Starting phenix.real_space_refine
on Wed Mar  4 21:15:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7nkk_12442/03_2026/7nkk_12442.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7nkk_12442/03_2026/7nkk_12442.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7nkk_12442/03_2026/7nkk_12442.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7nkk_12442/03_2026/7nkk_12442.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7nkk_12442/03_2026/7nkk_12442.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7nkk_12442/03_2026/7nkk_12442.map"
  }
  resolution = 3.6
  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      26      5.16       5
     C    5345      2.51       5
     N    1391      2.21       5
     O    1533      1.98       5
     H    8376      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16671
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "C"
      Number of atoms: 231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 231
          Classifications: {'peptide': 14}
          Link IDs: {'PTRANS': 2, 'TRANS': 11}
    Chain: "G"
      Number of atoms: 3794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 246, 3794
          Classifications: {'peptide': 246}
          Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 236}
          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: 1204
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 1204
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 4, 'TRANS': 80}
    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: 1204
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 1204
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 4, 'TRANS': 80}
    Chain: "P"
      Number of atoms: 1224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 1224
          Classifications: {'peptide': 86}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 81}
    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: 1204
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 1204
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 4, 'TRANS': 80}
    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: 1204
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 1204
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 4, 'TRANS': 80}
  Time building chain proxies: 3.05, per 1000 atoms: 0.18
  Number of scatterers: 16671
  At special positions: 0
  Unit cell: (66.4, 78.02, 149.4, 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      26     16.00
     O    1533      8.00
     N    1391      7.00
     C    5345      6.00
     H    8376      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: 1.64
  Conformation dependent library (CDL) restraints added in 395.4 milliseconds
  

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1954

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 3 sheets defined
      74.0% alpha, 7.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'G' and resid 19 through 43
    Processing helix  chain 'G' and resid 43 through 60
    Processing helix  chain 'G' and resid 65 through 69
    Processing helix  chain 'G' and resid 91 through 111
    Processing helix  chain 'G' and resid 120 through 131
      removed outlier: 3.620A  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 227 through 268
      Proline residue:  G 237  - end of helix
    Processing helix  chain 'H' and resid 91 through 99
    Processing helix  chain 'H' and resid 103 through 118
    Processing helix  chain 'L' and resid 4 through 46
    Processing helix  chain 'L' and resid 49 through 81
      removed outlier: 4.894A  pdb=" N   THR L  55 " --> pdb=" O   GLY L  51 " (cutoff:3.500A)
      Proline residue:  L  56  - end of helix
      removed outlier: 4.580A  pdb=" N   ALA L  67 " --> pdb=" O   LEU L  63 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 4 through 46
      removed outlier: 4.155A  pdb=" N   ILE M   8 " --> pdb=" O   ASP M   4 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 49 through 81
      removed outlier: 3.696A  pdb=" N   PHE M  54 " --> pdb=" O   GLN M  50 " (cutoff:3.500A)
      removed outlier: 5.121A  pdb=" N   THR M  55 " --> pdb=" O   GLY M  51 " (cutoff:3.500A)
      Proline residue:  M  56  - end of helix
      removed outlier: 3.691A  pdb=" N   ILE M  59 " --> pdb=" O   THR M  55 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   TYR M  68 " --> pdb=" O   VAL M  64 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 4 through 46
      removed outlier: 3.653A  pdb=" N   ILE N   8 " --> pdb=" O   ASP N   4 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 49 through 80
      removed outlier: 4.532A  pdb=" N   THR N  55 " --> pdb=" O   GLY N  51 " (cutoff:3.500A)
      Proline residue:  N  56  - end of helix
      removed outlier: 3.599A  pdb=" N   THR N  60 " --> pdb=" O   PRO N  56 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   VAL N  61 " --> pdb=" O   PHE N  57 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ALA N  66 " --> pdb=" O   GLY N  62 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 4 through 46
      removed outlier: 3.515A  pdb=" N   ILE O   8 " --> pdb=" O   ASP O   4 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 49 through 80
      removed outlier: 3.974A  pdb=" N   PHE O  54 " --> pdb=" O   GLN O  50 " (cutoff:3.500A)
