Starting phenix.real_space_refine
on Sun Jul 27 10:45:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f0x_50117/07_2025/9f0x_50117.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f0x_50117/07_2025/9f0x_50117.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9f0x_50117/07_2025/9f0x_50117.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f0x_50117/07_2025/9f0x_50117.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f0x_50117/07_2025/9f0x_50117.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f0x_50117/07_2025/9f0x_50117.cif"
  }
  resolution = 3.78
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.031
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     166      5.49       5
     S      22      5.16       5
     C    5408      2.51       5
     N    1700      2.21       5
     O    2127      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 9423
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1705
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 1705
          Classifications: {'DNA': 83}
          Link IDs: {'rna3p': 82}
    Chain: "B"
      Number of atoms: 1698
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 1698
          Classifications: {'DNA': 83}
          Link IDs: {'rna3p': 82}
    Chain: "C"
      Number of atoms: 759
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 759
          Classifications: {'peptide': 96}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 90}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "D"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 726
          Classifications: {'peptide': 94}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 88}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 17
    Chain: "E"
      Number of atoms: 900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 900
          Classifications: {'peptide': 113}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 3, 'TRANS': 109}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "F"
      Number of atoms: 924
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 924
          Classifications: {'peptide': 120}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
          Unresolved non-hydrogen bonds: 54
          Unresolved non-hydrogen angles: 64
          Unresolved non-hydrogen dihedrals: 49
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 34
    Chain: "G"
      Number of atoms: 764
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 764
          Classifications: {'peptide': 102}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 3, 'TRANS': 98}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 83
          Unresolved non-hydrogen angles: 102
          Unresolved non-hydrogen dihedrals: 73
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 46
    Chain: "H"
      Number of atoms: 1947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 1947
          Classifications: {'peptide': 266}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 14, 'TRANS': 251}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 104
          Unresolved non-hydrogen angles: 130
          Unresolved non-hydrogen dihedrals: 87
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 74
  Time building chain proxies: 8.67, per 1000 atoms: 0.92
  Number of scatterers: 9423
  At special positions: 0
  Unit cell: (94.05, 94.05, 183.15, 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      22     16.00
     P     166     15.00
     O    2127      8.00
     N    1700      7.00
     C    5408      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.52
  Conformation dependent library (CDL) restraints added in 820.6 milliseconds
  

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1490

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 11 sheets defined
      45.1% alpha, 16.6% beta
      77 base pairs and 142 stacking pairs defined.
    Time for finding SS restraints: 4.10
  Creating SS restraints...
    Processing helix  chain 'C' and resid 4 through 17
    Processing helix  chain 'C' and resid 19 through 40
      removed outlier: 3.676A  pdb=" N   PHE C  31 " --> pdb=" O   VAL C  27 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ILE C  34 " --> pdb=" O   PHE C  30 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 84 through 90
    Processing helix  chain 'D' and resid 2 through 14
      removed outlier: 3.723A  pdb=" N   GLU D   8 " --> pdb=" O   SER D   4 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 18 through 39
    Processing helix  chain 'D' and resid 83 through 91
    Processing helix  chain 'E' and resid 19 through 33
      removed outlier: 4.556A  pdb=" N   LEU E  25 " --> pdb=" O   ASP E  21 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 36 through 52
      removed outlier: 3.622A  pdb=" N   ARG E  44 " --> pdb=" O   GLU E  40 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 75 through 90
      removed outlier: 4.247A  pdb=" N   LEU E  81 " --> pdb=" O   GLU E  77 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 92 through 108
    Processing helix  chain 'F' and resid 22 through 34
      removed outlier: 3.656A  pdb=" N   LEU F  26 " --> pdb=" O   VAL F  22 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 36 through 52
    Processing helix  chain 'F' and resid 75 through 90
    Processing helix  chain 'F' and resid 92 through 108
    Processing helix  chain 'G' and resid 19 through 34
      removed outlier: 4.807A  pdb=" N   LEU G  25 " --> pdb=" O   ASP G  21 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 36 through 52
      removed outlier: 4.184A  pdb=" N   LEU G  49 " --> pdb=" O   LEU G  45 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   HIS G  50 " --> pdb=" O   LYS G  46 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ARG G  51 " --> pdb=" O   ASP G  47 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   TYR G  52 " --> pdb=" O   HIS G  48 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 61 through 65
    Processing helix  chain 'G' and resid 75 through 90
      removed outlier: 3.794A  pdb=" N   ARG G  88 " --> pdb=" O   ALA G  84 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 92 through 108
      removed outlier: 3.771A  pdb=" N   LYS G 107 " --> pdb=" O   ASP G 103 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 577 through 594
      removed outlier: 3.627A  pdb=" N   ALA H 581 " --> pdb=" O   ASN H 577 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ARG H 582 " --> pdb=" O   VAL H 578 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 604 through 622
    Processing helix  chain 'H' and resid 646 through 650
    Processing helix  chain 'H' and resid 696 through 698
      No H-bonds generated for 'chain 'H' and resid 696 through 698'
    Processing helix  chain 'H' and resid 763 through 767
    Processing helix  chain 'H' and resid 793 through 797
      removed outlier: 3.576A  pdb=" N   MET H 797 " --> pdb=" O   GLN H 794 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 798 through 808
    Processing helix  chain 'H' and resid 821 through 825
      removed outlier: 3.524A  pdb=" N   GLU H 825 " --> pdb=" O   ARG H 822 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 44 through 46
      removed outlier: 4.064A  pdb=" N   VAL C  44 " --> pdb=" O   PHE C  52 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 54 through 57
    Processing sheet with id=AA3, first strand: chain 'C' and resid 60 through 61
      removed outlier: 3.713A  pdb=" N   ARG C  60 " --> pdb=" O   ILE C  73 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 43 through 45
    Processing sheet with id=AA5, first strand: chain 'D' and resid 60 through 62
    Processing sheet with id=AA6, first strand: chain 'E' and resid 13 through 18
    Processing sheet with id=AA7, first strand: chain 'F' and resid 13 through 19
    Processing sheet with id=AA8, first strand: chain 'G' and resid 13 through 18
    Processing sheet with id=AA9, first strand: chain 'H' and resid 568 through 572
      removed outlier: 3.540A  pdb=" N   ALA H 790 " --> pdb=" O   ARG H 813 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   VAL H 598 " --> pdb=" O   PHE H 789 " (cutoff:3.500A)
      removed outlier: 7.740A  pdb=" N   SER H 791 " --> pdb=" O   VAL H 598 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   GLN H 600 " --> pdb=" O   SER H 791 " (cutoff:3.500A)
      removed outlier: 9.209A  pdb=" N   GLU H 776 " --> pdb=" O   SER H 597 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   ALA H 599 " --> pdb=" O   GLU H 776 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 632 through 637
      removed outlier: 4.572A  pdb=" N   LEU H 704 " --> pdb=" O   VAL H 637 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   THR H 682 " --> pdb=" O   ASP H 672 " (cutoff:3.500A)
      removed outlier: 4.660A  pdb=" N   VAL H 674 " --> pdb=" O   SER H 680 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   SER H 680 " --> pdb=" O   VAL H 674 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 756 through 759
      removed outlier: 3.864A  pdb=" N   SER H 739 " --> pdb=" O   THR H 746 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   VAL H 748 " --> pdb=" O   VAL H 737 " (cutoff:3.500A)
      removed outlier: 5.799A  pdb=" N   VAL H 737 " --> pdb=" O   VAL H 748 " (cutoff:3.500A)

    314 hydrogen bonds defined for protein.
