Starting phenix.real_space_refine
on Tue Feb  3 17:58:06 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9tgw_55912/02_2026/9tgw_55912.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9tgw_55912/02_2026/9tgw_55912.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9tgw_55912/02_2026/9tgw_55912.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9tgw_55912/02_2026/9tgw_55912.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9tgw_55912/02_2026/9tgw_55912.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9tgw_55912/02_2026/9tgw_55912.map"
  }
  resolution = 2.67
  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=   0.011
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      24      5.49       5
     S      33      5.16       5
     C    3585      2.51       5
     N     981      2.21       5
     O    1207      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5830
  Number of models: 1
  Model: ""
    Number of chains: 16
    Chain: "A"
      Number of atoms: 954
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 954
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 2, 'TRANS': 118}
    Chain: "B"
      Number of atoms: 820
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 820
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 4, 'TRANS': 101}
    Chain: "C"
      Number of atoms: 954
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 954
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 2, 'TRANS': 118}
    Chain: "D"
      Number of atoms: 954
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 954
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 2, 'TRANS': 118}
    Chain: "E"
      Number of atoms: 820
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 820
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 4, 'TRANS': 101}
    Chain: "F"
      Number of atoms: 820
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 820
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 4, 'TRANS': 101}
    Chain: "O"
      Number of atoms: 247
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 12, 246
          Classifications: {'DNA': 12}
          Link IDs: {'rna3p': 11}
      Conformer: "B"
        Number of residues, atoms: 12, 246
          Classifications: {'DNA': 12}
          Link IDs: {'rna3p': 11}
          bond proxies already assigned to first conformer: 273
    Chain: "P"
      Number of atoms: 246
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 246
          Classifications: {'DNA': 12}
          Link IDs: {'rna3p': 11}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "D"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "E"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "F"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "O"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "P"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 1.63, per 1000 atoms: 0.28
  Number of scatterers: 5830
  At special positions: 0
  Unit cell: (92.72, 98.04, 111.72, 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      33     16.00
     P      24     15.00
     O    1207      8.00
     N     981      7.00
     C    3585      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  98 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  98 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  98 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  23 " - pdb=" SG  CYS E  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  23 " - pdb=" SG  CYS F  88 " distance=2.04

  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: 0.52
  Conformation dependent library (CDL) restraints added in 353.8 milliseconds
  

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1248

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 16 sheets defined
      7.3% alpha, 44.8% beta
      12 base pairs and 10 stacking pairs defined.
    Time for finding SS restraints: 0.77
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 32
      removed outlier: 3.706A  pdb=" N   THR A  31 " --> pdb=" O   ASN A  28 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   TYR A  32 " --> pdb=" O   PHE A  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 28 through 32'
    Processing helix  chain 'A' and resid 53 through 57
    Processing helix  chain 'A' and resid 89 through 93
      removed outlier: 3.721A  pdb=" N   ASP A  92 " --> pdb=" O   LYS A  89 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   THR A  93 " --> pdb=" O   ALA A  90 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 89 through 93'
    Processing helix  chain 'B' and resid 79 through 83
      removed outlier: 4.029A  pdb=" N   ILE B  83 " --> pdb=" O   PRO B  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 32
      removed outlier: 3.726A  pdb=" N   TYR C  32 " --> pdb=" O   PHE C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 53 through 57
    Processing helix  chain 'C' and resid 89 through 93
      removed outlier: 3.890A  pdb=" N   THR C  93 " --> pdb=" O   ALA C  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 28 through 32
      removed outlier: 3.562A  pdb=" N   THR D  31 " --> pdb=" O   ASN D  28 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   TYR D  32 " --> pdb=" O   PHE D  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 28 through 32'
    Processing helix  chain 'D' and resid 89 through 93
      removed outlier: 3.809A  pdb=" N   THR D  93 " --> pdb=" O   ALA D  90 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 79 through 83
      removed outlier: 3.771A  pdb=" N   ILE E  83 " --> pdb=" O   PRO E  80 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12
      removed outlier: 6.842A  pdb=" N   MET A  34 " --> pdb=" O   ARG A  50 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   ARG A  50 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   TRP A  36 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12
      removed outlier: 3.654A  pdb=" N   ILE B  48 " --> pdb=" O   TRP B  35 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   GLN B  37 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
      removed outlier: 5.475A  pdb=" N   LEU B  46 " --> pdb=" O   GLN B  37 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12
      removed outlier: 4.118A  pdb=" N   THR B  97 " --> pdb=" O   GLN B  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 19 through 24
      removed outlier: 3.737A  pdb=" N   ASP B  70 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 7
    Processing sheet with id=AA7, first strand: chain 'C' and resid 11 through 12
      removed outlier: 6.962A  pdb=" N   MET C  34 " --> pdb=" O   ARG C  50 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   ARG C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 3 through 7
    Processing sheet with id=AA9, first strand: chain 'D' and resid 10 through 12
      removed outlier: 6.307A  pdb=" N   GLY D  10 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   MET D  34 " --> pdb=" O   ARG D  50 " (cutoff:3.500A)
      removed outlier: 4.760A  pdb=" N   ARG D  50 " --> pdb=" O   MET D  34 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12
      removed outlier: 6.307A  pdb=" N   GLY D  10 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   TYR D 111 " --> pdb=" O   ARG D 100 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 4 through 5
      removed outlier: 3.554A  pdb=" N   VAL E  19 " --> pdb=" O   ILE E  75 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ASP E  70 " --> pdb=" O   SER E  67 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.119A  pdb=" N   LEU E  11 " --> pdb=" O   GLU E 105 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   LEU E  33 " --> pdb=" O   TYR E  49 " (cutoff:3.500A)
      removed outlier: 4.820A  pdb=" N   TYR E  49 " --> pdb=" O   LEU E  33 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   TRP E  35 " --> pdb=" O   LEU E  47 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.119A  pdb=" N   LEU E  11 " --> pdb=" O   GLU E 105 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   GLN E  90 " --> pdb=" O   THR E  97 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   THR E  97 " --> pdb=" O   GLN E  90 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'F' and resid 4 through 5
      removed outlier: 3.553A  pdb=" N   ASP F  70 " --> pdb=" O   SER F  67 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'F' and resid 10 through 12
      removed outlier: 6.339A  pdb=" N   LEU F  11 " --> pdb=" O   GLU F 105 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ILE F  48 " --> pdb=" O   TRP F  35 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   GLN F  37 " --> pdb=" O   LEU F  46 " (cutoff:3.500A)
      removed outlier: 5.571A  pdb=" N   LEU F  46 " --> pdb=" O   GLN F  37 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 10 through 12
      removed outlier: 6.339A  pdb=" N   LEU F  11 " --> pdb=" O   GLU F 105 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   THR F  97 " --> pdb=" O   GLN F  90 " (cutoff:3.500A)

