Starting phenix.real_space_refine
on Sat Sep 12 15:09:09 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7ea8_31040/09_2026/7ea8_31040.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ea8_31040/09_2026/7ea8_31040.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ea8_31040/09_2026/7ea8_31040.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ea8_31040/09_2026/7ea8_31040.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ea8_31040/09_2026/7ea8_31040.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ea8_31040/09_2026/7ea8_31040.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7ea8_31040/09_2026/7ea8_31040.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7ea8_31040/09_2026/7ea8_31040.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 4902 atoms to isotropic.
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: 6
    Type Number    sf(0)   Gaussians
     Zn      3      6.06       5
     P     244      5.49       5
     S      33      5.16       5
     C    7305      2.51       5
     N    2401      2.21       5
     O    2879      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12865
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "L"
      Number of atoms: 1993
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 245, 1993
          Classifications: {'peptide': 245}
          Link IDs: {'PTRANS': 7, 'TRANS': 237}
    Chain: "A"
      Number of atoms: 818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 818
          Classifications: {'peptide': 101}
          Link IDs: {'PTRANS': 4, 'TRANS': 96}
    Chain: "B"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "C"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 799
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "D"
      Number of atoms: 720
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 720
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 771
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 771
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 3, 'TRANS': 90}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "G"
      Number of atoms: 794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 794
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
    Chain: "H"
      Number of atoms: 694
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 694
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 2, 'TRANS': 86}
    Chain: "I"
      Number of atoms: 2485
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 2485
          Classifications: {'DNA': 122}
          Link IDs: {'rna3p': 121}
    Chain: "J"
      Number of atoms: 2517
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 2517
          Classifications: {'DNA': 122}
          Link IDs: {'rna3p': 121}
    Chain: "L"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 30
          Unusual residues: {' ZN': 3}
          Classifications: {'peptide': 1, 'undetermined': 3}
          Link IDs: {None: 3}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    542  SG  CYS L1516      43.708  62.969  53.053  1.00 45.67           S
  ATOM    643  SG  CYS L1529      40.601  58.945  52.919  1.00 46.92           S
  ATOM    672  SG  CYS L1533      40.198  62.627  55.544  1.00 53.00           S
  ATOM    717  SG  CYS L1539      40.330  62.668  51.612  1.00 47.82           S
  ATOM    416  SG  CYS L1499      43.510  60.073  56.178  1.00 47.21           S
  ATOM    431  SG  CYS L1501      46.699  61.864  55.722  1.00 51.47           S
  ATOM    542  SG  CYS L1516      43.708  62.969  53.053  1.00 45.67           S
  ATOM    569  SG  CYS L1520      45.259  58.912  52.403  1.00 43.65           S
  ATOM   1863  SG  CYS L1678      39.772  46.170  17.879  1.00 67.56           S
  ATOM   1909  SG  CYS L1685      43.414  44.340  16.211  1.00 57.15           S

  Time building chain proxies: 2.74, per 1000 atoms: 0.21
  Number of scatterers: 12865
  At special positions: 0
  Unit cell: (132, 88, 141.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      3     29.99
     S      33     16.00
     P     244     15.00
     O    2879      8.00
     N    2401      7.00
     C    7305      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.05
  Conformation dependent library (CDL) restraints added in 427.2 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN L1801 "
        pdb="ZN    ZN L1801 " - pdb=" SG  CYS L1539 "
        pdb="ZN    ZN L1801 " - pdb=" SG  CYS L1516 "
        pdb="ZN    ZN L1801 " - pdb=" SG  CYS L1533 "
        pdb="ZN    ZN L1801 " - pdb=" SG  CYS L1529 "
      pdb="  ZN L1802 "
        pdb="ZN    ZN L1802 " - pdb=" SG  CYS L1520 "
        pdb="ZN    ZN L1802 " - pdb=" SG  CYS L1499 "
        pdb="ZN    ZN L1802 " - pdb=" SG  CYS L1516 "
        pdb="ZN    ZN L1802 " - pdb=" SG  CYS L1501 "
      pdb="  ZN L1803 "
        pdb="ZN    ZN L1803 " - pdb=" SG  CYS L1678 "
        pdb="ZN    ZN L1803 " - pdb=" SG  CYS L1685 "
      Number of angles added : 12


  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1830

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 12 sheets defined
      57.7% alpha, 4.6% beta
      121 base pairs and 214 stacking pairs defined.
    Time for finding SS restraints: 1.53
  Creating SS restraints...