    888 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      171 hydrogen bonds
      342 hydrogen bond angles
      0 basepair planarities
      77 basepair parallelities
      142 stacking parallelities
  Total time for adding SS restraints: 4.13

  Time building geometry restraints manager: 3.01 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1735
        1.33 -     1.45: 3012
        1.45 -     1.57: 4814
        1.57 -     1.68: 330
        1.68 -     1.80: 41
  Bond restraints: 9932
  Sorted by residual:
  bond pdb=" C   PHE C  81 "
       pdb=" N   ARG C  82 "
    ideal  model  delta    sigma   weight residual
    1.332  1.306  0.025 8.60e-03 1.35e+04 8.75e+00
  bond pdb=" C   TYR H 650 "
       pdb=" N   ARG H 651 "
    ideal  model  delta    sigma   weight residual
    1.332  1.302  0.030 1.92e-02 2.71e+03 2.37e+00
  bond pdb=" C   ARG H 576 "
       pdb=" N   ASN H 577 "
    ideal  model  delta    sigma   weight residual
    1.332  1.313  0.019 1.40e-02 5.10e+03 1.90e+00
  bond pdb=" CA  ARG E  73 "
       pdb=" CB  ARG E  73 "
    ideal  model  delta    sigma   weight residual
    1.528  1.494  0.034 2.61e-02 1.47e+03 1.72e+00
  bond pdb=" C3'  DC B  75 "
       pdb=" C2'  DC B  75 "
    ideal  model  delta    sigma   weight residual
    1.525  1.551 -0.026 2.00e-02 2.50e+03 1.65e+00
  ... (remaining 9927 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 13485
        1.42 -     2.84: 609
        2.84 -     4.27: 44
        4.27 -     5.69: 6
        5.69 -     7.11: 2
  Bond angle restraints: 14146
  Sorted by residual:
  angle pdb=" C   TYR H 650 "
        pdb=" N   ARG H 651 "
        pdb=" CA  ARG H 651 "
      ideal   model   delta    sigma   weight residual
     122.31  115.20    7.11 2.34e+00 1.83e-01 9.24e+00
  angle pdb=" N   PHE C  49 "
        pdb=" CA  PHE C  49 "
        pdb=" C   PHE C  49 "
      ideal   model   delta    sigma   weight residual
     113.18  109.18    4.00 1.33e+00 5.65e-01 9.05e+00
  angle pdb=" N   PHE E   4 "
        pdb=" CA  PHE E   4 "
        pdb=" C   PHE E   4 "
      ideal   model   delta    sigma   weight residual
     114.75  111.39    3.36 1.26e+00 6.30e-01 7.11e+00
  angle pdb=" C3'  DT B  89 "
        pdb=" C2'  DT B  89 "
        pdb=" C1'  DT B  89 "
      ideal   model   delta    sigma   weight residual
     101.60   97.89    3.71 1.50e+00 4.44e-01 6.10e+00
  angle pdb=" N   GLY E   5 "
        pdb=" CA  GLY E   5 "
        pdb=" C   GLY E   5 "
      ideal   model   delta    sigma   weight residual
     113.18  118.46   -5.28 2.37e+00 1.78e-01 4.95e+00
  ... (remaining 14141 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.29: 4901
       35.29 -    70.58: 759
       70.58 -   105.87: 12
      105.87 -   141.15: 1
      141.15 -   176.44: 1
  Dihedral angle restraints: 5674
    sinusoidal: 3384
      harmonic: 2290
  Sorted by residual:
  dihedral pdb=" C4'  DG B  47 "
           pdb=" C3'  DG B  47 "
           pdb=" O3'  DG B  47 "
           pdb=" P    DA B  48 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   36.44 -176.44     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" CA  LYS G  68 "
           pdb=" C   LYS G  68 "
           pdb=" N   TYR G  69 "
           pdb=" CA  TYR G  69 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.52  -19.48     0      5.00e+00 4.00e-02 1.52e+01
  dihedral pdb=" CA  SER H 665 "
           pdb=" C   SER H 665 "
           pdb=" N   HIS H 666 "
           pdb=" CA  HIS H 666 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.01  -17.99     0      5.00e+00 4.00e-02 1.29e+01
  ... (remaining 5671 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 966
       0.027 -    0.054: 431
       0.054 -    0.081: 137
       0.081 -    0.108: 55
       0.108 -    0.135: 19
  Chirality restraints: 1608
  Sorted by residual:
  chirality pdb=" P    DT B  91 "
            pdb=" OP1  DT B  91 "
            pdb=" OP2  DT B  91 "
            pdb=" O5'  DT B  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.48   -0.14 2.00e-01 2.50e+01 4.57e-01
  chirality pdb=" C4'  DA B  64 "
            pdb=" C5'  DA B  64 "
            pdb=" O4'  DA B  64 "
            pdb=" C3'  DA B  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.39   -0.13 2.00e-01 2.50e+01 4.53e-01
  chirality pdb=" CA  ILE D  17 "
            pdb=" N   ILE D  17 "
            pdb=" C   ILE D  17 "
            pdb=" CB  ILE D  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.52e-01
  ... (remaining 1605 not shown)

  Planarity restraints: 1241
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA A  63 "   -0.027 2.00e-02 2.50e+03   1.18e-02 3.80e+00
        pdb=" N9   DA A  63 "    0.024 2.00e-02 2.50e+03
        pdb=" C8   DA A  63 "    0.002 2.00e-02 2.50e+03
        pdb=" N7   DA A  63 "    0.000 2.00e-02 2.50e+03
        pdb=" C5   DA A  63 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DA A  63 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6   DA A  63 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1   DA A  63 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DA A  63 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3   DA A  63 "    0.007 2.00e-02 2.50e+03
        pdb=" C4   DA A  63 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT A  93 "    0.006 2.00e-02 2.50e+03   1.10e-02 3.01e+00
        pdb=" N1   DT A  93 "   -0.018 2.00e-02 2.50e+03
        pdb=" C2   DT A  93 "    0.021 2.00e-02 2.50e+03
        pdb=" O2   DT A  93 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3   DT A  93 "   -0.016 2.00e-02 2.50e+03
        pdb=" C4   DT A  93 "    0.010 2.00e-02 2.50e+03
        pdb=" O4   DT A  93 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5   DT A  93 "    0.001 2.00e-02 2.50e+03
        pdb=" C7   DT A  93 "    0.004 2.00e-02 2.50e+03
        pdb=" C6   DT A  93 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA B  61 "    0.023 2.00e-02 2.50e+03   1.02e-02 2.83e+00
        pdb=" N9   DA B  61 "   -0.022 2.00e-02 2.50e+03
        pdb=" C8   DA B  61 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7   DA B  61 "    0.000 2.00e-02 2.50e+03
        pdb=" C5   DA B  61 "    0.000 2.00e-02 2.50e+03
        pdb=" C6   DA B  61 "    0.004 2.00e-02 2.50e+03
        pdb=" N6   DA B  61 "    0.006 2.00e-02 2.50e+03
        pdb=" N1   DA B  61 "    0.003 2.00e-02 2.50e+03
