Starting phenix.real_space_refine
on Mon Aug 25 17:58:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c98_16505/08_2025/8c98_16505.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c98_16505/08_2025/8c98_16505.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c98_16505/08_2025/8c98_16505.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c98_16505/08_2025/8c98_16505.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c98_16505/08_2025/8c98_16505.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c98_16505/08_2025/8c98_16505.map"
  }
  resolution = 3.66
  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=   0.023 sd=   0.113
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P    1017      5.49       5
     S      20      5.16       5
     C   15050      2.51       5
     N    5646      2.21       5
     O    8551      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  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: 30284
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "2"
      Number of atoms: 286
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 286
          Classifications: {'peptide': 35}
          Link IDs: {'TRANS': 34}
    Chain: "E"
      Number of atoms: 1454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 189, 1454
          Classifications: {'peptide': 189}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 184}
          Chain breaks: 1
    Chain: "J"
      Number of atoms: 1055
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 1055
          Classifications: {'peptide': 132}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 125}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 671
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 671
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          Chain breaks: 1
    Chain: "Q"
      Number of atoms: 947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 947
          Classifications: {'peptide': 117}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 116}
    Chain: "R"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 816
          Classifications: {'peptide': 103}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 101}
    Chain: "S"
      Number of atoms: 734
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 734
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 93}
          Chain breaks: 1
    Chain: "T"
      Number of atoms: 738
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 738
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 1, 'TRANS': 91}
    Chain: "U"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 779
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 3, 'TRANS': 98}
    Chain: "Y"
      Number of atoms: 509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 509
          Classifications: {'peptide': 63}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 62}
    Chain: "Z"
      Number of atoms: 449
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 449
          Classifications: {'peptide': 58}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 55}
    Chain: "A"
      Number of atoms: 21846
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1018, 21846
          Classifications: {'DNA': 1, 'RNA': 1017}
          Modifications used: {'rna2p_pur': 95, 'rna2p_pyr': 52, 'rna3p_pur': 499, 'rna3p_pyr': 371}
          Incomplete info: {'p_only': 1}
          Link IDs: {'rna2p': 147, 'rna3p': 870}
          Unresolved chain links: 2
          Chain breaks: 6
          Unresolved chain link angles: 11
          Unresolved chain link dihedrals: 8
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'  G:plan': 1, '  G:plan2': 1}
          Unresolved non-hydrogen planarities: 14
  Time building chain proxies: 5.30, per 1000 atoms: 0.18
  Number of scatterers: 30284
  At special positions: 0
  Unit cell: (131.25, 190, 167.5, 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      20     16.00
     P    1017     15.00
     O    8551      8.00
     N    5646      7.00
     C   15050      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.00
  Conformation dependent library (CDL) restraints added in 454.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2006

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 12 sheets defined
      39.5% alpha, 13.6% beta
      335 base pairs and 521 stacking pairs defined.
    Time for finding SS restraints: 4.44
  Creating SS restraints...
