Starting phenix.real_space_refine
on Sun Aug 24 10:15:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9chr_45599/08_2025/9chr_45599.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9chr_45599/08_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_45599/08_2025/9chr_45599.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9chr_45599/08_2025/9chr_45599.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9chr_45599/08_2025/9chr_45599.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9chr_45599/08_2025/9chr_45599.cif"
  }
  resolution = 3.5
  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=   0.003
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.82, per 1000 atoms: 0.20
  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: 1.53
  Conformation dependent library (CDL) restraints added in 654.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.83
  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: 4.39

  Time building geometry restraints manager: 2.19 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: 0.01
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:             1.790
  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:             0.130
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.870
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.910
-------------------------------------------------------------------------------
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= 0.766
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.008   0.001   ARG D 531 
 TYR   0.184   0.022   TYR B 652 
 PHE   0.086   0.012   PHE D 701 
 TRP   0.122   0.016   TRP B 705 
 HIS   0.013   0.003   HIS A 587 

Details of bonding type rmsd
  covalent geometry    : bond        0.01289 ( 9776)
  covalent geometry    : angle       1.69908 (13288)
  hydrogen bonds       : bond        0.15507 (  651)
  hydrogen bonds       : angle       6.46674 ( 1917)

*********************** 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  : 0.502 
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: 0.7958 (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: 0.7554 (mt)
REVERT: B  472 ARG cc_start: 0.6638 (mmt180) cc_final: 0.6428 (mmm160)
REVERT: B  578 HIS cc_start: 0.5045 (t-170) cc_final: 0.3683 (m170)
REVERT: B  583 ILE cc_start: 0.8712 (mm) cc_final: 0.8477 (mt)
REVERT: C  574 MET cc_start: 0.7535 (mtt) cc_final: 0.7330 (mtp)
REVERT: C  591 ASP cc_start: 0.7814 (m-30) cc_final: 0.7216 (m-30)
REVERT: C  677 MET cc_start: 0.8348 (tpp) cc_final: 0.8114 (tpt)
REVERT: D  578 HIS cc_start: 0.6452 (t-170) cc_final: 0.5726 (t70)
REVERT: D  673 TYR cc_start: 0.8452 (t80) cc_final: 0.8171 (t80)
REVERT: D  682 GLU cc_start: 0.8304 (tt0) cc_final: 0.7916 (tt0)
REVERT: D  696 ARG cc_start: 0.8301 (mtp180) cc_final: 0.8052 (mtm-85)
REVERT: D  702 GLN cc_start: 0.7913 (mt0) cc_final: 0.7701 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 254
  average time/residue: 0.3288
  time to fit residues: 106.4805
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  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 587 HIS
B 674 HIS
** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3715 r_free = 0.3715 target = 0.156361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.105869 restraints weight = 31707.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.108996 restraints weight = 22380.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.111015 restraints weight = 18267.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.111766 restraints weight = 16238.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.112654 restraints weight = 15342.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
moved from start:          0.3126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9776  Z= 0.155
  Angle     :  0.571   4.694  13288  Z= 0.325
  Chirality :  0.040   0.148   1496
  Planarity :  0.005   0.061   1620
  Dihedral  :  5.011  25.488   1280
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 1.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.25), residues: 1140
  helix:  0.66 (0.16), residues: 888
  sheet:  None (None), residues: 0
  loop :  1.20 (0.49), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 528 
 TYR   0.016   0.002   TYR D 700 
 PHE   0.018   0.002   PHE B 701 
 TRP   0.015   0.001   TRP C 585 
 HIS   0.014   0.001   HIS C 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 9776)
  covalent geometry    : angle       0.57055 (13288)
  hydrogen bonds       : bond        0.05156 (  651)
  hydrogen bonds       : angle       4.18638 ( 1917)

*********************** 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
  192 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 181
  time to evaluate  : 0.510 
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  673 TYR cc_start: 0.8257 (t80) cc_final: 0.8025 (t80)
REVERT: B  681 ARG cc_start: 0.7870 (ttp-170) cc_final: 0.7597 (mtm-85)
REVERT: D  578 HIS cc_start: 0.6155 (t-170) cc_final: 0.5342 (t70)
REVERT: D  673 TYR cc_start: 0.8329 (t80) cc_final: 0.8029 (t80)
  outliers start: 11
  outliers final: 6
  residues processed: 187
  average time/residue: 0.2394
  time to fit residues: 61.9524
Evaluate side-chains
  163 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 157
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  454 VAL
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  703 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 64 optimal weight:    4.9990
   chunk 36 optimal weight:    0.2980
   chunk 41 optimal weight:    0.0170
   chunk 22 optimal weight:    0.9980
   chunk 113 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.8420