        pdb=" C2   DA B  61 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3   DA B  61 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DA B  61 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 1238 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 127
        2.64 -     3.20: 8406
        3.20 -     3.77: 16879
        3.77 -     4.33: 21350
        4.33 -     4.90: 31138
  Nonbonded interactions: 77900
  Sorted by model distance:
  nonbonded pdb=" OP1  DT A  61 "
            pdb=" OG1 THR E   6 "
     model   vdw
     2.069 3.040
  nonbonded pdb=" OP1  DG A  71 "
            pdb=" OG1 THR F   6 "
     model   vdw
     2.158 3.040
  nonbonded pdb=" OG  SER H 761 "
            pdb=" OG1 THR H 766 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" NE2 HIS F  48 "
            pdb=" OD2 ASP F 103 "
     model   vdw
     2.195 3.120
  nonbonded pdb=" OD1 ASP H 699 "
            pdb=" OG  SER H 701 "
     model   vdw
     2.201 3.040
  ... (remaining 77895 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'E' and (resid 12 through 16 or (resid 17 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 18 through 22 or (resid 23 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 24 through 45 or (resid 46 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 47 or (resid 48 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 49 or (resid 50 t \ 
hrough 51 and (name N or name CA or name C or name O or name CB )) or resid 52 t \ 
hrough 53 or (resid 54 and (name N or name CA or name C or name O or name CB ))  \ 
or resid 55 or (resid 61 through 62 and (name N or name CA or name C or name O o \ 
r name CB )) or resid 63 or (resid 64 and (name N or name CA or name C or name O \ 
 or name CB )) or resid 65 or (resid 66 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 67 through 73 or (resid 74 through 75 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 76 or (resid 77 and (name N or \ 
 name CA or name C or name O or name CB )) or resid 78 or (resid 79 through 80 a \ 
nd (name N or name CA or name C or name O or name CB )) or resid 81 through 85 o \ 
r (resid 86 and (name N or name CA or name C or name O or name CB )) or resid 87 \ 
 through 92 or (resid 93 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 94 or (resid 95 and (name N or name CA or name C or name O or name CB \ 
 )) or resid 96 through 101 or (resid 102 and (name N or name CA or name C or na \ 
me O or name CB )) or resid 103 through 107 or (resid 108 and (name N or name CA \ 
 or name C or name O or name CB )) or resid 109 through 111 or (resid 112 and (n \ 
ame N or name CA or name C or name O or name CB )) or resid 113))
  selection = (chain 'F' and (resid 12 through 25 or (resid 26 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 27 or (resid 28 through 29 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 30 through 47 or (resid 48 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 49 through 55 or (r \ 
esid 61 through 62 and (name N or name CA or name C or name O or name CB )) or r \ 
esid 63 through 65 or (resid 66 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 67 or (resid 68 and (name N or name CA or name C or name O or  \ 
name CB )) or resid 69 through 73 or (resid 74 through 75 and (name N or name CA \ 
 or name C or name O or name CB )) or resid 76 or (resid 77 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 78 or (resid 79 through 80 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 81 through 85 or (res \ 
id 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throu \ 
gh 92 or (resid 93 and (name N or name CA or name C or name O or name CB )) or r \ 
esid 94 or (resid 95 and (name N or name CA or name C or name O or name CB )) or \ 
 resid 96 through 101 or (resid 102 and (name N or name CA or name C or name O o \ 
r name CB )) or resid 103 through 107 or (resid 108 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 109 through 113))
  selection = (chain 'G' and (resid 12 through 22 or (resid 23 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 24 through 25 or (resid 26 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 27 or (resid 28 through 29 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 30 through 45 or (r \ 
esid 46 and (name N or name CA or name C or name O or name CB )) or resid 47 thr \ 
ough 49 or (resid 50 through 51 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 52 through 67 or (resid 68 and (name N or name CA or name C or \ 
 name O or name CB )) or resid 69 through 79 or (resid 80 and (name N or name CA \ 
 or name C or name O or name CB )) or resid 81 through 111 or (resid 112 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 113))
}

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:             18.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     30.820
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   53.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7129
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      :  0.005   0.037   9932  Z= 0.245
  Angle     :  0.636   7.111  14146  Z= 0.381
  Chirality :  0.037   0.135   1608
  Planarity :  0.004   0.038   1241
  Dihedral  : 24.698 176.442   4184
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  2.91 %
    Favored  : 96.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.31), residues: 773
  helix:  1.10 (0.28), residues: 321
  sheet: -0.67 (0.41), residues: 155
  loop : -0.92 (0.39), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP H 774 
 HIS   0.002   0.001   HIS D  16 
 PHE   0.021   0.002   PHE C  49 
 TYR   0.019   0.001   TYR H 669 
 ARG   0.004   0.000   ARG C  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12746 (  485)
  hydrogen bonds       : angle       5.85956 ( 1230)
  covalent geometry    : bond        0.00522 ( 9932)
  covalent geometry    : angle       0.63589 (14146)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 212
  time to evaluate  : 0.803 
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: D    1 MET cc_start: 0.7020 (ttp) cc_final: 0.6163 (ptm)
REVERT: E   61 ILE cc_start: 0.8880 (mt) cc_final: 0.8677 (mm)
REVERT: E   95 ASP cc_start: 0.7720 (m-30) cc_final: 0.7417 (m-30)
REVERT: F   22 VAL cc_start: 0.8605 (m) cc_final: 0.8362 (p)
REVERT: G   39 PHE cc_start: 0.6983 (t80) cc_final: 0.6710 (t80)
REVERT: H  719 ARG cc_start: 0.8113 (ptp90) cc_final: 0.7731 (mtm-85)
  outliers start: 5
  outliers final: 3
  residues processed: 216
  average time/residue: 0.2244
  time to fit residues: 65.5308
Evaluate side-chains