    200 hydrogen bonds defined for protein.
    486 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      36 hydrogen bonds
      72 hydrogen bond angles
      0 basepair planarities
      12 basepair parallelities
      10 stacking parallelities
  Total time for adding SS restraints: 0.88

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1790
        1.35 -     1.46: 1689
        1.46 -     1.58: 2408
        1.58 -     1.70: 47
        1.70 -     1.82: 54
  Bond restraints: 5988
  Sorted by residual:
  bond pdb=" C3'  DG O   8 "
       pdb=" O3'  DG O   8 "
    ideal  model  delta    sigma   weight residual
    1.422  1.458 -0.036 3.00e-02 1.11e+03 1.41e+00
  bond pdb=" C3'  DG P   8 "
       pdb=" O3'  DG P   8 "
    ideal  model  delta    sigma   weight residual
    1.422  1.451 -0.029 3.00e-02 1.11e+03 9.07e-01
  bond pdb=" C3'  DG O   6 "
       pdb=" C2'  DG O   6 "
    ideal  model  delta    sigma   weight residual
    1.525  1.543 -0.018 2.00e-02 2.50e+03 7.94e-01
  bond pdb=" CB  ILE E   8 "
       pdb=" CG1 ILE E   8 "
    ideal  model  delta    sigma   weight residual
    1.530  1.547 -0.017 2.00e-02 2.50e+03 7.13e-01
  bond pdb=" C4'  DG O   6 "
       pdb=" O4'  DG O   6 "
    ideal  model  delta    sigma   weight residual
    1.450  1.433  0.017 2.00e-02 2.50e+03 7.11e-01
  ... (remaining 5983 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.31: 8012
        1.31 -     2.63: 141
        2.63 -     3.94: 34
        3.94 -     5.26: 10
        5.26 -     6.57: 3
  Bond angle restraints: 8200
  Sorted by residual:
  angle pdb=" CA  ILE E   8 "
        pdb=" CB  ILE E   8 "
        pdb=" CG1 ILE E   8 "
      ideal   model   delta    sigma   weight residual
     110.40  115.19   -4.79 1.70e+00 3.46e-01 7.92e+00
  angle pdb=" C   TYR F  50 "
        pdb=" N   THR F  51 "
        pdb=" CA  THR F  51 "
      ideal   model   delta    sigma   weight residual
     121.54  126.74   -5.20 1.91e+00 2.74e-01 7.41e+00
  angle pdb=" N   PHE E  94 "
        pdb=" CA  PHE E  94 "
        pdb=" C   PHE E  94 "
      ideal   model   delta    sigma   weight residual
     109.81  115.67   -5.86 2.21e+00 2.05e-01 7.03e+00
  angle pdb=" C   TYR E  50 "
        pdb=" N   THR E  51 "
        pdb=" CA  THR E  51 "
      ideal   model   delta    sigma   weight residual
     121.54  126.37   -4.83 1.91e+00 2.74e-01 6.39e+00
  angle pdb=" C   TYR B  50 "
        pdb=" N   THR B  51 "
        pdb=" CA  THR B  51 "
      ideal   model   delta    sigma   weight residual
     121.54  126.35   -4.81 1.91e+00 2.74e-01 6.35e+00
  ... (remaining 8195 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.99: 3142
       29.99 -    59.99: 290
       59.99 -    89.98: 26
       89.98 -   119.98: 1
      119.98 -   149.97: 1
  Dihedral angle restraints: 3460
    sinusoidal: 1486
      harmonic: 1974
  Sorted by residual:
  dihedral pdb=" CB  CYS E  23 "
           pdb=" SG  CYS E  23 "
           pdb=" SG  CYS E  88 "
           pdb=" CB  CYS E  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  137.63  -44.63     1      1.00e+01 1.00e-02 2.77e+01
  dihedral pdb=" CA  LYS F  93 "
           pdb=" C   LYS F  93 "
           pdb=" N   PHE F  94 "
           pdb=" CA  PHE F  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.28  -23.72     0      5.00e+00 4.00e-02 2.25e+01
  dihedral pdb=" CA  LYS E  93 "
           pdb=" C   LYS E  93 "
           pdb=" N   PHE E  94 "
           pdb=" CA  PHE E  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.46  -20.54     0      5.00e+00 4.00e-02 1.69e+01
  ... (remaining 3457 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 602
       0.033 -    0.066: 182
       0.066 -    0.099: 59
       0.099 -    0.132: 40
       0.132 -    0.165: 3
  Chirality restraints: 886
  Sorted by residual:
  chirality pdb=" CA  PHE E  94 "
            pdb=" N   PHE E  94 "
            pdb=" C   PHE E  94 "
            pdb=" CB  PHE E  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.17 2.00e-01 2.50e+01 6.82e-01
  chirality pdb=" CA  PHE F  94 "
            pdb=" N   PHE F  94 "
            pdb=" C   PHE F  94 "
            pdb=" CB  PHE F  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.80e-01
  chirality pdb=" CA  PHE B  94 "
            pdb=" N   PHE B  94 "
            pdb=" C   PHE B  94 "
            pdb=" CB  PHE B  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.48e-01
  ... (remaining 883 not shown)

