Starting phenix.real_space_refine
on Sun Aug 24 02:55:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7nkb_12436/08_2025/7nkb_12436.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7nkb_12436/08_2025/7nkb_12436.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7nkb_12436/08_2025/7nkb_12436.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7nkb_12436/08_2025/7nkb_12436.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7nkb_12436/08_2025/7nkb_12436.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7nkb_12436/08_2025/7nkb_12436.map"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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
     S      25      5.16       5
     C    5376      2.51       5
     N    1401      2.21       5
     O    1538      1.98       5
     H    8429      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16769
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "C"
      Number of atoms: 326
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 326
          Classifications: {'peptide': 21}
          Link IDs: {'PTRANS': 3, 'TRANS': 17}
    Chain: "G"
      Number of atoms: 3865
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 251, 3865
          Classifications: {'peptide': 251}
          Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 240}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 1802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 1802
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 3, 'TRANS': 114}
    Chain: "L"
      Number of atoms: 1204
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 1204
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 4, 'TRANS': 80}
    Chain: "M"
      Number of atoms: 1192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1192
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 4, 'TRANS': 79}
    Chain: "N"
      Number of atoms: 1192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1192
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 4, 'TRANS': 79}
    Chain: "O"
      Number of atoms: 1192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1192
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 4, 'TRANS': 79}
    Chain: "P"
      Number of atoms: 1204
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 1204
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 4, 'TRANS': 80}
    Chain: "Q"
      Number of atoms: 1204
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 1204
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 4, 'TRANS': 80}
    Chain: "R"
      Number of atoms: 1192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1192
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 4, 'TRANS': 79}
    Chain: "S"
      Number of atoms: 1204
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 1204
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 4, 'TRANS': 80}
    Chain: "T"
      Number of atoms: 1192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1192
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 4, 'TRANS': 79}
  Time building chain proxies: 3.01, per 1000 atoms: 0.18
  Number of scatterers: 16769
  At special positions: 0
  Unit cell: (78.02, 70.55, 150.23, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      25     16.00
     O    1538      8.00
     N    1401      7.00
     C    5376      6.00
     H    8429      1.00
    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: 1.70
  Conformation dependent library (CDL) restraints added in 495.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1966

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 3 sheets defined
      74.2% alpha, 9.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'C' and resid 529 through 533
      removed outlier: 3.569A  pdb=" N   LEU C 533 " --> pdb=" O   PRO C 530 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 19 through 43
    Processing helix  chain 'G' and resid 43 through 60
    Processing helix  chain 'G' and resid 91 through 110
    Processing helix  chain 'G' and resid 120 through 130
      removed outlier: 3.609A  pdb=" N   LEU G 124 " --> pdb=" O   GLY G 120 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 146 through 164
    Processing helix  chain 'G' and resid 172 through 176
      removed outlier: 3.679A  pdb=" N   ASP G 175 " --> pdb=" O   ALA G 172 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 227 through 270
      Proline residue:  G 237  - end of helix
    Processing helix  chain 'H' and resid 91 through 99
    Processing helix  chain 'H' and resid 103 through 117
    Processing helix  chain 'L' and resid 4 through 46
    Processing helix  chain 'L' and resid 49 through 80
      removed outlier: 4.392A  pdb=" N   THR L  55 " --> pdb=" O   GLY L  51 " (cutoff:3.500A)
      Proline residue:  L  56  - end of helix
      removed outlier: 3.681A  pdb=" N   ALA L  66 " --> pdb=" O   GLY L  62 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 4 through 46
      removed outlier: 3.519A  pdb=" N   ILE M   8 " --> pdb=" O   ASP M   4 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 48 through 80
      removed outlier: 4.307A  pdb=" N   ARG M  52 " --> pdb=" O   GLU M  48 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   PHE M  54 " --> pdb=" O   GLN M  50 " (cutoff:3.500A)
      removed outlier: 5.179A  pdb=" N   THR M  55 " --> pdb=" O   GLY M  51 " (cutoff:3.500A)
      Proline residue:  M  56  - end of helix
      removed outlier: 3.760A  pdb=" N   LEU M  63 " --> pdb=" O   ILE M  59 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   ALA M  67 " --> pdb=" O   LEU M  63 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 4 through 46
      removed outlier: 3.574A  pdb=" N   ILE N   8 " --> pdb=" O   ASP N   4 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 47 through 52
      removed outlier: 4.160A  pdb=" N   GLY N  51 " --> pdb=" O   GLU N  48 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 53 through 81
      removed outlier: 3.977A  pdb=" N   PHE N  57 " --> pdb=" O   LEU N  53 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 4 through 46
      removed outlier: 3.506A  pdb=" N   ILE O   8 " --> pdb=" O   ASP O   4 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 49 through 81
      removed outlier: 3.717A  pdb=" N   PHE O  54 " --> pdb=" O   GLN O  50 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   THR O  55 " --> pdb=" O   GLY O  51 " (cutoff:3.500A)
      Proline residue:  O  56  - end of helix