  136 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 133
  time to evaluate  : 0.744 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  655 VAL
Chi-restraints excluded: chain H residue  692 VAL
Chi-restraints excluded: chain H residue  729 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 24 optimal weight:    0.3980
   chunk 47 optimal weight:    0.6980
   chunk 37 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   chunk 44 optimal weight:    0.0570
   chunk 54 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
D  13 GLN
E  56 ASN
H 803 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.075395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.061672 restraints weight = 48133.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.063195 restraints weight = 26400.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.064171 restraints weight = 17996.293|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.2516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9932  Z= 0.161
  Angle     :  0.636  11.579  14146  Z= 0.365
  Chirality :  0.036   0.141   1608
  Planarity :  0.004   0.040   1241
  Dihedral  : 28.448 169.119   2786
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 14.05 %
    Favored  : 83.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.31), residues: 773
  helix:  1.54 (0.28), residues: 332
  sheet: -0.65 (0.37), residues: 180
  loop : -0.89 (0.42), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 659 
 HIS   0.004   0.001   HIS E 104 
 PHE   0.021   0.002   PHE F  55 
 TYR   0.010   0.001   TYR E  52 
 ARG   0.006   0.001   ARG E   3 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04075 (  485)
  hydrogen bonds       : angle       4.22889 ( 1230)
  covalent geometry    : bond        0.00348 ( 9932)
  covalent geometry    : angle       0.63646 (14146)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 147
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   28 GLU cc_start: 0.8657 (tp30) cc_final: 0.8004 (tm-30)
REVERT: D   29 MET cc_start: 0.8237 (mtm) cc_final: 0.6789 (mtm)
REVERT: D   33 MET cc_start: 0.7658 (mtm) cc_final: 0.7240 (mpp)
REVERT: D   39 GLN cc_start: 0.8479 (tt0) cc_final: 0.8125 (tm-30)
REVERT: E   61 ILE cc_start: 0.8773 (mt) cc_final: 0.8503 (tt)
REVERT: F   24 SER cc_start: 0.9265 (t) cc_final: 0.8980 (p)
REVERT: F  117 PHE cc_start: 0.6551 (t80) cc_final: 0.6345 (t80)
REVERT: G   39 PHE cc_start: 0.7464 (t80) cc_final: 0.7030 (t80)
REVERT: H  654 MET cc_start: 0.6879 (mtt) cc_final: 0.6649 (mmm)
  outliers start: 17
  outliers final: 13
  residues processed: 154
  average time/residue: 0.2497
  time to fit residues: 53.8561
Evaluate side-chains
  128 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 1.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue  113 ASN
Chi-restraints excluded: chain F residue   18 LEU
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain G residue   14 VAL
Chi-restraints excluded: chain G residue   82 LEU
Chi-restraints excluded: chain G residue  110 ASP
Chi-restraints excluded: chain H residue  566 ARG
Chi-restraints excluded: chain H residue  655 VAL
Chi-restraints excluded: chain H residue  692 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 86 optimal weight:    0.4980
   chunk 71 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 52 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   chunk 60 optimal weight:    0.2980
   chunk 43 optimal weight:    0.6980
   chunk 22 optimal weight:    3.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
E  56 ASN
H 666 HIS
H 803 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.075181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.061468 restraints weight = 48864.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.062836 restraints weight = 28235.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.063753 restraints weight = 19907.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.3190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9932  Z= 0.162
  Angle     :  0.614   8.641  14146  Z= 0.355
  Chirality :  0.035   0.163   1608
  Planarity :  0.004   0.028   1241
  Dihedral  : 28.277 171.377   2785
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 15.99 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.31), residues: 773
  helix:  1.63 (0.28), residues: 328
  sheet: -0.69 (0.39), residues: 166
  loop : -0.85 (0.41), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H 659 
 HIS   0.003   0.001   HIS E 104 
 PHE   0.022   0.001   PHE F  55 
 TYR   0.008   0.001   TYR H 650 
 ARG   0.005   0.000   ARG E   3 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03958 (  485)
  hydrogen bonds       : angle       4.06601 ( 1230)
  covalent geometry    : bond        0.00351 ( 9932)
  covalent geometry    : angle       0.61397 (14146)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 135
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   28 GLU cc_start: 0.8702 (tp30) cc_final: 0.8052 (tm-30)
REVERT: C   32 GLU cc_start: 0.8418 (tp30) cc_final: 0.8036 (tp30)
REVERT: C   92 GLU cc_start: 0.6137 (pm20) cc_final: 0.5877 (pm20)
REVERT: D   29 MET cc_start: 0.8339 (mtm) cc_final: 0.8053 (mtm)
REVERT: D   39 GLN cc_start: 0.8390 (tt0) cc_final: 0.8135 (tm-30)
REVERT: E   40 GLU cc_start: 0.7246 (tp30) cc_final: 0.6744 (tp30)
REVERT: E   61 ILE cc_start: 0.8797 (mt) cc_final: 0.8538 (tt)
REVERT: E   72 MET cc_start: 0.7664 (ttm) cc_final: 0.7460 (ttm)
REVERT: F   72 MET cc_start: 0.7013 (ttt) cc_final: 0.6519 (tmm)
REVERT: F   74 LEU cc_start: 0.8588 (mt) cc_final: 0.8351 (mt)
REVERT: F   81 LEU cc_start: 0.8759 (mm) cc_final: 0.8260 (mm)
REVERT: F  106 ILE cc_start: 0.7827 (mm) cc_final: 0.7549 (tt)
REVERT: G   39 PHE cc_start: 0.7432 (t80) cc_final: 0.7064 (t80)
REVERT: G   52 TYR cc_start: 0.7632 (m-80) cc_final: 0.7302 (m-10)
  outliers start: 22
  outliers final: 15
  residues processed: 148
  average time/residue: 0.2248
  time to fit residues: 47.5480
Evaluate side-chains
  135 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 1.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain D residue   22 VAL
Chi-restraints excluded: chain D residue   26 VAL
Chi-restraints excluded: chain D residue   66 THR
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  112 TYR
Chi-restraints excluded: chain E residue  113 ASN
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain G residue   82 LEU
Chi-restraints excluded: chain H residue  566 ARG