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

Flipped N/Q/H residues before XYZ refinement:
A 450 GLN
A 688 GLN
B 687 HIS
C 477 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.157139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.106907 restraints weight = 31640.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.109993 restraints weight = 22034.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.112128 restraints weight = 17910.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.113255 restraints weight = 15923.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.113727 restraints weight = 14854.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.3798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   9776  Z= 0.121
  Angle     :  0.491   6.036  13288  Z= 0.270
  Chirality :  0.038   0.151   1496
  Planarity :  0.004   0.051   1620
  Dihedral  :  4.506  24.241   1280
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 1.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  4.51 %
    Favored  : 94.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.82 (0.26), residues: 1140
  helix:  1.19 (0.17), residues: 884
  sheet:  None (None), residues: 0
  loop :  1.73 (0.49), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 528 
 TYR   0.012   0.001   TYR D 700 
 PHE   0.015   0.001   PHE B 701 
 TRP   0.011   0.001   TRP C 585 
 HIS   0.012   0.001   HIS D 703 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 9776)
  covalent geometry    : angle       0.49070 (13288)
  hydrogen bonds       : bond        0.04132 (  651)
  hydrogen bonds       : angle       3.84785 ( 1917)

*********************** 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
  180 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 170
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  578 HIS cc_start: 0.5051 (t-170) cc_final: 0.3416 (m90)
REVERT: B  673 TYR cc_start: 0.8271 (t80) cc_final: 0.7963 (t80)
REVERT: B  681 ARG cc_start: 0.7892 (ttp-170) cc_final: 0.7628 (mtm-85)
REVERT: B  688 GLN cc_start: 0.8609 (mt0) cc_final: 0.8321 (mt0)
REVERT: C  677 MET cc_start: 0.8709 (tpp) cc_final: 0.8326 (tpt)
REVERT: D  578 HIS cc_start: 0.6385 (t-170) cc_final: 0.5420 (t70)
REVERT: D  673 TYR cc_start: 0.8404 (t80) cc_final: 0.8082 (t80)
REVERT: D  688 GLN cc_start: 0.8743 (mt0) cc_final: 0.8362 (mm-40)
REVERT: D  699 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7981 (mt-10)
  outliers start: 10
  outliers final: 6
  residues processed: 173
  average time/residue: 0.1880
  time to fit residues: 46.9455
Evaluate side-chains
  161 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 155
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain A residue  682 GLU
Chi-restraints excluded: chain B residue  649 SER
Chi-restraints excluded: chain C residue  464 ILE
Chi-restraints excluded: chain D residue  698 GLU
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 48 optimal weight:    0.9980
   chunk 104 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 76 optimal weight:    4.9990
   chunk 111 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 56 optimal weight:    5.9990
   chunk 103 optimal weight:    0.9980
   overall best weight:    1.3984

-------------------------------------------------------------------------------
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
D 702 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 = 0.3706 r_free = 0.3706 target = 0.155117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.104298 restraints weight = 31877.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.107569 restraints weight = 22020.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.109381 restraints weight = 17974.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.110826 restraints weight = 15953.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.111297 restraints weight = 14924.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
moved from start:          0.4108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   9776  Z= 0.157
  Angle     :  0.499   5.017  13288  Z= 0.274
  Chirality :  0.038   0.154   1496
  Planarity :  0.004   0.048   1620
  Dihedral  :  4.346  23.766   1280
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  5.88 %
    Favored  : 93.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.93 (0.26), residues: 1140
  helix:  1.28 (0.17), residues: 884
  sheet:  None (None), residues: 0
  loop :  1.73 (0.49), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 528 
 TYR   0.014   0.002   TYR B 616 
 PHE   0.016   0.001   PHE B 494 
 TRP   0.010   0.001   TRP A 568 
 HIS   0.008   0.001   HIS C 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 9776)
  covalent geometry    : angle       0.49907 (13288)
  hydrogen bonds       : bond        0.03884 (  651)
  hydrogen bonds       : angle       3.74441 ( 1917)