      removed outlier: 5.991A  pdb=" N   THR O  55 " --> pdb=" O   GLY O  51 " (cutoff:3.500A)
      Proline residue:  O  56  - end of helix
      removed outlier: 3.627A  pdb=" N   ASN O  71 " --> pdb=" O   ALA O  67 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 4 through 46
    Processing helix  chain 'P' and resid 49 through 81
      removed outlier: 4.424A  pdb=" N   THR P  55 " --> pdb=" O   GLY P  51 " (cutoff:3.500A)
      Proline residue:  P  56  - end of helix
    Processing helix  chain 'Q' and resid 4 through 46
      removed outlier: 3.574A  pdb=" N   ILE Q   8 " --> pdb=" O   ASP Q   4 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 49 through 80
      removed outlier: 3.520A  pdb=" N   PHE Q  54 " --> pdb=" O   GLN Q  50 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   THR Q  55 " --> pdb=" O   GLY Q  51 " (cutoff:3.500A)
      Proline residue:  Q  56  - end of helix
      removed outlier: 3.558A  pdb=" N   ALA Q  66 " --> pdb=" O   GLY Q  62 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 4 through 46
    Processing helix  chain 'R' and resid 49 through 80
      removed outlier: 4.375A  pdb=" N   THR R  55 " --> pdb=" O   GLY R  51 " (cutoff:3.500A)
      Proline residue:  R  56  - end of helix
      removed outlier: 3.883A  pdb=" N   ILE R  59 " --> pdb=" O   THR R  55 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   ALA R  67 " --> pdb=" O   LEU R  63 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 4 through 46
      removed outlier: 3.737A  pdb=" N   ILE S   8 " --> pdb=" O   ASP S   4 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 49 through 80
      removed outlier: 3.600A  pdb=" N   PHE S  54 " --> pdb=" O   GLN S  50 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   THR S  55 " --> pdb=" O   GLY S  51 " (cutoff:3.500A)
      Proline residue:  S  56  - end of helix
      removed outlier: 3.755A  pdb=" N   ALA S  66 " --> pdb=" O   GLY S  62 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ALA S  67 " --> pdb=" O   LEU S  63 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ASN S  71 " --> pdb=" O   ALA S  67 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 4 through 46
    Processing helix  chain 'T' and resid 49 through 81
      removed outlier: 3.794A  pdb=" N   THR T  55 " --> pdb=" O   GLY T  51 " (cutoff:3.500A)
      Proline residue:  T  56  - end of helix
      removed outlier: 4.094A  pdb=" N   ALA T  67 " --> pdb=" O   LEU T  63 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 534 through 541
      removed outlier: 11.260A  pdb=" N   GLU C 534 " --> pdb=" O   PRO G 205 " (cutoff:3.500A)
      removed outlier: 9.344A  pdb=" N   GLU G 207 " --> pdb=" O   GLU C 534 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   GLU C 536 " --> pdb=" O   GLU G 207 " (cutoff:3.500A)
      removed outlier: 7.502A  pdb=" N   GLU G 209 " --> pdb=" O   GLU C 536 " (cutoff:3.500A)
      removed outlier: 5.990A  pdb=" N   VAL C 538 " --> pdb=" O   GLU G 209 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   VAL G 211 " --> pdb=" O   VAL C 538 " (cutoff:3.500A)
      removed outlier: 5.601A  pdb=" N   VAL C 540 " --> pdb=" O   VAL G 211 " (cutoff:3.500A)
      removed outlier: 5.450A  pdb=" N   ALA G 198 " --> pdb=" O   GLU G 189 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   GLU G 189 " --> pdb=" O   ALA G 198 " (cutoff:3.500A)
      removed outlier: 5.158A  pdb=" N   ALA G 200 " --> pdb=" O   PHE G 187 " (cutoff:3.500A)
      removed outlier: 7.261A  pdb=" N   PHE G 187 " --> pdb=" O   ALA G 200 " (cutoff:3.500A)
      removed outlier: 5.509A  pdb=" N   ARG G 202 " --> pdb=" O   ILE G 185 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   ILE G 185 " --> pdb=" O   ARG G 202 " (cutoff:3.500A)
      removed outlier: 8.514A  pdb=" N   HIS G 184 " --> pdb=" O   ARG G  76 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   GLY G  78 " --> pdb=" O   HIS G 184 " (cutoff:3.500A)
      removed outlier: 7.528A  pdb=" N   VAL G 186 " --> pdb=" O   GLY G  78 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   LEU G  80 " --> pdb=" O   VAL G 186 " (cutoff:3.500A)
      removed outlier: 8.475A  pdb=" N   THR G 188 " --> pdb=" O   LEU G  80 " (cutoff:3.500A)
      removed outlier: 9.309A  pdb=" N   VAL G  82 " --> pdb=" O   THR G 188 " (cutoff:3.500A)
      removed outlier: 11.236A  pdb=" N   PHE G 190 " --> pdb=" O   VAL G  82 " (cutoff:3.500A)
      removed outlier: 5.871A  pdb=" N   ALA G  77 " --> pdb=" O   VAL G 115 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   TYR G 117 " --> pdb=" O   ALA G  77 " (cutoff:3.500A)
      removed outlier: 6.015A  pdb=" N   VAL G  79 " --> pdb=" O   TYR G 117 " (cutoff:3.500A)
      removed outlier: 7.703A  pdb=" N   VAL G 119 " --> pdb=" O   VAL G  79 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   VAL G  81 " --> pdb=" O   VAL G 119 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   GLU G 136 " --> pdb=" O   LEU G 116 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'G' and resid 223 through 225
      removed outlier: 6.178A  pdb=" N   SER G 223 " --> pdb=" O   VAL H  42 " (cutoff:3.500A)
      removed outlier: 8.431A  pdb=" N   GLN H  44 " --> pdb=" O   SER G 223 " (cutoff:3.500A)