      removed outlier: 3.652A  pdb=" N   ILE O  70 " --> pdb=" O   ALA O  66 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 4 through 46
      removed outlier: 3.761A  pdb=" N   ILE P   8 " --> pdb=" O   ASP P   4 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 49 through 80
      removed outlier: 4.325A  pdb=" N   THR P  55 " --> pdb=" O   GLY P  51 " (cutoff:3.500A)
      Proline residue:  P  56  - end of helix
      removed outlier: 3.565A  pdb=" N   ILE P  59 " --> pdb=" O   THR P  55 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ALA P  67 " --> pdb=" O   LEU P  63 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 4 through 46
    Processing helix  chain 'Q' and resid 49 through 80
      removed outlier: 4.369A  pdb=" N   THR Q  55 " --> pdb=" O   GLY Q  51 " (cutoff:3.500A)
      Proline residue:  Q  56  - end of helix
    Processing helix  chain 'R' and resid 4 through 46
      removed outlier: 3.963A  pdb=" N   ILE R   8 " --> pdb=" O   ASP R   4 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 49 through 80
      removed outlier: 4.557A  pdb=" N   THR R  55 " --> pdb=" O   GLY R  51 " (cutoff:3.500A)
      Proline residue:  R  56  - end of helix
    Processing helix  chain 'S' and resid 4 through 46
    Processing helix  chain 'S' and resid 47 through 51
    Processing helix  chain 'S' and resid 53 through 81
    Processing helix  chain 'T' and resid 4 through 46
      removed outlier: 3.771A  pdb=" N   ILE T   8 " --> pdb=" O   ASP T   4 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 49 through 80
      removed outlier: 3.751A  pdb=" N   THR T  55 " --> pdb=" O   GLY T  51 " (cutoff:3.500A)
      Proline residue:  T  56  - end of helix
      removed outlier: 3.618A  pdb=" N   LEU T  63 " --> pdb=" O   ILE T  59 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ALA T  67 " --> pdb=" O   LEU T  63 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ASN T  71 " --> pdb=" O   ALA T  67 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 534 through 540
      removed outlier: 6.860A  pdb=" N   GLU C 534 " --> pdb=" O   ARG G 202 " (cutoff:3.500A)
      removed outlier: 7.699A  pdb=" N   ALA G 204 " --> pdb=" O   GLU C 534 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   GLU C 536 " --> pdb=" O   ALA G 204 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   MET G 206 " --> pdb=" O   GLU C 536 " (cutoff:3.500A)
      removed outlier: 5.740A  pdb=" N   VAL C 538 " --> pdb=" O   MET G 206 " (cutoff:3.500A)
      removed outlier: 4.891A  pdb=" N   VAL G 208 " --> pdb=" O   VAL C 538 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   VAL C 540 " --> pdb=" O   VAL G 208 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   TYR G 210 " --> pdb=" O   VAL C 540 " (cutoff:3.500A)
      removed outlier: 5.387A  pdb=" N   ALA G 198 " --> pdb=" O   GLU G 189 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   GLU G 189 " --> pdb=" O   ALA G 198 " (cutoff:3.500A)
      removed outlier: 5.241A  pdb=" N   ALA G 200 " --> pdb=" O   PHE G 187 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   PHE G 187 " --> pdb=" O   ALA G 200 " (cutoff:3.500A)
      removed outlier: 5.438A  pdb=" N   ARG G 202 " --> pdb=" O   ILE G 185 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   ILE G 185 " --> pdb=" O   ARG G 202 " (cutoff:3.500A)
      removed outlier: 4.961A  pdb=" N   THR G 188 " --> pdb=" O   VAL G  82 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   ALA G  77 " --> pdb=" O   VAL G 115 " (cutoff:3.500A)
      removed outlier: 7.264A  pdb=" N   TYR G 117 " --> pdb=" O   ALA G  77 " (cutoff:3.500A)
      removed outlier: 5.949A  pdb=" N   VAL G  79 " --> pdb=" O   TYR G 117 " (cutoff:3.500A)
      removed outlier: 7.547A  pdb=" N   VAL G 119 " --> pdb=" O   VAL G  79 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   VAL G  81 " --> pdb=" O   VAL G 119 " (cutoff:3.500A)
      removed outlier: 10.238A  pdb=" N   GLU G 136 " --> pdb=" O   PRO G 114 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   LEU G 116 " --> pdb=" O   GLU G 136 " (cutoff:3.500A)
      removed outlier: 8.842A  pdb=" N   TRP G 138 " --> pdb=" O   LEU G 116 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   VAL G 118 " --> pdb=" O   TRP G 138 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'G' and resid 223 through 225
      removed outlier: 6.335A  pdb=" N   SER G 223 " --> pdb=" O   VAL H  42 " (cutoff:3.500A)
      removed outlier: 8.391A  pdb=" N   GLN H  44 " --> pdb=" O   SER G 223 " (cutoff:3.500A)
      removed outlier: 7.936A  pdb=" N   GLU G 225 " --> pdb=" O   GLN H  44 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   ILE H  63 " --> pdb=" O   PHE H  86 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   PHE H  86 " --> pdb=" O   ILE H  63 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   VAL H  65 " --> pdb=" O   ALA H  84 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   ALA H  84 " --> pdb=" O   VAL H  65 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   GLY H  67 " --> pdb=" O   GLU H  82 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   ASN H   5 " --> pdb=" O   VAL H  77 " (cutoff:3.500A)
      removed outlier: 7.484A  pdb=" N   ILE H  79 " --> pdb=" O   ASN H   5 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   GLU H   7 " --> pdb=" O   ILE H  79 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   VAL H  81 " --> pdb=" O   GLU H   7 " (cutoff:3.500A)
      removed outlier: 6.225A  pdb=" N   VAL H   9 " --> pdb=" O   VAL H  81 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   ASN H  83 " --> pdb=" O   VAL H   9 " (cutoff:3.500A)
      removed outlier: 6.003A  pdb=" N   ALA H  10 " --> pdb=" O   GLU H  14 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   GLU H  14 " --> pdb=" O   ALA H  10 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'G' and resid 223 through 225
      removed outlier: 6.335A  pdb=" N   SER G 223 " --> pdb=" O   VAL H  42 " (cutoff:3.500A)
      removed outlier: 8.391A  pdb=" N   GLN H  44 " --> pdb=" O   SER G 223 " (cutoff:3.500A)
      removed outlier: 7.936A  pdb=" N   GLU G 225 " --> pdb=" O   GLN H  44 " (cutoff:3.500A)
      removed outlier: 5.782A  pdb=" N   MET H  50 " --> pdb=" O   ARG H  26 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   ARG H  26 " --> pdb=" O   MET H  50 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   PHE H  22 " --> pdb=" O   GLU H  54 " (cutoff:3.500A)

    723 hydrogen bonds defined for protein.