    Processing helix  chain 'L' and resid 1520 through 1525
      removed outlier: 3.660A  pdb=" N   LEU L1524 " --> pdb=" O   CYS L1520 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   LEU L1525 " --> pdb=" O   LEU L1521 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 1520 through 1525'
    Processing helix  chain 'L' and resid 1535 through 1539
      removed outlier: 4.046A  pdb=" N   CYS L1539 " --> pdb=" O   GLY L1536 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1585 through 1597
      removed outlier: 4.080A  pdb=" N   PHE L1589 " --> pdb=" O   ASP L1585 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   LYS L1590 " --> pdb=" O   HIS L1586 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   ALA L1591 " --> pdb=" O   LYS L1587 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   LYS L1594 " --> pdb=" O   LYS L1590 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1598 through 1600
      No H-bonds generated for 'chain 'L' and resid 1598 through 1600'
    Processing helix  chain 'L' and resid 1622 through 1626
      removed outlier: 3.531A  pdb=" N   ARG L1625 " --> pdb=" O   ASN L1622 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   PHE L1626 " --> pdb=" O   CYS L1623 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 1622 through 1626'
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.597A  pdb=" N   SER A  57 " --> pdb=" O   ARG A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 76
      removed outlier: 3.657A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 114
      removed outlier: 3.849A  pdb=" N   LEU A  92 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LEU A 109 " --> pdb=" O   GLU A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.748A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.738A  pdb=" N   GLY B  56 " --> pdb=" O   GLU B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
      removed outlier: 3.996A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 27 through 36
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.706A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.815A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   VAL D  48 " --> pdb=" O   VAL D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.659A  pdb=" N   HIS D  82 " --> pdb=" O   SER D  78 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   TYR D  83 " --> pdb=" O   ARG D  79 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 104 through 123
      removed outlier: 3.905A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   THR D 122 " --> pdb=" O   VAL D 118 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   SER D 123 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 75
      removed outlier: 3.792A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 4.044A  pdb=" N   ILE E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLU E  94 " --> pdb=" O   GLY E  90 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ASP E 106 " --> pdb=" O   GLY E 102 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.718A  pdb=" N   GLY E 132 " --> pdb=" O   ARG E 128 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.026A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLY F  56 " --> pdb=" O   GLU F  52 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.978A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 27 through 37
    Processing helix  chain 'G' and resid 46 through 72
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 92 through 97
    Processing helix  chain 'H' and resid 37 through 49
      removed outlier: 3.912A  pdb=" N   GLN H  47 " --> pdb=" O   LYS H  43 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   VAL H  48 " --> pdb=" O   VAL H  44 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.718A  pdb=" N   HIS H  82 " --> pdb=" O   SER H  78 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   TYR H  83 " --> pdb=" O   ARG H  79 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 103 through 123
      removed outlier: 3.613A  pdb=" N   LYS H 108 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   HIS H 109 " --> pdb=" O   GLU H 105 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   THR H 122 " --> pdb=" O   VAL H 118 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'L' and resid 1556 through 1558
      removed outlier: 4.337A  pdb=" N   GLU L1558 " --> pdb=" O   GLY L1561 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'L' and resid 1575 through 1578
      removed outlier: 6.954A  pdb=" N   PHE L1650 " --> pdb=" O   VAL L1576 " (cutoff:3.500A)
      removed outlier: 5.112A  pdb=" N   GLU L1578 " --> pdb=" O   VAL L1648 " (cutoff:3.500A)
      removed outlier: 7.601A  pdb=" N   VAL L1648 " --> pdb=" O   GLU L1578 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 1582 through 1583
    Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.068A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.322A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.110A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA9, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.904A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AB2, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.302A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'G' and resid 77 through 78

    392 hydrogen bonds defined for protein.
    1155 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      314 hydrogen bonds
      628 hydrogen bond angles
      0 basepair planarities
      121 basepair parallelities
      214 stacking parallelities
  Total time for adding SS restraints: 2.63

  Time building geometry restraints manager: 1.42 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2951
        1.34 -     1.46: 4033
        1.46 -     1.58: 6070
