Starting phenix.real_space_refine
on Wed Feb  4 04:55:24 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9o1b_70001/02_2026/9o1b_70001_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9o1b_70001/02_2026/9o1b_70001.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.37
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9o1b_70001/02_2026/9o1b_70001.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9o1b_70001/02_2026/9o1b_70001.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9o1b_70001/02_2026/9o1b_70001_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9o1b_70001/02_2026/9o1b_70001_neut.cif"
  }
  resolution = 2.37
  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=   0.002 sd=   0.010
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
     Zn      1      6.06       5
     S      65      5.16       5
     C    5960      2.51       5
     N    1392      2.21       5
     O    1502      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8920
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "I"
      Number of atoms: 594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 594
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 3, 'TRANS': 79}
    Chain: "J"
      Number of atoms: 594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 594
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 3, 'TRANS': 79}
    Chain: "L"
      Number of atoms: 594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 594
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 3, 'TRANS': 79}
    Chain: "M"
      Number of atoms: 594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 594
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 3, 'TRANS': 79}
    Chain: "N"
      Number of atoms: 594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 594
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 3, 'TRANS': 79}
    Chain: "O"
      Number of atoms: 594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 594
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 3, 'TRANS': 79}
    Chain: "P"
      Number of atoms: 591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 591
          Classifications: {'peptide': 83}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 79}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "Q"
      Number of atoms: 594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 594
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 3, 'TRANS': 79}
    Chain: "R"
      Number of atoms: 594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 594
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 3, 'TRANS': 79}
    Chain: "S"
      Number of atoms: 594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 594
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 3, 'TRANS': 79}
    Chain: "X"
      Number of atoms: 367
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 367
          Classifications: {'peptide': 47}
          Link IDs: {'PTRANS': 2, 'TRANS': 44}
    Chain: "Y"
      Number of atoms: 367
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 367
          Classifications: {'peptide': 47}
          Link IDs: {'PTRANS': 2, 'TRANS': 44}
    Chain: "a"
      Number of atoms: 2243
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2243
          Classifications: {'peptide': 286}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 275}
    Chain: "a"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1, 'water': 5}
          Link IDs: {None: 5}
  Time building chain proxies: 2.08, per 1000 atoms: 0.23
  Number of scatterers: 8920
  At special positions: 0
  Unit cell: (90.47, 102.09, 95.45, 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)
     Zn      1     29.99
     S      65     16.00
     O    1502      8.00
     N    1392      7.00
     C    5960      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.59
  Conformation dependent library (CDL) restraints added in 350.7 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN a 301 "
        pdb="ZN    ZN a 301 " - pdb=" ND1 HIS a 289 "
        pdb="ZN    ZN a 301 " - pdb=" ND1 HIS a 186 "