    2133 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: 3.94

  Time building geometry restraints manager: 2.06 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 8428
        1.03 -     1.23: 19
        1.23 -     1.42: 3435
        1.42 -     1.62: 4980
        1.62 -     1.81: 49
  Bond restraints: 16911
  Sorted by residual:
  bond pdb=" CB  MET R  21 "
       pdb=" CG  MET R  21 "
    ideal  model  delta    sigma   weight residual
    1.520  1.487  0.033 3.00e-02 1.11e+03 1.20e+00
  bond pdb=" CG  LEU T  63 "
       pdb=" CD2 LEU T  63 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.18e+00
  bond pdb=" CB  PRO G 205 "
       pdb=" CG  PRO G 205 "
    ideal  model  delta    sigma   weight residual
    1.506  1.470  0.036 3.90e-02 6.57e+02 8.48e-01
  bond pdb=" CG1 ILE S  43 "
       pdb=" CD1 ILE S  43 "
    ideal  model  delta    sigma   weight residual
    1.513  1.477  0.036 3.90e-02 6.57e+02 8.45e-01
  bond pdb=" CB  VAL L  61 "
       pdb=" CG1 VAL L  61 "
    ideal  model  delta    sigma   weight residual
    1.521  1.491  0.030 3.30e-02 9.18e+02 8.36e-01
  ... (remaining 16906 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.13: 29189
        1.13 -     2.26: 1346
        2.26 -     3.39: 52
        3.39 -     4.51: 34
        4.51 -     5.64: 4
  Bond angle restraints: 30625
  Sorted by residual:
  angle pdb=" CB  ARG R  52 "
        pdb=" CG  ARG R  52 "
        pdb=" CD  ARG R  52 "
      ideal   model   delta    sigma   weight residual
     111.30  116.94   -5.64 2.30e+00 1.89e-01 6.02e+00
  angle pdb=" N   GLY L  62 "
        pdb=" CA  GLY L  62 "
        pdb=" C   GLY L  62 "
      ideal   model   delta    sigma   weight residual
     113.99  110.98    3.01 1.28e+00 6.10e-01 5.53e+00
  angle pdb=" N   PRO H  36 "
        pdb=" CA  PRO H  36 "
        pdb=" C   PRO H  36 "
      ideal   model   delta    sigma   weight residual
     113.75  116.47   -2.72 1.49e+00 4.50e-01 3.33e+00
  angle pdb=" C   LEU H  35 "
        pdb=" CA  LEU H  35 "
        pdb=" CB  LEU H  35 "
      ideal   model   delta    sigma   weight residual
     109.48  112.05   -2.57 1.46e+00 4.69e-01 3.10e+00
  angle pdb=" N   LEU H  35 "
        pdb=" CA  LEU H  35 "
        pdb=" C   LEU H  35 "
      ideal   model   delta    sigma   weight residual
     110.58  107.96    2.62 1.56e+00 4.11e-01 2.83e+00
  ... (remaining 30620 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 6923
       17.58 -    35.16: 593
       35.16 -    52.74: 265
       52.74 -    70.32: 118
       70.32 -    87.90: 6
  Dihedral angle restraints: 7905
    sinusoidal: 4305
      harmonic: 3600
  Sorted by residual:
  dihedral pdb=" CA  VAL G 115 "
           pdb=" C   VAL G 115 "
           pdb=" N   LEU G 116 "
           pdb=" CA  LEU G 116 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.44  -18.56     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CA  LEU H  35 "
           pdb=" C   LEU H  35 "
           pdb=" N   PRO H  36 "
           pdb=" CA  PRO H  36 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.22  -16.78     0      5.00e+00 4.00e-02 1.13e+01
  dihedral pdb=" CA  LEU C 528 "
           pdb=" C   LEU C 528 "
           pdb=" N   ASP C 529 "
           pdb=" CA  ASP C 529 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.78   16.22     0      5.00e+00 4.00e-02 1.05e+01
  ... (remaining 7902 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 889
       0.034 -    0.069: 290
       0.069 -    0.103: 133
       0.103 -    0.137: 19
       0.137 -    0.171: 2
  Chirality restraints: 1333
  Sorted by residual:
  chirality pdb=" CA  PRO H  36 "
            pdb=" N   PRO H  36 "
            pdb=" C   PRO H  36 "
            pdb=" CB  PRO H  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 7.33e-01
  chirality pdb=" CA  PRO L  47 "
            pdb=" N   PRO L  47 "
            pdb=" C   PRO L  47 "
            pdb=" CB  PRO L  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.77e-01
  chirality pdb=" CA  ILE H  63 "
            pdb=" N   ILE H  63 "
            pdb=" C   ILE H  63 "
            pdb=" CB  ILE H  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.08e-01
  ... (remaining 1330 not shown)

  Planarity restraints: 2604
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU H  35 "    0.032 5.00e-02 4.00e+02   4.76e-02 3.62e+00
        pdb=" N   PRO H  36 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO H  36 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO H  36 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY M  62 "    0.007 2.00e-02 2.50e+03   1.33e-02 1.77e+00
        pdb=" C   GLY M  62 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   GLY M  62 "    0.009 2.00e-02 2.50e+03
        pdb=" N   LEU M  63 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA L  66 "    0.007 2.00e-02 2.50e+03   1.32e-02 1.75e+00