  Planarity restraints: 960
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B  79 "   -0.026 5.00e-02 4.00e+02   4.00e-02 2.56e+00
        pdb=" N   PRO B  80 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B  80 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B  80 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE E  94 "   -0.020 5.00e-02 4.00e+02   3.07e-02 1.50e+00
        pdb=" N   PRO E  95 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO E  95 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO E  95 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS F  39 "   -0.020 5.00e-02 4.00e+02   3.06e-02 1.50e+00
        pdb=" N   PRO F  40 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO F  40 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO F  40 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 957 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1460
        2.80 -     3.32: 4319
        3.32 -     3.85: 9193
        3.85 -     4.37: 11260
        4.37 -     4.90: 19763
  Nonbonded interactions: 45995
  Sorted by model distance:
  nonbonded pdb=" O   SER D 121 "
            pdb=" OG  SER D 121 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" NH2 ARG F  61 "
            pdb=" OD1 ASP F  82 "
     model   vdw
     2.344 3.120
  nonbonded pdb=" NH2 ARG B  61 "
            pdb=" OD2 ASP B  82 "
     model   vdw
     2.377 3.120
  nonbonded pdb=" O   ILE B  29 "
            pdb=" OH  TYR B  71 "
     model   vdw
     2.418 3.040
  nonbonded pdb=" O   TYR F  50 "
            pdb=" OG1 THR F  51 "
     model   vdw
     2.446 3.040
  ... (remaining 45990 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'E'
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'O' and (resid 1 through 5 or resid 7 through 12))
  selection = (chain 'P' and (resid 1 through 5 or resid 7 through 12))
}

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=0.02 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:             4.190
  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:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.220
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  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:8.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7243
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      :  0.002   0.036   5994  Z= 0.113
  Angle     :  0.500   6.570   8212  Z= 0.274
  Chirality :  0.042   0.165    886
  Planarity :  0.004   0.040    960
  Dihedral  : 20.067 149.970   2194
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 29.73 %
    Favored  : 66.67 %
  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: -0.01 (0.33), residues: 669
  helix:  None (None), residues: 0
  sheet:  0.52 (0.30), residues: 327
  loop : -0.48 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  38 
 TYR   0.011   0.001   TYR F  91 
 PHE   0.020   0.001   PHE F  94 
 TRP   0.004   0.001   TRP D 112 
 HIS   0.000   0.000   HIS E  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 5988)
  covalent geometry    : angle       0.49935 ( 8200)
  SS BOND              : bond        0.00419 (    6)
  SS BOND              : angle       0.70638 (   12)
  hydrogen bonds       : bond        0.21962 (  224)
  hydrogen bonds       : angle       8.11182 (  558)

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

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

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 152
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
REVERT: E    3 GLN cc_start: 0.7222 (mp10) cc_final: 0.6944 (mp-120)
REVERT: E   97 THR cc_start: 0.6741 (p) cc_final: 0.6530 (p)
REVERT: F   43 THR cc_start: 0.7675 (m) cc_final: 0.7443 (p)
  outliers start: 21
  outliers final: 4
  residues processed: 168
  average time/residue: 0.4759
  time to fit residues: 84.2206
Evaluate side-chains
  107 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 103
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain E residue   23 CYS
Chi-restraints excluded: chain F residue   67 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A  28 ASN
A  84 GLN
A 101 GLN
B  31 ASN
C  35 ASN
C  39 GLN
D  39 GLN
D  79 ASN
E  37 GLN
E  38 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.132401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.106205 restraints weight = 6254.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 2.02
r_work: 0.3083 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2954 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2962
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2962 r_free = 0.2962    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2962 r_free = 0.2962    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2962
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.5724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5994  Z= 0.181
  Angle     :  0.665   6.892   8212  Z= 0.368
  Chirality :  0.047   0.240    886
  Planarity :  0.005   0.039    960
  Dihedral  : 16.193 152.557    995
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  5.84 %
    Allowed  : 29.38 %
    Favored  : 64.78 %
  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:  0.07 (0.33), residues: 669
  helix:  None (None), residues: 0
  sheet:  0.58 (0.29), residues: 342
  loop : -0.48 (0.32), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG F  61 
 TYR   0.018   0.002   TYR D  97 
 PHE   0.030   0.002   PHE B  94 
 TRP   0.009   0.001   TRP C  36 
 HIS   0.003   0.001   HIS F  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 5988)
  covalent geometry    : angle       0.66284 ( 8200)
  SS BOND              : bond        0.00800 (    6)
  SS BOND              : angle       1.42674 (   12)
  hydrogen bonds       : bond        0.03765 (  224)
  hydrogen bonds       : angle       5.04266 (  558)

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

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

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 127
  time to evaluate  : 0.222 
Fit side-chains
REVERT: A   11 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7170 (mp)
REVERT: A   46 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7850 (tt0)
REVERT: B   15 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.6415 (tp)
REVERT: C   43 LYS cc_start: 0.7850 (mppt) cc_final: 0.7549 (mmtm)
REVERT: D    3 GLN cc_start: 0.8210 (mt0) cc_final: 0.7961 (mt0)
REVERT: D   66 MET cc_start: 0.8074 (mtm) cc_final: 0.7868 (ptt)
REVERT: D   72 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8368 (tt)
REVERT: F   74 THR cc_start: 0.8531 (m) cc_final: 0.8297 (m)
REVERT: F   81 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7343 (pm20)
  outliers start: 34
  outliers final: 13
  residues processed: 152
  average time/residue: 0.4394
  time to fit residues: 70.3192
Evaluate side-chains
  130 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   95 MET
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   24 SER
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue   25 SER
Chi-restraints excluded: chain D residue   72 ILE
Chi-restraints excluded: chain D residue   73 SER
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain E residue   54 LEU
Chi-restraints excluded: chain E residue  106 ILE
Chi-restraints excluded: chain F residue   81 GLU
Chi-restraints excluded: chain F residue  100 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 20 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 17 optimal weight:    3.9990
   chunk 23 optimal weight:   30.0000
   chunk 52 optimal weight:   10.0000
   chunk 49 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0570
   chunk 36 optimal weight:    5.9990
   overall best weight:    2.4104