  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2108

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 1 sheets defined
      89.9% alpha, 0.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'I' and resid 1 through 41
      removed outlier: 3.510A  pdb=" N   GLY I  19 " --> pdb=" O   LEU I  15 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 44 through 60
      removed outlier: 4.222A  pdb=" N   GLY I  57 " --> pdb=" O   PHE I  53 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU I  58 " --> pdb=" O   ILE I  54 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 60 through 76
    Processing helix  chain 'I' and resid 77 through 82
      removed outlier: 3.929A  pdb=" N   GLY I  81 " --> pdb=" O   ASN I  77 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   GLN I  82 " --> pdb=" O   PRO I  78 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'I' and resid 77 through 82'
    Processing helix  chain 'J' and resid 2 through 41
      removed outlier: 3.514A  pdb=" N   LYS J  33 " --> pdb=" O   LEU J  29 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 44 through 60
    Processing helix  chain 'J' and resid 61 through 76
      removed outlier: 3.589A  pdb=" N   ILE J  65 " --> pdb=" O   ALA J  61 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 79 through 83
    Processing helix  chain 'L' and resid 2 through 41
    Processing helix  chain 'L' and resid 44 through 75
      removed outlier: 3.826A  pdb=" N   VAL L  50 " --> pdb=" O   PRO L  46 " (cutoff:3.500A)
      removed outlier: 5.504A  pdb=" N   VAL L  62 " --> pdb=" O   LEU L  58 " (cutoff:3.500A)
      removed outlier: 5.157A  pdb=" N   THR L  63 " --> pdb=" O   LEU L  59 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 77 through 82
      removed outlier: 3.677A  pdb=" N   GLY L  81 " --> pdb=" O   ASN L  77 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 2 through 41
    Processing helix  chain 'M' and resid 44 through 75
      removed outlier: 3.876A  pdb=" N   VAL M  50 " --> pdb=" O   PRO M  46 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   LEU M  58 " --> pdb=" O   ILE M  54 " (cutoff:3.500A)
      removed outlier: 5.217A  pdb=" N   VAL M  62 " --> pdb=" O   LEU M  58 " (cutoff:3.500A)
      removed outlier: 5.153A  pdb=" N   THR M  63 " --> pdb=" O   LEU M  59 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 2 through 41
    Processing helix  chain 'N' and resid 44 through 60
      removed outlier: 3.515A  pdb=" N   LEU N  58 " --> pdb=" O   ILE N  54 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ASP N  60 " --> pdb=" O   ALA N  56 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 60 through 76
      removed outlier: 3.769A  pdb=" N   PHE N  75 " --> pdb=" O   LEU N  71 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 77 through 82
      removed outlier: 3.986A  pdb=" N   GLY N  81 " --> pdb=" O   ASN N  77 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   GLN N  82 " --> pdb=" O   PRO N  78 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 77 through 82'
    Processing helix  chain 'O' and resid 2 through 41
      removed outlier: 3.527A  pdb=" N   LYS O  33 " --> pdb=" O   LEU O  29 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 44 through 75
      removed outlier: 3.914A  pdb=" N   VAL O  50 " --> pdb=" O   PRO O  46 " (cutoff:3.500A)
      removed outlier: 5.282A  pdb=" N   VAL O  62 " --> pdb=" O   LEU O  58 " (cutoff:3.500A)
      removed outlier: 5.165A  pdb=" N   THR O  63 " --> pdb=" O   LEU O  59 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LEU O  71 " --> pdb=" O   VAL O  67 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   PHE O  75 " --> pdb=" O   LEU O  71 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 77 through 83
      removed outlier: 4.405A  pdb=" N   GLY O  81 " --> pdb=" O   ASN O  77 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   GLN O  82 " --> pdb=" O   PRO O  78 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ILE O  83 " --> pdb=" O   PHE O  79 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'O' and resid 77 through 83'
    Processing helix  chain 'P' and resid 2 through 41
    Processing helix  chain 'P' and resid 44 through 60
      removed outlier: 3.797A  pdb=" N   VAL P  50 " --> pdb=" O   PRO P  46 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 60 through 76
    Processing helix  chain 'Q' and resid 2 through 41
    Processing helix  chain 'Q' and resid 44 through 60
      removed outlier: 3.707A  pdb=" N   VAL Q  50 " --> pdb=" O   PRO Q  46 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 60 through 76
    Processing helix  chain 'Q' and resid 79 through 83
    Processing helix  chain 'R' and resid 2 through 41
      removed outlier: 3.527A  pdb=" N   LYS R  33 " --> pdb=" O   LEU R  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 44 through 60
      removed outlier: 4.169A  pdb=" N   VAL R  50 " --> pdb=" O   PRO R  46 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 60 through 76
    Processing helix  chain 'R' and resid 78 through 82
      removed outlier: 3.574A  pdb=" N   GLN R  82 " --> pdb=" O   PHE R  79 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 2 through 41
      removed outlier: 3.561A  pdb=" N   LYS S  33 " --> pdb=" O   LEU S  29 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 44 through 75
      removed outlier: 3.843A  pdb=" N   VAL S  50 " --> pdb=" O   PRO S  46 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   LEU S  58 " --> pdb=" O   ILE S  54 " (cutoff:3.500A)
      removed outlier: 5.342A  pdb=" N   VAL S  62 " --> pdb=" O   LEU S  58 " (cutoff:3.500A)
      removed outlier: 5.148A  pdb=" N   THR S  63 " --> pdb=" O   LEU S  59 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 79 through 83
    Processing helix  chain 'X' and resid 5 through 24
      removed outlier: 3.702A  pdb=" N   SER X  11 " --> pdb=" O   LEU X   7 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 25 through 45
      removed outlier: 3.615A  pdb=" N   VAL X  29 " --> pdb=" O   VAL X  25 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 5 through 25
      removed outlier: 3.563A  pdb=" N   GLY Y   9 " --> pdb=" O   ALA Y   5 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 25 through 47
      removed outlier: 3.721A  pdb=" N   VAL Y  29 " --> pdb=" O   VAL Y  25 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 5 through 15
    Processing helix  chain 'a' and resid 32 through 39
    Processing helix  chain 'a' and resid 46 through 66
      removed outlier: 3.584A  pdb=" N   ALA a  66 " --> pdb=" O   ILE a  62 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 76 through 95
      removed outlier: 3.542A  pdb=" N   PHE a  81 " --> pdb=" O   GLY a  77 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 103 through 121
      removed outlier: 3.729A  pdb=" N   ILE a 121 " --> pdb=" O   LEU a 117 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 122 through 124
      No H-bonds generated for 'chain 'a' and resid 122 through 124'
    Processing helix  chain 'a' and resid 127 through 138
    Processing helix  chain 'a' and resid 147 through 150
      removed outlier: 3.650A  pdb=" N   THR a 150 " --> pdb=" O   VAL a 147 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'a' and resid 147 through 150'
    Processing helix  chain 'a' and resid 151 through 185
      removed outlier: 3.953A  pdb=" N   THR a 155 " --> pdb=" O   ASP a 151 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   ILE a 176 " --> pdb=" O   LYS a 172 " (cutoff:3.500A)
      removed outlier: 8.809A  pdb=" N   GLY a 177 " --> pdb=" O   VAL a 173 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 192 through 199
    Processing helix  chain 'a' and resid 199 through 242
      removed outlier: 3.718A  pdb=" N   ASN a 203 " --> pdb=" O   LEU a 199 " (cutoff:3.500A)
      Proline residue:  a 215  - end of helix
      removed outlier: 4.143A  pdb=" N   LEU a 222 " --> pdb=" O   LEU a 218 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   SER a 242 " --> pdb=" O   VAL a 238 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 244 through 284
      removed outlier: 3.775A  pdb=" N   SER a 248 " --> pdb=" O   MET a 244 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ALA a 249 " --> pdb=" O   PHE a 245 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   LEU a 250 " --> pdb=" O   LEU a 246 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   LEU a 264 " --> pdb=" O   VAL a 260 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'a' and resid 18 through 19

    836 hydrogen bonds defined for protein.
    2484 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.53