        pdb=" C   ALA L  66 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   ALA L  66 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ALA L  67 "    0.008 2.00e-02 2.50e+03
  ... (remaining 2601 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 711
        2.18 -     2.78: 34221
        2.78 -     3.39: 51341
        3.39 -     3.99: 66895
        3.99 -     4.60: 104733
  Nonbonded interactions: 257901
  Sorted by model distance:
  nonbonded pdb="HH21 ARG R  52 "
            pdb=" O   ILE S  43 "
     model   vdw
     1.572 2.450
  nonbonded pdb="HH12 ARG G  39 "
            pdb=" O   PRO G 145 "
     model   vdw
     1.618 2.450
  nonbonded pdb=" OD2 ASP G 167 "
            pdb=" H   GLY G 179 "
     model   vdw
     1.642 2.450
  nonbonded pdb="HD21 ASN T   6 "
            pdb=" O   GLN T  86 "
     model   vdw
     1.643 2.450
  nonbonded pdb=" OE1 GLU Q  48 "
            pdb=" H   GLU Q  48 "
     model   vdw
     1.651 2.450
  ... (remaining 257896 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 'L' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ 
r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG  \ 
or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23))  \ 
or resid 4 through 86))
  selection = chain 'M'
  selection = chain 'N'
  selection = chain 'O'
  selection = (chain 'P' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ 
r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG  \ 
or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23))  \ 
or resid 4 through 86))
  selection = (chain 'Q' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ 
r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG  \ 
or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23))  \ 
or resid 4 through 86))
  selection = chain 'R'
  selection = (chain 'S' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ 
r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG  \ 
or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23))  \ 
or resid 4 through 86))
  selection = chain 'T'
}

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:             9.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.120
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     16.280
  Find NCS groups from input model:        0.180
  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:             0.010
  Load rotamer database and sin/cos tables:6.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
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      :  0.004   0.036   8482  Z= 0.198
  Angle     :  0.501   5.642  11500  Z= 0.278
  Chirality :  0.040   0.171   1333
  Planarity :  0.004   0.048   1519
  Dihedral  : 13.118  87.900   2960
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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 aren not related in a simple way.
  whole:  1.81 (0.26), residues: 1124
  helix:  1.65 (0.19), residues: 811
  sheet: -1.24 (0.53), residues: 89
  loop :  0.88 (0.45), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG R  52 
 TYR   0.010   0.001   TYR G 147 
 PHE   0.017   0.002   PHE M  78 
 TRP   0.004   0.001   TRP H 109 
 HIS   0.002   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 ( 8482)
  covalent geometry    : angle       0.50117 (11500)
  hydrogen bonds       : bond        0.13537 (  719)
  hydrogen bonds       : angle       6.46992 ( 2133)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.276 
Fit side-chains
REVERT: P   75 MET cc_start: 0.8181 (tmm) cc_final: 0.7942 (tmm)
REVERT: R   21 MET cc_start: 0.8568 (mmm) cc_final: 0.8311 (mmm)
REVERT: R   50 GLN cc_start: 0.8339 (tt0) cc_final: 0.7929 (tm130)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 1.0529
  time to fit residues: 103.7157
Evaluate side-chains
  60 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9990
   chunk 106 optimal weight:    0.0970
   overall best weight:    0.7578

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

Flipped N/Q/H residues before XYZ refinement:
G  73 GLN
N  71 ASN
Q  86 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.085305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.065496 restraints weight = 45789.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.2914 rms_B_bonded: 2.14
r_work: 0.2800 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2668 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.1003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8482  Z= 0.203
  Angle     :  0.536   5.162  11500  Z= 0.291
  Chirality :  0.042   0.171   1333
  Planarity :  0.004   0.049   1519
  Dihedral  :  4.066  18.584   1208
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  :  6.88 %
    Favored  : 91.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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 aren not related in a simple way.