        1.58 -     1.70: 486
        1.70 -     1.82: 49
  Bond restraints: 13589
  Sorted by residual:
  bond pdb=" C5'  DA I  39 "
       pdb=" C4'  DA I  39 "
    ideal  model  delta    sigma   weight residual
    1.512  1.538 -0.026 7.00e-03 2.04e+04 1.33e+01
  bond pdb=" C3'  DG J  95 "
       pdb=" C2'  DG J  95 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.19e+01
  bond pdb=" C3'  DC I  12 "
       pdb=" C2'  DC I  12 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.06e+01
  bond pdb=" C3'  DT I 104 "
       pdb=" C2'  DT I 104 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.05e+01
  bond pdb=" C3'  DG I  94 "
       pdb=" C2'  DG I  94 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.04e+01
  ... (remaining 13584 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 18176
        1.70 -     3.39: 1126
        3.39 -     5.09: 54
        5.09 -     6.79: 14
        6.79 -     8.48: 5
  Bond angle restraints: 19375
  Sorted by residual:
  angle pdb=" O5'  DA I  39 "
        pdb=" C5'  DA I  39 "
        pdb=" C4'  DA I  39 "
      ideal   model   delta    sigma   weight residual
     109.40  113.25   -3.85 8.00e-01 1.56e+00 2.31e+01
  angle pdb=" N3   DT J  42 "
        pdb=" C4   DT J  42 "
        pdb=" O4   DT J  42 "
      ideal   model   delta    sigma   weight residual
     119.90  122.70   -2.80 6.00e-01 2.78e+00 2.18e+01
  angle pdb=" N3   DT J  50 "
        pdb=" C4   DT J  50 "
        pdb=" O4   DT J  50 "
      ideal   model   delta    sigma   weight residual
     119.90  122.64   -2.74 6.00e-01 2.78e+00 2.09e+01
  angle pdb=" N3   DT J  83 "
        pdb=" C4   DT J  83 "
        pdb=" O4   DT J  83 "
      ideal   model   delta    sigma   weight residual
     119.90  122.63   -2.73 6.00e-01 2.78e+00 2.08e+01
  angle pdb=" N3   DT I  35 "
        pdb=" C4   DT I  35 "
        pdb=" O4   DT I  35 "
      ideal   model   delta    sigma   weight residual
     119.90  122.55   -2.65 6.00e-01 2.78e+00 1.96e+01
  ... (remaining 19370 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.88: 6124
       27.88 -    55.77: 1292
       55.77 -    83.65: 111
       83.65 -   111.53: 0
      111.53 -   139.41: 3
  Dihedral angle restraints: 7530
    sinusoidal: 4686
      harmonic: 2844
  Sorted by residual:
  dihedral pdb=" CA  TYR L1666 "
           pdb=" C   TYR L1666 "
           pdb=" N   GLN L1667 "
           pdb=" CA  GLN L1667 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.21   20.79     0      5.00e+00 4.00e-02 1.73e+01
  dihedral pdb=" CA  GLU L1478 "
           pdb=" C   GLU L1478 "
           pdb=" N   ASN L1479 "
           pdb=" CA  ASN L1479 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.36  -20.64     0      5.00e+00 4.00e-02 1.70e+01
  dihedral pdb=" C4'  DC J 126 "
           pdb=" C3'  DC J 126 "
           pdb=" O3'  DC J 126 "
           pdb=" P    DC J 127 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   80.59  139.41     1      3.50e+01 8.16e-04 1.38e+01
  ... (remaining 7527 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1609
       0.052 -    0.104: 489
       0.104 -    0.156: 69
       0.156 -    0.208: 5
       0.208 -    0.260: 1
  Chirality restraints: 2173
  Sorted by residual:
  chirality pdb=" CB  ILE A 119 "
            pdb=" CA  ILE A 119 "
            pdb=" CG1 ILE A 119 "
            pdb=" CG2 ILE A 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.69e+00
  chirality pdb=" CB  ILE L1494 "
            pdb=" CA  ILE L1494 "
            pdb=" CG1 ILE L1494 "
            pdb=" CG2 ILE L1494 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.84   -0.19 2.00e-01 2.50e+01 9.30e-01
  chirality pdb=" CG  LEU E  61 "
            pdb=" CB  LEU E  61 "
            pdb=" CD1 LEU E  61 "
            pdb=" CD2 LEU E  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 8.92e-01
  ... (remaining 2170 not shown)

  Planarity restraints: 1621
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU H 102 "   -0.034 5.00e-02 4.00e+02   5.10e-02 4.16e+00
        pdb=" N   PRO H 103 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO H 103 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO H 103 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C  79 "    0.033 5.00e-02 4.00e+02   5.01e-02 4.02e+00
        pdb=" N   PRO C  80 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO C  80 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO C  80 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 102 "    0.033 5.00e-02 4.00e+02   5.00e-02 3.99e+00
        pdb=" N   PRO D 103 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO D 103 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO D 103 "    0.028 5.00e-02 4.00e+02
  ... (remaining 1618 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.82: 3109
        2.82 -     3.34: 10018
        3.34 -     3.86: 22773
        3.86 -     4.38: 26823
        4.38 -     4.90: 39763
  Nonbonded interactions: 102486
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D  90 "
            pdb=" OE1 GLU D  93 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" ND2 ASN L1634 "
            pdb=" O   GLU L1661 "
     model   vdw
     2.379 3.120
  nonbonded pdb=" OD2 ASP A 106 "
            pdb=" NH2 ARG A 131 "
     model   vdw
     2.381 3.120
  nonbonded pdb=" O   LEU A 103 "
            pdb=" OG1 THR A 107 "
     model   vdw
     2.382 3.040
  nonbonded pdb=" O   GLU L1578 "
            pdb=" ND2 ASN L1622 "
     model   vdw
     2.387 3.120
  ... (remaining 102481 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 39 through 76 or resid 78 through 133))
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 15 through 117)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 35 through 123)
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     14.870