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

Flipped N/Q/H residues before XYZ refinement:
A 101 GLN
C  79 ASN
D   3 GLN
D 105 ASN
E  27 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.124805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.098928 restraints weight = 6217.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 1.83
r_work: 0.2985 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2856 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2859
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2859 r_free = 0.2859    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2858 r_free = 0.2858    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2858
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8780
moved from start:          0.6939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   5994  Z= 0.241
  Angle     :  0.706   7.585   8212  Z= 0.391
  Chirality :  0.051   0.284    886
  Planarity :  0.005   0.039    960
  Dihedral  : 16.295 157.384    991
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  7.39 %
    Allowed  : 26.98 %
    Favored  : 65.64 %
  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:  0.02 (0.32), residues: 669
  helix:  None (None), residues: 0
  sheet:  0.58 (0.30), residues: 327
  loop : -0.51 (0.31), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  50 
 TYR   0.021   0.002   TYR D  97 
 PHE   0.040   0.003   PHE F  94 
 TRP   0.005   0.001   TRP A  36 
 HIS   0.005   0.002   HIS E  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00564 ( 5988)
  covalent geometry    : angle       0.70396 ( 8200)
  SS BOND              : bond        0.00984 (    6)
  SS BOND              : angle       1.63377 (   12)
  hydrogen bonds       : bond        0.04750 (  224)
  hydrogen bonds       : angle       5.07103 (  558)

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

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

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 120
  time to evaluate  : 0.224 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.8758 (mtmt) cc_final: 0.8507 (mtmm)
REVERT: A   46 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7962 (tt0)
REVERT: A  119 THR cc_start: 0.8542 (m) cc_final: 0.8275 (t)
REVERT: B   54 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9004 (mp)
REVERT: C   43 LYS cc_start: 0.8174 (mppt) cc_final: 0.7859 (mmtm)
REVERT: C  117 SER cc_start: 0.8775 (OUTLIER) cc_final: 0.8376 (t)
REVERT: D    3 GLN cc_start: 0.8386 (mt0) cc_final: 0.8176 (mt0)
REVERT: F   41 ASP cc_start: 0.7923 (p0) cc_final: 0.7722 (p0)
REVERT: F   81 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7619 (pm20)
  outliers start: 43
  outliers final: 18
  residues processed: 150
  average time/residue: 0.4485
  time to fit residues: 71.1614
Evaluate side-chains
  130 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 108
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   95 MET
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain C residue   65 SER
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue   25 SER
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain D residue   73 SER
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain E residue    8 ILE
Chi-restraints excluded: chain E residue   43 THR
Chi-restraints excluded: chain E residue   54 LEU
Chi-restraints excluded: chain E residue  106 ILE
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   81 GLU
Chi-restraints excluded: chain F residue  100 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 2 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 41 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 57 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    2.1188

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

Flipped N/Q/H residues before XYZ refinement:
C  79 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.124383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.098973 restraints weight = 6301.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 1.87
r_work: 0.2992 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2865 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2868
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2868 r_free = 0.2868    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2868 r_free = 0.2868    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2868
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8782
moved from start:          0.7198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   5994  Z= 0.214
  Angle     :  0.671   7.516   8212  Z= 0.372
  Chirality :  0.049   0.273    886
  Planarity :  0.004   0.037    960
  Dihedral  : 16.206 155.309    991
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  7.04 %
    Allowed  : 27.15 %
    Favored  : 65.81 %
  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: -0.09 (0.32), residues: 669
  helix:  None (None), residues: 0
  sheet:  0.46 (0.28), residues: 342
  loop : -0.57 (0.32), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  50 
 TYR   0.018   0.002   TYR D  97 
 PHE   0.038   0.003   PHE F  94 
 TRP   0.006   0.001   TRP A  47 
 HIS   0.004   0.001   HIS E  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 ( 5988)
  covalent geometry    : angle       0.66820 ( 8200)
  SS BOND              : bond        0.00928 (    6)
  SS BOND              : angle       1.81403 (   12)
  hydrogen bonds       : bond        0.04061 (  224)
  hydrogen bonds       : angle       4.80721 (  558)