  whole:  2.69 (0.26), residues: 1124
  helix:  2.38 (0.18), residues: 813
  sheet: -1.38 (0.52), residues: 89
  loop :  1.04 (0.45), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H 113 
 TYR   0.011   0.001   TYR G 147 
 PHE   0.014   0.002   PHE M  78 
 TRP   0.004   0.001   TRP H 109 
 HIS   0.003   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 8482)
  covalent geometry    : angle       0.53593 (11500)
  hydrogen bonds       : bond        0.05289 (  719)
  hydrogen bonds       : angle       4.33171 ( 2133)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.303 
Fit side-chains
REVERT: L   46 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.7823 (tm130)
REVERT: L   63 LEU cc_start: 0.7852 (tt) cc_final: 0.7623 (tt)
REVERT: M   65 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7152 (mp0)
REVERT: P   75 MET cc_start: 0.8783 (tmm) cc_final: 0.8359 (tmm)
REVERT: R   21 MET cc_start: 0.8947 (mmm) cc_final: 0.8742 (mmm)
REVERT: R   50 GLN cc_start: 0.8086 (tt0) cc_final: 0.7353 (tm130)
  outliers start: 11
  outliers final: 3
  residues processed: 74
  average time/residue: 1.1623
  time to fit residues: 91.5885
Evaluate side-chains
  64 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   46 GLN
Chi-restraints excluded: chain L residue   75 MET
Chi-restraints excluded: chain M residue   65 GLU
Chi-restraints excluded: chain Q residue   86 GLN
Chi-restraints excluded: chain S residue    3 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 11 optimal weight:    0.0270
   chunk 2 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 22 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 33 optimal weight:    0.1980
   overall best weight:    0.5038

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

Flipped N/Q/H residues before XYZ refinement:
G  73 GLN
H   5 ASN
Q  86 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.086325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.066497 restraints weight = 45640.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.2937 rms_B_bonded: 2.15
r_work: 0.2818 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2682 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8661
moved from start:          0.1234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8482  Z= 0.158
  Angle     :  0.499   4.901  11500  Z= 0.267
  Chirality :  0.041   0.157   1333
  Planarity :  0.004   0.046   1519
  Dihedral  :  4.012  18.093   1208
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  :  7.76 %
    Favored  : 90.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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 aren not related in a simple way.
  whole:  3.16 (0.26), residues: 1124
  helix:  2.79 (0.18), residues: 813
  sheet: -1.28 (0.54), residues: 79
  loop :  0.86 (0.44), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  52 
 TYR   0.010   0.001   TYR G 147 
 PHE   0.016   0.001   PHE R  74 
 TRP   0.004   0.001   TRP H 109 
 HIS   0.002   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 8482)
  covalent geometry    : angle       0.49877 (11500)
  hydrogen bonds       : bond        0.04904 (  719)
  hydrogen bonds       : angle       4.09206 ( 2133)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
REVERT: L   46 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.7751 (tm130)
REVERT: M   32 ASP cc_start: 0.8135 (m-30) cc_final: 0.7894 (m-30)
REVERT: M   65 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7168 (mp0)
REVERT: O   75 MET cc_start: 0.9247 (tmm) cc_final: 0.8919 (tmt)
REVERT: P   75 MET cc_start: 0.8884 (tmm) cc_final: 0.8451 (tmm)
REVERT: R   50 GLN cc_start: 0.8098 (tt0) cc_final: 0.7415 (tm-30)
  outliers start: 12
  outliers final: 4
  residues processed: 70
  average time/residue: 1.1470
  time to fit residues: 85.0655
Evaluate side-chains
  61 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  194 LEU
Chi-restraints excluded: chain H residue   75 GLU
Chi-restraints excluded: chain L residue   46 GLN
Chi-restraints excluded: chain L residue   75 MET
Chi-restraints excluded: chain M residue   65 GLU
Chi-restraints excluded: chain S residue    3 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 50 optimal weight:    0.8980
   chunk 43 optimal weight:    0.2980
   chunk 79 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 82 optimal weight:    0.6980
   chunk 41 optimal weight:    0.5980
   chunk 23 optimal weight:    0.0470
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
G  73 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.086443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.066578 restraints weight = 45521.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.2942 rms_B_bonded: 2.15
r_work: 0.2822 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2684 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8660
moved from start:          0.1435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8482  Z= 0.156
  Angle     :  0.495   5.208  11500  Z= 0.263
  Chirality :  0.040   0.156   1333
  Planarity :  0.004   0.046   1519
  Dihedral  :  3.943  17.676   1208
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  8.76 %
    Favored  : 89.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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 aren not related in a simple way.