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
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      :  0.011   0.487  13600  Z= 0.601
  Angle     :  0.906  27.780  19387  Z= 0.682
  Chirality :  0.048   0.260   2173
  Planarity :  0.006   0.051   1621
  Dihedral  : 24.015 139.413   5700
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.23 (0.21), residues: 964
  helix: -1.58 (0.17), residues: 540
  sheet: -2.04 (0.90), residues: 31
  loop : -2.88 (0.25), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 116 
 TYR   0.024   0.002   TYR H  42 
 PHE   0.021   0.002   PHE L1664 
 TRP   0.014   0.002   TRP L1640 
 HIS   0.005   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00564 /  0.50 (13589)
  covalent geometry    : angle       0.83618 /  0.68 (19375)
  hydrogen bonds       : bond        0.10867 /  7.23 (  706)
  hydrogen bonds       : angle       4.47227 /  3.00 ( 1783)
  metal coordination   : bond        0.35222 / 21.15 (   10)
  metal coordination   : angle      14.08458 /  7.21 (   12)
  Misc. bond           : bond        0.00016 /  0.01 (    1)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
REVERT: L 1486 LYS cc_start: 0.4525 (pmtt) cc_final: 0.4283 (mmtt)
REVERT: L 1599 ASN cc_start: 0.4018 (m-40) cc_final: 0.3670 (t0)
REVERT: B   68 ASP cc_start: 0.7662 (m-30) cc_final: 0.7440 (m-30)
REVERT: C   75 LYS cc_start: 0.8601 (mmtp) cc_final: 0.8335 (mmtt)
REVERT: D   62 MET cc_start: 0.8493 (mmm) cc_final: 0.8249 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 238
  average time/residue: 0.2067
  time to fit residues: 61.5338
Evaluate side-chains
  157 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:   20.0000
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:   20.0000
   chunk 113 optimal weight:   20.0000
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:   20.0000
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    7.9990
   chunk 117 optimal weight:   50.0000
   overall best weight:    3.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** L1541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L1548 GLN
L1601 ASN
A  39 HIS
A  68 GLN
B  93 GLN
C  68 ASN
F  27 GLN
H  47 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.189060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.145897 restraints weight = 14127.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3609 rms_B_bonded: 1.31
r_work: 0.3104 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8563
moved from start:          0.2162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  13600  Z= 0.246
  Angle     :  0.729  12.588  19387  Z= 0.406
  Chirality :  0.049   0.186   2173
  Planarity :  0.006   0.047   1621
  Dihedral  : 29.000 145.984   3741
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  8.56 %
    Favored  : 90.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.39 (0.25), residues: 964
  helix:  0.38 (0.22), residues: 547
  sheet: -1.69 (0.86), residues: 31
  loop : -2.86 (0.25), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  55 
 TYR   0.017   0.002   TYR C  50 
 PHE   0.020   0.003   PHE C  25 
 TRP   0.013   0.003   TRP L1562 
 HIS   0.008   0.002   HIS H  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00535 /  0.25 (13589)
  covalent geometry    : angle       0.70976 /  0.41 (19375)
  hydrogen bonds       : bond        0.07937 /  5.16 (  706)
  hydrogen bonds       : angle       3.22332 /  2.14 ( 1783)
  metal coordination   : bond        0.01819 /  1.11 (   10)
  metal coordination   : angle       6.77951 /  3.53 (   12)
  Misc. bond           : bond        0.00048 /  0.03 (    1)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 149
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
REVERT: L 1477 GLU cc_start: 0.4949 (tp30) cc_final: 0.4636 (tm-30)
REVERT: A  115 LYS cc_start: 0.7749 (mttp) cc_final: 0.7445 (mtmm)
REVERT: C   75 LYS cc_start: 0.8924 (mmtp) cc_final: 0.8662 (mmtt)
REVERT: C  104 GLN cc_start: 0.8329 (mm-40) cc_final: 0.8062 (mt0)
REVERT: G   36 LYS cc_start: 0.8432 (tttt) cc_final: 0.7785 (mmtm)
REVERT: H   47 GLN cc_start: 0.8288 (mt0) cc_final: 0.7978 (mt0)
  outliers start: 11
  outliers final: 4
  residues processed: 155
  average time/residue: 0.1855
  time to fit residues: 36.8877
Evaluate side-chains
  142 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 138
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue 1636 GLU
Chi-restraints excluded: chain L residue 1642 VAL
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain E residue   73 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 94 optimal weight:   50.0000
   chunk 24 optimal weight:    3.9990
   chunk 34 optimal weight:    0.5980
   chunk 39 optimal weight:    0.7980
   chunk 26 optimal weight:    0.5980
   chunk 117 optimal weight:   50.0000
   chunk 28 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   overall best weight:    0.9982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** L1541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L1545 GLN
E  68 GLN
F  27 GLN
H  63 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.192619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.149291 restraints weight = 14261.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 1.19
r_work: 0.3173 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.2238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  13600  Z= 0.138
  Angle     :  0.594   9.689  19387  Z= 0.343
  Chirality :  0.043   0.192   2173
  Planarity :  0.004   0.044   1621
  Dihedral  : 29.055 147.727   3741
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  :  7.96 %
    Favored  : 90.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.27), residues: 964
  helix:  1.43 (0.23), residues: 549
  sheet: -1.81 (0.92), residues: 28