*********************** 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
  162 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 151
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  464 ILE cc_start: 0.8335 (tp) cc_final: 0.8027 (tp)
REVERT: B  578 HIS cc_start: 0.5104 (t-170) cc_final: 0.3453 (m90)
REVERT: B  673 TYR cc_start: 0.8309 (t80) cc_final: 0.7914 (t80)
REVERT: B  681 ARG cc_start: 0.7951 (ttp-170) cc_final: 0.7694 (mtm-85)
REVERT: C  677 MET cc_start: 0.8693 (tpp) cc_final: 0.7981 (tpt)
REVERT: D  578 HIS cc_start: 0.6465 (t-170) cc_final: 0.5481 (t70)
REVERT: D  579 MET cc_start: 0.6021 (mtp) cc_final: 0.5795 (mtp)
REVERT: D  673 TYR cc_start: 0.8498 (t80) cc_final: 0.8127 (t80)
REVERT: D  688 GLN cc_start: 0.8716 (mt0) cc_final: 0.8348 (mm-40)
  outliers start: 11
  outliers final: 11
  residues processed: 154
  average time/residue: 0.2008
  time to fit residues: 44.5269
Evaluate side-chains
  160 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 149
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
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  682 GLU
Chi-restraints excluded: chain C residue  462 MET
Chi-restraints excluded: chain C residue  464 ILE
Chi-restraints excluded: chain C residue  702 GLN
Chi-restraints excluded: chain D residue  651 MET
Chi-restraints excluded: chain D residue  662 ILE
Chi-restraints excluded: chain D residue  698 GLU
Chi-restraints excluded: chain D residue  702 GLN
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 102 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9990
   chunk 51 optimal weight:    0.5980
   chunk 69 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 477 ASN
C 578 HIS
C 687 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.156016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.105673 restraints weight = 31591.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.108810 restraints weight = 21484.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.110763 restraints weight = 17531.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.112029 restraints weight = 15565.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.112411 restraints weight = 14570.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.4267

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= 0.131
  Angle     :  0.468   4.949  13288  Z= 0.257
  Chirality :  0.037   0.153   1496
  Planarity :  0.004   0.046   1620
  Dihedral  :  4.191  22.089   1280
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 2.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  7.35 %
    Favored  : 91.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.09 (0.26), residues: 1140
  helix:  1.43 (0.17), residues: 880
  sheet:  None (None), residues: 0
  loop :  1.66 (0.49), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 679 
 TYR   0.013   0.001   TYR B 616 
 PHE   0.011   0.001   PHE A 656 
 TRP   0.009   0.001   TRP A 568 
 HIS   0.008   0.001   HIS C 578 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9776)
  covalent geometry    : angle       0.46845 (13288)
  hydrogen bonds       : bond        0.03713 (  651)
  hydrogen bonds       : angle       3.63868 ( 1917)

*********************** 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
  164 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 153
  time to evaluate  : 0.462 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  524 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8100 (mp)
REVERT: B  578 HIS cc_start: 0.5131 (t-170) cc_final: 0.3506 (m90)
REVERT: B  673 TYR cc_start: 0.8227 (t80) cc_final: 0.7796 (t80)
REVERT: B  681 ARG cc_start: 0.7909 (ttp-170) cc_final: 0.7699 (mtm-85)
REVERT: C  501 ASP cc_start: 0.7383 (m-30) cc_final: 0.7128 (m-30)
REVERT: C  677 MET cc_start: 0.8674 (tpp) cc_final: 0.7966 (tpt)
REVERT: D  578 HIS cc_start: 0.6608 (t-170) cc_final: 0.5599 (t70)
REVERT: D  579 MET cc_start: 0.5878 (mtp) cc_final: 0.5640 (mtp)
REVERT: D  673 TYR cc_start: 0.8449 (t80) cc_final: 0.7994 (t80)
REVERT: D  688 GLN cc_start: 0.8728 (mt0) cc_final: 0.8363 (mm-40)
REVERT: D  699 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7760 (mt-10)
REVERT: D  702 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7434 (mm-40)
  outliers start: 11
  outliers final: 6
  residues processed: 155
  average time/residue: 0.1970
  time to fit residues: 44.7757
Evaluate side-chains
  159 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 151
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  462 MET
Chi-restraints excluded: chain C residue  464 ILE
Chi-restraints excluded: chain D residue  651 MET
Chi-restraints excluded: chain D residue  702 GLN
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 95 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 113 optimal weight:    0.7980
   chunk 112 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 77 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9980
   chunk 88 optimal weight:    2.9990
   chunk 99 optimal weight:    0.7980
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 635 ASN
C 477 ASN
C 635 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.156909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.106515 restraints weight = 31386.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.109904 restraints weight = 21299.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.111775 restraints weight = 17262.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.113284 restraints weight = 15288.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.113942 restraints weight = 14270.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.4440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   9776  Z= 0.114
  Angle     :  0.450   7.187  13288  Z= 0.241
  Chirality :  0.036   0.152   1496
  Planarity :  0.004   0.045   1620
  Dihedral  :  4.020  20.333   1280
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 2.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  8.24 %
    Favored  : 90.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.35 (0.26), residues: 1140
  helix:  1.62 (0.17), residues: 880
  sheet:  None (None), residues: 0
  loop :  1.68 (0.49), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 679 
 TYR   0.013   0.001   TYR B 616 
 PHE   0.010   0.001   PHE D 686 
 TRP   0.009   0.001   TRP A 568 
 HIS   0.009   0.001   HIS D 703 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 9776)
  covalent geometry    : angle       0.44964 (13288)
  hydrogen bonds       : bond        0.03464 (  651)
  hydrogen bonds       : angle       3.52075 ( 1917)

