Starting phenix.real_space_refine
on Thu Jul  2 02:34:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9tgw_55912/07_2026/9tgw_55912.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9tgw_55912/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9tgw_55912/07_2026/9tgw_55912.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9tgw_55912/07_2026/9tgw_55912.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9tgw_55912/07_2026/9tgw_55912.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9tgw_55912/07_2026/9tgw_55912.cif"
  }
  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-dev-6108/lib/python3.11/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: 1.42, per 1000 atoms: 0.24
  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: 0.39
  Conformation dependent library (CDL) restraints added in 175.8 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: 0.63
  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: 0.86

  Time building geometry restraints manager: 0.55 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   6 "
       pdb=" C2'  DG O   6 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.12e+01
  bond pdb=" C3'  DG P   6 "
       pdb=" C2'  DG P   6 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 8.76e+00
  bond pdb=" C3'  DG P   2 "
       pdb=" C2'  DG P   2 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 8.00e-03 1.56e+04 8.16e+00
  bond pdb=" C3'  DG O  10 "
       pdb=" C2'  DG O  10 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 8.00e-03 1.56e+04 7.95e+00
  bond pdb=" C3'  DG O   2 "
       pdb=" C2'  DG O   2 "
    ideal  model  delta    sigma   weight residual
    1.516  1.538 -0.022 8.00e-03 1.56e+04 7.27e+00
  ... (remaining 5983 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.31: 7966
        1.31 -     2.63: 192
        2.63 -     3.94: 27
        3.94 -     5.26: 12
        5.26 -     6.57: 3
  Bond angle restraints: 8200
  Sorted by residual:
  angle pdb=" O4'  DG O   8 "
        pdb=" C4'  DG O   8 "
        pdb=" C3'  DG O   8 "
      ideal   model   delta    sigma   weight residual
     106.00  103.08    2.92 6.00e-01 2.78e+00 2.36e+01
  angle pdb=" O4'  DG P   4 "
        pdb=" C1'  DG P   4 "
        pdb=" C2'  DG P   4 "
      ideal   model   delta    sigma   weight residual
     105.90  108.83   -2.93 8.00e-01 1.56e+00 1.35e+01
  angle pdb=" O4'  DC O   9 "
        pdb=" C4'  DC O   9 "
        pdb=" C3'  DC O   9 "
      ideal   model   delta    sigma   weight residual
     106.00  103.84    2.16 6.00e-01 2.78e+00 1.30e+01
  angle pdb=" O4'  DG O   4 "
        pdb=" C1'  DG O   4 "
        pdb=" C2'  DG O   4 "
      ideal   model   delta    sigma   weight residual
     105.90  108.33   -2.43 8.00e-01 1.56e+00 9.20e+00
  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
  ... (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: 570
       0.033 -    0.066: 193
       0.066 -    0.099: 78
       0.099 -    0.132: 40
       0.132 -    0.165: 5
  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:             3.450
  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:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.880
  Find NCS groups from input model:        0.100
  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:6.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
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      :  0.003   0.027   5994  Z= 0.255
  Angle     :  0.529   6.570   8212  Z= 0.353
  Chirality :  0.044   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/Z
  covalent geometry    : bond        0.00306 /  0.26 ( 5988)
  covalent geometry    : angle       0.52853 /  0.35 ( 8200)
  SS BOND              : bond        0.00419 /  0.20 (    6)
  SS BOND              : angle       0.70638 /  0.37 (   12)
  hydrogen bonds       : bond        0.21962 / 14.65 (  224)
  hydrogen bonds       : angle       8.11182 /  5.66 (  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  : 0.200 
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: 0.3869
  time to fit residues: 68.7050
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  : 0.200 
-------------------------------------------------------------------------------
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:    0.7980
   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:    1.0984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  28 ASN
A 101 GLN
C  35 ASN
D  79 ASN
E  37 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.141512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.115910 restraints weight = 6712.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 1.89
r_work: 0.3303 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3198 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3195