  loop : -2.61 (0.26), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  81 
 TYR   0.012   0.001   TYR L1596 
 PHE   0.034   0.002   PHE L1589 
 TRP   0.006   0.001   TRP L1562 
 HIS   0.004   0.001   HIS L1586 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00232 /  0.14 (13589)
  covalent geometry    : angle       0.58192 /  0.34 (19375)
  hydrogen bonds       : bond        0.05809 /  3.79 (  706)
  hydrogen bonds       : angle       2.87820 /  1.92 ( 1783)
  metal coordination   : bond        0.00888 /  0.44 (   10)
  metal coordination   : angle       4.86526 /  2.60 (   12)
  Misc. bond           : bond        0.00032 /  0.02 (    1)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 142
  time to evaluate  : 0.595 
Fit side-chains
   revert: symmetry clash
REVERT: L 1465 LYS cc_start: 0.3906 (ttpt) cc_final: 0.3055 (mtmt)
REVERT: L 1514 ILE cc_start: 0.6089 (OUTLIER) cc_final: 0.5748 (pp)
REVERT: L 1545 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7051 (mp10)
REVERT: A  115 LYS cc_start: 0.7456 (mttp) cc_final: 0.7171 (mtmm)
REVERT: C   75 LYS cc_start: 0.8952 (mmtp) cc_final: 0.8737 (mmtt)
REVERT: C   89 ASN cc_start: 0.8740 (m-40) cc_final: 0.8539 (m-40)
REVERT: G   36 LYS cc_start: 0.8340 (tttt) cc_final: 0.7725 (mmtm)
  outliers start: 14
  outliers final: 7
  residues processed: 150
  average time/residue: 0.1726
  time to fit residues: 33.8478
Evaluate side-chains
  145 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 136
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue 1514 ILE
Chi-restraints excluded: chain L residue 1545 GLN
Chi-restraints excluded: chain L residue 1636 GLU
Chi-restraints excluded: chain L residue 1642 VAL
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue   87 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 64 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 117 optimal weight:   50.0000
   chunk 87 optimal weight:    1.9990
   overall best weight:    1.3588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** L1541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L1545 GLN
L1599 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.191530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.148515 restraints weight = 14187.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 1.15
r_work: 0.3223 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.2375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  13600  Z= 0.144
  Angle     :  0.580   7.399  19387  Z= 0.337
  Chirality :  0.043   0.182   2173
  Planarity :  0.004   0.042   1621
  Dihedral  : 29.089 147.955   3741
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  9.17 %
    Favored  : 89.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.27), residues: 964
  helix:  1.83 (0.23), residues: 548
  sheet: -1.25 (0.89), residues: 33
  loop : -2.54 (0.26), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG L1546 
 TYR   0.009   0.001   TYR C  57 
 PHE   0.013   0.002   PHE L1589 
 TRP   0.008   0.001   TRP L1562 
 HIS   0.004   0.001   HIS D  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.14 (13589)
  covalent geometry    : angle       0.57190 /  0.34 (19375)
  hydrogen bonds       : bond        0.05822 /  3.79 (  706)
  hydrogen bonds       : angle       2.84048 /  1.88 ( 1783)
  metal coordination   : bond        0.00561 /  0.29 (   10)
  metal coordination   : angle       3.98461 /  2.11 (   12)
  Misc. bond           : bond        0.00016 /  0.01 (    1)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 139
  time to evaluate  : 0.364 
Fit side-chains
REVERT: L 1514 ILE cc_start: 0.6112 (OUTLIER) cc_final: 0.5768 (pp)
REVERT: A  115 LYS cc_start: 0.7499 (mttp) cc_final: 0.7201 (mtmm)
REVERT: C   89 ASN cc_start: 0.8733 (m-40) cc_final: 0.8521 (m-40)
REVERT: G   36 LYS cc_start: 0.8321 (tttt) cc_final: 0.7729 (mmtm)
  outliers start: 12
  outliers final: 10
  residues processed: 146
  average time/residue: 0.1720
  time to fit residues: 32.7629
Evaluate side-chains
  146 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 135
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue 1514 ILE
Chi-restraints excluded: chain L residue 1636 GLU
Chi-restraints excluded: chain L residue 1642 VAL
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain H residue  101 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 69 optimal weight:    0.4980
   chunk 115 optimal weight:   20.0000
   chunk 59 optimal weight:    0.6980
   chunk 97 optimal weight:   20.0000
   chunk 90 optimal weight:    4.9990
   chunk 114 optimal weight:   20.0000
   chunk 110 optimal weight:   20.0000
   chunk 20 optimal weight:   10.0000
   chunk 52 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   overall best weight:    2.4184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L1541 ASN
L1643 ASN
E  68 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.188393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.144516 restraints weight = 14281.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.3595 rms_B_bonded: 1.09
r_work: 0.3159 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          0.2653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13600  Z= 0.186
  Angle     :  0.628   6.993  19387  Z= 0.358
  Chirality :  0.045   0.187   2173
  Planarity :  0.004   0.043   1621
  Dihedral  : 29.152 148.554   3741
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  9.65 %
    Favored  : 88.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.28), residues: 964
  helix:  1.89 (0.23), residues: 543
  sheet: -1.10 (0.92), residues: 33
  loop : -2.54 (0.27), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  55 
 TYR   0.011   0.002   TYR D 121 
 PHE   0.021   0.002   PHE C  25 
 TRP   0.011   0.002   TRP L1562 