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

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

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 109
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A   13 GLN cc_start: 0.7932 (mp10) cc_final: 0.7551 (mp10)
REVERT: A   15 LYS cc_start: 0.8698 (mtmt) cc_final: 0.8461 (mtmm)
REVERT: A   46 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7990 (tt0)
REVERT: B   11 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7652 (tp)
REVERT: B   54 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9042 (mp)
REVERT: B   82 ASP cc_start: 0.8415 (m-30) cc_final: 0.8101 (m-30)
REVERT: C   43 LYS cc_start: 0.8197 (mppt) cc_final: 0.7838 (mmtm)
REVERT: C  117 SER cc_start: 0.8838 (OUTLIER) cc_final: 0.8512 (t)
REVERT: D    3 GLN cc_start: 0.8385 (mt0) cc_final: 0.8159 (mt0)
REVERT: E  103 LYS cc_start: 0.8716 (ttpp) cc_final: 0.8078 (tptp)
REVERT: F    3 GLN cc_start: 0.8395 (mp10) cc_final: 0.7788 (mm-40)
REVERT: F   12 SER cc_start: 0.7965 (OUTLIER) cc_final: 0.7644 (m)
REVERT: F  103 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8633 (ttmm)
  outliers start: 41
  outliers final: 22
  residues processed: 136
  average time/residue: 0.4444
  time to fit residues: 63.8781
Evaluate side-chains
  134 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 106
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   95 MET
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   24 SER
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain C residue   65 SER
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain D residue   25 SER
Chi-restraints excluded: chain D residue   73 SER
Chi-restraints excluded: chain D residue   91 GLU
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain E residue    8 ILE
Chi-restraints excluded: chain E residue   43 THR
Chi-restraints excluded: chain E residue   54 LEU
Chi-restraints excluded: chain E residue   81 GLU
Chi-restraints excluded: chain E residue  106 ILE
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   27 GLN
Chi-restraints excluded: chain F residue   33 LEU
Chi-restraints excluded: chain F residue  100 SER
Chi-restraints excluded: chain F residue  103 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 13 optimal weight:   10.0000
   chunk 28 optimal weight:    0.0040
   chunk 6 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 46 optimal weight:    5.9990
   chunk 27 optimal weight:    0.6980
   chunk 60 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    2.1398

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

Flipped N/Q/H residues before XYZ refinement:
C  79 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.123975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.098284 restraints weight = 6435.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 1.90
r_work: 0.2982 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2854 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2858
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2858 r_free = 0.2858    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2858 r_free = 0.2858    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2858
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8792
moved from start:          0.7289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   5994  Z= 0.216
  Angle     :  0.673   7.510   8212  Z= 0.373
  Chirality :  0.049   0.275    886
  Planarity :  0.004   0.038    960
  Dihedral  : 16.227 155.794    991
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  6.87 %
    Allowed  : 28.18 %
    Favored  : 64.95 %
  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: -0.09 (0.32), residues: 669
  helix:  None (None), residues: 0
  sheet:  0.44 (0.28), residues: 342
  loop : -0.56 (0.32), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  50 
 TYR   0.018   0.002   TYR D  97 
 PHE   0.039   0.003   PHE F  94 
 TRP   0.006   0.001   TRP A  47 
 HIS   0.004   0.002   HIS E  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 ( 5988)
  covalent geometry    : angle       0.66789 ( 8200)
  SS BOND              : bond        0.00963 (    6)
  SS BOND              : angle       2.26698 (   12)
  hydrogen bonds       : bond        0.04027 (  224)
  hydrogen bonds       : angle       4.71995 (  558)

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

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

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 108
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A   13 GLN cc_start: 0.7913 (mp10) cc_final: 0.7488 (mp10)
REVERT: A   15 LYS cc_start: 0.8674 (mtmt) cc_final: 0.8453 (mtmm)
REVERT: A   46 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8016 (tt0)
REVERT: B   11 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7601 (tp)
REVERT: C  117 SER cc_start: 0.8881 (OUTLIER) cc_final: 0.8520 (t)
REVERT: D    3 GLN cc_start: 0.8399 (mt0) cc_final: 0.8171 (mt0)
REVERT: E   73 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8483 (tp)
REVERT: E  103 LYS cc_start: 0.8708 (ttpp) cc_final: 0.8049 (tptp)
REVERT: F    3 GLN cc_start: 0.8390 (mp10) cc_final: 0.7806 (mm-40)
REVERT: F   12 SER cc_start: 0.7975 (OUTLIER) cc_final: 0.7660 (m)
REVERT: F  103 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8607 (ttmm)
  outliers start: 40
  outliers final: 25
  residues processed: 134
  average time/residue: 0.4800
  time to fit residues: 67.7530
Evaluate side-chains
  138 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 107
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   95 MET
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue   65 SER
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain D residue   17 SER
Chi-restraints excluded: chain D residue   25 SER
Chi-restraints excluded: chain D residue   65 SER
Chi-restraints excluded: chain D residue   73 SER
Chi-restraints excluded: chain D residue   91 GLU
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain E residue    5 THR
Chi-restraints excluded: chain E residue    8 ILE
Chi-restraints excluded: chain E residue   43 THR
Chi-restraints excluded: chain E residue   54 LEU
Chi-restraints excluded: chain E residue   73 LEU
Chi-restraints excluded: chain E residue  106 ILE
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   27 GLN
Chi-restraints excluded: chain F residue   33 LEU
Chi-restraints excluded: chain F residue  100 SER
Chi-restraints excluded: chain F residue  103 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 11 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 7 optimal weight:    7.9990
   chunk 56 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0870
   chunk 25 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.8760

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

Flipped N/Q/H residues before XYZ refinement:
C  79 ASN
C 105 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.127038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.101916 restraints weight = 6324.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 1.89
r_work: 0.3028 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2900 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2904
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2904 r_free = 0.2904    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2904 r_free = 0.2904    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2904
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8727
moved from start:          0.7316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5994  Z= 0.126
  Angle     :  0.553   6.497   8212  Z= 0.309
  Chirality :  0.044   0.222    886
  Planarity :  0.004   0.038    960
  Dihedral  : 16.093 154.528    991
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 29.38 %
    Favored  : 65.12 %
  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:  0.08 (0.32), residues: 669
  helix:  None (None), residues: 0
  sheet:  0.56 (0.28), residues: 342
  loop : -0.44 (0.32), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  50 
 TYR   0.012   0.001   TYR D  97 
 PHE   0.028   0.002   PHE F  94 
 TRP   0.005   0.001   TRP A  47 
 HIS   0.001   0.001   HIS E  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 5988)
  covalent geometry    : angle       0.55068 ( 8200)
  SS BOND              : bond        0.00657 (    6)
  SS BOND              : angle       1.31527 (   12)
  hydrogen bonds       : bond        0.02973 (  224)
  hydrogen bonds       : angle       4.45125 (  558)