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (12 function evaluations)
r_final: 0.3195
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.3595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5994  Z= 0.210
  Angle     :  0.756   8.105   8212  Z= 0.419
  Chirality :  0.053   0.362    886
  Planarity :  0.005   0.053    960
  Dihedral  : 16.148 154.207    995
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  6.87 %
    Allowed  : 27.84 %
    Favored  : 65.29 %
  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: -0.21 (0.31), residues: 669
  helix:  None (None), residues: 0
  sheet:  0.45 (0.28), residues: 336
  loop : -0.73 (0.31), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG F  61 
 TYR   0.025   0.002   TYR A  62 
 PHE   0.036   0.003   PHE B  94 
 TRP   0.017   0.002   TRP A  47 
 HIS   0.002   0.001   HIS B  55 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00431 /  0.21 ( 5988)
  covalent geometry    : angle       0.75432 /  0.42 ( 8200)
  SS BOND              : bond        0.00739 /  0.36 (    6)
  SS BOND              : angle       1.39843 /  0.69 (   12)
  hydrogen bonds       : bond        0.03800 /  2.52 (  224)
  hydrogen bonds       : angle       5.44636 /  3.77 (  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
  172 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 132
  time to evaluate  : 0.207 
Fit side-chains
REVERT: B   15 LEU cc_start: 0.6277 (OUTLIER) cc_final: 0.5997 (tp)
REVERT: C   43 LYS cc_start: 0.7650 (mppt) cc_final: 0.7343 (mmtm)
REVERT: C   60 THR cc_start: 0.8414 (p) cc_final: 0.8170 (p)
REVERT: E    3 GLN cc_start: 0.7719 (mp10) cc_final: 0.7446 (mp-120)
REVERT: E  104 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6850 (mp)
REVERT: F   60 SER cc_start: 0.8043 (OUTLIER) cc_final: 0.7594 (p)
REVERT: F   72 SER cc_start: 0.8491 (OUTLIER) cc_final: 0.8247 (p)
REVERT: F   82 ASP cc_start: 0.7385 (m-30) cc_final: 0.7168 (m-30)
  outliers start: 40
  outliers final: 10
  residues processed: 159
  average time/residue: 0.4419
  time to fit residues: 73.9822
Evaluate side-chains
  130 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   55 SER
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 B residue   73 LEU
Chi-restraints excluded: chain D residue   80 MET
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain E residue   54 LEU
Chi-restraints excluded: chain E residue   85 THR
Chi-restraints excluded: chain E residue  104 LEU
Chi-restraints excluded: chain F residue   33 LEU
Chi-restraints excluded: chain F residue   60 SER
Chi-restraints excluded: chain F residue   72 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 19 optimal weight:    0.3980
   chunk 10 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 23 optimal weight:    0.0170
   chunk 52 optimal weight:    7.9990
   chunk 49 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0000
   chunk 36 optimal weight:    6.9990
   overall best weight:    1.2826

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  84 GLN
A 101 GLN
C  39 GLN
D  39 GLN
D  57 ASN
E  27 GLN
E  38 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.132725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.106404 restraints weight = 6167.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 2.03
r_work: 0.3080 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2950 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2953
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2953 r_free = 0.2953    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2953 r_free = 0.2953    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (9 function evaluations)
r_final: 0.2953
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8812
moved from start:          0.4965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5994  Z= 0.174
  Angle     :  0.649   7.907   8212  Z= 0.368
  Chirality :  0.049   0.400    886
  Planarity :  0.004   0.048    960
  Dihedral  : 15.885 144.243    991
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  7.04 %
    Allowed  : 27.66 %
    Favored  : 65.29 %
  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:  0.43 (0.28), residues: 360
  loop : -0.47 (0.34), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 100 
 TYR   0.017   0.002   TYR D  97 
 PHE   0.029   0.002   PHE F  94 
 TRP   0.007   0.001   TRP C  36 
 HIS   0.003   0.001   HIS E  55 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00355 /  0.17 ( 5988)
  covalent geometry    : angle       0.64802 /  0.37 ( 8200)
  SS BOND              : bond        0.00711 /  0.33 (    6)
  SS BOND              : angle       1.12464 /  0.69 (   12)
  hydrogen bonds       : bond        0.05333 /  3.52 (  224)
  hydrogen bonds       : angle       5.10233 /  3.55 (  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