  Time building geometry restraints manager: 0.74 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1452
        1.32 -     1.45: 2169
        1.45 -     1.57: 5334
        1.57 -     1.69: 0
        1.69 -     1.82: 128
  Bond restraints: 9083
  Sorted by residual:
  bond pdb=" C   PRO a 130 "
       pdb=" O   PRO a 130 "
    ideal  model  delta    sigma   weight residual
    1.238  1.203  0.034 1.24e-02 6.50e+03 7.60e+00
  bond pdb=" C   PRO a 125 "
       pdb=" O   PRO a 125 "
    ideal  model  delta    sigma   weight residual
    1.233  1.202  0.031 1.24e-02 6.50e+03 6.34e+00
  bond pdb=" N   PHE a 143 "
       pdb=" CA  PHE a 143 "
    ideal  model  delta    sigma   weight residual
    1.456  1.484 -0.027 1.23e-02 6.61e+03 4.92e+00
  bond pdb=" N   VAL a 126 "
       pdb=" CA  VAL a 126 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.41e-02 5.03e+03 4.89e+00
  bond pdb=" N   MET a 131 "
       pdb=" CA  MET a 131 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.029 1.30e-02 5.92e+03 4.84e+00
  ... (remaining 9078 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.50: 12013
        1.50 -     2.99: 237
        2.99 -     4.49: 37
        4.49 -     5.98: 18
        5.98 -     7.48: 8
  Bond angle restraints: 12313
  Sorted by residual:
  angle pdb=" C   ASN Y   2 "
        pdb=" CA  ASN Y   2 "
        pdb=" CB  ASN Y   2 "
      ideal   model   delta    sigma   weight residual
     117.23  110.42    6.81 1.36e+00 5.41e-01 2.51e+01
  angle pdb=" N   GLN I  82 "
        pdb=" CA  GLN I  82 "
        pdb=" C   GLN I  82 "
      ideal   model   delta    sigma   weight residual
     113.37  107.30    6.07 1.38e+00 5.25e-01 1.93e+01
  angle pdb=" CA  ASN Y   2 "
        pdb=" C   ASN Y   2 "
        pdb=" N   ILE Y   3 "
      ideal   model   delta    sigma   weight residual
     119.98  116.70    3.28 8.50e-01 1.38e+00 1.49e+01
  angle pdb=" CA  MET I  52 "
        pdb=" CB  MET I  52 "
        pdb=" CG  MET I  52 "
      ideal   model   delta    sigma   weight residual
     114.10  121.58   -7.48 2.00e+00 2.50e-01 1.40e+01
  angle pdb=" C   ALA N  76 "
        pdb=" N   ASN N  77 "
        pdb=" CA  ASN N  77 "
      ideal   model   delta    sigma   weight residual
     122.26  118.32    3.94 1.10e+00 8.26e-01 1.28e+01
  ... (remaining 12308 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 4804
       17.95 -    35.89: 342
       35.89 -    53.84: 60
       53.84 -    71.78: 8
       71.78 -    89.73: 7
  Dihedral angle restraints: 5221
    sinusoidal: 1911
      harmonic: 3310
  Sorted by residual:
  dihedral pdb=" CA  GLY R  81 "
           pdb=" C   GLY R  81 "
           pdb=" N   GLN R  82 "
           pdb=" CA  GLN R  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.91  -20.09     0      5.00e+00 4.00e-02 1.61e+01
  dihedral pdb=" CA  ALA a 284 "
           pdb=" C   ALA a 284 "
           pdb=" N   HIS a 285 "
           pdb=" CA  HIS a 285 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.37  -15.63     0      5.00e+00 4.00e-02 9.77e+00
  dihedral pdb=" CB  GLU a 182 "
           pdb=" CG  GLU a 182 "
           pdb=" CD  GLU a 182 "
           pdb=" OE1 GLU a 182 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   83.64  -83.64     1      3.00e+01 1.11e-03 9.48e+00
  ... (remaining 5218 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 962
       0.028 -    0.056: 327
       0.056 -    0.084: 176
       0.084 -    0.112: 44
       0.112 -    0.140: 9
  Chirality restraints: 1518
  Sorted by residual:
  chirality pdb=" CA  PHE a 143 "
            pdb=" N   PHE a 143 "
            pdb=" C   PHE a 143 "
            pdb=" CB  PHE a 143 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 4.91e-01
  chirality pdb=" CB  VAL a 126 "
            pdb=" CA  VAL a 126 "
            pdb=" CG1 VAL a 126 "
            pdb=" CG2 VAL a 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 4.59e-01
  chirality pdb=" CA  VAL I  80 "
            pdb=" N   VAL I  80 "
            pdb=" C   VAL I  80 "
            pdb=" CB  VAL I  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.41e-01
  ... (remaining 1515 not shown)

  Planarity restraints: 1522
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE I  79 "   -0.018 2.00e-02 2.50e+03   3.63e-02 1.32e+01
        pdb=" C   PHE I  79 "    0.063 2.00e-02 2.50e+03
        pdb=" O   PHE I  79 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   VAL I  80 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY R  81 "    0.017 2.00e-02 2.50e+03   3.20e-02 1.02e+01
        pdb=" C   GLY R  81 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   GLY R  81 "    0.020 2.00e-02 2.50e+03
        pdb=" N   GLN R  82 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA a 284 "    0.013 2.00e-02 2.50e+03   2.55e-02 6.50e+00
        pdb=" C   ALA a 284 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   ALA a 284 "    0.016 2.00e-02 2.50e+03
        pdb=" N   HIS a 285 "    0.015 2.00e-02 2.50e+03
  ... (remaining 1519 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.24: 5
        2.24 -     2.91: 3501
        2.91 -     3.57: 14015
        3.57 -     4.24: 19272
        4.24 -     4.90: 35581
  Nonbonded interactions: 72374
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU a 182 "
            pdb="ZN    ZN a 301 "
     model   vdw
     1.578 2.230
  nonbonded pdb=" OE2 GLU a 182 "
            pdb="ZN    ZN a 301 "
     model   vdw
     1.721 2.230
  nonbonded pdb=" CD  GLU a 182 "
            pdb="ZN    ZN a 301 "
     model   vdw
     1.829 2.460
  nonbonded pdb=" OE2 GLU a 182 "
            pdb=" OD1 ASP a 287 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" OE2 GLU a 182 "
            pdb=" ND1 HIS a 289 "
     model   vdw
     2.234 3.120
  ... (remaining 72369 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 'I' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ 
 or name O or name CB ))))
  selection = (chain 'J' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ 
 or name O or name CB ))))
  selection = (chain 'L' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ 
 or name O or name CB ))))
  selection = (chain 'M' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ 
 or name O or name CB ))))
  selection = (chain 'N' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ 
 or name O or name CB ))))
  selection = (chain 'O' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ 
 or name O or name CB ))))
  selection = chain 'P'
  selection = (chain 'Q' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ 
 or name O or name CB ))))
  selection = (chain 'R' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ 
 or name O or name CB ))))
  selection = (chain 'S' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ 
 or name O or name CB ))))
}
ncs_group {
  reference = chain 'X'
  selection = chain 'Y'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.510
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.860
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
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      :  0.006   0.364   9085  Z= 0.233
  Angle     :  0.549   7.479  12313  Z= 0.330
  Chirality :  0.037   0.140   1518
  Planarity :  0.004   0.036   1522
  Dihedral  : 13.074  89.730   3113
  Min Nonbonded Distance : 1.578

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  9.63 %
    Favored  : 89.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  2.31 (0.24), residues: 1184
  helix:  1.99 (0.16), residues: 1023
  sheet:  None (None), residues: 0
  loop : -1.50 (0.39), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG a 145 
 TYR   0.007   0.001   TYR a   9 
 PHE   0.009   0.001   PHE a 143 
 TRP   0.012   0.001   TRP a 256 
 HIS   0.001   0.000   HIS a 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 9083)
  covalent geometry    : angle       0.54872 (12313)
  hydrogen bonds       : bond        0.12142 (  836)
  hydrogen bonds       : angle       5.85277 ( 2484)
  metal coordination   : bond        0.32990 (    2)

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

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

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 228
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
REVERT: X   23 LYS cc_start: 0.7928 (mtpt) cc_final: 0.7680 (mttt)
REVERT: Y   23 LYS cc_start: 0.7791 (ttpt) cc_final: 0.7418 (tptp)
  outliers start: 10
  outliers final: 1
  residues processed: 233
  average time/residue: 0.5721
  time to fit residues: 140.8257
Evaluate side-chains
  149 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 148
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue  186 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    3.9990
   overall best weight:    2.1184