    Processing helix  chain '2' and resid 10 through 17
    Processing helix  chain '2' and resid 17 through 24
      removed outlier: 3.894A  pdb=" N   THR 2  24 " --> pdb=" O   ALA 2  20 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 24 through 38
    Processing helix  chain 'E' and resid 15 through 20
    Processing helix  chain 'E' and resid 24 through 39
    Processing helix  chain 'E' and resid 97 through 115
    Processing helix  chain 'E' and resid 130 through 141
    Processing helix  chain 'E' and resid 154 through 164
      removed outlier: 4.359A  pdb=" N   ASN E 163 " --> pdb=" O   LEU E 159 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   LEU E 164 " --> pdb=" O   ALA E 160 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 173 through 175
      No H-bonds generated for 'chain 'E' and resid 173 through 175'
    Processing helix  chain 'E' and resid 176 through 183
    Processing helix  chain 'E' and resid 190 through 201
    Processing helix  chain 'J' and resid 25 through 37
    Processing helix  chain 'J' and resid 67 through 72
    Processing helix  chain 'J' and resid 89 through 96
    Processing helix  chain 'J' and resid 97 through 108
      removed outlier: 4.084A  pdb=" N   ILE J 101 " --> pdb=" O   PRO J  97 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 112 through 121
      removed outlier: 3.655A  pdb=" N   LYS J 121 " --> pdb=" O   ALA J 117 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 130 through 136
      removed outlier: 3.682A  pdb=" N   ALA J 134 " --> pdb=" O   ASN J 131 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 130 through 136
      removed outlier: 3.957A  pdb=" N   ALA L 134 " --> pdb=" O   GLY L 130 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 5 through 19
      removed outlier: 3.916A  pdb=" N   GLN Q  19 " --> pdb=" O   LYS Q  15 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 24 through 29
      removed outlier: 4.435A  pdb=" N   ARG Q  27 " --> pdb=" O   TYR Q  24 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 30 through 70
      removed outlier: 4.321A  pdb=" N   GLN Q  36 " --> pdb=" O   ARG Q  32 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ARG Q  50 " --> pdb=" O   TYR Q  46 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   LYS Q  53 " --> pdb=" O   ARG Q  49 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ARG Q  54 " --> pdb=" O   ARG Q  50 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   GLN Q  70 " --> pdb=" O   ALA Q  66 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 74 through 85
    Processing helix  chain 'Q' and resid 90 through 101
    Processing helix  chain 'Q' and resid 101 through 117
      removed outlier: 4.000A  pdb=" N   PHE Q 105 " --> pdb=" O   ASP Q 101 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   ALA Q 117 " --> pdb=" O   LYS Q 113 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 13 through 23
      removed outlier: 3.865A  pdb=" N   LEU S  23 " --> pdb=" O   LEU S  19 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 38
      removed outlier: 3.860A  pdb=" N   ASP S  34 " --> pdb=" O   SER S  30 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   TYR S  38 " --> pdb=" O   ASP S  34 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 41 through 62
      removed outlier: 4.098A  pdb=" N   VAL S  45 " --> pdb=" O   LYS S  41 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   LEU S  46 " --> pdb=" O   LYS S  42 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 4 through 11
      removed outlier: 3.840A  pdb=" N   LEU T  11 " --> pdb=" O   LEU T   7 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 17 through 27
      removed outlier: 3.857A  pdb=" N   GLU T  25 " --> pdb=" O   SER T  21 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 39 through 52
    Processing helix  chain 'Y' and resid 9 through 34
      removed outlier: 3.809A  pdb=" N   PHE Y  26 " --> pdb=" O   LEU Y  22 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 40 through 56
      removed outlier: 4.017A  pdb=" N   LYS Y  44 " --> pdb=" O   SER Y  40 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 16 through 27
    Processing helix  chain 'Z' and resid 40 through 50
    Processing sheet with id=AA1, first strand: chain 'E' and resid 118 through 121