  whole:  3.36 (0.26), residues: 1124
  helix:  2.96 (0.18), residues: 813
  sheet: -1.49 (0.52), residues: 83
  loop :  0.96 (0.44), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N  52 
 TYR   0.010   0.001   TYR G 147 
 PHE   0.015   0.001   PHE R  74 
 TRP   0.004   0.001   TRP H 109 
 HIS   0.002   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 8482)
  covalent geometry    : angle       0.49547 (11500)
  hydrogen bonds       : bond        0.04720 (  719)
  hydrogen bonds       : angle       3.95791 ( 2133)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
REVERT: H   75 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6685 (tm-30)
REVERT: M   65 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7170 (mp0)
REVERT: O   65 GLU cc_start: 0.8123 (mp0) cc_final: 0.7874 (mp0)
REVERT: O   75 MET cc_start: 0.9272 (tmm) cc_final: 0.8992 (tmm)
REVERT: P   75 MET cc_start: 0.8937 (tmm) cc_final: 0.8555 (tmm)
REVERT: Q   86 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.6223 (pm20)
REVERT: R   50 GLN cc_start: 0.8081 (tt0) cc_final: 0.7377 (tm-30)
  outliers start: 13
  outliers final: 3
  residues processed: 71
  average time/residue: 1.3656
  time to fit residues: 103.2575
Evaluate side-chains
  64 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  194 LEU
Chi-restraints excluded: chain H residue   75 GLU
Chi-restraints excluded: chain L residue   75 MET
Chi-restraints excluded: chain M residue   65 GLU
Chi-restraints excluded: chain Q residue   86 GLN
Chi-restraints excluded: chain S residue    3 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 102 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 93 optimal weight:    0.9980
   chunk 98 optimal weight:    0.9990
   chunk 23 optimal weight:    0.3980
   chunk 61 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
G  73 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.085108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.065169 restraints weight = 45707.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.2910 rms_B_bonded: 2.15
r_work: 0.2788 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2652 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8684
moved from start:          0.1468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   8482  Z= 0.211
  Angle     :  0.520   5.295  11500  Z= 0.281
  Chirality :  0.041   0.178   1333
  Planarity :  0.004   0.050   1519
  Dihedral  :  4.016  18.339   1208
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 10.01 %
    Favored  : 88.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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 aren not related in a simple way.
  whole:  3.24 (0.26), residues: 1124
  helix:  2.89 (0.18), residues: 813
  sheet: -1.45 (0.52), residues: 83
  loop :  0.87 (0.43), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG P  52 
 TYR   0.013   0.001   TYR G 147 
 PHE   0.017   0.002   PHE R  74 
 TRP   0.004   0.001   TRP H 109 
 HIS   0.003   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 8482)
  covalent geometry    : angle       0.51981 (11500)
  hydrogen bonds       : bond        0.04946 (  719)
  hydrogen bonds       : angle       3.98957 ( 2133)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.482 
Fit side-chains
REVERT: M   65 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7270 (mp0)
REVERT: O   75 MET cc_start: 0.9297 (tmm) cc_final: 0.9015 (tmm)
REVERT: P   75 MET cc_start: 0.8969 (tmm) cc_final: 0.8565 (tmm)
REVERT: R   50 GLN cc_start: 0.8077 (tt0) cc_final: 0.7398 (tm-30)
  outliers start: 15
  outliers final: 8
  residues processed: 67
  average time/residue: 1.3884
  time to fit residues: 99.0505
Evaluate side-chains
  66 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  177 ILE
Chi-restraints excluded: chain G residue  194 LEU
Chi-restraints excluded: chain H residue   75 GLU
Chi-restraints excluded: chain L residue   72 LEU
Chi-restraints excluded: chain L residue   75 MET
Chi-restraints excluded: chain M residue   65 GLU
Chi-restraints excluded: chain R residue   75 MET
Chi-restraints excluded: chain S residue    3 LEU
Chi-restraints excluded: chain S residue   75 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0980
   chunk 5 optimal weight:    0.0970
   chunk 69 optimal weight:    0.9990
   chunk 21 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.5178

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.086259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.066395 restraints weight = 45424.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.2938 rms_B_bonded: 2.14
r_work: 0.2816 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2682 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8664
moved from start:          0.1565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8482  Z= 0.154
  Angle     :  0.490   5.752  11500  Z= 0.261
  Chirality :  0.040   0.154   1333
  Planarity :  0.004   0.046   1519
  Dihedral  :  3.930  18.201   1208
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 10.14 %
    Favored  : 87.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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 aren not related in a simple way.
  whole:  3.46 (0.26), residues: 1124
  helix:  3.06 (0.18), residues: 813
  sheet: -1.52 (0.51), residues: 83
  loop :  0.95 (0.44), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG O  45 
 TYR   0.009   0.001   TYR G 147 
 PHE   0.016   0.001   PHE R  74 
 TRP   0.004   0.001   TRP H 109 
 HIS   0.002   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 8482)
  covalent geometry    : angle       0.49018 (11500)
  hydrogen bonds       : bond        0.04649 (  719)
  hydrogen bonds       : angle       3.86604 ( 2133)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.462 
Fit side-chains
   revert: symmetry clash
REVERT: M   65 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7260 (mp0)
REVERT: O   75 MET cc_start: 0.9293 (tmm) cc_final: 0.9020 (tmt)
REVERT: P   75 MET cc_start: 0.8983 (tmm) cc_final: 0.8578 (tmm)
REVERT: R   50 GLN cc_start: 0.8068 (tt0) cc_final: 0.7394 (tm-30)
  outliers start: 16
  outliers final: 8
  residues processed: 67
  average time/residue: 1.2961
  time to fit residues: 92.7570
Evaluate side-chains
  64 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  175 ASP
Chi-restraints excluded: chain G residue  177 ILE
Chi-restraints excluded: chain G residue  194 LEU
Chi-restraints excluded: chain H residue   75 GLU
Chi-restraints excluded: chain L residue   75 MET
Chi-restraints excluded: chain M residue   65 GLU
Chi-restraints excluded: chain R residue   75 MET
Chi-restraints excluded: chain S residue    3 LEU
Chi-restraints excluded: chain S residue   75 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 61 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 106 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 93 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
G  73 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.084963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.065056 restraints weight = 45563.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.2910 rms_B_bonded: 2.14
r_work: 0.2787 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2650 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8688
moved from start:          0.1572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   8482  Z= 0.221
  Angle     :  0.531   6.988  11500  Z= 0.285
  Chirality :  0.041   0.180   1333
  Planarity :  0.004   0.050   1519
  Dihedral  :  4.012  18.726   1208
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 10.51 %
    Favored  : 87.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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 aren not related in a simple way.