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

Flipped N/Q/H residues before XYZ refinement:
M  41 GLN
N  82 GLN
P  41 GLN
P  82 GLN
R  82 GLN
S  41 GLN
S  82 GLN
X   4 ASN
X  34 GLN
a  45 HIS
a  79 GLN
a 196 GLN
a 269 GLN
a 285 HIS

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.081458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.062887 restraints weight = 14707.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.3016 rms_B_bonded: 1.82
r_work: 0.2900 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2792 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8749
moved from start:          0.3376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9085  Z= 0.186
  Angle     :  0.609   7.034  12313  Z= 0.314
  Chirality :  0.042   0.147   1518
  Planarity :  0.005   0.039   1522
  Dihedral  :  4.009  51.768   1222
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 13.62 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  2.92 (0.23), residues: 1184
  helix:  2.38 (0.15), residues: 1028
  sheet:  None (None), residues: 0
  loop : -1.23 (0.43), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG Q  40 
 TYR   0.015   0.002   TYR a   9 
 PHE   0.014   0.002   PHE L  34 
 TRP   0.006   0.001   TRP X  26 
 HIS   0.003   0.001   HIS a  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 9083)
  covalent geometry    : angle       0.60865 (12313)
  hydrogen bonds       : bond        0.06605 (  836)
  hydrogen bonds       : angle       4.10023 ( 2484)
  metal coordination   : bond        0.00632 (    2)

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

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

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 157
  time to evaluate  : 0.335 
Fit side-chains
REVERT: L    1 MET cc_start: 0.6941 (ttp) cc_final: 0.6648 (ttt)
REVERT: L   44 MET cc_start: 0.7522 (mmt) cc_final: 0.7157 (mtt)
REVERT: X   23 LYS cc_start: 0.8366 (mtpt) cc_final: 0.7951 (mtmt)
REVERT: X   35 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7564 (mt-10)
REVERT: Y   23 LYS cc_start: 0.8079 (ttpt) cc_final: 0.7485 (tptp)
REVERT: a  183 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8022 (mp)
REVERT: a  230 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8192 (tt0)
REVERT: a  246 LEU cc_start: 0.7835 (tp) cc_final: 0.7553 (tm)
REVERT: a  286 GLU cc_start: 0.7794 (pp20) cc_final: 0.7327 (pp20)
  outliers start: 37
  outliers final: 12
  residues processed: 181
  average time/residue: 0.7159
  time to fit residues: 135.6329
Evaluate side-chains
  157 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 143
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   23 THR
Chi-restraints excluded: chain M residue   47 MET
Chi-restraints excluded: chain N residue   23 THR
Chi-restraints excluded: chain O residue   23 THR
Chi-restraints excluded: chain P residue   23 THR
Chi-restraints excluded: chain S residue   23 THR
Chi-restraints excluded: chain X residue   19 LEU
Chi-restraints excluded: chain X residue   30 ILE
Chi-restraints excluded: chain X residue   35 GLU
Chi-restraints excluded: chain Y residue   30 ILE
Chi-restraints excluded: chain a residue   37 LYS
Chi-restraints excluded: chain a residue  149 THR
Chi-restraints excluded: chain a residue  183 LEU
Chi-restraints excluded: chain a residue  231 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 59 optimal weight:    5.9990
   chunk 39 optimal weight:    0.0570
   chunk 53 optimal weight:    3.9990
   chunk 101 optimal weight:    0.7980
   chunk 95 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    1.9704

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

Flipped N/Q/H residues before XYZ refinement:
N  41 GLN
a  79 GLN
a 262 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.079422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.060995 restraints weight = 14713.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.2974 rms_B_bonded: 1.80
r_work: 0.2860 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2753 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8780
moved from start:          0.3793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9085  Z= 0.166
  Angle     :  0.548   6.971  12313  Z= 0.287
  Chirality :  0.040   0.144   1518
  Planarity :  0.005   0.040   1522
  Dihedral  :  3.774  18.891   1220
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 15.06 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.11 (0.23), residues: 1184
  helix:  2.50 (0.15), residues: 1029
  sheet:  None (None), residues: 0
  loop : -1.18 (0.44), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG Q  40 
 TYR   0.011   0.002   TYR a   9 
 PHE   0.014   0.001   PHE L  75 
 TRP   0.008   0.001   TRP Y  26 
 HIS   0.002   0.001   HIS a  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 9083)
  covalent geometry    : angle       0.54819 (12313)
  hydrogen bonds       : bond        0.06485 (  836)
  hydrogen bonds       : angle       3.94585 ( 2484)
  metal coordination   : bond        0.00267 (    2)

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

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

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 144
  time to evaluate  : 0.226 
Fit side-chains
REVERT: I   43 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7813 (pm20)
REVERT: L   44 MET cc_start: 0.7655 (mmt) cc_final: 0.7382 (mtt)
REVERT: L   52 MET cc_start: 0.8888 (ttp) cc_final: 0.8509 (ttp)
REVERT: N   43 GLU cc_start: 0.7914 (pm20) cc_final: 0.7589 (pm20)
REVERT: O    2 GLU cc_start: 0.8057 (pm20) cc_final: 0.7688 (mp0)
REVERT: X   23 LYS cc_start: 0.8459 (mtpt) cc_final: 0.7999 (mtmt)
REVERT: Y   23 LYS cc_start: 0.8042 (ttpt) cc_final: 0.7505 (tptp)
REVERT: a  140 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7261 (tm-30)
REVERT: a  230 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8273 (tt0)
REVERT: a  246 LEU cc_start: 0.8176 (tp) cc_final: 0.7878 (tm)
  outliers start: 25
  outliers final: 11
  residues processed: 162
  average time/residue: 0.7531
  time to fit residues: 127.6435
Evaluate side-chains
  147 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 135
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue    1 MET
Chi-restraints excluded: chain I residue   43 GLU
Chi-restraints excluded: chain J residue   23 THR
Chi-restraints excluded: chain N residue   23 THR
Chi-restraints excluded: chain O residue   23 THR
Chi-restraints excluded: chain S residue   23 THR
Chi-restraints excluded: chain X residue   30 ILE
Chi-restraints excluded: chain Y residue   30 ILE
Chi-restraints excluded: chain a residue   24 ASN
Chi-restraints excluded: chain a residue   37 LYS
Chi-restraints excluded: chain a residue  149 THR
Chi-restraints excluded: chain a residue  231 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 39 optimal weight:    4.9990
   chunk 60 optimal weight:    0.0570
   chunk 45 optimal weight:    0.9990
   chunk 76 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 108 optimal weight:    3.9990
   chunk 84 optimal weight:    8.9990
   chunk 72 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    1.6106