 HIS   0.005   0.001   HIS D  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00390 /  0.19 (13589)
  covalent geometry    : angle       0.62212 /  0.36 (19375)
  hydrogen bonds       : bond        0.06924 /  4.51 (  706)
  hydrogen bonds       : angle       2.96259 /  1.96 ( 1783)
  metal coordination   : bond        0.00495 /  0.26 (   10)
  metal coordination   : angle       3.50970 /  1.84 (   12)
  Misc. bond           : bond        0.00013 /  0.01 (    1)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 141
  time to evaluate  : 0.370 
Fit side-chains
REVERT: L 1514 ILE cc_start: 0.6109 (OUTLIER) cc_final: 0.5742 (pp)
REVERT: L 1582 GLU cc_start: 0.6117 (mt-10) cc_final: 0.5439 (tp30)
REVERT: A   73 GLU cc_start: 0.8176 (tt0) cc_final: 0.7934 (tt0)
REVERT: A  115 LYS cc_start: 0.7737 (mttp) cc_final: 0.7460 (mtmm)
REVERT: G   36 LYS cc_start: 0.8412 (tttt) cc_final: 0.7775 (mmtm)
  outliers start: 12
  outliers final: 10
  residues processed: 148
  average time/residue: 0.1703
  time to fit residues: 33.2316
Evaluate side-chains
  148 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 137
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue 1514 ILE
Chi-restraints excluded: chain L residue 1636 GLU
Chi-restraints excluded: chain L residue 1642 VAL
Chi-restraints excluded: chain L residue 1643 ASN
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain H residue  101 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 88 optimal weight:    0.8980
   chunk 111 optimal weight:   20.0000
   chunk 77 optimal weight:    0.0270
   chunk 89 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 78 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9980
   chunk 81 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 97 optimal weight:   20.0000
   chunk 2 optimal weight:   20.0000
   overall best weight:    1.3840

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L1643 ASN
E  68 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.189827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.145379 restraints weight = 14164.703|
|-----------------------------------------------------------------------------|
r_work (start): 0.3599 rms_B_bonded: 1.12
r_work: 0.3188 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13600  Z= 0.146
  Angle     :  0.591   6.814  19387  Z= 0.341
  Chirality :  0.043   0.187   2173
  Planarity :  0.004   0.042   1621
  Dihedral  : 29.155 149.402   3741
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 10.86 %
    Favored  : 87.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.28), residues: 964
  helix:  2.12 (0.23), residues: 541
  sheet: -0.95 (0.92), residues: 33
  loop : -2.41 (0.27), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G  81 
 TYR   0.021   0.001   TYR D  42 
 PHE   0.015   0.002   PHE L1589 
 TRP   0.010   0.002   TRP L1562 
 HIS   0.004   0.001   HIS D  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00270 /  0.15 (13589)
  covalent geometry    : angle       0.58633 /  0.34 (19375)
  hydrogen bonds       : bond        0.06105 /  3.98 (  706)
  hydrogen bonds       : angle       2.86088 /  1.89 ( 1783)
  metal coordination   : bond        0.00444 /  0.23 (   10)
  metal coordination   : angle       3.03809 /  1.59 (   12)
  Misc. bond           : bond        0.00002 /  0.00 (    1)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 143
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
REVERT: L 1544 PHE cc_start: 0.7291 (m-10) cc_final: 0.7064 (m-10)
REVERT: L 1582 GLU cc_start: 0.6081 (mt-10) cc_final: 0.5479 (tp30)
REVERT: L 1606 PHE cc_start: 0.6509 (m-10) cc_final: 0.6299 (m-80)
REVERT: L 1627 MET cc_start: 0.5556 (mmm) cc_final: 0.5286 (mmm)
REVERT: A   73 GLU cc_start: 0.8121 (tt0) cc_final: 0.7857 (tt0)
REVERT: A  115 LYS cc_start: 0.7647 (mttp) cc_final: 0.7374 (mtmm)
  outliers start: 10
  outliers final: 7
  residues processed: 149
  average time/residue: 0.1739
  time to fit residues: 33.8640
Evaluate side-chains
  150 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 143
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue 1636 GLU
Chi-restraints excluded: chain L residue 1642 VAL
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain F residue   80 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 115 optimal weight:   20.0000
   chunk 117 optimal weight:   50.0000
   chunk 45 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 66 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   chunk 10 optimal weight:    4.9990
   chunk 104 optimal weight:   20.0000
   chunk 75 optimal weight:    3.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E  68 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.186735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.141744 restraints weight = 14111.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 1.03
r_work: 0.3153 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8547
moved from start:          0.2906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13600  Z= 0.203
  Angle     :  0.643   6.658  19387  Z= 0.364
  Chirality :  0.046   0.182   2173
  Planarity :  0.005   0.044   1621
  Dihedral  : 29.200 149.068   3741
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 11.34 %
    Favored  : 87.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.27), residues: 964
  helix:  1.84 (0.23), residues: 548
  sheet: -0.95 (0.90), residues: 33
  loop : -2.50 (0.27), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  55 
 TYR   0.013   0.002   TYR C  57 
 PHE   0.021   0.002   PHE A  84 
 TRP   0.006   0.002   TRP L1562 
 HIS   0.006   0.001   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00445 /  0.20 (13589)
  covalent geometry    : angle       0.63828 /  0.36 (19375)
  hydrogen bonds       : bond        0.07396 /  4.82 (  706)