      removed outlier: 7.961A  pdb=" N   GLU G 225 " --> pdb=" O   GLN H  44 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   ASN H   5 " --> pdb=" O   VAL H  77 " (cutoff:3.500A)
      removed outlier: 8.113A  pdb=" N   ILE H  79 " --> pdb=" O   ASN H   5 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   GLU H   7 " --> pdb=" O   ILE H  79 " (cutoff:3.500A)
      removed outlier: 7.461A  pdb=" N   VAL H  81 " --> pdb=" O   GLU H   7 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   VAL H   9 " --> pdb=" O   VAL H  81 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   ALA H  10 " --> pdb=" O   GLU H  14 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   GLU H  14 " --> pdb=" O   ALA H  10 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 32 through 34

    712 hydrogen bonds defined for protein.
    2103 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: 3.75

  Time building geometry restraints manager: 2.21 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: 8375
        1.03 -     1.23: 112
        1.23 -     1.43: 3327
        1.43 -     1.62: 4946
        1.62 -     1.82: 51
  Bond restraints: 16811
  Sorted by residual:
  bond pdb=" CG1 ILE Q  20 "
       pdb=" CD1 ILE Q  20 "
    ideal  model  delta    sigma   weight residual
    1.513  1.469  0.044 3.90e-02 6.57e+02 1.29e+00
  bond pdb=" CG1 ILE M  20 "
       pdb=" CD1 ILE M  20 "
    ideal  model  delta    sigma   weight residual
    1.513  1.472  0.041 3.90e-02 6.57e+02 1.10e+00
  bond pdb=" CG1 ILE R  30 "
       pdb=" CD1 ILE R  30 "
    ideal  model  delta    sigma   weight residual
    1.513  1.472  0.041 3.90e-02 6.57e+02 1.10e+00
  bond pdb=" SD  MET R  21 "
       pdb=" CE  MET R  21 "
    ideal  model  delta    sigma   weight residual
    1.791  1.767  0.024 2.50e-02 1.60e+03 9.12e-01
  bond pdb=" CG  LEU Q  19 "
       pdb=" CD1 LEU Q  19 "
    ideal  model  delta    sigma   weight residual
    1.521  1.490  0.031 3.30e-02 9.18e+02 8.81e-01
  ... (remaining 16806 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 29991
        1.55 -     3.10: 387
        3.10 -     4.65: 51
        4.65 -     6.20: 7
        6.20 -     7.75: 1
  Bond angle restraints: 30437
  Sorted by residual:
  angle pdb=" CB  MET R  21 "
        pdb=" CG  MET R  21 "
        pdb=" SD  MET R  21 "
      ideal   model   delta    sigma   weight residual
     112.70  120.45   -7.75 3.00e+00 1.11e-01 6.68e+00
  angle pdb=" C   ILE R  20 "
        pdb=" N   MET R  21 "
        pdb=" CA  MET R  21 "
      ideal   model   delta    sigma   weight residual
     121.14  117.37    3.77 1.75e+00 3.27e-01 4.63e+00
  angle pdb=" CG  MET S  21 "
        pdb=" SD  MET S  21 "
        pdb=" CE  MET S  21 "
      ideal   model   delta    sigma   weight residual
     100.90  104.93   -4.03 2.20e+00 2.07e-01 3.36e+00
  angle pdb=" C   PHE T  74 "
        pdb=" N   MET T  75 "
        pdb=" CA  MET T  75 "
      ideal   model   delta    sigma   weight residual
     120.29  117.75    2.54 1.42e+00 4.96e-01 3.19e+00
  angle pdb=" CB  MET L  21 "
        pdb=" CG  MET L  21 "
        pdb=" SD  MET L  21 "
      ideal   model   delta    sigma   weight residual
     112.70  118.04   -5.34 3.00e+00 1.11e-01 3.17e+00
  ... (remaining 30432 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.18: 6797
       17.18 -    34.36: 635
       34.36 -    51.55: 240
       51.55 -    68.73: 178
       68.73 -    85.91: 6
  Dihedral angle restraints: 7856
    sinusoidal: 4275
      harmonic: 3581
  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 -161.82  -18.18     0      5.00e+00 4.00e-02 1.32e+01
  dihedral pdb=" CA  ASP G 227 "
           pdb=" CB  ASP G 227 "
           pdb=" CG  ASP G 227 "
           pdb=" OD1 ASP G 227 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.98   54.98     1      2.00e+01 2.50e-03 1.02e+01
  dihedral pdb=" CB  GLU R  65 "
           pdb=" CG  GLU R  65 "
           pdb=" CD  GLU R  65 "
           pdb=" OE1 GLU R  65 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -83.37   83.37     1      3.00e+01 1.11e-03 9.43e+00
  ... (remaining 7853 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 885
       0.030 -    0.061: 247
       0.061 -    0.091: 136
       0.091 -    0.122: 51
       0.122 -    0.152: 6
  Chirality restraints: 1325
  Sorted by residual:
  chirality pdb=" CA  ILE G 185 "
            pdb=" N   ILE G 185 "
            pdb=" C   ILE G 185 "
            pdb=" CB  ILE G 185 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.79e-01
  chirality pdb=" CA  ILE O  20 "
            pdb=" N   ILE O  20 "
            pdb=" C   ILE O  20 "
            pdb=" CB  ILE O  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.89e-01
  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    2.59    0.13 2.00e-01 2.50e+01 4.34e-01
  ... (remaining 1322 not shown)

  Planarity restraints: 2590
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE N  70 "    0.007 2.00e-02 2.50e+03   1.46e-02 2.12e+00
        pdb=" C   ILE N  70 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   ILE N  70 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ASN N  71 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU H  35 "    0.024 5.00e-02 4.00e+02   3.61e-02 2.08e+00