      removed outlier: 3.843A  pdb=" N   VAL E 121 " --> pdb=" O   MET E 188 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   VAL E 146 " --> pdb=" O   ASP E 168 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   ARG E 170 " --> pdb=" O   VAL E 146 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   ILE E 148 " --> pdb=" O   ARG E 170 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'J' and resid 123 through 125
      removed outlier: 6.306A  pdb=" N   ILE J  54 " --> pdb=" O   LYS J 123 " (cutoff:3.500A)
      removed outlier: 8.000A  pdb=" N   TYR J 125 " --> pdb=" O   ILE J  54 " (cutoff:3.500A)
      removed outlier: 6.122A  pdb=" N   VAL J  56 " --> pdb=" O   TYR J 125 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'J' and resid 23 through 24
      removed outlier: 5.779A  pdb=" N   LYS J  23 " --> pdb=" O   ALA J  63 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'J' and resid 73 through 74
    Processing sheet with id=AA5, first strand: chain 'R' and resid 11 through 14
      removed outlier: 6.870A  pdb=" N   GLN R   6 " --> pdb=" O   VAL R  38 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   VAL R  38 " --> pdb=" O   GLN R   6 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'R' and resid 19 through 22
      removed outlier: 7.023A  pdb=" N   PHE R  93 " --> pdb=" O   HIS R  66 " (cutoff:3.500A)
      removed outlier: 5.270A  pdb=" N   HIS R  66 " --> pdb=" O   PHE R  93 " (cutoff:3.500A)
      removed outlier: 7.902A  pdb=" N   ASP R  95 " --> pdb=" O   VAL R  64 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   VAL R  64 " --> pdb=" O   ASP R  95 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   THR R  99 " --> pdb=" O   LYS R  60 " (cutoff:3.500A)
      removed outlier: 4.894A  pdb=" N   LYS R  60 " --> pdb=" O   THR R  99 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'R' and resid 72 through 75
    Processing sheet with id=AA8, first strand: chain 'S' and resid 2 through 10
      removed outlier: 5.611A  pdb=" N   SER S 101 " --> pdb=" O   HIS S   9 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   HIS S 102 " --> pdb=" O   VAL S  76 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   VAL S  76 " --> pdb=" O   HIS S 102 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   THR S 104 " --> pdb=" O   ILE S  74 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   ILE S  74 " --> pdb=" O   THR S 104 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   VAL S 106 " --> pdb=" O   THR S  72 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'T' and resid 13 through 14
      removed outlier: 4.033A  pdb=" N   LYS T  81 " --> pdb=" O   VAL T  34 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   TRP T  80 " --> pdb=" O   VAL T  62 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   VAL T  62 " --> pdb=" O   TRP T  80 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   LYS T  82 " --> pdb=" O   THR T  60 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   THR T  60 " --> pdb=" O   LYS T  82 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   TYR T  84 " --> pdb=" O   VAL T  58 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   VAL T  58 " --> pdb=" O   TYR T  84 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   THR T  86 " --> pdb=" O   GLU T  56 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'U' and resid 64 through 65
      removed outlier: 6.676A  pdb=" N   LYS U  32 " --> pdb=" O   VAL U  27 " (cutoff:3.500A)
      removed outlier: 4.883A  pdb=" N   VAL U  27 " --> pdb=" O   LYS U  32 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   ILE U  34 " --> pdb=" O   LYS U  25 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'U' and resid 82 through 86
    Processing sheet with id=AB3, first strand: chain 'Z' and resid 34 through 38

    340 hydrogen bonds defined for protein.
    981 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      853 hydrogen bonds
      1378 hydrogen bond angles
      0 basepair planarities
      335 basepair parallelities
      521 stacking parallelities
  Total time for adding SS restraints: 7.15

  Time building geometry restraints manager: 2.88 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 4501