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

Flipped N/Q/H residues before XYZ refinement:
** N  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  79 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.079432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.060952 restraints weight = 15056.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.2972 rms_B_bonded: 1.82
r_work: 0.2857 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2750 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8776
moved from start:          0.3931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9085  Z= 0.152
  Angle     :  0.534   6.687  12313  Z= 0.279
  Chirality :  0.039   0.139   1518
  Planarity :  0.004   0.040   1522
  Dihedral  :  3.796  19.011   1220
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 14.51 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.27 (0.23), residues: 1184
  helix:  2.61 (0.15), residues: 1029
  sheet:  None (None), residues: 0
  loop : -1.16 (0.44), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG Q  40 
 TYR   0.012   0.002   TYR a   9 
 PHE   0.012   0.001   PHE N  75 
 TRP   0.010   0.001   TRP Y  26 
 HIS   0.002   0.000   HIS a 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 9083)
  covalent geometry    : angle       0.53406 (12313)
  hydrogen bonds       : bond        0.06140 (  836)
  hydrogen bonds       : angle       3.83522 ( 2484)
  metal coordination   : bond        0.00295 (    2)

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

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

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 135
  time to evaluate  : 0.342 
Fit side-chains
REVERT: L    1 MET cc_start: 0.7710 (ttt) cc_final: 0.7351 (tpp)
REVERT: L   44 MET cc_start: 0.7648 (mmt) cc_final: 0.7349 (mtt)
REVERT: L   52 MET cc_start: 0.8880 (ttp) cc_final: 0.8491 (ttp)
REVERT: N    1 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.6979 (tpt)
REVERT: N   41 GLN cc_start: 0.7485 (pt0) cc_final: 0.6900 (pt0)
REVERT: N   44 MET cc_start: 0.8124 (mmt) cc_final: 0.7279 (mtp)
REVERT: Q    2 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7682 (mm-30)
REVERT: S   33 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8940 (mmpt)
REVERT: X   23 LYS cc_start: 0.8434 (mtpt) cc_final: 0.7961 (mtmt)
REVERT: Y   23 LYS cc_start: 0.7951 (ttpt) cc_final: 0.7559 (mmmt)
REVERT: a  140 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7422 (tm-30)
REVERT: a  206 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6842 (mp)
REVERT: a  230 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8222 (tt0)
  outliers start: 30
  outliers final: 14
  residues processed: 154
  average time/residue: 0.7540
  time to fit residues: 121.4998
Evaluate side-chains
  148 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   23 THR
Chi-restraints excluded: chain N residue    1 MET
Chi-restraints excluded: chain N residue   23 THR
Chi-restraints excluded: chain O residue   23 THR
Chi-restraints excluded: chain P residue   23 THR
Chi-restraints excluded: chain Q residue    2 GLU
Chi-restraints excluded: chain S residue   23 THR
Chi-restraints excluded: chain S residue   33 LYS
Chi-restraints excluded: chain X residue   19 LEU
Chi-restraints excluded: chain X residue   35 GLU
Chi-restraints excluded: chain X residue   40 ILE
Chi-restraints excluded: chain Y residue   30 ILE
Chi-restraints excluded: chain a residue   37 LYS
Chi-restraints excluded: chain a residue  111 VAL
Chi-restraints excluded: chain a residue  149 THR
Chi-restraints excluded: chain a residue  206 LEU
Chi-restraints excluded: chain a residue  231 LEU
Chi-restraints excluded: chain a residue  275 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 95 optimal weight:    0.6980
   chunk 109 optimal weight:    0.4980
   chunk 32 optimal weight:    4.9990
   chunk 91 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 59 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 58 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
** N  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  79 GLN
a 262 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.080535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.062196 restraints weight = 14844.839|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 1.81
r_work: 0.2889 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2784 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8750
moved from start:          0.3933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9085  Z= 0.137
  Angle     :  0.509   6.683  12313  Z= 0.266
  Chirality :  0.038   0.126   1518
  Planarity :  0.004   0.040   1522
  Dihedral  :  3.707  18.473   1220
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 15.84 %
    Favored  : 81.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.47 (0.23), residues: 1184
  helix:  2.75 (0.15), residues: 1029
  sheet:  None (None), residues: 0
  loop : -1.13 (0.44), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG Q  40 
 TYR   0.011   0.001   TYR a   9 
 PHE   0.011   0.001   PHE N  75 
 TRP   0.012   0.001   TRP Y  26 
 HIS   0.001   0.000   HIS a 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 9083)
  covalent geometry    : angle       0.50943 (12313)
  hydrogen bonds       : bond        0.05675 (  836)
  hydrogen bonds       : angle       3.73938 ( 2484)
  metal coordination   : bond        0.00388 (    2)

