  524 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8097 (mp)
REVERT: B  578 HIS cc_start: 0.5139 (t-170) cc_final: 0.3511 (m90)
REVERT: C  677 MET cc_start: 0.8784 (tpp) cc_final: 0.8372 (tpt)
REVERT: C  699 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7156 (mt-10)
REVERT: D  401 LEU cc_start: 0.8107 (mm) cc_final: 0.7833 (mt)
REVERT: D  578 HIS cc_start: 0.6548 (t-170) cc_final: 0.5554 (t70)
REVERT: D  673 TYR cc_start: 0.8462 (t80) cc_final: 0.8049 (t80)
REVERT: D  688 GLN cc_start: 0.8711 (mt0) cc_final: 0.8363 (mm-40)
  outliers start: 8
  outliers final: 5
  residues processed: 159
  average time/residue: 0.4470
  time to fit residues: 100.4765
Evaluate side-chains
  162 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 156
  time to evaluate  : 1.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  682 GLU
Chi-restraints excluded: chain C residue  464 ILE
Chi-restraints excluded: chain D residue  703 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 110 optimal weight:    0.5980
   chunk 27 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 114 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 90 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 95 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 111 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 635 ASN
C 635 ASN
C 687 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.155743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.105231 restraints weight = 31723.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.108278 restraints weight = 22200.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.110463 restraints weight = 17955.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.4445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   9776  Z= 0.186
  Angle     :  0.457   5.005  13288  Z= 0.249
  Chirality :  0.037   0.153   1496
  Planarity :  0.004   0.046   1620
  Dihedral  :  4.091  20.004   1280
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 2.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  8.33 %
    Favored  : 91.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.17 (0.26), residues: 1140
  helix:  1.51 (0.17), residues: 880
  sheet:  None (None), residues: 0
  loop :  1.55 (0.48), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 585 
 HIS   0.003   0.001   HIS D 687 
 PHE   0.012   0.001   PHE D 701 
 TYR   0.013   0.001   TYR B 616 
 ARG   0.003   0.000   ARG B 534 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 161
  time to evaluate  : 1.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  652 TYR cc_start: 0.7427 (OUTLIER) cc_final: 0.6519 (m-80)
REVERT: B  578 HIS cc_start: 0.5192 (t-170) cc_final: 0.3607 (m90)
REVERT: D  401 LEU cc_start: 0.8128 (mm) cc_final: 0.7829 (mt)
REVERT: D  578 HIS cc_start: 0.6502 (t-170) cc_final: 0.5519 (t70)
REVERT: D  579 MET cc_start: 0.6084 (mtp) cc_final: 0.5845 (mtp)
REVERT: D  673 TYR cc_start: 0.8452 (t80) cc_final: 0.8016 (t80)
REVERT: D  688 GLN cc_start: 0.8668 (mt0) cc_final: 0.8353 (mm-40)
  outliers start: 6
  outliers final: 5
  residues processed: 162
  average time/residue: 0.4457
  time to fit residues: 103.1703
Evaluate side-chains
  166 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 160
  time to evaluate  : 1.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain A residue  652 TYR
Chi-restraints excluded: chain A residue  682 GLU
Chi-restraints excluded: chain C residue  464 ILE
Chi-restraints excluded: chain D residue  703 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 115 optimal weight:    5.9990
   chunk 98 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 107 optimal weight:    0.5980
   chunk 74 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
A 635 ASN
C 635 ASN
D 576 GLN
D 703 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.152847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.102945 restraints weight = 32011.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.105962 restraints weight = 22441.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.107896 restraints weight = 18404.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.4539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   9776  Z= 0.296
  Angle     :  0.517   8.164  13288  Z= 0.283
  Chirality :  0.039   0.157   1496
  Planarity :  0.004   0.047   1620
  Dihedral  :  4.198  20.832   1280
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  8.53 %
    Favored  : 90.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.26), residues: 1140
  helix:  1.35 (0.17), residues: 880
  sheet:  None (None), residues: 0
  loop :  1.38 (0.48), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 568 
 HIS   0.006   0.001   HIS D 703 
 PHE   0.015   0.002   PHE C 656 
 TYR   0.016   0.002   TYR B 616 
 ARG   0.003   0.000   ARG B 534 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 158
  time to evaluate  : 1.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  524 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8115 (mp)