        1.33 -     1.45: 13501
        1.45 -     1.57: 12918
        1.57 -     1.69: 2027
        1.69 -     1.81: 40
  Bond restraints: 32987
  Sorted by residual:
  bond pdb=" C1'   U A 546 "
       pdb=" N1    U A 546 "
    ideal  model  delta    sigma   weight residual
    1.480  1.573 -0.093 1.50e-02 4.44e+03 3.88e+01
  bond pdb=" C1'   U A 827 "
       pdb=" N1    U A 827 "
    ideal  model  delta    sigma   weight residual
    1.480  1.573 -0.093 1.50e-02 4.44e+03 3.84e+01
  bond pdb=" N   MET Y   1 "
       pdb=" CA  MET Y   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.08e+00
  bond pdb=" N   MET J   1 "
       pdb=" CA  MET J   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.07e+00
  bond pdb=" N   MET T   1 "
       pdb=" CA  MET T   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.06e+00
  ... (remaining 32982 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.22: 48869
        1.22 -     2.43: 589
        2.43 -     3.65: 84
        3.65 -     4.87: 14
        4.87 -     6.08: 2
  Bond angle restraints: 49558
  Sorted by residual:
  angle pdb=" N   ALA S  64 "
        pdb=" CA  ALA S  64 "
        pdb=" C   ALA S  64 "
      ideal   model   delta    sigma   weight residual
     107.73  112.44   -4.71 1.34e+00 5.57e-01 1.24e+01
  angle pdb=" C4'   U A1019 "
        pdb=" C3'   U A1019 "
        pdb=" O3'   U A1019 "
      ideal   model   delta    sigma   weight residual
     109.40  113.45   -4.05 1.50e+00 4.44e-01 7.29e+00
  angle pdb=" C3'   U A1019 "
        pdb=" O3'   U A1019 "
        pdb=" P     A A1020 "
      ideal   model   delta    sigma   weight residual
     120.20  123.94   -3.74 1.50e+00 4.44e-01 6.23e+00
  angle pdb=" C4'   A A 404 "
        pdb=" C3'   A A 404 "
        pdb=" O3'   A A 404 "
      ideal   model   delta    sigma   weight residual
     109.40  112.81   -3.41 1.50e+00 4.44e-01 5.17e+00
  angle pdb=" N   LYS E   6 "
        pdb=" CA  LYS E   6 "
        pdb=" CB  LYS E   6 "
      ideal   model   delta    sigma   weight residual
     113.65  110.36    3.29 1.47e+00 4.63e-01 5.00e+00
  ... (remaining 49553 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.81: 18569
       35.81 -    71.61: 2226
       71.61 -   107.42: 276
      107.42 -   143.23: 7
      143.23 -   179.04: 3
  Dihedral angle restraints: 21081
    sinusoidal: 17992
      harmonic: 3089
  Sorted by residual:
  dihedral pdb=" O4'   C A 323 "
           pdb=" C1'   C A 323 "
           pdb=" N1    C A 323 "
           pdb=" C2    C A 323 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   29.07 -157.07     1      1.70e+01 3.46e-03 6.38e+01
  dihedral pdb=" O4'   U A1313 "
           pdb=" C1'   U A1313 "
           pdb=" N1    U A1313 "
           pdb=" C2    U A1313 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   98.74  101.26     1      1.50e+01 4.44e-03 5.10e+01
  dihedral pdb=" C4'   U A 276 "
           pdb=" C3'   U A 276 "
           pdb=" O3'   U A 276 "
           pdb=" P     G A 277 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   40.96  179.04     1      3.50e+01 8.16e-04 1.57e+01
  ... (remaining 21078 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 5571
       0.036 -    0.072: 663
       0.072 -    0.108: 125
       0.108 -    0.143: 47
       0.143 -    0.179: 2
  Chirality restraints: 6408
  Sorted by residual:
  chirality pdb=" C3'   U A1019 "
            pdb=" C4'   U A1019 "
            pdb=" O3'   U A1019 "
            pdb=" C2'   U A1019 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.57   -0.18 2.00e-01 2.50e+01 8.03e-01
  chirality pdb=" C1'   U A 827 "
            pdb=" O4'   U A 827 "
            pdb=" C2'   U A 827 "
            pdb=" N1    U A 827 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.62   -0.16 2.00e-01 2.50e+01 6.24e-01
  chirality pdb=" CA  ILE S 103 "
            pdb=" N   ILE S 103 "
            pdb=" C   ILE S 103 "
            pdb=" CB  ILE S 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.46e-01
  ... (remaining 6405 not shown)

  Planarity restraints: 2468
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A 259 "    0.009 2.00e-02 2.50e+03   1.47e-02 6.47e+00
        pdb=" N9    G A 259 "   -0.002 2.00e-02 2.50e+03