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

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

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 133
  time to evaluate  : 0.327 
Fit side-chains
REVERT: L    1 MET cc_start: 0.7763 (ttt) cc_final: 0.7354 (tpp)
REVERT: L    2 GLU cc_start: 0.8033 (pm20) cc_final: 0.7822 (mp0)
REVERT: L   44 MET cc_start: 0.7602 (mmt) cc_final: 0.7309 (mtt)
REVERT: L   52 MET cc_start: 0.8847 (ttp) cc_final: 0.8467 (ttp)
REVERT: N    1 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.6765 (tpt)
REVERT: N   41 GLN cc_start: 0.7386 (pt0) cc_final: 0.6810 (pt0)
REVERT: N   44 MET cc_start: 0.8130 (mmt) cc_final: 0.7236 (mtp)
REVERT: N   83 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7683 (mp)
REVERT: Q    2 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7623 (mm-30)
REVERT: S   33 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8937 (mmpt)
REVERT: X   23 LYS cc_start: 0.8459 (mtpt) cc_final: 0.7969 (mtmt)
REVERT: Y   23 LYS cc_start: 0.7876 (ttpt) cc_final: 0.7497 (mmmt)
REVERT: a  140 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7616 (tt0)
REVERT: a  206 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6965 (mp)
  outliers start: 24
  outliers final: 10
  residues processed: 148
  average time/residue: 0.7228
  time to fit residues: 111.9707
Evaluate side-chains
  144 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 129
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   23 THR
Chi-restraints excluded: chain N residue    1 MET
Chi-restraints excluded: chain N residue   23 THR
Chi-restraints excluded: chain N residue   83 ILE
Chi-restraints excluded: chain P residue   23 THR
Chi-restraints excluded: chain Q residue    2 GLU
Chi-restraints excluded: chain S residue   23 THR
Chi-restraints excluded: chain S residue   33 LYS
Chi-restraints excluded: chain Y residue   30 ILE
Chi-restraints excluded: chain a residue   24 ASN
Chi-restraints excluded: chain a residue   37 LYS
Chi-restraints excluded: chain a residue  149 THR
Chi-restraints excluded: chain a residue  186 HIS
Chi-restraints excluded: chain a residue  206 LEU
Chi-restraints excluded: chain a residue  275 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   chunk 14 optimal weight:    7.9990
   chunk 76 optimal weight:    1.9990
   chunk 105 optimal weight:    3.9990
   chunk 109 optimal weight:    0.9980
   chunk 8 optimal weight:   10.0000
   chunk 41 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** N  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  79 GLN
a 262 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.079939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.062073 restraints weight = 14816.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.3012 rms_B_bonded: 1.78
r_work: 0.2898 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2792 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8736
moved from start:          0.3948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9085  Z= 0.134
  Angle     :  0.511   6.746  12313  Z= 0.265
  Chirality :  0.038   0.127   1518
  Planarity :  0.004   0.046   1522
  Dihedral  :  3.678  18.456   1220
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.61 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.55 (0.23), residues: 1184
  helix:  2.81 (0.15), residues: 1029
  sheet:  None (None), residues: 0
  loop : -1.11 (0.45), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG Q  40 
 TYR   0.011   0.001   TYR a   9 
 PHE   0.011   0.001   PHE N  75 
 TRP   0.014   0.001   TRP Y  26 
 HIS   0.001   0.000   HIS a 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 9083)
  covalent geometry    : angle       0.51142 (12313)
  hydrogen bonds       : bond        0.05572 (  836)
  hydrogen bonds       : angle       3.70161 ( 2484)
  metal coordination   : bond        0.00172 (    2)

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

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

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 133
  time to evaluate  : 0.227 
Fit side-chains
REVERT: L    1 MET cc_start: 0.7818 (ttt) cc_final: 0.7372 (tpp)
REVERT: L   44 MET cc_start: 0.7603 (mmt) cc_final: 0.7302 (mtt)
REVERT: L   52 MET cc_start: 0.8819 (ttp) cc_final: 0.8451 (ttp)
REVERT: N   41 GLN cc_start: 0.7284 (pt0) cc_final: 0.6727 (pt0)
REVERT: N   44 MET cc_start: 0.8106 (mmt) cc_final: 0.7178 (mtp)
REVERT: N   83 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7710 (mp)
REVERT: Q    2 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7561 (mm-30)
REVERT: S   33 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8925 (mmtt)
REVERT: X    1 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.6531 (mmt)
REVERT: X   23 LYS cc_start: 0.8417 (mtpt) cc_final: 0.7983 (ttmt)
REVERT: Y   23 LYS cc_start: 0.7838 (ttpt) cc_final: 0.7450 (mmmt)
REVERT: a  140 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7653 (tt0)
REVERT: a  206 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6897 (mp)
  outliers start: 26
  outliers final: 11
  residues processed: 150
  average time/residue: 0.7369
  time to fit residues: 115.6042
Evaluate side-chains
  144 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   23 THR
Chi-restraints excluded: chain N residue   23 THR
Chi-restraints excluded: chain N residue   83 ILE
Chi-restraints excluded: chain O residue   23 THR
Chi-restraints excluded: chain P residue   23 THR
Chi-restraints excluded: chain Q residue    2 GLU
Chi-restraints excluded: chain S residue   23 THR
Chi-restraints excluded: chain S residue   33 LYS
Chi-restraints excluded: chain X residue    1 MET
Chi-restraints excluded: chain X residue   35 GLU
Chi-restraints excluded: chain X residue   40 ILE
Chi-restraints excluded: chain Y residue   30 ILE
Chi-restraints excluded: chain a residue   24 ASN
Chi-restraints excluded: chain a residue   37 LYS
Chi-restraints excluded: chain a residue  149 THR
Chi-restraints excluded: chain a residue  206 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 46 optimal weight:    6.9990
   chunk 65 optimal weight:    0.7980
   chunk 42 optimal weight:    6.9990
   chunk 83 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9980
   chunk 15 optimal weight:    6.9990
   chunk 90 optimal weight:    0.7980
   chunk 61 optimal weight:    4.9990
   chunk 105 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    2.1184

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

Flipped N/Q/H residues before XYZ refinement:
** N  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  79 GLN
a 262 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.077742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.059355 restraints weight = 14914.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.2941 rms_B_bonded: 1.80
r_work: 0.2825 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2719 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8798
moved from start:          0.4140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9085  Z= 0.171
  Angle     :  0.568   7.958  12313  Z= 0.294
  Chirality :  0.039   0.139   1518
  Planarity :  0.005   0.047   1522
  Dihedral  :  3.887  20.380   1220
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 15.50 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.28 (0.23), residues: 1184
  helix:  2.63 (0.15), residues: 1029
  sheet:  None (None), residues: 0
  loop : -1.26 (0.44), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG Q  40 
 TYR   0.012   0.002   TYR a   9 
 PHE   0.015   0.002   PHE I  75 
 TRP   0.014   0.001   TRP Y  26 
 HIS   0.002   0.001   HIS a 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 9083)
  covalent geometry    : angle       0.56831 (12313)
  hydrogen bonds       : bond        0.06576 (  836)
  hydrogen bonds       : angle       3.84291 ( 2484)
  metal coordination   : bond        0.00467 (    2)