  whole:  3.29 (0.26), residues: 1124
  helix:  2.92 (0.18), residues: 813
  sheet: -1.52 (0.51), residues: 83
  loop :  0.91 (0.43), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG O  45 
 TYR   0.011   0.001   TYR G 147 
 PHE   0.016   0.001   PHE R  74 
 TRP   0.004   0.001   TRP H 109 
 HIS   0.003   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 ( 8482)
  covalent geometry    : angle       0.53112 (11500)
  hydrogen bonds       : bond        0.04919 (  719)
  hydrogen bonds       : angle       3.93761 ( 2133)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 60
  time to evaluate  : 0.479 
Fit side-chains
REVERT: M   65 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7304 (mp0)
REVERT: O   75 MET cc_start: 0.9300 (tmm) cc_final: 0.8972 (tmm)
REVERT: R   50 GLN cc_start: 0.8106 (tt0) cc_final: 0.7454 (tm-30)
  outliers start: 18
  outliers final: 9
  residues processed: 69
  average time/residue: 1.2578
  time to fit residues: 92.8554
Evaluate side-chains
  67 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  115 VAL
Chi-restraints excluded: chain G residue  175 ASP
Chi-restraints excluded: chain G residue  177 ILE
Chi-restraints excluded: chain G residue  194 LEU
Chi-restraints excluded: chain H residue   75 GLU
Chi-restraints excluded: chain L residue   75 MET
Chi-restraints excluded: chain M residue   65 GLU
Chi-restraints excluded: chain R residue   75 MET
Chi-restraints excluded: chain S residue    3 LEU
Chi-restraints excluded: chain S residue   75 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 101 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.9980

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

Flipped N/Q/H residues before XYZ refinement:
S  50 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.084450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.064529 restraints weight = 46004.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.2898 rms_B_bonded: 2.14
r_work: 0.2773 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2637 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8694
moved from start:          0.1621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   8482  Z= 0.237
  Angle     :  0.541   7.429  11500  Z= 0.291
  Chirality :  0.041   0.183   1333
  Planarity :  0.004   0.051   1519
  Dihedral  :  4.090  19.304   1208
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 11.14 %
    Favored  : 86.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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 aren not related in a simple way.
  whole:  3.19 (0.26), residues: 1124
  helix:  2.85 (0.18), residues: 813
  sheet: -1.53 (0.50), residues: 83
  loop :  0.87 (0.43), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG O  45 
 TYR   0.011   0.001   TYR G 147 
 PHE   0.016   0.002   PHE R  74 
 TRP   0.004   0.001   TRP H 109 
 HIS   0.003   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00520 ( 8482)
  covalent geometry    : angle       0.54075 (11500)
  hydrogen bonds       : bond        0.05015 (  719)
  hydrogen bonds       : angle       3.97517 ( 2133)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 59
  time to evaluate  : 0.466 
Fit side-chains
REVERT: G  264 LYS cc_start: 0.8759 (tptm) cc_final: 0.8545 (tptp)
REVERT: M   65 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7270 (mp0)
REVERT: O   75 MET cc_start: 0.9289 (tmm) cc_final: 0.9004 (tmt)
REVERT: R   50 GLN cc_start: 0.8110 (tt0) cc_final: 0.7455 (tm-30)
  outliers start: 15
  outliers final: 10
  residues processed: 67
  average time/residue: 1.3736
  time to fit residues: 98.2146
Evaluate side-chains
  66 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  115 VAL
Chi-restraints excluded: chain G residue  175 ASP
Chi-restraints excluded: chain G residue  177 ILE
Chi-restraints excluded: chain G residue  194 LEU
Chi-restraints excluded: chain H residue   75 GLU
Chi-restraints excluded: chain L residue   72 LEU
Chi-restraints excluded: chain L residue   75 MET
Chi-restraints excluded: chain M residue   65 GLU
Chi-restraints excluded: chain R residue   75 MET
Chi-restraints excluded: chain S residue    3 LEU
Chi-restraints excluded: chain S residue   75 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 55 optimal weight:    0.1980
   chunk 76 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.085791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.065607 restraints weight = 45435.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.2921 rms_B_bonded: 2.15
r_work: 0.2798 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2663 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8679
moved from start:          0.1652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8482  Z= 0.181
  Angle     :  0.523   8.660  11500  Z= 0.278
  Chirality :  0.040   0.164   1333
  Planarity :  0.004   0.049   1519
  Dihedral  :  4.025  18.905   1208
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 11.64 %
    Favored  : 86.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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 aren not related in a simple way.