        pdb=" C8    G A 259 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7    G A 259 "    0.003 2.00e-02 2.50e+03
        pdb=" C5    G A 259 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    G A 259 "   -0.011 2.00e-02 2.50e+03
        pdb=" O6    G A 259 "    0.013 2.00e-02 2.50e+03
        pdb=" N1    G A 259 "    0.003 2.00e-02 2.50e+03
        pdb=" C2    G A 259 "   -0.039 2.00e-02 2.50e+03
        pdb=" N2    G A 259 "    0.025 2.00e-02 2.50e+03
        pdb=" N3    G A 259 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    G A 259 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C A 269 "   -0.014 2.00e-02 2.50e+03   1.51e-02 5.13e+00
        pdb=" N1    C A 269 "    0.017 2.00e-02 2.50e+03
        pdb=" C2    C A 269 "    0.033 2.00e-02 2.50e+03
        pdb=" O2    C A 269 "   -0.019 2.00e-02 2.50e+03
        pdb=" N3    C A 269 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    C A 269 "    0.002 2.00e-02 2.50e+03
        pdb=" N4    C A 269 "   -0.006 2.00e-02 2.50e+03
        pdb=" C5    C A 269 "   -0.007 2.00e-02 2.50e+03
        pdb=" C6    C A 269 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C A 239 "   -0.009 2.00e-02 2.50e+03   1.44e-02 4.69e+00
        pdb=" N1    C A 239 "    0.007 2.00e-02 2.50e+03
        pdb=" C2    C A 239 "    0.035 2.00e-02 2.50e+03
        pdb=" O2    C A 239 "   -0.019 2.00e-02 2.50e+03
        pdb=" N3    C A 239 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    C A 239 "    0.007 2.00e-02 2.50e+03
        pdb=" N4    C A 239 "   -0.009 2.00e-02 2.50e+03
        pdb=" C5    C A 239 "   -0.005 2.00e-02 2.50e+03
        pdb=" C6    C A 239 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 2465 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.52: 241
        2.52 -     3.11: 21985
        3.11 -     3.71: 57922
        3.71 -     4.30: 79359
        4.30 -     4.90: 110115
  Nonbonded interactions: 269622
  Sorted by model distance:
  nonbonded pdb=" O2'   A A 126 "
            pdb=" O4'   A A 127 "
     model   vdw
     1.923 3.040
  nonbonded pdb=" OD2 ASP Q  48 "
            pdb=" O2'   U A 534 "
     model   vdw
     1.941 3.040
  nonbonded pdb=" OP2   G A 117 "
            pdb=" O2'   A A 119 "
     model   vdw
     1.983 3.040
  nonbonded pdb=" O2'   A A1383 "
            pdb=" O4'   A A1384 "
     model   vdw
     1.996 3.040
  nonbonded pdb=" O2'   A A 299 "
            pdb=" O4'   A A 300 "
     model   vdw
     2.004 3.040
  ... (remaining 269617 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             1.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.080
  Set scattering table:                    0.050
  Process input model:                     26.920
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7199
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.093  32987  Z= 0.096
  Angle     :  0.375   6.083  49558  Z= 0.199
  Chirality :  0.027   0.179   6408
  Planarity :  0.002   0.021   2468
  Dihedral  : 22.599 179.037  19075
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.28), residues: 1050
  helix:  2.69 (0.27), residues: 369
  sheet:  0.18 (0.43), residues: 155
  loop : -0.16 (0.29), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG Q  27 
 TYR   0.006   0.001   TYR T  84 
 PHE   0.005   0.001   PHE S  75 
 TRP   0.002   0.000   TRP R  92 
 HIS   0.005   0.001   HIS Y  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00170 (32987)
  covalent geometry    : angle       0.37513 (49558)
  hydrogen bonds       : bond        0.09130 ( 1193)
  hydrogen bonds       : angle       4.23535 ( 2359)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   95 LEU cc_start: 0.4567 (pt) cc_final: 0.3917 (tt)
REVERT: T    1 MET cc_start: 0.4070 (pmm) cc_final: 0.3846 (pmm)
REVERT: Y    1 MET cc_start: 0.6249 (tpp) cc_final: 0.5874 (tpp)
REVERT: Z   36 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6380 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.1816
  time to fit residues: 19.6278
Evaluate side-chains
  41 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 194 optimal weight:   10.0000
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:   20.0000
   chunk 124 optimal weight:   30.0000
   chunk 103 optimal weight:   10.0000
   chunk 200 optimal weight:   50.0000