*********************** 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
  164 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 156
  time to evaluate  : 0.526 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  524 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8114 (mp)
REVERT: B  578 HIS cc_start: 0.5184 (t-170) cc_final: 0.3629 (m90)
REVERT: D  578 HIS cc_start: 0.6505 (t-170) cc_final: 0.5545 (t70)
REVERT: D  673 TYR cc_start: 0.8456 (t80) cc_final: 0.8010 (t80)
REVERT: D  688 GLN cc_start: 0.8673 (mt0) cc_final: 0.8390 (mm-40)
REVERT: D  698 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6456 (mt-10)
REVERT: D  702 GLN cc_start: 0.8163 (mt0) cc_final: 0.7768 (mt0)
  outliers start: 8
  outliers final: 4
  residues processed: 158
  average time/residue: 0.2039
  time to fit residues: 46.3830
Evaluate side-chains
  158 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 152
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  462 MET
Chi-restraints excluded: chain C residue  464 ILE
Chi-restraints excluded: chain D residue  698 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 95 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 115 optimal weight:    5.9990
   chunk 79 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 67 optimal weight:    3.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 635 ASN
C 477 ASN
C 635 ASN
D 702 GLN
D 703 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.155077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.106226 restraints weight = 31740.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.107323 restraints weight = 23040.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.107274 restraints weight = 22718.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.108317 restraints weight = 19852.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.108606 restraints weight = 17706.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.4492

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= 0.150
  Angle     :  0.479   7.780  13288  Z= 0.259
  Chirality :  0.037   0.154   1496
  Planarity :  0.004   0.046   1620
  Dihedral  :  4.033  19.597   1280
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 2.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  :  8.14 %
    Favored  : 90.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.24 (0.26), residues: 1140
  helix:  1.56 (0.17), residues: 880
  sheet:  None (None), residues: 0
  loop :  1.58 (0.49), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 679 
 TYR   0.014   0.001   TYR B 616 
 PHE   0.012   0.001   PHE C 656 
 TRP   0.010   0.001   TRP A 568 
 HIS   0.004   0.001   HIS D 703 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 9776)
  covalent geometry    : angle       0.47884 (13288)
  hydrogen bonds       : bond        0.03588 (  651)
  hydrogen bonds       : angle       3.53593 ( 1917)

*********************** 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
  173 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 161
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  524 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8114 (mp)
REVERT: A  554 MET cc_start: 0.7953 (mmm) cc_final: 0.7593 (mmp)
REVERT: A  652 TYR cc_start: 0.7441 (OUTLIER) cc_final: 0.6479 (m-80)
REVERT: A  678 LEU cc_start: 0.8670 (tp) cc_final: 0.8437 (tt)
REVERT: B  578 HIS cc_start: 0.5149 (t-170) cc_final: 0.3582 (m90)
REVERT: C  501 ASP cc_start: 0.7530 (m-30) cc_final: 0.7256 (m-30)
REVERT: D  401 LEU cc_start: 0.8060 (mm) cc_final: 0.7775 (mt)
REVERT: D  578 HIS cc_start: 0.6589 (t-170) cc_final: 0.5595 (t70)
REVERT: D  673 TYR cc_start: 0.8441 (t80) cc_final: 0.7984 (t80)
REVERT: D  688 GLN cc_start: 0.8708 (mt0) cc_final: 0.8428 (mm-40)
  outliers start: 12
  outliers final: 8
  residues processed: 164
  average time/residue: 0.2019
  time to fit residues: 48.3455
Evaluate side-chains
  169 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 159
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
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  462 MET
Chi-restraints excluded: chain C residue  464 ILE
Chi-restraints excluded: chain C residue  702 GLN
Chi-restraints excluded: chain D residue  698 GLU
Chi-restraints excluded: chain D residue  702 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 105 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 102 optimal weight:    1.9990
   overall best weight:    1.3384