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

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

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 135
  time to evaluate  : 0.361 
Fit side-chains
REVERT: J   41 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7878 (mt0)
REVERT: L    1 MET cc_start: 0.7843 (ttt) cc_final: 0.7473 (tpp)
REVERT: L   44 MET cc_start: 0.7685 (mmt) cc_final: 0.7374 (mtt)
REVERT: M   44 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7897 (mmp)
REVERT: N   41 GLN cc_start: 0.7437 (pt0) cc_final: 0.6848 (pt0)
REVERT: N   44 MET cc_start: 0.8169 (mmt) cc_final: 0.7266 (mtp)
REVERT: N   83 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7648 (mp)
REVERT: O    2 GLU cc_start: 0.8123 (pm20) cc_final: 0.7727 (mp0)
REVERT: S   33 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8945 (mmpt)
REVERT: X   23 LYS cc_start: 0.8476 (mtpt) cc_final: 0.7966 (mtmt)
REVERT: Y   23 LYS cc_start: 0.7887 (ttpt) cc_final: 0.7515 (mmmt)
REVERT: a  140 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7815 (tt0)
REVERT: a  230 GLU cc_start: 0.8694 (tp30) cc_final: 0.8069 (tt0)
  outliers start: 32
  outliers final: 14
  residues processed: 156
  average time/residue: 0.7879
  time to fit residues: 128.6125
Evaluate side-chains
  150 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   23 THR
Chi-restraints excluded: chain J residue   41 GLN
Chi-restraints excluded: chain M residue   44 MET
Chi-restraints excluded: chain N residue   23 THR
Chi-restraints excluded: chain N residue   83 ILE
Chi-restraints excluded: chain O residue   23 THR
Chi-restraints excluded: chain P residue   23 THR
Chi-restraints excluded: chain R residue   50 VAL
Chi-restraints excluded: chain S residue   23 THR
Chi-restraints excluded: chain S residue   33 LYS
Chi-restraints excluded: chain S residue   60 ASP
Chi-restraints excluded: chain X residue   35 GLU
Chi-restraints excluded: chain X residue   40 ILE
Chi-restraints excluded: chain Y residue   30 ILE
Chi-restraints excluded: chain a residue   24 ASN
Chi-restraints excluded: chain a residue   37 LYS
Chi-restraints excluded: chain a residue  111 VAL
Chi-restraints excluded: chain a residue  149 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 72 optimal weight:    4.9990
   chunk 31 optimal weight:    4.9990
   chunk 96 optimal weight:    1.9990
   chunk 86 optimal weight:    0.0470
   chunk 30 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   overall best weight:    1.0080

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

Flipped N/Q/H residues before XYZ refinement:
N  41 GLN
a  79 GLN
a 262 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.080284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.062046 restraints weight = 14846.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 1.80
r_work: 0.2887 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2781 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8750
moved from start:          0.4067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9085  Z= 0.135
  Angle     :  0.531   8.413  12313  Z= 0.274
  Chirality :  0.037   0.135   1518
  Planarity :  0.004   0.049   1522
  Dihedral  :  3.747  19.502   1220
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 16.94 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.56 (0.24), residues: 1184
  helix:  2.81 (0.15), residues: 1030
  sheet:  None (None), residues: 0
  loop : -1.17 (0.45), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG Q  40 
 TYR   0.011   0.001   TYR a   9 
 PHE   0.011   0.001   PHE N  75 
 TRP   0.019   0.001   TRP Y  26 
 HIS   0.001   0.000   HIS a 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 9083)
  covalent geometry    : angle       0.53099 (12313)
  hydrogen bonds       : bond        0.05565 (  836)
  hydrogen bonds       : angle       3.70473 ( 2484)
  metal coordination   : bond        0.00309 (    2)

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

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

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 133
  time to evaluate  : 0.324 
Fit side-chains
REVERT: L    1 MET cc_start: 0.7865 (ttt) cc_final: 0.7463 (tpp)
REVERT: L   44 MET cc_start: 0.7594 (mmt) cc_final: 0.7322 (mtt)
REVERT: L   52 MET cc_start: 0.8819 (ttp) cc_final: 0.8465 (ttp)
REVERT: N   41 GLN cc_start: 0.7240 (pt0) cc_final: 0.6637 (pt0)
REVERT: N   44 MET cc_start: 0.8194 (mmt) cc_final: 0.7208 (mtp)
REVERT: N   83 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7668 (mp)
REVERT: Q    2 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7517 (mm-30)
REVERT: R   43 GLU cc_start: 0.8424 (pm20) cc_final: 0.8005 (pm20)
REVERT: S   33 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8930 (mmpt)
REVERT: X   23 LYS cc_start: 0.8465 (mtpt) cc_final: 0.8008 (mtmt)
REVERT: Y   23 LYS cc_start: 0.7834 (ttpt) cc_final: 0.7466 (mmmt)
REVERT: a  140 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7833 (tt0)
REVERT: a  230 GLU cc_start: 0.8653 (tp30) cc_final: 0.8006 (tt0)
  outliers start: 23
  outliers final: 14
  residues processed: 150
  average time/residue: 0.7630
  time to fit residues: 119.7346
Evaluate side-chains
  148 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   23 THR
Chi-restraints excluded: chain M residue   47 MET
Chi-restraints excluded: chain N residue   23 THR
Chi-restraints excluded: chain N residue   83 ILE
Chi-restraints excluded: chain O residue   23 THR
Chi-restraints excluded: chain P residue   23 THR
Chi-restraints excluded: chain Q residue    2 GLU
Chi-restraints excluded: chain R residue   50 VAL
Chi-restraints excluded: chain S residue   23 THR
Chi-restraints excluded: chain S residue   33 LYS
Chi-restraints excluded: chain X residue   35 GLU
Chi-restraints excluded: chain X residue   40 ILE
Chi-restraints excluded: chain Y residue   30 ILE
Chi-restraints excluded: chain a residue   24 ASN
Chi-restraints excluded: chain a residue   37 LYS
Chi-restraints excluded: chain a residue  111 VAL
Chi-restraints excluded: chain a residue  149 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 60 optimal weight:    0.0270
   chunk 82 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 103 optimal weight:    0.7980
   chunk 88 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 108 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 105 optimal weight:    3.9990
   chunk 113 optimal weight:    0.8980
   overall best weight:    0.6638

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

Flipped N/Q/H residues before XYZ refinement:
a 262 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.082646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.064559 restraints weight = 14927.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3064 rms_B_bonded: 1.79
r_work: 0.2954 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2850 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8723
moved from start:          0.3994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9085  Z= 0.126
  Angle     :  0.522   8.991  12313  Z= 0.267
  Chirality :  0.037   0.137   1518
  Planarity :  0.004   0.046   1522
  Dihedral  :  3.617  18.251   1220
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 17.72 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.70 (0.24), residues: 1184
  helix:  2.92 (0.15), residues: 1029
  sheet:  None (None), residues: 0
  loop : -1.18 (0.45), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG Q  40 
 TYR   0.010   0.001   TYR a   9 
 PHE   0.010   0.001   PHE N  75 
 TRP   0.024   0.001   TRP Y  26 
 HIS   0.001   0.000   HIS a 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 9083)
  covalent geometry    : angle       0.52179 (12313)
  hydrogen bonds       : bond        0.05028 (  836)
  hydrogen bonds       : angle       3.60696 ( 2484)
  metal coordination   : bond        0.00153 (    2)