Chi-restraints excluded: chain H residue  655 VAL
Chi-restraints excluded: chain H residue  692 VAL
Chi-restraints excluded: chain H residue  694 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 89 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0470
   chunk 55 optimal weight:    0.9990
   chunk 74 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 69 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 67 optimal weight:    7.9990
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
C  59 GLN
E  56 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.074920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.061278 restraints weight = 49175.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.062679 restraints weight = 28484.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.063576 restraints weight = 20020.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.3551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9932  Z= 0.164
  Angle     :  0.618  10.698  14146  Z= 0.352
  Chirality :  0.036   0.155   1608
  Planarity :  0.004   0.034   1241
  Dihedral  : 28.223 170.254   2785
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 16.16 %
    Favored  : 79.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.31), residues: 773
  helix:  1.57 (0.28), residues: 329
  sheet: -0.71 (0.39), residues: 165
  loop : -0.90 (0.40), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H 659 
 HIS   0.003   0.001   HIS E 104 
 PHE   0.010   0.001   PHE F 117 
 TYR   0.010   0.001   TYR H 669 
 ARG   0.004   0.000   ARG F  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03827 (  485)
  hydrogen bonds       : angle       3.97996 ( 1230)
  covalent geometry    : bond        0.00359 ( 9932)
  covalent geometry    : angle       0.61770 (14146)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 121
  time to evaluate  : 1.619 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   28 GLU cc_start: 0.8722 (tp30) cc_final: 0.8051 (tm-30)
REVERT: C   32 GLU cc_start: 0.8427 (tp30) cc_final: 0.8004 (tp30)
REVERT: D   39 GLN cc_start: 0.8403 (tt0) cc_final: 0.8155 (tm-30)
REVERT: F   72 MET cc_start: 0.7018 (ttt) cc_final: 0.6560 (tmm)
REVERT: F   99 ASP cc_start: 0.7727 (t0) cc_final: 0.7143 (m-30)
REVERT: F  106 ILE cc_start: 0.7873 (mm) cc_final: 0.7626 (tt)
REVERT: G   39 PHE cc_start: 0.7427 (t80) cc_final: 0.7057 (t80)
REVERT: H  640 ASP cc_start: 0.8571 (p0) cc_final: 0.8213 (p0)
REVERT: H  687 GLN cc_start: 0.8523 (mp10) cc_final: 0.8264 (mp10)
  outliers start: 28
  outliers final: 20
  residues processed: 137
  average time/residue: 0.1958
  time to fit residues: 39.6382
Evaluate side-chains
  126 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain D residue   22 VAL
Chi-restraints excluded: chain D residue   26 VAL
Chi-restraints excluded: chain D residue   66 THR
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  113 ASN
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain G residue   14 VAL
Chi-restraints excluded: chain G residue   21 ASP
Chi-restraints excluded: chain G residue   82 LEU
Chi-restraints excluded: chain H residue  655 VAL
Chi-restraints excluded: chain H residue  656 MET
Chi-restraints excluded: chain H residue  692 VAL
Chi-restraints excluded: chain H residue  694 ARG
Chi-restraints excluded: chain H residue  695 ILE
Chi-restraints excluded: chain H residue  735 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 67 optimal weight:    6.9990
   chunk 25 optimal weight:    0.0970
   chunk 83 optimal weight:    3.9990
   chunk 47 optimal weight:    0.6980
   chunk 29 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 39 optimal weight:    0.4980
   chunk 27 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 41 optimal weight:    0.5980
   chunk 15 optimal weight:    3.9990
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
C  93 ASN
E  56 ASN
** H 830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.074837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.061504 restraints weight = 49729.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.062953 restraints weight = 27595.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.063922 restraints weight = 18974.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7383
moved from start:          0.3858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9932  Z= 0.152
  Angle     :  0.608  11.844  14146  Z= 0.347
  Chirality :  0.035   0.157   1608
  Planarity :  0.004   0.029   1241
  Dihedral  : 28.166 169.683   2785
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 18.09 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.32), residues: 773
  helix:  1.58 (0.28), residues: 329
  sheet: -0.70 (0.39), residues: 181
  loop : -0.94 (0.42), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H 659 
 HIS   0.002   0.001   HIS E 104 
 PHE   0.017   0.001   PHE G  55 
 TYR   0.008   0.001   TYR F  62 
 ARG   0.005   0.000   ARG H 566 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03678 (  485)
  hydrogen bonds       : angle       3.88730 ( 1230)
  covalent geometry    : bond        0.00329 ( 9932)
  covalent geometry    : angle       0.60833 (14146)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 119
  time to evaluate  : 0.648 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   28 GLU cc_start: 0.8687 (tp30) cc_final: 0.8061 (tm-30)
REVERT: C   32 GLU cc_start: 0.8470 (tp30) cc_final: 0.8060 (tp30)
REVERT: D   39 GLN cc_start: 0.8447 (tt0) cc_final: 0.8129 (tm-30)
REVERT: D   79 HIS cc_start: 0.7701 (OUTLIER) cc_final: 0.6728 (t70)
REVERT: E   78 THR cc_start: 0.7300 (p) cc_final: 0.6493 (t)
REVERT: F   72 MET cc_start: 0.7036 (ttt) cc_final: 0.6573 (tmm)
REVERT: F   77 GLU cc_start: 0.8866 (tp30) cc_final: 0.8614 (tp30)
REVERT: F   81 LEU cc_start: 0.8772 (mm) cc_final: 0.8206 (mm)
REVERT: F  106 ILE cc_start: 0.7792 (mm) cc_final: 0.7579 (tt)
REVERT: G   39 PHE cc_start: 0.7415 (t80) cc_final: 0.7027 (t80)
REVERT: G   99 ASP cc_start: 0.8240 (m-30) cc_final: 0.7956 (p0)
REVERT: H  640 ASP cc_start: 0.8560 (p0) cc_final: 0.8237 (p0)
  outliers start: 24
  outliers final: 18
  residues processed: 134
  average time/residue: 0.2629
  time to fit residues: 51.9385
Evaluate side-chains
  123 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain D residue   22 VAL
Chi-restraints excluded: chain D residue   26 VAL
Chi-restraints excluded: chain D residue   79 HIS
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  113 ASN