  160 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 119
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A   46 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8014 (tt0)
REVERT: B    4 MET cc_start: 0.8659 (mmm) cc_final: 0.8442 (mmm)
REVERT: B   15 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6321 (tp)
REVERT: C   43 LYS cc_start: 0.7882 (mppt) cc_final: 0.7580 (mmtm)
REVERT: C   73 SER cc_start: 0.8703 (p) cc_final: 0.8434 (p)
REVERT: D   46 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8594 (tt0)
REVERT: D   72 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8214 (tt)
REVERT: E    3 GLN cc_start: 0.8240 (mp10) cc_final: 0.8036 (mp-120)
REVERT: E  104 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7499 (mp)
REVERT: F   60 SER cc_start: 0.8125 (t) cc_final: 0.7899 (p)
REVERT: F   81 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7250 (pm20)
  outliers start: 41
  outliers final: 17
  residues processed: 146
  average time/residue: 0.4108
  time to fit residues: 63.2936
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  : 0.204 
-------------------------------------------------------------------------------
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   95 MET
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   24 SER
Chi-restraints excluded: chain C residue   55 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   46 GLU
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 D residue  110 ASP
Chi-restraints excluded: chain E residue   54 LEU
Chi-restraints excluded: chain E residue  104 LEU
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   63 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:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 67 optimal weight:    8.9990
   chunk 41 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0170
   chunk 61 optimal weight:    0.8980
   overall best weight:    1.3824

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 101 GLN
C  79 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.130464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.103613 restraints weight = 6214.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 1.78
r_work: 0.3074 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2945 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2952
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2952 r_free = 0.2952    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2952 r_free = 0.2952    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2952
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8872
moved from start:          0.5816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5994  Z= 0.164
  Angle     :  0.624   6.843   8212  Z= 0.353
  Chirality :  0.049   0.340    886
  Planarity :  0.004   0.034    960
  Dihedral  : 16.012 152.441    991
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  6.87 %
    Allowed  : 28.87 %
    Favored  : 64.26 %
  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: -0.05 (0.32), residues: 669
  helix:  None (None), residues: 0
  sheet:  0.40 (0.28), residues: 360
  loop : -0.47 (0.33), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  61 
 TYR   0.014   0.002   TYR C  97 
 PHE   0.029   0.003   PHE F  94 
 TRP   0.009   0.001   TRP A  47 
 HIS   0.002   0.001   HIS E  55 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.16 ( 5988)
  covalent geometry    : angle       0.62264 /  0.35 ( 8200)
  SS BOND              : bond        0.00697 /  0.32 (    6)
  SS BOND              : angle       1.33654 /  0.74 (   12)
  hydrogen bonds       : bond        0.03507 /  2.35 (  224)
  hydrogen bonds       : angle       4.78907 /  3.34 (  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
  157 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 117
  time to evaluate  : 0.199 
Fit side-chains
REVERT: A    6 GLU cc_start: 0.8665 (mp0) cc_final: 0.8397 (mp0)
REVERT: A   46 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7975 (tt0)
REVERT: B   15 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6497 (tp)
REVERT: C   43 LYS cc_start: 0.7991 (mppt) cc_final: 0.7644 (mmtm)
REVERT: D    3 GLN cc_start: 0.8447 (mt0) cc_final: 0.8070 (mt0)
REVERT: E    3 GLN cc_start: 0.8275 (mp10) cc_final: 0.8034 (mp-120)
REVERT: E   73 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8141 (tp)
REVERT: F   47 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8543 (mp)
REVERT: F   81 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7395 (pm20)
  outliers start: 40
  outliers final: 22
  residues processed: 145
  average time/residue: 0.3978
  time to fit residues: 60.9857
Evaluate side-chains
  133 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 107