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

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

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 111
  time to evaluate  : 0.238 
Fit side-chains
REVERT: A   13 GLN cc_start: 0.7897 (mp10) cc_final: 0.7393 (mp10)
REVERT: A   15 LYS cc_start: 0.8622 (mtmt) cc_final: 0.8393 (mtmm)
REVERT: A   46 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7939 (tt0)
REVERT: B   61 ARG cc_start: 0.7894 (mtm-85) cc_final: 0.7459 (mtm110)
REVERT: C  105 ASN cc_start: 0.8830 (OUTLIER) cc_final: 0.8490 (t0)
REVERT: C  117 SER cc_start: 0.8787 (OUTLIER) cc_final: 0.8467 (t)
REVERT: D    3 GLN cc_start: 0.8332 (mt0) cc_final: 0.8071 (mt0)
REVERT: E   73 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8424 (tp)
REVERT: E  103 LYS cc_start: 0.8694 (ttpp) cc_final: 0.8056 (tmtt)
REVERT: F    3 GLN cc_start: 0.8362 (mp10) cc_final: 0.7755 (mm-40)
REVERT: F  103 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8642 (ttmm)
  outliers start: 32
  outliers final: 17
  residues processed: 135
  average time/residue: 0.5071
  time to fit residues: 71.9688
Evaluate side-chains
  131 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 109
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   95 MET
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain C residue   65 SER
Chi-restraints excluded: chain C residue  105 ASN
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain D residue   17 SER
Chi-restraints excluded: chain D residue   25 SER
Chi-restraints excluded: chain D residue   65 SER
Chi-restraints excluded: chain D residue   73 SER
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain E residue    8 ILE
Chi-restraints excluded: chain E residue   73 LEU
Chi-restraints excluded: chain E residue   81 GLU
Chi-restraints excluded: chain E residue  106 ILE
Chi-restraints excluded: chain F residue   33 LEU
Chi-restraints excluded: chain F residue  103 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 36 optimal weight:    6.9990
   chunk 3 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 16 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 12 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 5 optimal weight:    0.3980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
C  79 ASN
F   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.127986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.102065 restraints weight = 6287.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 1.73
r_work: 0.3055 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2928 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2934
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2934 r_free = 0.2934    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2934 r_free = 0.2934    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2934
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8705
moved from start:          0.7335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5994  Z= 0.122
  Angle     :  0.545   6.351   8212  Z= 0.305
  Chirality :  0.044   0.215    886
  Planarity :  0.004   0.040    960
  Dihedral  : 16.063 154.668    991
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 30.93 %
    Favored  : 64.78 %
  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:  0.17 (0.32), residues: 669
  helix:  None (None), residues: 0
  sheet:  0.60 (0.28), residues: 342
  loop : -0.36 (0.32), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  50 
 TYR   0.013   0.001   TYR D  97 
 PHE   0.027   0.002   PHE F  94 
 TRP   0.006   0.001   TRP C  47 
 HIS   0.001   0.001   HIS E  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 5988)
  covalent geometry    : angle       0.54304 ( 8200)
  SS BOND              : bond        0.00586 (    6)
  SS BOND              : angle       1.19716 (   12)
  hydrogen bonds       : bond        0.02891 (  224)
  hydrogen bonds       : angle       4.40382 (  558)

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

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

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.147 
Fit side-chains
REVERT: A   13 GLN cc_start: 0.7854 (mp10) cc_final: 0.7341 (mp10)
REVERT: A   15 LYS cc_start: 0.8610 (mtmt) cc_final: 0.8404 (mtmm)
REVERT: A   46 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7920 (tt0)
REVERT: C  117 SER cc_start: 0.8772 (OUTLIER) cc_final: 0.8470 (t)
REVERT: D    3 GLN cc_start: 0.8336 (mt0) cc_final: 0.8077 (mt0)
REVERT: E   73 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8423 (tp)
REVERT: E  103 LYS cc_start: 0.8674 (ttpp) cc_final: 0.8047 (tmtt)
REVERT: F    3 GLN cc_start: 0.8377 (mp10) cc_final: 0.7825 (mm-40)
REVERT: F  103 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8644 (ttmm)
  outliers start: 25
  outliers final: 17
  residues processed: 127
  average time/residue: 0.5245
  time to fit residues: 69.7833
Evaluate side-chains
  129 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   85 MET
Chi-restraints excluded: chain A residue   95 MET
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain D residue   17 SER
Chi-restraints excluded: chain D residue   25 SER
Chi-restraints excluded: chain D residue   65 SER
Chi-restraints excluded: chain D residue   73 SER
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain E residue    8 ILE
Chi-restraints excluded: chain E residue   73 LEU
Chi-restraints excluded: chain E residue  106 ILE
Chi-restraints excluded: chain F residue   27 GLN
Chi-restraints excluded: chain F residue   33 LEU
Chi-restraints excluded: chain F residue  103 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 66 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 13 optimal weight:    9.9990
   chunk 36 optimal weight:    8.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    2.3586

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

Flipped N/Q/H residues before XYZ refinement:
C  79 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.123698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.098357 restraints weight = 6317.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 1.86
r_work: 0.2982 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2853 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2854
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2854 r_free = 0.2854    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2854 r_free = 0.2854    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2854
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8792
moved from start:          0.7384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   5994  Z= 0.233
  Angle     :  0.684   7.581   8212  Z= 0.379
  Chirality :  0.050   0.275    886
  Planarity :  0.004   0.041    960
  Dihedral  : 16.210 155.841    991
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 30.07 %
    Favored  : 64.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -0.02 (0.31), residues: 669
  helix:  None (None), residues: 0
  sheet:  0.41 (0.28), residues: 348
  loop : -0.42 (0.32), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  50 
 TYR   0.019   0.002   TYR D  97 
 PHE   0.039   0.003   PHE F  94 
 TRP   0.006   0.001   TRP A  47 
 HIS   0.004   0.002   HIS E  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00543 ( 5988)
  covalent geometry    : angle       0.68015 ( 8200)
  SS BOND              : bond        0.00944 (    6)
  SS BOND              : angle       1.96286 (   12)
  hydrogen bonds       : bond        0.04067 (  224)
  hydrogen bonds       : angle       4.62752 (  558)