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain F residue   62 TYR
Chi-restraints excluded: chain G residue   14 VAL
Chi-restraints excluded: chain G residue   21 ASP
Chi-restraints excluded: chain G residue   82 LEU
Chi-restraints excluded: chain H residue  655 VAL
Chi-restraints excluded: chain H residue  683 LEU
Chi-restraints excluded: chain H residue  692 VAL
Chi-restraints excluded: chain H residue  694 ARG
Chi-restraints excluded: chain H residue  735 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 76 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9980
   chunk 59 optimal weight:    6.9990
   chunk 6 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 25 optimal weight:    0.8980
   chunk 45 optimal weight:    0.3980
   chunk 26 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
E  56 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.072570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.059054 restraints weight = 48291.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.060498 restraints weight = 26647.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.061450 restraints weight = 17991.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.4110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9932  Z= 0.176
  Angle     :  0.637  13.353  14146  Z= 0.357
  Chirality :  0.036   0.170   1608
  Planarity :  0.004   0.030   1241
  Dihedral  : 28.207 169.887   2785
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 18.42 %
    Favored  : 77.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.31), residues: 773
  helix:  1.54 (0.28), residues: 328
  sheet: -0.71 (0.40), residues: 168
  loop : -0.94 (0.40), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 659 
 HIS   0.003   0.001   HIS E  48 
 PHE   0.022   0.002   PHE F  55 
 TYR   0.016   0.001   TYR H 815 
 ARG   0.005   0.000   ARG F 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04008 (  485)
  hydrogen bonds       : angle       3.96381 ( 1230)
  covalent geometry    : bond        0.00388 ( 9932)
  covalent geometry    : angle       0.63671 (14146)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 108
  time to evaluate  : 2.027 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   10 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7482 (mm-30)
REVERT: C   28 GLU cc_start: 0.8643 (tp30) cc_final: 0.8062 (tm-30)
REVERT: C   32 GLU cc_start: 0.8529 (tp30) cc_final: 0.8099 (tp30)
REVERT: D   39 GLN cc_start: 0.8465 (tt0) cc_final: 0.8062 (tm-30)
REVERT: D   79 HIS cc_start: 0.7729 (OUTLIER) cc_final: 0.6810 (t70)
REVERT: E   78 THR cc_start: 0.7198 (p) cc_final: 0.6892 (t)
REVERT: E   95 ASP cc_start: 0.7802 (m-30) cc_final: 0.7360 (m-30)
REVERT: F   72 MET cc_start: 0.7093 (ttt) cc_final: 0.6624 (tmm)
REVERT: F   81 LEU cc_start: 0.8818 (mm) cc_final: 0.8269 (mm)
REVERT: F   99 ASP cc_start: 0.7778 (t0) cc_final: 0.7351 (m-30)
REVERT: F  106 ILE cc_start: 0.7809 (mm) cc_final: 0.7579 (tt)
REVERT: G   39 PHE cc_start: 0.7506 (t80) cc_final: 0.7135 (t80)
REVERT: H  650 TYR cc_start: 0.7623 (m-10) cc_final: 0.7420 (m-10)
  outliers start: 27
  outliers final: 20
  residues processed: 123
  average time/residue: 0.2537
  time to fit residues: 46.1565
Evaluate side-chains
  128 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain D residue   22 VAL
Chi-restraints excluded: chain D residue   26 VAL
Chi-restraints excluded: chain D residue   79 HIS
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  113 ASN
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain F residue   87 ASN
Chi-restraints excluded: chain G residue   14 VAL
Chi-restraints excluded: chain G residue   21 ASP
Chi-restraints excluded: chain H residue  655 VAL
Chi-restraints excluded: chain H residue  656 MET
Chi-restraints excluded: chain H residue  683 LEU
Chi-restraints excluded: chain H residue  692 VAL
Chi-restraints excluded: chain H residue  694 ARG
Chi-restraints excluded: chain H residue  695 ILE
Chi-restraints excluded: chain H residue  735 LEU
Chi-restraints excluded: chain H residue  740 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 84 optimal weight:   10.0000
   chunk 17 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
E  50 HIS
E  56 ASN
E  80 GLN
G  31 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.069661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.056070 restraints weight = 49982.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.057455 restraints weight = 27902.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.058410 restraints weight = 19064.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.4497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   9932  Z= 0.254
  Angle     :  0.722  15.307  14146  Z= 0.401
  Chirality :  0.040   0.327   1608
  Planarity :  0.005   0.040   1241
  Dihedral  : 28.626 170.248   2785
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 18.26 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.30), residues: 773
  helix:  1.07 (0.28), residues: 327
  sheet: -0.83 (0.40), residues: 169
  loop : -1.20 (0.39), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H 659 
 HIS   0.006   0.002   HIS E 104 
 PHE   0.021   0.002   PHE C  49 
 TYR   0.010   0.001   TYR H 669 
 ARG   0.008   0.001   ARG F 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05136 (  485)
  hydrogen bonds       : angle       4.36115 ( 1230)
  covalent geometry    : bond        0.00565 ( 9932)
  covalent geometry    : angle       0.72200 (14146)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 104
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   32 GLU cc_start: 0.8573 (tp30) cc_final: 0.8315 (tp30)
REVERT: D   39 GLN cc_start: 0.8460 (tt0) cc_final: 0.8087 (tm-30)
REVERT: D   42 ARG cc_start: 0.6356 (OUTLIER) cc_final: 0.6026 (ttt-90)
REVERT: D   79 HIS cc_start: 0.7888 (OUTLIER) cc_final: 0.6941 (t70)
REVERT: E   75 ASP cc_start: 0.8906 (p0) cc_final: 0.8631 (p0)
REVERT: F   69 TYR cc_start: 0.8085 (m-80) cc_final: 0.7755 (m-80)
REVERT: F   72 MET cc_start: 0.7362 (ttt) cc_final: 0.6843 (tmm)
REVERT: G   99 ASP cc_start: 0.8548 (m-30) cc_final: 0.8069 (p0)
REVERT: H  650 TYR cc_start: 0.7818 (m-10) cc_final: 0.7479 (m-10)
REVERT: H  736 GLN cc_start: 0.7845 (tp40) cc_final: 0.7362 (tm-30)
  outliers start: 32
  outliers final: 23
  residues processed: 124
  average time/residue: 0.1989
  time to fit residues: 34.7545
Evaluate side-chains
  122 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 97