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
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   55 SER
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   21 SER
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain C residue   89 LYS
Chi-restraints excluded: chain D residue   12 VAL
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   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   11 LEU
Chi-restraints excluded: chain F residue   14 SER
Chi-restraints excluded: chain F residue   47 LEU
Chi-restraints excluded: chain F residue   63 SER
Chi-restraints excluded: chain F residue   81 GLU
Chi-restraints excluded: chain F residue  100 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 28 optimal weight:    0.3980
   chunk 6 optimal weight:    3.9990
   chunk 2 optimal weight:    8.9990
   chunk 46 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 60 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 32 optimal weight:    0.5980
   chunk 17 optimal weight:    0.8980
   chunk 42 optimal weight:    5.9990
   overall best weight:    1.3784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 101 GLN
C  79 ASN
D 105 ASN
D 114 GLN
E   6 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.128629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.101727 restraints weight = 6323.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 1.79
r_work: 0.3047 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2918 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2923
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2923 r_free = 0.2923    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2923 r_free = 0.2923    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2923
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8903
moved from start:          0.6151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   5994  Z= 0.160
  Angle     :  0.607   7.200   8212  Z= 0.346
  Chirality :  0.049   0.377    886
  Planarity :  0.004   0.037    960
  Dihedral  : 15.941 149.115    991
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  7.22 %
    Allowed  : 27.84 %
    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: -0.03 (0.32), residues: 669
  helix:  None (None), residues: 0
  sheet:  0.39 (0.28), residues: 360
  loop : -0.42 (0.33), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  61 
 TYR   0.016   0.002   TYR D  97 
 PHE   0.033   0.003   PHE F  94 
 TRP   0.006   0.001   TRP A  47 
 HIS   0.002   0.001   HIS E  55 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00341 /  0.16 ( 5988)
  covalent geometry    : angle       0.60633 /  0.35 ( 8200)
  SS BOND              : bond        0.00716 /  0.37 (    6)
  SS BOND              : angle       1.13277 /  0.64 (   12)
  hydrogen bonds       : bond        0.03648 /  2.41 (  224)
  hydrogen bonds       : angle       4.78069 /  3.32 (  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
  154 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 112
  time to evaluate  : 0.179 
Fit side-chains
REVERT: A   46 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7946 (tt0)
REVERT: B   15 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6509 (tp)
REVERT: B   24 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8580 (p)
REVERT: B   54 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8983 (mp)
REVERT: C   43 LYS cc_start: 0.8019 (mppt) cc_final: 0.7727 (mmtm)
REVERT: D    3 GLN cc_start: 0.8512 (mt0) cc_final: 0.8224 (mt0)
REVERT: D   72 ILE cc_start: 0.8709 (pt) cc_final: 0.8485 (tt)
REVERT: E   73 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8233 (tp)
REVERT: F   47 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8584 (mp)
REVERT: F   81 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7434 (pm20)
  outliers start: 42
  outliers final: 18
  residues processed: 142
  average time/residue: 0.3954
  time to fit residues: 59.4676
Evaluate side-chains
  131 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    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   55 SER
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   54 LEU
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain C residue   55 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  104 SER
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   14 SER
Chi-restraints excluded: chain F residue   27 GLN
Chi-restraints excluded: chain F residue   33 LEU
Chi-restraints excluded: chain F residue   47 LEU
Chi-restraints excluded: chain F residue   63 SER
Chi-restraints excluded: chain F residue   81 GLU
Chi-restraints excluded: chain F residue  100 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 56 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 45 optimal weight:    6.9990