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

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

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 105
  time to evaluate  : 0.223 
Fit side-chains
REVERT: A   13 GLN cc_start: 0.7911 (mp10) cc_final: 0.7385 (mp10)
REVERT: A   46 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8017 (tt0)
REVERT: B   11 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7572 (tp)
REVERT: C  117 SER cc_start: 0.8832 (OUTLIER) cc_final: 0.8503 (t)
REVERT: D    3 GLN cc_start: 0.8407 (mt0) cc_final: 0.8180 (mt0)
REVERT: D   15 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7998 (mtmt)
REVERT: E   73 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8514 (tp)
REVERT: E  103 LYS cc_start: 0.8699 (ttpp) cc_final: 0.8052 (tptp)
REVERT: F    3 GLN cc_start: 0.8448 (mp10) cc_final: 0.7869 (mm-40)
REVERT: F  103 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8625 (ttmm)
  outliers start: 32
  outliers final: 23
  residues processed: 131
  average time/residue: 0.4842
  time to fit residues: 66.8314
Evaluate side-chains
  133 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 104
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   95 MET
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue   65 SER
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain D residue   15 LYS
Chi-restraints excluded: chain D residue   17 SER
Chi-restraints excluded: chain D residue   25 SER
Chi-restraints excluded: chain D residue   65 SER
Chi-restraints excluded: chain D residue   73 SER
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain E residue    8 ILE
Chi-restraints excluded: chain E residue   54 LEU
Chi-restraints excluded: chain E residue   73 LEU
Chi-restraints excluded: chain E residue  106 ILE
Chi-restraints excluded: chain F residue   11 LEU
Chi-restraints excluded: chain F residue   27 GLN
Chi-restraints excluded: chain F residue   33 LEU
Chi-restraints excluded: chain F residue  103 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 61 optimal weight:    0.2980
   chunk 50 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 63 optimal weight:    1.9990
   chunk 41 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   chunk 1 optimal weight:    0.3980
   chunk 66 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
C 105 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.128344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.102290 restraints weight = 6293.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3179 rms_B_bonded: 1.74
r_work: 0.3059 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2930 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2938
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2938 r_free = 0.2938    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2938 r_free = 0.2938    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2938
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8700
moved from start:          0.7403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5994  Z= 0.119
  Angle     :  0.540   6.304   8212  Z= 0.302
  Chirality :  0.044   0.215    886
  Planarity :  0.004   0.039    960
  Dihedral  : 16.072 154.307    991
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 30.24 %
    Favored  : 64.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.32), residues: 669
  helix:  None (None), residues: 0
  sheet:  0.57 (0.28), residues: 342
  loop : -0.35 (0.32), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  50 
 TYR   0.012   0.001   TYR D  97 
 PHE   0.027   0.002   PHE F  94 
 TRP   0.006   0.001   TRP D  47 
 HIS   0.001   0.001   HIS E  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 5988)
  covalent geometry    : angle       0.53856 ( 8200)
  SS BOND              : bond        0.00577 (    6)
  SS BOND              : angle       1.14482 (   12)
  hydrogen bonds       : bond        0.02763 (  224)
  hydrogen bonds       : angle       4.33520 (  558)

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

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

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 107
  time to evaluate  : 0.253 
Fit side-chains
REVERT: A   13 GLN cc_start: 0.7877 (mp10) cc_final: 0.7350 (mp10)
REVERT: A   46 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7934 (tt0)
REVERT: C  105 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8593 (t0)
REVERT: C  117 SER cc_start: 0.8779 (OUTLIER) cc_final: 0.8488 (t)
REVERT: D    3 GLN cc_start: 0.8338 (mt0) cc_final: 0.8034 (mt0)
REVERT: D   15 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7991 (mtmt)
REVERT: E   73 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8328 (tp)
REVERT: E  103 LYS cc_start: 0.8659 (ttpp) cc_final: 0.8013 (tmtt)
REVERT: F    3 GLN cc_start: 0.8406 (mp10) cc_final: 0.7890 (mm-40)
REVERT: F   12 SER cc_start: 0.7931 (OUTLIER) cc_final: 0.7668 (m)
REVERT: F   27 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8246 (mt0)
REVERT: F  103 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8643 (ttmm)
  outliers start: 31
  outliers final: 15
  residues processed: 131
  average time/residue: 0.4973
  time to fit residues: 68.5403
Evaluate side-chains
  128 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue  105 ASN
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain D residue   15 LYS
Chi-restraints excluded: chain D residue   17 SER
Chi-restraints excluded: chain D residue   25 SER
Chi-restraints excluded: chain D residue   73 SER
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain E residue    8 ILE
Chi-restraints excluded: chain E residue   73 LEU
Chi-restraints excluded: chain E residue   81 GLU
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   27 GLN
Chi-restraints excluded: chain F residue   33 LEU
Chi-restraints excluded: chain F residue  103 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0570
   chunk 63 optimal weight:    0.9980
   chunk 2 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 66 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9980
   overall best weight:    0.7698