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

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

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 0.331 
Fit side-chains
REVERT: L    1 MET cc_start: 0.7900 (ttt) cc_final: 0.7503 (tpp)
REVERT: L   44 MET cc_start: 0.7556 (mmt) cc_final: 0.7278 (mtt)
REVERT: N   41 GLN cc_start: 0.7088 (pt0) cc_final: 0.6495 (pt0)
REVERT: N   44 MET cc_start: 0.8306 (mmt) cc_final: 0.7261 (mtp)
REVERT: N   83 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7734 (mp)
REVERT: X   23 LYS cc_start: 0.8437 (mtpt) cc_final: 0.8031 (ttmt)
REVERT: Y   23 LYS cc_start: 0.7896 (ttpt) cc_final: 0.7522 (mmmt)
REVERT: a  140 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7856 (tt0)
  outliers start: 20
  outliers final: 12
  residues processed: 148
  average time/residue: 0.7892
  time to fit residues: 122.1519
Evaluate side-chains
  143 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 130
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   23 THR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain N residue   23 THR
Chi-restraints excluded: chain N residue   83 ILE
Chi-restraints excluded: chain O residue   23 THR
Chi-restraints excluded: chain P residue   23 THR
Chi-restraints excluded: chain P residue   80 VAL
Chi-restraints excluded: chain R residue   50 VAL
Chi-restraints excluded: chain S residue   23 THR
Chi-restraints excluded: chain X residue   35 GLU
Chi-restraints excluded: chain Y residue   30 ILE
Chi-restraints excluded: chain a residue   24 ASN
Chi-restraints excluded: chain a residue  149 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 18 optimal weight:    7.9990
   chunk 27 optimal weight:    5.9990
   chunk 9 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
J  41 GLN
a  79 GLN
a 262 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.081697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.063548 restraints weight = 14830.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.3032 rms_B_bonded: 1.80
r_work: 0.2921 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2816 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8722
moved from start:          0.4037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9085  Z= 0.131
  Angle     :  0.543   9.663  12313  Z= 0.275
  Chirality :  0.037   0.145   1518
  Planarity :  0.004   0.044   1522
  Dihedral  :  3.626  18.565   1220
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 18.38 %
    Favored  : 79.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.69 (0.23), residues: 1184
  helix:  2.91 (0.15), residues: 1029
  sheet:  None (None), residues: 0
  loop : -1.20 (0.45), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG Q  40 
 TYR   0.011   0.001   TYR a   9 
 PHE   0.011   0.001   PHE N  75 
 TRP   0.025   0.001   TRP Y  26 
 HIS   0.001   0.000   HIS a 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 9083)
  covalent geometry    : angle       0.54287 (12313)
  hydrogen bonds       : bond        0.05242 (  836)
  hydrogen bonds       : angle       3.61122 ( 2484)
  metal coordination   : bond        0.00173 (    2)

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

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

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 130
  time to evaluate  : 0.273 
Fit side-chains
REVERT: L    1 MET cc_start: 0.7835 (ttt) cc_final: 0.7492 (tpp)
REVERT: L   44 MET cc_start: 0.7536 (mmt) cc_final: 0.7253 (mtt)
REVERT: N   41 GLN cc_start: 0.7080 (pt0) cc_final: 0.6487 (pt0)
REVERT: N   44 MET cc_start: 0.8198 (mmt) cc_final: 0.7159 (mtp)
REVERT: N   83 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7734 (mp)
REVERT: X   23 LYS cc_start: 0.8406 (mtpt) cc_final: 0.7980 (ttmt)
REVERT: Y   23 LYS cc_start: 0.7820 (ttpt) cc_final: 0.7442 (mmmt)
REVERT: a  140 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7897 (tt0)
  outliers start: 15
  outliers final: 12
  residues processed: 142
  average time/residue: 0.7957
  time to fit residues: 118.0671
Evaluate side-chains
  142 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 129
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   23 THR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain N residue   23 THR
Chi-restraints excluded: chain N residue   83 ILE
Chi-restraints excluded: chain O residue   23 THR
Chi-restraints excluded: chain P residue   23 THR
Chi-restraints excluded: chain P residue   80 VAL
Chi-restraints excluded: chain R residue   50 VAL
Chi-restraints excluded: chain S residue   23 THR
Chi-restraints excluded: chain X residue   35 GLU
Chi-restraints excluded: chain Y residue   30 ILE
Chi-restraints excluded: chain a residue   24 ASN
Chi-restraints excluded: chain a residue  149 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 112 optimal weight:    4.9990
   chunk 4 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 9 optimal weight:    8.9990
   chunk 62 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   chunk 93 optimal weight:    6.9990
   chunk 88 optimal weight:    2.9990
   overall best weight:    2.1188

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

Flipped N/Q/H residues before XYZ refinement:
J  41 GLN
a  79 GLN
a 262 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.077440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.059182 restraints weight = 14681.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.2939 rms_B_bonded: 1.78
r_work: 0.2823 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2717 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8800
moved from start:          0.4255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9085  Z= 0.174
  Angle     :  0.604  10.060  12313  Z= 0.308
  Chirality :  0.040   0.164   1518
  Planarity :  0.005   0.043   1522
  Dihedral  :  3.925  21.226   1220
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 17.72 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.31 (0.23), residues: 1184
  helix:  2.65 (0.15), residues: 1031
  sheet:  None (None), residues: 0
  loop : -1.33 (0.44), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG Q  40 
 TYR   0.012   0.002   TYR a   9 
 PHE   0.016   0.002   PHE I  75 
 TRP   0.025   0.001   TRP Y  26 
 HIS   0.002   0.001   HIS a 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 9083)
  covalent geometry    : angle       0.60370 (12313)
  hydrogen bonds       : bond        0.06633 (  836)
  hydrogen bonds       : angle       3.83543 ( 2484)
  metal coordination   : bond        0.00364 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3615.03 seconds
wall clock time: 62 minutes 6.74 seconds (3726.74 seconds total)