   chunk 32 optimal weight:    0.8980
   overall best weight:    1.9386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 101 GLN
C  79 ASN
E   6 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.126364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.099504 restraints weight = 6261.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 1.78
r_work: 0.3014 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2894
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2894 r_free = 0.2894    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2894 r_free = 0.2894    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2894
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8939
moved from start:          0.6560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5994  Z= 0.192
  Angle     :  0.655   7.738   8212  Z= 0.371
  Chirality :  0.051   0.405    886
  Planarity :  0.004   0.037    960
  Dihedral  : 15.974 150.113    991
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 2.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  6.36 %
    Allowed  : 29.73 %
    Favored  : 63.92 %
  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 (0.32), residues: 669
  helix:  None (None), residues: 0
  sheet:  0.43 (0.28), residues: 360
  loop : -0.42 (0.33), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  61 
 TYR   0.018   0.002   TYR D  97 
 PHE   0.036   0.003   PHE F  94 
 TRP   0.007   0.001   TRP A  47 
 HIS   0.003   0.002   HIS E  55 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00426 /  0.19 ( 5988)
  covalent geometry    : angle       0.65192 /  0.37 ( 8200)
  SS BOND              : bond        0.00908 /  0.42 (    6)
  SS BOND              : angle       1.66113 /  0.94 (   12)
  hydrogen bonds       : bond        0.04040 /  2.67 (  224)
  hydrogen bonds       : angle       4.88279 /  3.39 (  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
  152 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 115
  time to evaluate  : 0.226 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.8766 (mtmt) cc_final: 0.8457 (mttt)
REVERT: A   46 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7958 (tt0)
REVERT: A   57 ASN cc_start: 0.9016 (m-40) cc_final: 0.8813 (m-40)
REVERT: B   54 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.9015 (mp)
REVERT: C   43 LYS cc_start: 0.8080 (mppt) cc_final: 0.7765 (mmtm)
REVERT: D    3 GLN cc_start: 0.8476 (mt0) cc_final: 0.8191 (mt0)
REVERT: E    4 MET cc_start: 0.9066 (mmp) cc_final: 0.8805 (mmm)
REVERT: E   73 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8339 (tp)
REVERT: F   47 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8601 (mp)
  outliers start: 37
  outliers final: 17
  residues processed: 142
  average time/residue: 0.4267
  time to fit residues: 63.9239
Evaluate side-chains
  129 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   95 MET
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue   55 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  104 SER
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 F residue   12 SER
Chi-restraints excluded: chain F residue   14 SER
Chi-restraints excluded: chain F residue   33 LEU
Chi-restraints excluded: chain F residue   47 LEU
Chi-restraints excluded: chain F residue   63 SER
Chi-restraints excluded: chain F residue  100 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 36 optimal weight:    6.9990
   chunk 3 optimal weight:    8.9990
   chunk 51 optimal weight:    6.9990
   chunk 30 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    1.3988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 101 GLN
C  79 ASN
D   3 GLN
F   6 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.125874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.099953 restraints weight = 6299.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 1.92
r_work: 0.3003 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2873 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2879
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2879 r_free = 0.2879    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2879 r_free = 0.2879    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (13 function evaluations)
r_final: 0.2879
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8942
moved from start:          0.6705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5994  Z= 0.155
  Angle     :  0.610   6.877   8212  Z= 0.347
  Chirality :  0.049   0.361    886
  Planarity :  0.004   0.036    960
  Dihedral  : 15.998 149.912    991
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  5.84 %
    Allowed  : 29.21 %
    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:  0.03 (0.32), residues: 669
  helix:  None (None), residues: 0