  hydrogen bonds       : angle       2.99840 /  1.97 ( 1783)
  metal coordination   : bond        0.00437 /  0.24 (   10)
  metal coordination   : angle       3.09533 /  1.58 (   12)
  Misc. bond           : bond        0.00005 /  0.00 (    1)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 145
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
REVERT: L 1582 GLU cc_start: 0.6122 (mt-10) cc_final: 0.5522 (tp30)
REVERT: L 1606 PHE cc_start: 0.6665 (m-10) cc_final: 0.6289 (m-80)
REVERT: L 1627 MET cc_start: 0.5648 (mmm) cc_final: 0.5287 (mmm)
REVERT: A  115 LYS cc_start: 0.7840 (mttp) cc_final: 0.7487 (mtmm)
  outliers start: 10
  outliers final: 9
  residues processed: 150
  average time/residue: 0.1685
  time to fit residues: 33.1282
Evaluate side-chains
  152 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 143
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue 1636 GLU
Chi-restraints excluded: chain L residue 1642 VAL
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain H residue  101 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 72 optimal weight:    0.9980
   chunk 113 optimal weight:   20.0000
   chunk 114 optimal weight:   20.0000
   chunk 54 optimal weight:    0.6980
   chunk 42 optimal weight:    0.7980
   chunk 107 optimal weight:   20.0000
   chunk 9 optimal weight:   10.0000
   chunk 36 optimal weight:    3.9990
   chunk 14 optimal weight:   20.0000
   chunk 55 optimal weight:    0.7980
   overall best weight:    1.4582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L1548 GLN
E  68 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.188406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.144215 restraints weight = 14052.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 1.06
r_work: 0.3180 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.2904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13600  Z= 0.152
  Angle     :  0.606   7.340  19387  Z= 0.346
  Chirality :  0.044   0.190   2173
  Planarity :  0.004   0.044   1621
  Dihedral  : 29.184 149.817   3741
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 11.82 %
    Favored  : 87.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.28), residues: 964
  helix:  2.04 (0.23), residues: 548
  sheet: -0.87 (0.90), residues: 33
  loop : -2.36 (0.28), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  35 
 TYR   0.018   0.001   TYR D  42 
 PHE   0.025   0.002   PHE L1575 
 TRP   0.005   0.001   TRP L1562 
 HIS   0.004   0.001   HIS D  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.15 (13589)
  covalent geometry    : angle       0.60224 /  0.35 (19375)
  hydrogen bonds       : bond        0.06435 /  4.20 (  706)
  hydrogen bonds       : angle       2.90413 /  1.92 ( 1783)
  metal coordination   : bond        0.00445 /  0.24 (   10)
  metal coordination   : angle       2.66046 /  1.35 (   12)
  Misc. bond           : bond        0.00003 /  0.00 (    1)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 146
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
REVERT: L 1582 GLU cc_start: 0.6088 (mt-10) cc_final: 0.5527 (tp30)
REVERT: L 1606 PHE cc_start: 0.6685 (m-10) cc_final: 0.6320 (m-80)
REVERT: L 1627 MET cc_start: 0.5706 (mmm) cc_final: 0.5354 (mmm)
REVERT: A  115 LYS cc_start: 0.7770 (mttp) cc_final: 0.7407 (mtmm)
  outliers start: 8
  outliers final: 8
  residues processed: 150
  average time/residue: 0.1721
  time to fit residues: 34.0140
Evaluate side-chains
  146 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 138
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue 1636 GLU
Chi-restraints excluded: chain L residue 1642 VAL
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain D residue   51 ASP
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain F residue   80 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 78 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 18 optimal weight:    8.9990
   chunk 29 optimal weight:    2.9990
   chunk 9 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 21 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   overall best weight:    1.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L1548 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.187999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.144095 restraints weight = 14148.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.3585 rms_B_bonded: 1.10
r_work: 0.3166 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.2949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13600  Z= 0.166
  Angle     :  0.605   7.215  19387  Z= 0.347
  Chirality :  0.044   0.184   2173
  Planarity :  0.004   0.044   1621
  Dihedral  : 29.189 149.600   3741
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 12.18 %
    Favored  : 86.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.47 (0.28), residues: 964
  helix:  2.05 (0.23), residues: 546
  sheet: -0.84 (0.91), residues: 33
  loop : -2.32 (0.28), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG G  35 
 TYR   0.012   0.001   TYR C  57 
 PHE   0.017   0.002   PHE L1575 
 TRP   0.003   0.001   TRP L1562 
 HIS   0.004   0.001   HIS D  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00336 /  0.17 (13589)
  covalent geometry    : angle       0.60115 /  0.35 (19375)
  hydrogen bonds       : bond        0.06597 /  4.29 (  706)
  hydrogen bonds       : angle       2.90102 /  1.92 ( 1783)
  metal coordination   : bond        0.00371 /  0.20 (   10)
  metal coordination   : angle       2.62805 /  1.33 (   12)
  Misc. bond           : bond        0.00004 /  0.00 (    1)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 142
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
REVERT: L 1582 GLU cc_start: 0.6209 (mt-10) cc_final: 0.5593 (tp30)