REVERT: A  652 TYR cc_start: 0.7442 (OUTLIER) cc_final: 0.6667 (m-80)
REVERT: B  578 HIS cc_start: 0.5193 (t-170) cc_final: 0.3639 (m90)
REVERT: C  551 PHE cc_start: 0.7642 (t80) cc_final: 0.7276 (t80)
REVERT: D  578 HIS cc_start: 0.6537 (t-170) cc_final: 0.5544 (t70)
REVERT: D  673 TYR cc_start: 0.8481 (t80) cc_final: 0.8036 (t80)
REVERT: D  688 GLN cc_start: 0.8659 (mt0) cc_final: 0.8342 (mm-40)
  outliers start: 10
  outliers final: 8
  residues processed: 160
  average time/residue: 0.4446
  time to fit residues: 101.5670
Evaluate side-chains
  166 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 156
  time to evaluate  : 1.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  652 TYR
Chi-restraints excluded: chain A residue  682 GLU
Chi-restraints excluded: chain C residue  464 ILE
Chi-restraints excluded: chain C residue  682 GLU
Chi-restraints excluded: chain C residue  702 GLN
Chi-restraints excluded: chain D residue  651 MET
Chi-restraints excluded: chain D residue  703 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 83 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   chunk 96 optimal weight:    2.9990
   chunk 113 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 109 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 97 optimal weight:    0.9980
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 635 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.153538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.102395 restraints weight = 32107.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.105556 restraints weight = 21877.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.107763 restraints weight = 17561.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.4593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   9776  Z= 0.262
  Angle     :  0.500   8.183  13288  Z= 0.272
  Chirality :  0.038   0.155   1496
  Planarity :  0.004   0.047   1620
  Dihedral  :  4.161  20.282   1280
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  8.43 %
    Favored  : 90.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.26), residues: 1140
  helix:  1.44 (0.17), residues: 872
  sheet:  None (None), residues: 0
  loop :  1.38 (0.47), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 585 
 HIS   0.006   0.001   HIS D 703 
 PHE   0.014   0.001   PHE C 656 
 TYR   0.015   0.002   TYR B 616 
 ARG   0.002   0.000   ARG D 582 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 156
  time to evaluate  : 1.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  578 HIS cc_start: 0.5406 (t-170) cc_final: 0.4234 (m-70)
REVERT: A  652 TYR cc_start: 0.7326 (OUTLIER) cc_final: 0.6630 (m-80)
REVERT: B  578 HIS cc_start: 0.5092 (t-170) cc_final: 0.3772 (m90)
REVERT: D  578 HIS cc_start: 0.6601 (t-170) cc_final: 0.5614 (t70)
REVERT: D  673 TYR cc_start: 0.8451 (t80) cc_final: 0.7980 (t80)
REVERT: D  688 GLN cc_start: 0.8687 (mt0) cc_final: 0.8369 (mm-40)
  outliers start: 10
  outliers final: 7
  residues processed: 159
  average time/residue: 0.4600
  time to fit residues: 106.0267
Evaluate side-chains
  163 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 155
  time to evaluate  : 1.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain A residue  652 TYR
Chi-restraints excluded: chain A residue  682 GLU
Chi-restraints excluded: chain C residue  464 ILE
Chi-restraints excluded: chain C residue  682 GLU
Chi-restraints excluded: chain C residue  702 GLN
Chi-restraints excluded: chain D residue  703 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 80 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   chunk 102 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 108 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 97 optimal weight:    0.5980
   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 635 ASN
C 635 ASN
D 703 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.155235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.105057 restraints weight = 31713.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.108248 restraints weight = 21755.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.110001 restraints weight = 17734.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.4700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   9776  Z= 0.176
  Angle     :  0.459   9.024  13288  Z= 0.245
  Chirality :  0.037   0.151   1496
  Planarity :  0.004   0.046   1620
  Dihedral  :  4.007  19.115   1280
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 2.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  9.22 %
    Favored  : 90.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.32 (0.26), residues: 1140
  helix:  1.65 (0.17), residues: 872
  sheet:  None (None), residues: 0
  loop :  1.50 (0.47), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 568 
 HIS   0.007   0.001   HIS D 703 
 PHE   0.012   0.001   PHE C 656 
 TYR   0.013   0.001   TYR B 616 
 ARG   0.002   0.000   ARG C 679 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 157