  sheet:  0.45 (0.28), residues: 360
  loop : -0.42 (0.33), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  18 
 TYR   0.016   0.002   TYR D  97 
 PHE   0.032   0.002   PHE F  94 
 TRP   0.006   0.001   TRP A  47 
 HIS   0.003   0.001   HIS E  55 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00327 /  0.15 ( 5988)
  covalent geometry    : angle       0.60443 /  0.34 ( 8200)
  SS BOND              : bond        0.00791 /  0.36 (    6)
  SS BOND              : angle       2.29744 /  1.18 (   12)
  hydrogen bonds       : bond        0.03487 /  2.31 (  224)
  hydrogen bonds       : angle       4.75237 /  3.28 (  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
  142 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 108
  time to evaluate  : 0.215 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.8767 (mtmt) cc_final: 0.8456 (mttt)
REVERT: A   46 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7998 (tt0)
REVERT: A   87 ASN cc_start: 0.8889 (t0) cc_final: 0.8654 (t0)
REVERT: C   43 LYS cc_start: 0.8109 (mppt) cc_final: 0.7771 (mmtm)
REVERT: D    3 GLN cc_start: 0.8447 (mt0) cc_final: 0.8178 (mt0)
REVERT: E   73 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8342 (tp)
REVERT: E  103 LYS cc_start: 0.8676 (ttpp) cc_final: 0.8038 (tptp)
REVERT: F    3 GLN cc_start: 0.8344 (mp10) cc_final: 0.7683 (mm-40)
REVERT: F   38 GLN cc_start: 0.9395 (OUTLIER) cc_final: 0.9184 (tt0)
REVERT: F   47 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8592 (mp)
REVERT: F   81 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7639 (pm20)
  outliers start: 34
  outliers final: 16
  residues processed: 135
  average time/residue: 0.4106
  time to fit residues: 58.7019
Evaluate side-chains
  127 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain D residue   25 SER
Chi-restraints excluded: chain D residue   65 SER
Chi-restraints excluded: chain D residue  104 SER
Chi-restraints excluded: chain E residue   54 LEU
Chi-restraints excluded: chain E residue   73 LEU
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   14 SER
Chi-restraints excluded: chain F residue   27 GLN
Chi-restraints excluded: chain F residue   33 LEU
Chi-restraints excluded: chain F residue   38 GLN
Chi-restraints excluded: chain F residue   47 LEU
Chi-restraints excluded: chain F residue   63 SER
Chi-restraints excluded: chain F residue   81 GLU
Chi-restraints excluded: chain F residue  100 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 3 optimal weight:    8.9990
   chunk 66 optimal weight:    8.9990
   chunk 55 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0370
   chunk 27 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 13 optimal weight:    0.0040
   chunk 36 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.4870

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 101 GLN
B  31 ASN
C  79 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.130122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.103394 restraints weight = 6213.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 1.78
r_work: 0.3073 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2944 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2948
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2948 r_free = 0.2948    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2948 r_free = 0.2948    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2948
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8884
moved from start:          0.6784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   5994  Z= 0.107
  Angle     :  0.524   6.284   8212  Z= 0.302
  Chirality :  0.045   0.293    886
  Planarity :  0.004   0.038    960
  Dihedral  : 15.977 149.106    991
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 32.13 %
    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:  0.19 (0.32), residues: 669
  helix:  None (None), residues: 0
  sheet:  0.55 (0.28), residues: 360
  loop : -0.30 (0.33), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  61 
 TYR   0.011   0.001   TYR F  91 
 PHE   0.022   0.002   PHE E  94 
 TRP   0.007   0.001   TRP D  47 
 HIS   0.000   0.000   HIS B  55 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00192 /  0.11 ( 5988)
  covalent geometry    : angle       0.52290 /  0.30 ( 8200)
  SS BOND              : bond        0.00368 /  0.18 (    6)
  SS BOND              : angle       1.10113 /  0.58 (   12)
  hydrogen bonds       : bond        0.02748 /  1.82 (  224)
  hydrogen bonds       : angle       4.57690 /  3.14 (  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
  128 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A   13 GLN cc_start: 0.7278 (mm-40) cc_final: 0.7026 (mp10)
REVERT: A   15 LYS cc_start: 0.8775 (mtmt) cc_final: 0.8471 (mttt)