REVERT: L 1606 PHE cc_start: 0.6667 (m-10) cc_final: 0.6312 (m-80)
REVERT: L 1627 MET cc_start: 0.5821 (mmm) cc_final: 0.5454 (mmm)
REVERT: A  115 LYS cc_start: 0.7824 (mttp) cc_final: 0.7471 (mtmm)
REVERT: C   36 LYS cc_start: 0.8509 (mptt) cc_final: 0.8291 (mptt)
  outliers start: 9
  outliers final: 7
  residues processed: 147
  average time/residue: 0.1717
  time to fit residues: 33.1318
Evaluate side-chains
  147 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 140
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue 1636 GLU
Chi-restraints excluded: chain L residue 1642 VAL
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain D residue   51 ASP
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain F residue   80 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 94 optimal weight:   50.0000
   chunk 117 optimal weight:   50.0000
   chunk 79 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 52 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 83 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9980
   chunk 22 optimal weight:    9.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    1.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L1548 GLN
B  25 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.187944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.143901 restraints weight = 14133.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3588 rms_B_bonded: 1.16
r_work: 0.3136 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.2984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  13600  Z= 0.165
  Angle     :  0.605   7.274  19387  Z= 0.347
  Chirality :  0.044   0.186   2173
  Planarity :  0.004   0.044   1621
  Dihedral  : 29.189 149.824   3741
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 12.30 %
    Favored  : 86.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.28), residues: 964
  helix:  2.07 (0.23), residues: 546
  sheet: -0.90 (0.91), residues: 33
  loop : -2.24 (0.28), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  35 
 TYR   0.011   0.001   TYR C  57 
 PHE   0.015   0.002   PHE L1589 
 TRP   0.003   0.001   TRP L1562 
 HIS   0.004   0.001   HIS D  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00335 /  0.17 (13589)
  covalent geometry    : angle       0.60174 /  0.35 (19375)
  hydrogen bonds       : bond        0.06556 /  4.27 (  706)
  hydrogen bonds       : angle       2.90538 /  1.92 ( 1783)
  metal coordination   : bond        0.00374 /  0.20 (   10)
  metal coordination   : angle       2.47397 /  1.24 (   12)
  Misc. bond           : bond        0.00002 /  0.00 (    1)

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

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

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1928 Ramachandran restraints generated.
    964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 142
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
REVERT: L 1582 GLU cc_start: 0.6243 (mt-10) cc_final: 0.5578 (tp30)
REVERT: L 1606 PHE cc_start: 0.6705 (m-10) cc_final: 0.6291 (m-80)
REVERT: L 1627 MET cc_start: 0.5845 (mmm) cc_final: 0.5420 (mmm)
REVERT: L 1638 GLN cc_start: 0.8110 (mt0) cc_final: 0.7764 (mt0)
REVERT: A  115 LYS cc_start: 0.7817 (mttp) cc_final: 0.7442 (mtmm)
REVERT: C   36 LYS cc_start: 0.8528 (mptt) cc_final: 0.8311 (mptt)
  outliers start: 8
  outliers final: 8
  residues processed: 146
  average time/residue: 0.1690
  time to fit residues: 32.3620
Evaluate side-chains
  150 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 142
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue 1636 GLU
Chi-restraints excluded: chain L residue 1642 VAL
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain D residue   51 ASP
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain F residue   80 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 12 optimal weight:    6.9990
   chunk 56 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 117 optimal weight:   50.0000
   chunk 96 optimal weight:   20.0000
   chunk 99 optimal weight:   20.0000
   chunk 77 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   overall best weight:    2.1588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L1548 GLN
B  25 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.187413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.143187 restraints weight = 14152.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 1.07
r_work: 0.3139 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8555
moved from start:          0.3049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  13600  Z= 0.173
  Angle     :  0.612   7.661  19387  Z= 0.350
  Chirality :  0.044   0.185   2173
  Planarity :  0.004   0.044   1621
  Dihedral  : 29.193 149.759   3741
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 12.55 %
    Favored  : 86.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.49 (0.28), residues: 964
  helix:  2.02 (0.23), residues: 546
  sheet: -0.89 (0.93), residues: 33
  loop : -2.23 (0.28), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G  35 
 TYR   0.012   0.001   TYR C  57 
 PHE   0.014   0.002   PHE C  25 
 TRP   0.004   0.001   TRP L1562 
 HIS   0.004   0.001   HIS D  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00359 /  0.17 (13589)
  covalent geometry    : angle       0.60950 /  0.35 (19375)
  hydrogen bonds       : bond        0.06757 /  4.40 (  706)
  hydrogen bonds       : angle       2.92868 /  1.94 ( 1783)
  metal coordination   : bond        0.00352 /  0.20 (   10)
  metal coordination   : angle       2.35850 /  1.20 (   12)
  Misc. bond           : bond        0.00004 /  0.00 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2802.66 seconds
wall clock time: 48 minutes 38.09 seconds (2918.09 seconds total)