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.155351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.105046 restraints weight = 31928.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.108335 restraints weight = 21848.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.110390 restraints weight = 17768.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.111493 restraints weight = 15778.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.112339 restraints weight = 14698.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.4585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9776  Z= 0.147
  Angle     :  0.475   8.465  13288  Z= 0.256
  Chirality :  0.037   0.153   1496
  Planarity :  0.004   0.045   1620
  Dihedral  :  4.015  19.194   1280
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  8.82 %
    Favored  : 90.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.22 (0.26), residues: 1140
  helix:  1.55 (0.17), residues: 880
  sheet:  None (None), residues: 0
  loop :  1.57 (0.49), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 679 
 TYR   0.015   0.001   TYR B 616 
 PHE   0.012   0.001   PHE C 656 
 TRP   0.010   0.001   TRP A 568 
 HIS   0.008   0.001   HIS D 703 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 9776)
  covalent geometry    : angle       0.47524 (13288)
  hydrogen bonds       : bond        0.03573 (  651)
  hydrogen bonds       : angle       3.54107 ( 1917)

*********************** 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
  173 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 163
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  554 MET cc_start: 0.7927 (mmm) cc_final: 0.7582 (mmp)
REVERT: A  578 HIS cc_start: 0.5373 (t-170) cc_final: 0.4273 (m-70)
REVERT: A  652 TYR cc_start: 0.7413 (OUTLIER) cc_final: 0.6431 (m-80)
REVERT: B  578 HIS cc_start: 0.5092 (t-170) cc_final: 0.3803 (m90)
REVERT: D  401 LEU cc_start: 0.8071 (mm) cc_final: 0.7778 (mt)
REVERT: D  578 HIS cc_start: 0.6550 (t-170) cc_final: 0.5599 (t70)
REVERT: D  673 TYR cc_start: 0.8447 (t80) cc_final: 0.7998 (t80)
REVERT: D  688 GLN cc_start: 0.8676 (mt0) cc_final: 0.8404 (mm-40)
  outliers start: 10
  outliers final: 6
  residues processed: 165
  average time/residue: 0.1962
  time to fit residues: 47.2177
Evaluate side-chains
  169 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 162
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
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  462 MET
Chi-restraints excluded: chain C residue  464 ILE
Chi-restraints excluded: chain C residue  702 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 113 optimal weight:    0.5980
   chunk 0 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 115 optimal weight:    0.4980
   chunk 37 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 87 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9990
   overall best weight:    1.2186

-------------------------------------------------------------------------------
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 = 0.3714 r_free = 0.3714 target = 0.155710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.105523 restraints weight = 31476.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.108736 restraints weight = 21586.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.110519 restraints weight = 17601.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.111995 restraints weight = 15694.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.112473 restraints weight = 14634.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.4628

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= 0.138
  Angle     :  0.472   9.013  13288  Z= 0.253
  Chirality :  0.037   0.153   1496
  Planarity :  0.004   0.045   1620
  Dihedral  :  3.964  19.127   1280
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.29 (0.26), residues: 1140
  helix:  1.60 (0.17), residues: 880
  sheet:  None (None), residues: 0
  loop :  1.56 (0.48), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 679 
 TYR   0.014   0.001   TYR A 616 
 PHE   0.014   0.001   PHE C 686 
 TRP   0.010   0.001   TRP A 568 
 HIS   0.009   0.001   HIS D 703 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 9776)
  covalent geometry    : angle       0.47233 (13288)
  hydrogen bonds       : bond        0.03517 (  651)
  hydrogen bonds       : angle       3.51683 ( 1917)