        pdb=" N   PRO H  36 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO H  36 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO H  36 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET R  21 "    0.007 2.00e-02 2.50e+03   1.44e-02 2.06e+00
        pdb=" C   MET R  21 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   MET R  21 "    0.009 2.00e-02 2.50e+03
        pdb=" N   GLY R  22 "    0.008 2.00e-02 2.50e+03
  ... (remaining 2587 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.20: 1100
        2.20 -     2.80: 35044
        2.80 -     3.40: 50710
        3.40 -     4.00: 64280
        4.00 -     4.60: 100622
  Nonbonded interactions: 251756
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN Q  71 "
            pdb=" HH  TYR R  68 "
     model   vdw
     1.594 2.450
  nonbonded pdb=" OE1 GLU H 104 "
            pdb=" H   GLU H 104 "
     model   vdw
     1.607 2.450
  nonbonded pdb=" OE1 GLU G 143 "
            pdb=" H   GLU G 143 "
     model   vdw
     1.625 2.450
  nonbonded pdb=" HG  SER G 192 "
            pdb=" OG  SER G 195 "
     model   vdw
     1.625 2.450
  nonbonded pdb=" O   PHE S  78 "
            pdb=" HG1 THR S  82 "
     model   vdw
     1.626 2.450
  ... (remaining 251751 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' 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 'N'
  selection = (chain 'O' 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 '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' 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 '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' 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))
}

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 group one per residue
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:             8.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.010
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.130
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     16.810
  Find NCS groups from input model:        0.190
  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:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8435  Z= 0.143
  Angle     :  0.509   7.752  11434  Z= 0.272
  Chirality :  0.040   0.152   1325
  Planarity :  0.004   0.036   1510
  Dihedral  : 13.865  85.910   2942
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.95 (0.26), residues: 1117
  helix:  1.82 (0.19), residues: 820
  sheet: -0.88 (0.54), residues: 86
  loop :  0.36 (0.45), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R  52 
 TYR   0.007   0.001   TYR G  46 
 PHE   0.019   0.001   PHE P  54 
 TRP   0.017   0.002   TRP H 109 
 HIS   0.002   0.001   HIS G  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 8435)
  covalent geometry    : angle       0.50866 (11434)
  hydrogen bonds       : bond        0.14728 (  712)
  hydrogen bonds       : angle       6.47802 ( 2103)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  193 MET cc_start: 0.8467 (tpp) cc_final: 0.8250 (tpp)
REVERT: S    6 ASN cc_start: 0.8693 (m-40) cc_final: 0.8469 (t0)
REVERT: S   21 MET cc_start: 0.8289 (mmp) cc_final: 0.8038 (mmp)
REVERT: S   32 ASP cc_start: 0.7071 (m-30) cc_final: 0.6858 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.1499
  time to fit residues: 14.1567
Evaluate side-chains
  46 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.4980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0770
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9980
   chunk 106 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.7138

-------------------------------------------------------------------------------
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 = 0.3695 r_free = 0.3695 target = 0.075473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.062542 restraints weight = 89124.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.064713 restraints weight = 34211.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.066030 restraints weight = 17770.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.066800 restraints weight = 11392.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.067246 restraints weight = 8677.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.0831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8435  Z= 0.167
  Angle     :  0.535   6.276  11434  Z= 0.283
  Chirality :  0.041   0.135   1325
  Planarity :  0.004   0.038   1510
  Dihedral  :  3.656  18.464   1200
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  5.03 %
    Favored  : 94.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.62 (0.26), residues: 1117
  helix:  2.39 (0.18), residues: 833
  sheet: -0.91 (0.55), residues: 80
  loop :  0.15 (0.45), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  39 
 TYR   0.007   0.001   TYR G  92 
 PHE   0.016   0.001   PHE P  54 
 TRP   0.005   0.001   TRP H 109 
 HIS   0.002   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 8435)
  covalent geometry    : angle       0.53525 (11434)
  hydrogen bonds       : bond        0.04919 (  712)
  hydrogen bonds       : angle       4.68679 ( 2103)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  263 MET cc_start: 0.8112 (mmp) cc_final: 0.7861 (mmp)
REVERT: P   65 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7778 (mm-30)