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain D residue   22 VAL
Chi-restraints excluded: chain D residue   26 VAL
Chi-restraints excluded: chain D residue   42 ARG
Chi-restraints excluded: chain D residue   79 HIS
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  113 ASN
Chi-restraints excluded: chain F residue   18 LEU
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain F residue   87 ASN
Chi-restraints excluded: chain G residue   14 VAL
Chi-restraints excluded: chain G residue   21 ASP
Chi-restraints excluded: chain G residue   31 ASN
Chi-restraints excluded: chain H residue  655 VAL
Chi-restraints excluded: chain H residue  656 MET
Chi-restraints excluded: chain H residue  683 LEU
Chi-restraints excluded: chain H residue  692 VAL
Chi-restraints excluded: chain H residue  694 ARG
Chi-restraints excluded: chain H residue  695 ILE
Chi-restraints excluded: chain H residue  735 LEU
Chi-restraints excluded: chain H residue  740 VAL
Chi-restraints excluded: chain H residue  775 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 8 optimal weight:    3.9990
   chunk 33 optimal weight:    0.5980
   chunk 55 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 40 optimal weight:    9.9990
   chunk 27 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
E  56 ASN
G  31 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.070949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.057312 restraints weight = 51071.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.058735 restraints weight = 28388.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.059696 restraints weight = 19393.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.4680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9932  Z= 0.181
  Angle     :  0.677  15.386  14146  Z= 0.378
  Chirality :  0.037   0.281   1608
  Planarity :  0.004   0.038   1241
  Dihedral  : 28.542 167.089   2785
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 18.90 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.31), residues: 773
  helix:  1.25 (0.28), residues: 328
  sheet: -0.87 (0.40), residues: 169
  loop : -1.13 (0.40), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP G  91 
 HIS   0.003   0.001   HIS F 104 
 PHE   0.032   0.002   PHE G 111 
 TYR   0.009   0.001   TYR F  52 
 ARG   0.005   0.000   ARG F  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04219 (  485)
  hydrogen bonds       : angle       4.15583 ( 1230)
  covalent geometry    : bond        0.00397 ( 9932)
  covalent geometry    : angle       0.67716 (14146)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 104
  time to evaluate  : 0.879 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   39 GLN cc_start: 0.8492 (tt0) cc_final: 0.8133 (tm-30)
REVERT: D   79 HIS cc_start: 0.7714 (OUTLIER) cc_final: 0.6844 (t70)
REVERT: F   69 TYR cc_start: 0.8068 (m-80) cc_final: 0.7653 (m-80)
REVERT: F   72 MET cc_start: 0.7377 (ttt) cc_final: 0.6853 (tmm)
REVERT: F   83 ILE cc_start: 0.6585 (mm) cc_final: 0.6355 (mm)
REVERT: F   99 ASP cc_start: 0.7831 (t0) cc_final: 0.7331 (m-30)
REVERT: F  106 ILE cc_start: 0.7769 (mm) cc_final: 0.7558 (tt)
REVERT: G   99 ASP cc_start: 0.8548 (m-30) cc_final: 0.8064 (p0)
REVERT: H  650 TYR cc_start: 0.7741 (m-10) cc_final: 0.7422 (m-10)
REVERT: H  736 GLN cc_start: 0.7873 (tp40) cc_final: 0.7403 (tm-30)
  outliers start: 28
  outliers final: 19
  residues processed: 122
  average time/residue: 0.2558
  time to fit residues: 44.4264
Evaluate side-chains
  119 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain D residue   22 VAL
Chi-restraints excluded: chain D residue   26 VAL
Chi-restraints excluded: chain D residue   79 HIS
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  113 ASN
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain F residue   62 TYR
Chi-restraints excluded: chain G residue   14 VAL
Chi-restraints excluded: chain G residue   21 ASP
Chi-restraints excluded: chain H residue  655 VAL
Chi-restraints excluded: chain H residue  656 MET
Chi-restraints excluded: chain H residue  692 VAL
Chi-restraints excluded: chain H residue  694 ARG
Chi-restraints excluded: chain H residue  695 ILE
Chi-restraints excluded: chain H residue  735 LEU
Chi-restraints excluded: chain H residue  740 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 50 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 88 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 53 optimal weight:    0.7980
   chunk 62 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 69 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
E  56 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.071117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.057633 restraints weight = 50290.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.059066 restraints weight = 27876.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.060008 restraints weight = 19005.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.4826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9932  Z= 0.179
  Angle     :  0.677  15.611  14146  Z= 0.377
  Chirality :  0.037   0.267   1608
  Planarity :  0.004   0.040   1241
  Dihedral  : 28.455 167.643   2785
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 19.71 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.31), residues: 773
  helix:  1.32 (0.28), residues: 328
  sheet: -0.79 (0.41), residues: 167
  loop : -1.09 (0.40), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP G  91 
 HIS   0.004   0.001   HIS E  50 
 PHE   0.014   0.001   PHE G 111 
 TYR   0.010   0.001   TYR F  52 
 ARG   0.005   0.000   ARG H 673 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04179 (  485)
  hydrogen bonds       : angle       4.09047 ( 1230)
  covalent geometry    : bond        0.00396 ( 9932)
  covalent geometry    : angle       0.67744 (14146)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 103
  time to evaluate  : 0.833 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   29 MET cc_start: 0.7758 (mmt) cc_final: 0.6785 (mmt)
REVERT: D   33 MET cc_start: 0.8729 (mmt) cc_final: 0.8240 (mpp)
REVERT: D   39 GLN cc_start: 0.8500 (tt0) cc_final: 0.8055 (tm-30)
REVERT: D   79 HIS cc_start: 0.7731 (OUTLIER) cc_final: 0.6811 (t70)
REVERT: E   13 MET cc_start: 0.7757 (ppp) cc_final: 0.7128 (ttp)
REVERT: F   72 MET cc_start: 0.7309 (ttt) cc_final: 0.6815 (tmm)
REVERT: F   83 ILE cc_start: 0.6637 (mm) cc_final: 0.6418 (mm)