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:   20.0000
   overall best weight:    6.9994

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

Flipped N/Q/H residues before XYZ refinement:
J  47 HIS
Q  71 ASN
R   6 GLN
R  18 GLN
S  61 ASN
Y  41 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.050882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.036966 restraints weight = 289809.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.037378 restraints weight = 129303.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.037787 restraints weight = 88690.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.037945 restraints weight = 74716.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 62)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.038067 restraints weight = 70069.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.073  32987  Z= 0.283
  Angle     :  0.651  10.580  49558  Z= 0.325
  Chirality :  0.034   0.210   6408
  Planarity :  0.005   0.040   2468
  Dihedral  : 23.455 175.869  16959
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  6.25 %
    Favored  : 93.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.18 (0.26), residues: 1050
  helix:  1.31 (0.26), residues: 375
  sheet:  0.10 (0.44), residues: 145
  loop : -0.72 (0.28), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG T   3 
 TYR   0.014   0.002   TYR J  53 
 PHE   0.021   0.002   PHE 2  18 
 TRP   0.006   0.001   TRP J  15 
 HIS   0.009   0.002   HIS Z  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00556 (32987)
  covalent geometry    : angle       0.65051 (49558)
  hydrogen bonds       : bond        0.07673 ( 1193)
  hydrogen bonds       : angle       3.75087 ( 2359)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.540 
Fit side-chains
REVERT: L   95 LEU cc_start: 0.4471 (pt) cc_final: 0.4100 (tt)
REVERT: Z   36 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7002 (mm-30)
  outliers start: 6
  outliers final: 4
  residues processed: 53
  average time/residue: 0.1695
  time to fit residues: 15.3077
Evaluate side-chains
  45 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 41
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   32 LEU
Chi-restraints excluded: chain T residue   93 LEU
Chi-restraints excluded: chain Z residue    4 ILE
Chi-restraints excluded: chain Z residue   34 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 183 optimal weight:   10.0000
   chunk 61 optimal weight:    0.0670
   chunk 161 optimal weight:   10.0000
   chunk 62 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 77 optimal weight:    9.9990
   chunk 132 optimal weight:   10.0000
   chunk 154 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 127 optimal weight:   10.0000
   chunk 135 optimal weight:   10.0000
   overall best weight:    4.7926

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

Flipped N/Q/H residues before XYZ refinement:
T  48 GLN
** T  70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
T  91 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.050891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.037060 restraints weight = 289702.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.037499 restraints weight = 130457.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.037877 restraints weight = 88350.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.038067 restraints weight = 74787.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 61)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.038182 restraints weight = 69853.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.2560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  32987  Z= 0.198
  Angle     :  0.528   9.953  49558  Z= 0.269
  Chirality :  0.031   0.226   6408
  Planarity :  0.004   0.034   2468
  Dihedral  : 23.399 168.112  16959
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  :  8.07 %
    Favored  : 90.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.02 (0.26), residues: 1050
  helix:  1.14 (0.26), residues: 380
  sheet:  0.04 (0.44), residues: 145
  loop : -0.82 (0.27), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Y  52 
 TYR   0.008   0.002   TYR J  53 
 PHE   0.014   0.001   PHE 2  18 
 TRP   0.006   0.001   TRP J  15 