REVERT: S   21 MET cc_start: 0.8389 (mmp) cc_final: 0.7862 (mmp)
REVERT: S   32 ASP cc_start: 0.7122 (m-30) cc_final: 0.6821 (m-30)
  outliers start: 4
  outliers final: 1
  residues processed: 56
  average time/residue: 0.1415
  time to fit residues: 12.4640
Evaluate side-chains
  48 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 46
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue   72 LEU
Chi-restraints excluded: chain P residue   65 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 105 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 25 optimal weight:    0.4980
   chunk 9 optimal weight:    0.9980
   chunk 98 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
L  46 GLN
M  71 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.075311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.062355 restraints weight = 89431.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.064544 restraints weight = 34421.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.065833 restraints weight = 17708.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.066601 restraints weight = 11376.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.066958 restraints weight = 8638.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.1176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8435  Z= 0.171
  Angle     :  0.506   5.287  11434  Z= 0.269
  Chirality :  0.040   0.134   1325
  Planarity :  0.004   0.038   1510
  Dihedral  :  3.661  18.764   1200
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  7.66 %
    Favored  : 91.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.89 (0.25), residues: 1117
  helix:  2.62 (0.18), residues: 833
  sheet: -0.91 (0.55), residues: 80
  loop :  0.10 (0.45), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R  52 
 TYR   0.009   0.001   TYR M  68 
 PHE   0.013   0.001   PHE P  54 
 TRP   0.003   0.001   TRP H 109 
 HIS   0.002   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 8435)
  covalent geometry    : angle       0.50633 (11434)
  hydrogen bonds       : bond        0.04523 (  712)
  hydrogen bonds       : angle       4.40077 ( 2103)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  263 MET cc_start: 0.8140 (mmp) cc_final: 0.7838 (mmp)
REVERT: O   75 MET cc_start: 0.7610 (tmm) cc_final: 0.7305 (tmm)
REVERT: R   21 MET cc_start: 0.7729 (tmm) cc_final: 0.7388 (tmm)
REVERT: S   32 ASP cc_start: 0.7157 (m-30) cc_final: 0.6665 (m-30)
  outliers start: 5
  outliers final: 1
  residues processed: 48
  average time/residue: 0.1513
  time to fit residues: 11.4540
Evaluate side-chains
  45 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 44
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   63 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 104 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 52 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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 = 0.3664 r_free = 0.3664 target = 0.074163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.061206 restraints weight = 90182.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.063353 restraints weight = 34949.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.064629 restraints weight = 18125.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.065382 restraints weight = 11686.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.065734 restraints weight = 8896.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.1426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   8435  Z= 0.227
  Angle     :  0.543   6.570  11434  Z= 0.291
  Chirality :  0.041   0.143   1325
  Planarity :  0.004   0.040   1510
  Dihedral  :  3.796  19.532   1200
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  9.30 %
    Favored  : 90.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.76 (0.25), residues: 1117
  helix:  2.55 (0.17), residues: 834
  sheet: -1.19 (0.55), residues: 81
  loop :  0.06 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R  52 
 TYR   0.010   0.001   TYR M  68 
 PHE   0.014   0.001   PHE R  74 
 TRP   0.003   0.001   TRP H  16 
 HIS   0.002   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 ( 8435)
  covalent geometry    : angle       0.54268 (11434)
  hydrogen bonds       : bond        0.04431 (  712)
  hydrogen bonds       : angle       4.33920 ( 2103)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 43
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  263 MET cc_start: 0.8134 (mmp) cc_final: 0.7835 (mmp)
REVERT: O   75 MET cc_start: 0.7618 (tmm) cc_final: 0.7349 (tmm)
REVERT: S   32 ASP cc_start: 0.7346 (m-30) cc_final: 0.7016 (m-30)
  outliers start: 3
  outliers final: 2
  residues processed: 44
  average time/residue: 0.1480
  time to fit residues: 10.2153
Evaluate side-chains
  44 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 42
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   63 LEU
Chi-restraints excluded: chain P residue   65 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 3 optimal weight:    0.4980
   chunk 40 optimal weight:    0.0770
   chunk 8 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.6942

-------------------------------------------------------------------------------