  whole:  3.34 (0.26), residues: 1124
  helix:  2.97 (0.18), residues: 813
  sheet: -1.53 (0.53), residues: 74
  loop :  0.79 (0.42), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG O  45 
 TYR   0.011   0.001   TYR G 147 
 PHE   0.014   0.001   PHE R  74 
 TRP   0.004   0.001   TRP H 109 
 HIS   0.003   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 8482)
  covalent geometry    : angle       0.52339 (11500)
  hydrogen bonds       : bond        0.04787 (  719)
  hydrogen bonds       : angle       3.90194 ( 2133)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
REVERT: M   65 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7314 (mp0)
REVERT: O   75 MET cc_start: 0.9304 (tmm) cc_final: 0.8974 (tmm)
REVERT: R   50 GLN cc_start: 0.8055 (tt0) cc_final: 0.7411 (tm-30)
  outliers start: 14
  outliers final: 10
  residues processed: 63
  average time/residue: 1.2027
  time to fit residues: 80.8502
Evaluate side-chains
  67 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  115 VAL
Chi-restraints excluded: chain G residue  175 ASP
Chi-restraints excluded: chain G residue  177 ILE
Chi-restraints excluded: chain G residue  194 LEU
Chi-restraints excluded: chain H residue   75 GLU
Chi-restraints excluded: chain L residue   46 GLN
Chi-restraints excluded: chain L residue   75 MET
Chi-restraints excluded: chain M residue   65 GLU
Chi-restraints excluded: chain R residue   75 MET
Chi-restraints excluded: chain S residue    3 LEU
Chi-restraints excluded: chain S residue   75 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 102 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 109 optimal weight:    0.6980
   chunk 87 optimal weight:    1.9990
   chunk 91 optimal weight:    0.0980
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.085286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.065300 restraints weight = 45421.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.2912 rms_B_bonded: 2.14
r_work: 0.2789 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2653 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8681
moved from start:          0.1663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8482  Z= 0.193
  Angle     :  0.531   8.113  11500  Z= 0.283
  Chirality :  0.040   0.170   1333
  Planarity :  0.004   0.049   1519
  Dihedral  :  4.015  18.748   1208
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 11.76 %
    Favored  : 86.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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 aren not related in a simple way.
  whole:  3.34 (0.26), residues: 1124
  helix:  2.98 (0.18), residues: 813
  sheet: -1.52 (0.53), residues: 74
  loop :  0.76 (0.42), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG O  45 
 TYR   0.010   0.001   TYR G 147 
 PHE   0.014   0.001   PHE R  74 
 TRP   0.003   0.001   TRP H 109 
 HIS   0.003   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 8482)
  covalent geometry    : angle       0.53093 (11500)
  hydrogen bonds       : bond        0.04815 (  719)
  hydrogen bonds       : angle       3.90029 ( 2133)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
REVERT: M   65 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7285 (mp0)
REVERT: O   75 MET cc_start: 0.9304 (tmm) cc_final: 0.8984 (tmm)
REVERT: R   50 GLN cc_start: 0.8058 (tt0) cc_final: 0.7411 (tm-30)
  outliers start: 14
  outliers final: 10
  residues processed: 61
  average time/residue: 1.1872
  time to fit residues: 77.6163
Evaluate side-chains
  66 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  115 VAL
Chi-restraints excluded: chain G residue  175 ASP
Chi-restraints excluded: chain G residue  177 ILE
Chi-restraints excluded: chain G residue  194 LEU
Chi-restraints excluded: chain H residue   75 GLU
Chi-restraints excluded: chain L residue   46 GLN
Chi-restraints excluded: chain L residue   75 MET
Chi-restraints excluded: chain M residue   65 GLU
Chi-restraints excluded: chain R residue   75 MET
Chi-restraints excluded: chain S residue    3 LEU
Chi-restraints excluded: chain S residue   75 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 2 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 80 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 92 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9980
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.085145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.065157 restraints weight = 45828.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.2911 rms_B_bonded: 2.15
r_work: 0.2788 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2653 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8684
moved from start:          0.1691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8482  Z= 0.199
  Angle     :  0.534   8.336  11500  Z= 0.285
  Chirality :  0.041   0.171   1333
  Planarity :  0.004   0.049   1519
  Dihedral  :  4.027  18.816   1208
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 11.89 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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 aren not related in a simple way.
  whole:  3.34 (0.26), residues: 1124
  helix:  2.97 (0.18), residues: 813
  sheet: -1.50 (0.53), residues: 74
  loop :  0.76 (0.42), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG O  45 
 TYR   0.011   0.001   TYR G 147 
 PHE   0.014   0.001   PHE R  74 
 TRP   0.004   0.001   TRP H 109 
 HIS   0.003   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 8482)
  covalent geometry    : angle       0.53397 (11500)
  hydrogen bonds       : bond        0.04827 (  719)
  hydrogen bonds       : angle       3.90488 ( 2133)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5063.54 seconds
wall clock time: 86 minutes 26.83 seconds (5186.83 seconds total)