*********************** 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
  172 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 163
  time to evaluate  : 0.535 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  554 MET cc_start: 0.7916 (mmm) cc_final: 0.7581 (mmp)
REVERT: A  578 HIS cc_start: 0.5370 (t-170) cc_final: 0.4344 (m-70)
REVERT: A  652 TYR cc_start: 0.7448 (OUTLIER) cc_final: 0.6429 (m-80)
REVERT: B  578 HIS cc_start: 0.5184 (t-170) cc_final: 0.3978 (m90)
REVERT: D  401 LEU cc_start: 0.8084 (mm) cc_final: 0.7793 (mt)
REVERT: D  578 HIS cc_start: 0.6544 (t-170) cc_final: 0.5611 (t70)
REVERT: D  673 TYR cc_start: 0.8445 (t80) cc_final: 0.7975 (t80)
REVERT: D  688 GLN cc_start: 0.8644 (mt0) cc_final: 0.8395 (mm-40)
  outliers start: 9
  outliers final: 6
  residues processed: 166
  average time/residue: 0.2150
  time to fit residues: 51.1912
Evaluate side-chains
  167 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 160
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
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  462 MET
Chi-restraints excluded: chain C residue  464 ILE
Chi-restraints excluded: chain C residue  702 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 96 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 10 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 56 optimal weight:    3.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.156396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.105849 restraints weight = 31673.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.108860 restraints weight = 21798.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.111154 restraints weight = 17733.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.112201 restraints weight = 15710.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.112201 restraints weight = 14645.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.4740

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= 0.129
  Angle     :  0.462   9.225  13288  Z= 0.246
  Chirality :  0.037   0.152   1496
  Planarity :  0.004   0.045   1620
  Dihedral  :  3.913  18.703   1280
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.39 (0.26), residues: 1140
  helix:  1.68 (0.17), residues: 880
  sheet:  None (None), residues: 0
  loop :  1.58 (0.48), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 679 
 TYR   0.014   0.001   TYR A 616 
 PHE   0.012   0.001   PHE C 656 
 TRP   0.010   0.001   TRP A 568 
 HIS   0.008   0.001   HIS D 703 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9776)
  covalent geometry    : angle       0.46237 (13288)
  hydrogen bonds       : bond        0.03418 (  651)
  hydrogen bonds       : angle       3.47031 ( 1917)

********************** 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
  170 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 163
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  554 MET cc_start: 0.7907 (mmm) cc_final: 0.7575 (mmp)
REVERT: A  578 HIS cc_start: 0.5323 (t-170) cc_final: 0.4306 (m-70)
REVERT: A  652 TYR cc_start: 0.7418 (OUTLIER) cc_final: 0.6372 (m-80)
REVERT: B  578 HIS cc_start: 0.5115 (t-170) cc_final: 0.3929 (m90)
REVERT: D  401 LEU cc_start: 0.8109 (mm) cc_final: 0.7773 (mt)
REVERT: D  578 HIS cc_start: 0.6556 (t-170) cc_final: 0.5615 (t70)
REVERT: D  673 TYR cc_start: 0.8429 (t80) cc_final: 0.7935 (t80)
REVERT: D  688 GLN cc_start: 0.8689 (mt0) cc_final: 0.8435 (mm-40)
  outliers start: 7
  outliers final: 6
  residues processed: 164
  average time/residue: 0.2123
  time to fit residues: 49.8006
Evaluate side-chains
  170 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 163
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
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  462 MET
Chi-restraints excluded: chain C residue  464 ILE
Chi-restraints excluded: chain C residue  702 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 111 optimal weight:    0.9980
   chunk 29 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 98 optimal weight:    3.9990
   chunk 27 optimal weight:    0.3980
   chunk 17 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   chunk 68 optimal weight:    3.9990
   chunk 58 optimal weight:    4.9990
   chunk 75 optimal weight:    1.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 695 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.156677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.106098 restraints weight = 31692.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.109398 restraints weight = 21646.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.111264 restraints weight = 17592.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.112762 restraints weight = 15578.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.113202 restraints weight = 14536.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.4779

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= 0.124
  Angle     :  0.464   8.899  13288  Z= 0.246
  Chirality :  0.037   0.151   1496
  Planarity :  0.004   0.045   1620
  Dihedral  :  3.883  18.637   1280
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  9.51 %
    Favored  : 89.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.42 (0.26), residues: 1140
  helix:  1.71 (0.17), residues: 880
  sheet:  None (None), residues: 0
  loop :  1.58 (0.48), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 679 
 TYR   0.014   0.001   TYR A 616 
 PHE   0.012   0.001   PHE C 656 
 TRP   0.009   0.001   TRP A 568 
 HIS   0.008   0.001   HIS D 703 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 9776)
  covalent geometry    : angle       0.46419 (13288)
  hydrogen bonds       : bond        0.03384 (  651)
  hydrogen bonds       : angle       3.45662 ( 1917)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3420.68 seconds
wall clock time: 59 minutes 0.41 seconds (3540.41 seconds total)