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

Flipped N/Q/H residues before XYZ refinement:
C  79 ASN
C 105 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.128093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.102261 restraints weight = 6345.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 1.73
r_work: 0.3060 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2934 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2941
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2941
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8699
moved from start:          0.7428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5994  Z= 0.121
  Angle     :  0.542   6.310   8212  Z= 0.304
  Chirality :  0.044   0.212    886
  Planarity :  0.004   0.040    960
  Dihedral  : 16.042 154.722    991
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 30.76 %
    Favored  : 65.12 %
  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:  0.25 (0.31), residues: 669
  helix:  None (None), residues: 0
  sheet:  0.72 (0.28), residues: 336
  loop : -0.37 (0.32), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  50 
 TYR   0.014   0.001   TYR C 106 
 PHE   0.027   0.002   PHE F  94 
 TRP   0.007   0.001   TRP D  47 
 HIS   0.001   0.001   HIS E  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 5988)
  covalent geometry    : angle       0.54115 ( 8200)
  SS BOND              : bond        0.00567 (    6)
  SS BOND              : angle       1.11104 (   12)
  hydrogen bonds       : bond        0.02795 (  224)
  hydrogen bonds       : angle       4.33524 (  558)

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

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

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1338 Ramachandran restraints generated.
    669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 106
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A   13 GLN cc_start: 0.7880 (mp10) cc_final: 0.7347 (mp10)
REVERT: A   46 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7928 (tt0)
REVERT: C  105 ASN cc_start: 0.8795 (OUTLIER) cc_final: 0.8594 (t0)
REVERT: C  117 SER cc_start: 0.8785 (OUTLIER) cc_final: 0.8485 (t)
REVERT: D    3 GLN cc_start: 0.8341 (mt0) cc_final: 0.8039 (mt0)
REVERT: D   15 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7935 (mtmt)
REVERT: E   73 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8346 (tp)
REVERT: E  103 LYS cc_start: 0.8666 (ttpp) cc_final: 0.8023 (tmtt)
REVERT: F    3 GLN cc_start: 0.8412 (mp10) cc_final: 0.7905 (mm-40)
REVERT: F   12 SER cc_start: 0.7936 (OUTLIER) cc_final: 0.7664 (m)
REVERT: F   27 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8241 (mt0)
REVERT: F  103 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8650 (ttmm)
  outliers start: 24
  outliers final: 15
  residues processed: 125
  average time/residue: 0.4996
  time to fit residues: 65.7146
Evaluate side-chains
  129 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue  105 ASN
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain D residue   15 LYS
Chi-restraints excluded: chain D residue   17 SER
Chi-restraints excluded: chain D residue   25 SER
Chi-restraints excluded: chain D residue   73 SER
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain E residue    8 ILE
Chi-restraints excluded: chain E residue   73 LEU
Chi-restraints excluded: chain E residue   81 GLU
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   27 GLN
Chi-restraints excluded: chain F residue   33 LEU
Chi-restraints excluded: chain F residue  103 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run
    self.rsr_result = rsr_wrappers.run_real_space_refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__
    self._refined = macro_cycle_real_space.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs
    ro = mmtbx.refinement.real_space.individual_sites.easy(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__
    self.weight = mmtbx.refinement.real_space.weight.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine
    real_space_result = refinery(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine
    self.refined = maptbx.real_space_refinement_simple.lbfgs(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__
    O.minimizer = scitbx.lbfgs.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients
    gr_e = O.geometry_restraints_manager.energies_sites(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites
    pair_proxies = self.pair_proxies(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 50.614 > 50:
  distance: 11 - 12:   3.902
  distance: 12 - 13:   3.781
  distance: 12 - 15:   3.362
  distance: 13 - 14:   5.291
  distance: 13 - 17:   5.608
  distance: 15 - 16:   8.093
  distance: 17 - 18:   7.661
  distance: 18 - 19:  10.464
  distance: 18 - 21:  11.498
  distance: 19 - 20:  12.027
  distance: 19 - 25:   4.523
  distance: 21 - 22:   9.791
  distance: 22 - 23:  10.444
  distance: 22 - 24:  18.939
  distance: 25 - 26:   7.896
  distance: 26 - 27:  18.035
  distance: 26 - 29:  16.291
  distance: 27 - 28:  28.905
  distance: 27 - 31:  10.476
  distance: 29 - 30:  17.236
  distance: 31 - 32:  28.799
  distance: 32 - 33:  21.749
  distance: 32 - 35:  19.026
  distance: 33 - 34:  31.677
  distance: 33 - 36:   6.876
  distance: 36 - 37:   8.908
  distance: 37 - 38:  20.829
  distance: 37 - 40:  13.427
  distance: 38 - 39:   8.145
  distance: 38 - 42:   8.586
  distance: 40 - 41:  20.248
  distance: 42 - 43:   3.883
  distance: 43 - 44:   3.545
  distance: 43 - 46:   6.200
  distance: 44 - 45:   4.013
  distance: 44 - 50:   8.751
  distance: 46 - 47:   5.570
  distance: 47 - 48:   4.394
  distance: 47 - 49:   6.343
  distance: 50 - 51:   4.949
  distance: 51 - 52:   4.208
  distance: 52 - 53:   3.469
  distance: 54 - 55:   4.833
  distance: 55 - 56:   3.597
  distance: 56 - 57:   4.031
  distance: 56 - 62:   3.350
  distance: 58 - 59:   4.220
  distance: 59 - 60:   5.105
  distance: 59 - 61:   5.657
  distance: 62 - 63:   7.183
  distance: 63 - 64:   6.886
  distance: 64 - 65:  14.883
  distance: 64 - 73:   6.319
  distance: 66 - 67:   3.760
  distance: 67 - 68:   7.181
  distance: 68 - 69:   4.804
  distance: 69 - 70:   6.436
  distance: 70 - 71:  11.058
  distance: 70 - 72:   6.202
  distance: 73 - 74:   3.426
  distance: 74 - 75:   9.970
  distance: 74 - 77:   7.024
  distance: 75 - 76:   8.740
  distance: 75 - 80:   6.110
  distance: 77 - 78:   5.786
  distance: 77 - 79:   7.707