REVERT: A   46 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7967 (tt0)
REVERT: A   87 ASN cc_start: 0.8814 (t0) cc_final: 0.8593 (t0)
REVERT: A   95 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8636 (ttt)
REVERT: C   43 LYS cc_start: 0.8026 (mppt) cc_final: 0.7727 (mmtm)
REVERT: D    3 GLN cc_start: 0.8424 (mt0) cc_final: 0.8085 (mt0)
REVERT: E  103 LYS cc_start: 0.8628 (ttpp) cc_final: 0.7998 (tptp)
REVERT: F    3 GLN cc_start: 0.8362 (mp10) cc_final: 0.7751 (mm-40)
  outliers start: 18
  outliers final: 10
  residues processed: 122
  average time/residue: 0.4344
  time to fit residues: 55.9154
Evaluate side-chains
  119 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 MET
Chi-restraints excluded: chain A residue   95 MET
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain D residue   12 VAL
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 F residue   12 SER
Chi-restraints excluded: chain F residue   14 SER
Chi-restraints excluded: chain F residue   33 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 61 optimal weight:    0.4980
   chunk 50 optimal weight:    5.9990
   chunk 25 optimal weight:    7.9990
   chunk 63 optimal weight:    6.9990
   chunk 41 optimal weight:    6.9990
   chunk 38 optimal weight:    4.9990
   chunk 54 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 1 optimal weight:    0.4980
   chunk 66 optimal weight:    8.9990
   chunk 42 optimal weight:    0.7980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 101 GLN
C  79 ASN
D 114 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.127500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.101584 restraints weight = 6302.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 1.91
r_work: 0.3027 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2897 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2902
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2902 r_free = 0.2902    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2902 r_free = 0.2902    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2902
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8917
moved from start:          0.6870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5994  Z= 0.127
  Angle     :  0.562   6.907   8212  Z= 0.321
  Chirality :  0.047   0.340    886
  Planarity :  0.004   0.041    960
  Dihedral  : 15.876 148.198    991
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 32.65 %
    Favored  : 64.09 %
  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:  0.26 (0.32), residues: 669
  helix:  None (None), residues: 0
  sheet:  0.65 (0.28), residues: 357
  loop : -0.32 (0.33), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  52 
 TYR   0.014   0.001   TYR D  97 
 PHE   0.028   0.002   PHE F  94 
 TRP   0.006   0.001   TRP C  47 
 HIS   0.002   0.001   HIS E  55 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.13 ( 5988)
  covalent geometry    : angle       0.55922 /  0.32 ( 8200)
  SS BOND              : bond        0.00601 /  0.29 (    6)
  SS BOND              : angle       1.44682 /  0.78 (   12)
  hydrogen bonds       : bond        0.03010 /  2.00 (  224)
  hydrogen bonds       : angle       4.49925 /  3.09 (  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
  127 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.207 
Fit side-chains
REVERT: A   13 GLN cc_start: 0.7342 (mm-40) cc_final: 0.7039 (mp10)
REVERT: A   15 LYS cc_start: 0.8778 (mtmt) cc_final: 0.8526 (mtmm)
REVERT: A   46 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8019 (tt0)
REVERT: C   43 LYS cc_start: 0.8028 (mppt) cc_final: 0.7716 (mmtm)
REVERT: D    3 GLN cc_start: 0.8449 (mt0) cc_final: 0.8153 (mt0)
REVERT: E  103 LYS cc_start: 0.8636 (ttpp) cc_final: 0.8004 (tptp)
REVERT: F    3 GLN cc_start: 0.8399 (mp10) cc_final: 0.7754 (mm-40)
  outliers start: 19
  outliers final: 13
  residues processed: 121
  average time/residue: 0.4679
  time to fit residues: 59.5423
Evaluate side-chains
  119 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   85 MET
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 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  104 SER
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   14 SER
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:    2.9990
   chunk 58 optimal weight:    7.9990
   chunk 63 optimal weight:    3.9990
   chunk 2 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 66 optimal weight:    7.9990
   chunk 64 optimal weight:    6.9990
   overall best weight:    2.3986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 101 GLN
C  79 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.125054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.098080 restraints weight = 6297.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3119 rms_B_bonded: 1.78