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 = 0.3685 r_free = 0.3685 target = 0.075250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.062308 restraints weight = 88949.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.064485 restraints weight = 34211.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.065791 restraints weight = 17599.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.066525 restraints weight = 11285.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.066837 restraints weight = 8628.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.1510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8435  Z= 0.146
  Angle     :  0.501   7.547  11434  Z= 0.260
  Chirality :  0.040   0.134   1325
  Planarity :  0.004   0.037   1510
  Dihedral  :  3.686  19.342   1200
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  9.92 %
    Favored  : 89.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.08 (0.26), residues: 1117
  helix:  2.81 (0.18), residues: 833
  sheet: -1.15 (0.55), residues: 80
  loop :  0.05 (0.44), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R  52 
 TYR   0.008   0.001   TYR G  92 
 PHE   0.018   0.001   PHE Q  74 
 TRP   0.005   0.001   TRP H  16 
 HIS   0.002   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 8435)
  covalent geometry    : angle       0.50062 (11434)
  hydrogen bonds       : bond        0.04237 (  712)
  hydrogen bonds       : angle       4.12661 ( 2103)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  263 MET cc_start: 0.8114 (mmp) cc_final: 0.7836 (mmp)
REVERT: O   75 MET cc_start: 0.7653 (tmm) cc_final: 0.7297 (tmm)
REVERT: S   21 MET cc_start: 0.8373 (mmp) cc_final: 0.8108 (mmp)
REVERT: S   32 ASP cc_start: 0.7274 (m-30) cc_final: 0.6947 (m-30)
  outliers start: 6
  outliers final: 3
  residues processed: 48
  average time/residue: 0.1569
  time to fit residues: 11.5814
Evaluate side-chains
  44 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   74 PHE
Chi-restraints excluded: chain O residue   63 LEU
Chi-restraints excluded: chain P residue   65 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0980
   chunk 39 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0870
   chunk 29 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 98 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    0.5962

-------------------------------------------------------------------------------
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 = 0.3689 r_free = 0.3689 target = 0.075339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.062463 restraints weight = 89367.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.064674 restraints weight = 34331.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.066004 restraints weight = 17653.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.066710 restraints weight = 11281.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.067163 restraints weight = 8670.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.1644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8435  Z= 0.140
  Angle     :  0.491   7.397  11434  Z= 0.255
  Chirality :  0.040   0.133   1325
  Planarity :  0.004   0.037   1510
  Dihedral  :  3.609  18.726   1200
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 10.30 %
    Favored  : 88.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.28 (0.26), residues: 1117
  helix:  2.96 (0.18), residues: 834
  sheet: -1.21 (0.55), residues: 81
  loop :  0.17 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R  52 
 TYR   0.006   0.001   TYR G  92 
 PHE   0.011   0.001   PHE R  74 
 TRP   0.004   0.001   TRP H  16 
 HIS   0.002   0.001   HIS G  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 8435)
  covalent geometry    : angle       0.49135 (11434)
  hydrogen bonds       : bond        0.04098 (  712)
  hydrogen bonds       : angle       4.02098 ( 2103)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  263 MET cc_start: 0.8145 (mmp) cc_final: 0.7871 (mmp)
REVERT: O   75 MET cc_start: 0.7673 (tmm) cc_final: 0.7339 (tmm)
REVERT: S   21 MET cc_start: 0.8328 (mmp) cc_final: 0.8087 (mmp)
REVERT: S   32 ASP cc_start: 0.7193 (m-30) cc_final: 0.6894 (m-30)
  outliers start: 6
  outliers final: 4
  residues processed: 45
  average time/residue: 0.1561
  time to fit residues: 11.0059
Evaluate side-chains
  46 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   61 VAL
Chi-restraints excluded: chain M residue   74 PHE
Chi-restraints excluded: chain O residue   63 LEU
Chi-restraints excluded: chain P residue   65 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0980
   chunk 12 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 69 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
S   6 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.075318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.062433 restraints weight = 89304.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.064629 restraints weight = 34427.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.065936 restraints weight = 17747.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.066699 restraints weight = 11378.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.067090 restraints weight = 8621.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.1715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8435  Z= 0.146