  time to evaluate  : 1.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  578 HIS cc_start: 0.5362 (t-170) cc_final: 0.4258 (m-70)
REVERT: A  652 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.6403 (m-80)
REVERT: B  578 HIS cc_start: 0.5160 (t-170) cc_final: 0.3889 (m90)
REVERT: D  578 HIS cc_start: 0.6553 (t-170) cc_final: 0.5598 (t70)
REVERT: D  673 TYR cc_start: 0.8435 (t80) cc_final: 0.7960 (t80)
REVERT: D  688 GLN cc_start: 0.8655 (mt0) cc_final: 0.8359 (mm-40)
  outliers start: 7
  outliers final: 6
  residues processed: 159
  average time/residue: 0.4497
  time to fit residues: 103.1150
Evaluate side-chains
  161 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 154
  time to evaluate  : 1.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain A residue  652 TYR
Chi-restraints excluded: chain A residue  682 GLU
Chi-restraints excluded: chain C residue  464 ILE
Chi-restraints excluded: chain C residue  702 GLN
Chi-restraints excluded: chain D residue  703 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 91 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 80 optimal weight:    1.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 635 ASN
C 635 ASN
D 703 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.154758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.104493 restraints weight = 31889.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.107667 restraints weight = 22178.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.109725 restraints weight = 17898.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.4756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   9776  Z= 0.210
  Angle     :  0.475   8.510  13288  Z= 0.256
  Chirality :  0.037   0.152   1496
  Planarity :  0.004   0.046   1620
  Dihedral  :  3.998  19.357   1280
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  9.02 %
    Favored  : 90.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.30 (0.26), residues: 1140
  helix:  1.63 (0.17), residues: 872
  sheet:  None (None), residues: 0
  loop :  1.49 (0.47), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 568 
 HIS   0.004   0.001   HIS D 703 
 PHE   0.013   0.001   PHE C 656 
 TYR   0.017   0.001   TYR B 616 
 ARG   0.003   0.000   ARG C 534 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 154
  time to evaluate  : 1.469 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  578 HIS cc_start: 0.5301 (t-170) cc_final: 0.4294 (m-70)
REVERT: A  652 TYR cc_start: 0.7433 (OUTLIER) cc_final: 0.6443 (m-80)
REVERT: B  578 HIS cc_start: 0.5170 (t-170) cc_final: 0.4013 (m90)
REVERT: D  401 LEU cc_start: 0.8109 (mm) cc_final: 0.7836 (mt)
REVERT: D  578 HIS cc_start: 0.6520 (t-170) cc_final: 0.5612 (t70)
REVERT: D  673 TYR cc_start: 0.8455 (t80) cc_final: 0.7986 (t80)
REVERT: D  688 GLN cc_start: 0.8638 (mt0) cc_final: 0.8355 (mm-40)
  outliers start: 9
  outliers final: 7
  residues processed: 157
  average time/residue: 0.4295
  time to fit residues: 96.7439
Evaluate side-chains
  161 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 153
  time to evaluate  : 1.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain A residue  652 TYR
Chi-restraints excluded: chain C residue  464 ILE
Chi-restraints excluded: chain C residue  682 GLU
Chi-restraints excluded: chain C residue  702 GLN
Chi-restraints excluded: chain D residue  620 SER
Chi-restraints excluded: chain D residue  703 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 34 optimal weight:    3.9990
   chunk 85 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 65 optimal weight:    5.9990
   chunk 54 optimal weight:    5.9990
   chunk 71 optimal weight:    2.9990
   chunk 112 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   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 635 ASN
C 635 ASN
D 702 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.154767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.104386 restraints weight = 31872.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.107621 restraints weight = 21950.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.109594 restraints weight = 17841.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
moved from start:          0.4810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   9776  Z= 0.208
  Angle     :  0.473   8.410  13288  Z= 0.254
  Chirality :  0.037   0.152   1496
  Planarity :  0.004   0.046   1620
  Dihedral  :  3.980  19.472   1280
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  9.02 %
    Favored  : 90.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.32 (0.26), residues: 1140
  helix:  1.65 (0.17), residues: 872
  sheet:  None (None), residues: 0
  loop :  1.51 (0.46), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 568 
 HIS   0.004   0.001   HIS D 703 
 PHE   0.013   0.001   PHE C 656 
 TYR   0.014   0.001   TYR B 616 
 ARG   0.002   0.000   ARG B 534 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5874.74 seconds
wall clock time: 104 minutes 24.01 seconds (6264.01 seconds total)