r_work: 0.2994 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2865 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2873
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2873 r_free = 0.2873    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 = 0.2873 r_free = 0.2873    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2873
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8962
moved from start:          0.7028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   5994  Z= 0.226
  Angle     :  0.701   8.416   8212  Z= 0.394
  Chirality :  0.053   0.432    886
  Planarity :  0.005   0.040    960
  Dihedral  : 15.948 148.641    991
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 32.13 %
    Favored  : 64.26 %
  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:  0.49 (0.28), residues: 360
  loop : -0.38 (0.33), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  50 
 TYR   0.020   0.002   TYR D  97 
 PHE   0.037   0.003   PHE F  94 
 TRP   0.006   0.002   TRP A  47 
 HIS   0.005   0.002   HIS E  55 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00514 /  0.23 ( 5988)
  covalent geometry    : angle       0.69624 /  0.39 ( 8200)
  SS BOND              : bond        0.01003 /  0.46 (    6)
  SS BOND              : angle       2.33184 /  1.28 (   12)
  hydrogen bonds       : bond        0.04313 /  2.82 (  224)
  hydrogen bonds       : angle       4.76498 /  3.29 (  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
  122 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A   13 GLN cc_start: 0.7365 (mm-40) cc_final: 0.7066 (mp10)
REVERT: A   15 LYS cc_start: 0.8757 (mtmt) cc_final: 0.8513 (mtmm)
REVERT: A   46 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7991 (tt0)
REVERT: C   43 LYS cc_start: 0.8137 (mppt) cc_final: 0.7796 (mmtm)
REVERT: D    3 GLN cc_start: 0.8475 (mt0) cc_final: 0.8201 (mt0)
REVERT: E   73 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8462 (tp)
REVERT: E  103 LYS cc_start: 0.8631 (ttpp) cc_final: 0.7974 (tptp)
REVERT: F    3 GLN cc_start: 0.8415 (mp10) cc_final: 0.7862 (mm-40)
  outliers start: 21
  outliers final: 13
  residues processed: 115
  average time/residue: 0.4532
  time to fit residues: 54.8288
Evaluate side-chains
  115 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain D residue   12 VAL
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   73 LEU
Chi-restraints excluded: chain E residue  106 ILE
Chi-restraints excluded: chain F residue   12 SER
Chi-restraints excluded: chain F residue   14 SER
Chi-restraints excluded: chain F residue   27 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 66 optimal weight:    8.9990
   chunk 39 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0270
   chunk 22 optimal weight:    9.9990
   chunk 23 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 47 optimal weight:    5.9990
   overall best weight:    0.9444

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 101 GLN
C  79 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.127670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.100767 restraints weight = 6185.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 1.77
r_work: 0.3029 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2901 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2908
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2908 r_free = 0.2908    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2908 r_free = 0.2908    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (9 function evaluations)
r_final: 0.2908
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8927
moved from start:          0.7061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5994  Z= 0.133
  Angle     :  0.585   6.684   8212  Z= 0.335
  Chirality :  0.047   0.333    886
  Planarity :  0.004   0.039    960
  Dihedral  : 16.004 149.347    991
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 32.65 %
    Favored  : 63.75 %
  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:  0.51 (0.28), residues: 360
  loop : -0.27 (0.33), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  50 
 TYR   0.014   0.001   TYR D  97 
 PHE   0.029   0.002   PHE F  94 
 TRP   0.008   0.001   TRP D  47 
 HIS   0.002   0.001   HIS E  55 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.13 ( 5988)
  covalent geometry    : angle       0.58244 /  0.33 ( 8200)
  SS BOND              : bond        0.00580 /  0.27 (    6)
  SS BOND              : angle       1.41385 /  0.77 (   12)
  hydrogen bonds       : bond        0.03213 /  2.14 (  224)
  hydrogen bonds       : angle       4.60801 /  3.17 (  558)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 2628.71 seconds
wall clock time: 45 minutes 28.26 seconds (2728.26 seconds total)