  Angle     :  0.492   6.725  11434  Z= 0.254
  Chirality :  0.039   0.132   1325
  Planarity :  0.004   0.037   1510
  Dihedral  :  3.585  18.683   1200
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 10.68 %
    Favored  : 88.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.35 (0.25), residues: 1117
  helix:  3.02 (0.18), residues: 834
  sheet: -1.21 (0.55), residues: 81
  loop :  0.19 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R  52 
 TYR   0.007   0.001   TYR G  92 
 PHE   0.011   0.001   PHE Q  74 
 TRP   0.004   0.001   TRP H  16 
 HIS   0.002   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 8435)
  covalent geometry    : angle       0.49187 (11434)
  hydrogen bonds       : bond        0.04046 (  712)
  hydrogen bonds       : angle       3.96329 ( 2103)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  263 MET cc_start: 0.8143 (mmp) cc_final: 0.7876 (mmp)
REVERT: O   75 MET cc_start: 0.7709 (tmm) cc_final: 0.7390 (tmm)
REVERT: S   32 ASP cc_start: 0.7164 (m-30) cc_final: 0.6943 (m-30)
  outliers start: 8
  outliers final: 6
  residues processed: 47
  average time/residue: 0.1446
  time to fit residues: 10.7528
Evaluate side-chains
  47 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   61 VAL
Chi-restraints excluded: chain M residue   74 PHE
Chi-restraints excluded: chain N residue   21 MET
Chi-restraints excluded: chain O residue   63 LEU
Chi-restraints excluded: chain P residue   65 GLU
Chi-restraints excluded: chain S residue    6 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 90 optimal weight:    2.9990
   chunk 100 optimal weight:    0.6980
   chunk 50 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 84 optimal weight:    0.2980
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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 = 0.3686 r_free = 0.3686 target = 0.075119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.062212 restraints weight = 89295.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.064392 restraints weight = 34462.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.065674 restraints weight = 17859.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.066460 restraints weight = 11563.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.066846 restraints weight = 8705.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.1780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8435  Z= 0.156
  Angle     :  0.503   8.221  11434  Z= 0.260
  Chirality :  0.039   0.130   1325
  Planarity :  0.004   0.036   1510
  Dihedral  :  3.589  18.605   1200
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 11.06 %
    Favored  : 87.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.35 (0.25), residues: 1117
  helix:  3.01 (0.17), residues: 834
  sheet: -1.21 (0.55), residues: 81
  loop :  0.20 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R  52 
 TYR   0.007   0.001   TYR G  92 
 PHE   0.016   0.001   PHE Q  74 
 TRP   0.003   0.001   TRP H  16 
 HIS   0.002   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 8435)
  covalent geometry    : angle       0.50271 (11434)
  hydrogen bonds       : bond        0.04033 (  712)
  hydrogen bonds       : angle       3.96881 ( 2103)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  263 MET cc_start: 0.8144 (mmp) cc_final: 0.7880 (mmp)
REVERT: O   75 MET cc_start: 0.7694 (tmm) cc_final: 0.7378 (tmm)
REVERT: S   32 ASP cc_start: 0.7170 (m-30) cc_final: 0.6954 (m-30)
  outliers start: 8
  outliers final: 7
  residues processed: 45
  average time/residue: 0.1574
  time to fit residues: 11.0889
Evaluate side-chains
  48 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   61 VAL
Chi-restraints excluded: chain M residue   74 PHE
Chi-restraints excluded: chain N residue   21 MET
Chi-restraints excluded: chain N residue   72 LEU
Chi-restraints excluded: chain O residue   63 LEU
Chi-restraints excluded: chain P residue   65 GLU
Chi-restraints excluded: chain T residue    8 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 85 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 95 optimal weight:    1.9990
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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 = 0.3682 r_free = 0.3682 target = 0.074978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.062023 restraints weight = 89658.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.064206 restraints weight = 34611.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.065506 restraints weight = 17873.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.066289 restraints weight = 11463.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.066575 restraints weight = 8641.900|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.1834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8435  Z= 0.168
  Angle     :  0.514   8.233  11434  Z= 0.265
  Chirality :  0.040   0.133   1325
  Planarity :  0.004   0.037   1510
  Dihedral  :  3.621  18.768   1200
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 11.68 %
    Favored  : 87.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.30 (0.25), residues: 1117
  helix:  2.97 (0.17), residues: 834