REVERT: F   99 ASP cc_start: 0.7877 (t0) cc_final: 0.7370 (m-30)
REVERT: F  106 ILE cc_start: 0.7747 (mm) cc_final: 0.7525 (tt)
REVERT: G   72 MET cc_start: 0.6192 (tpt) cc_final: 0.5857 (tpp)
REVERT: G   99 ASP cc_start: 0.8550 (m-30) cc_final: 0.8068 (p0)
REVERT: H  650 TYR cc_start: 0.7668 (m-10) cc_final: 0.7332 (m-10)
REVERT: H  736 GLN cc_start: 0.7880 (tp40) cc_final: 0.7428 (tm-30)
  outliers start: 23
  outliers final: 20
  residues processed: 117
  average time/residue: 0.1839
  time to fit residues: 31.7687
Evaluate side-chains
  117 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain D residue   22 VAL
Chi-restraints excluded: chain D residue   26 VAL
Chi-restraints excluded: chain D residue   79 HIS
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  113 ASN
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain F residue   62 TYR
Chi-restraints excluded: chain F residue   87 ASN
Chi-restraints excluded: chain G residue   14 VAL
Chi-restraints excluded: chain G residue   21 ASP
Chi-restraints excluded: chain H residue  655 VAL
Chi-restraints excluded: chain H residue  692 VAL
Chi-restraints excluded: chain H residue  694 ARG
Chi-restraints excluded: chain H residue  695 ILE
Chi-restraints excluded: chain H residue  735 LEU
Chi-restraints excluded: chain H residue  740 VAL
Chi-restraints excluded: chain H residue  775 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 22 optimal weight:    0.1980
   chunk 39 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 74 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   chunk 27 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 90 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
E  56 ASN
G  31 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.071675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.058008 restraints weight = 51157.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.059469 restraints weight = 28471.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.060398 restraints weight = 19284.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.4914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9932  Z= 0.166
  Angle     :  0.673  15.348  14146  Z= 0.373
  Chirality :  0.036   0.249   1608
  Planarity :  0.004   0.037   1241
  Dihedral  : 28.418 166.928   2785
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 20.84 %
    Favored  : 75.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.32), residues: 773
  helix:  1.35 (0.28), residues: 328
  sheet: -0.77 (0.42), residues: 167
  loop : -1.10 (0.41), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP G  91 
 HIS   0.005   0.001   HIS E 104 
 PHE   0.025   0.002   PHE G 111 
 TYR   0.011   0.001   TYR F  52 
 ARG   0.004   0.000   ARG F  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04033 (  485)
  hydrogen bonds       : angle       4.04598 ( 1230)
  covalent geometry    : bond        0.00365 ( 9932)
  covalent geometry    : angle       0.67300 (14146)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   10 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7404 (mm-30)
REVERT: D   29 MET cc_start: 0.8001 (mmt) cc_final: 0.7521 (mmt)
REVERT: D   39 GLN cc_start: 0.8495 (tt0) cc_final: 0.8121 (tm-30)
REVERT: D   79 HIS cc_start: 0.7715 (OUTLIER) cc_final: 0.6776 (t70)
REVERT: E   13 MET cc_start: 0.7678 (ppp) cc_final: 0.6954 (ttp)
REVERT: F   72 MET cc_start: 0.7318 (ttt) cc_final: 0.6893 (tmm)
REVERT: F   83 ILE cc_start: 0.6621 (mm) cc_final: 0.6403 (mm)
REVERT: F   99 ASP cc_start: 0.7848 (t0) cc_final: 0.7352 (m-30)
REVERT: F  106 ILE cc_start: 0.7753 (mm) cc_final: 0.7539 (tt)
REVERT: G   72 MET cc_start: 0.6146 (tpt) cc_final: 0.5739 (tpt)
REVERT: G   99 ASP cc_start: 0.8589 (m-30) cc_final: 0.8104 (p0)
REVERT: H  650 TYR cc_start: 0.7610 (m-10) cc_final: 0.7276 (m-10)
REVERT: H  736 GLN cc_start: 0.7883 (tp40) cc_final: 0.7428 (tm-30)
  outliers start: 21
  outliers final: 18
  residues processed: 111
  average time/residue: 0.1910
  time to fit residues: 31.4776
Evaluate side-chains
  114 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain D residue   22 VAL
Chi-restraints excluded: chain D residue   26 VAL
Chi-restraints excluded: chain D residue   79 HIS
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   62 TYR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  113 ASN
Chi-restraints excluded: chain F residue   62 TYR
Chi-restraints excluded: chain F residue   87 ASN
Chi-restraints excluded: chain G residue   14 VAL
Chi-restraints excluded: chain G residue   21 ASP
Chi-restraints excluded: chain H residue  655 VAL
Chi-restraints excluded: chain H residue  692 VAL
Chi-restraints excluded: chain H residue  694 ARG
Chi-restraints excluded: chain H residue  695 ILE
Chi-restraints excluded: chain H residue  735 LEU
Chi-restraints excluded: chain H residue  740 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 40 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 73 optimal weight:    0.5980
   chunk 84 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
E  56 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.069365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.055757 restraints weight = 51402.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.057161 restraints weight = 29043.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.058073 restraints weight = 19935.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.5069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9932  Z= 0.244
  Angle     :  0.727  14.227  14146  Z= 0.403
  Chirality :  0.039   0.192   1608
  Planarity :  0.004   0.037   1241
  Dihedral  : 28.620 169.386   2785
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 21.00 %
    Favored  : 75.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.31), residues: 773
  helix:  0.98 (0.27), residues: 328
  sheet: -0.98 (0.41), residues: 167
  loop : -1.22 (0.39), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP H 659 
 HIS   0.006   0.002   HIS E 104 
 PHE   0.020   0.002   PHE C  49 
 TYR   0.010   0.001   TYR H 669 
 ARG   0.006   0.001   ARG F  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04968 (  485)
  hydrogen bonds       : angle       4.39973 ( 1230)
  covalent geometry    : bond        0.00545 ( 9932)
  covalent geometry    : angle       0.72661 (14146)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3591.76 seconds
wall clock time: 65 minutes 19.26 seconds (3919.26 seconds total)