  sheet: -1.25 (0.55), residues: 81
  loop :  0.21 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R  52 
 TYR   0.008   0.001   TYR G  92 
 PHE   0.010   0.001   PHE Q  74 
 TRP   0.003   0.001   TRP H  16 
 HIS   0.002   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 8435)
  covalent geometry    : angle       0.51392 (11434)
  hydrogen bonds       : bond        0.04057 (  712)
  hydrogen bonds       : angle       3.96964 ( 2103)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  263 MET cc_start: 0.8108 (mmp) cc_final: 0.7852 (mmp)
REVERT: S   32 ASP cc_start: 0.7211 (m-30) cc_final: 0.6990 (m-30)
  outliers start: 6
  outliers final: 5
  residues processed: 44
  average time/residue: 0.1571
  time to fit residues: 10.8493
Evaluate side-chains
  46 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   61 VAL
Chi-restraints excluded: chain M residue   74 PHE
Chi-restraints excluded: chain O residue   63 LEU
Chi-restraints excluded: chain P residue   65 GLU
Chi-restraints excluded: chain T residue    8 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 77 optimal weight:    0.0980
   chunk 101 optimal weight:    3.9990
   chunk 102 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 107 optimal weight:    0.7980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3687 r_free = 0.3687 target = 0.075183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.062059 restraints weight = 89188.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.064287 restraints weight = 33752.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.065642 restraints weight = 17323.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.066426 restraints weight = 11007.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.066814 restraints weight = 8270.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.1881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8435  Z= 0.150
  Angle     :  0.502   7.658  11434  Z= 0.259
  Chirality :  0.039   0.130   1325
  Planarity :  0.004   0.037   1510
  Dihedral  :  3.594  18.710   1200
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 11.56 %
    Favored  : 87.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.38 (0.25), residues: 1117
  helix:  3.04 (0.17), residues: 834
  sheet: -1.27 (0.55), residues: 81
  loop :  0.21 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R  52 
 TYR   0.007   0.001   TYR G  92 
 PHE   0.016   0.001   PHE R  74 
 TRP   0.004   0.001   TRP H  16 
 HIS   0.002   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 8435)
  covalent geometry    : angle       0.50235 (11434)
  hydrogen bonds       : bond        0.04006 (  712)
  hydrogen bonds       : angle       3.92118 ( 2103)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   76 THR cc_start: 0.8096 (OUTLIER) cc_final: 0.7865 (p)
REVERT: S   32 ASP cc_start: 0.7169 (m-30) cc_final: 0.6952 (m-30)
  outliers start: 8
  outliers final: 6
  residues processed: 47
  average time/residue: 0.1430
  time to fit residues: 10.6800
Evaluate side-chains
  48 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   76 THR
Chi-restraints excluded: chain M residue   61 VAL
Chi-restraints excluded: chain M residue   74 PHE
Chi-restraints excluded: chain N residue   72 LEU
Chi-restraints excluded: chain O residue   63 LEU
Chi-restraints excluded: chain P residue   65 GLU
Chi-restraints excluded: chain T residue    8 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 87 optimal weight:    0.3980
   chunk 92 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   chunk 85 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 89 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 1 optimal weight:    0.5980
   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 = 0.3691 r_free = 0.3691 target = 0.075410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.062461 restraints weight = 89188.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.064663 restraints weight = 34501.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.065952 restraints weight = 17834.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.066705 restraints weight = 11498.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.067138 restraints weight = 8742.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.1932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8435  Z= 0.143
  Angle     :  0.506   8.567  11434  Z= 0.258
  Chirality :  0.039   0.128   1325
  Planarity :  0.004   0.038   1510
  Dihedral  :  3.577  18.662   1200
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 11.81 %
    Favored  : 87.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.45 (0.25), residues: 1117
  helix:  3.09 (0.17), residues: 834
  sheet: -1.26 (0.55), residues: 81
  loop :  0.27 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R  52 
 TYR   0.007   0.001   TYR G  92 
 PHE   0.009   0.001   PHE Q  74 
 TRP   0.004   0.001   TRP H  16 
 HIS   0.002   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8435)
  covalent geometry    : angle       0.50565 (11434)
  hydrogen bonds       : bond        0.03957 (  712)
  hydrogen bonds       : angle       3.88779 ( 2103)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2609.60 seconds
wall clock time: 45 minutes 4.33 seconds (2704.33 seconds total)