 HIS   0.004   0.001   HIS Y  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (32987)
  covalent geometry    : angle       0.52830 (49558)
  hydrogen bonds       : bond        0.05680 ( 1193)
  hydrogen bonds       : angle       3.54514 ( 2359)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 46
  time to evaluate  : 0.573 
Fit side-chains
REVERT: L   95 LEU cc_start: 0.4487 (pt) cc_final: 0.4046 (tt)
REVERT: S    1 MET cc_start: 0.6638 (ttt) cc_final: 0.5640 (ttp)
  outliers start: 13
  outliers final: 6
  residues processed: 56
  average time/residue: 0.1504
  time to fit residues: 14.7146
Evaluate side-chains
  48 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   32 LEU
Chi-restraints excluded: chain Q residue   82 LEU
Chi-restraints excluded: chain T residue   93 LEU
Chi-restraints excluded: chain Z residue    4 ILE
Chi-restraints excluded: chain Z residue   31 ILE
Chi-restraints excluded: chain Z residue   51 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 142 optimal weight:   40.0000
   chunk 60 optimal weight:    7.9990
   chunk 122 optimal weight:   20.0000
   chunk 27 optimal weight:    4.9990
   chunk 180 optimal weight:   20.0000
   chunk 74 optimal weight:   20.0000
   chunk 106 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9990
   chunk 132 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   overall best weight:    5.7992

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

Flipped N/Q/H residues before XYZ refinement:
** T  70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.050531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.036666 restraints weight = 289338.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.037072 restraints weight = 127281.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.037416 restraints weight = 87630.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.037668 restraints weight = 75472.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.037748 restraints weight = 69649.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.3122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  32987  Z= 0.240
  Angle     :  0.577   9.816  49558  Z= 0.293
  Chirality :  0.032   0.231   6408
  Planarity :  0.004   0.051   2468
  Dihedral  : 23.492 174.210  16959
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 10.23 %
    Favored  : 87.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.17 (0.25), residues: 1050
  helix:  1.01 (0.26), residues: 375
  sheet: -0.06 (0.42), residues: 158
  loop : -0.95 (0.27), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG S 110 
 TYR   0.008   0.002   TYR S  38 
 PHE   0.019   0.002   PHE 2  18 
 TRP   0.004   0.001   TRP J  15 
 HIS   0.005   0.001   HIS Z  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 (32987)
  covalent geometry    : angle       0.57705 (49558)
  hydrogen bonds       : bond        0.06535 ( 1193)
  hydrogen bonds       : angle       3.56912 ( 2359)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 44
  time to evaluate  : 0.553 
Fit side-chains
REVERT: L   95 LEU cc_start: 0.4602 (pt) cc_final: 0.4197 (tt)
REVERT: Z   36 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6996 (mm-30)
  outliers start: 18
  outliers final: 14
  residues processed: 59
  average time/residue: 0.1518
  time to fit residues: 15.9063
Evaluate side-chains
  53 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 39
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   16 HIS
Chi-restraints excluded: chain E residue   31 VAL
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain J residue   32 LEU
Chi-restraints excluded: chain Q residue    3 VAL
Chi-restraints excluded: chain Q residue   82 LEU
Chi-restraints excluded: chain R residue   40 MET
Chi-restraints excluded: chain R residue   75 VAL
Chi-restraints excluded: chain S residue   74 ILE
Chi-restraints excluded: chain T residue   93 LEU
Chi-restraints excluded: chain Z residue    4 ILE
Chi-restraints excluded: chain Z residue   31 ILE
Chi-restraints excluded: chain Z residue   34 THR
Chi-restraints excluded: chain Z residue   51 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 36 optimal weight:    7.9990
   chunk 194 optimal weight:   10.0000
   chunk 8 optimal weight:    0.0980
   chunk 83 optimal weight:   10.0000
   chunk 199 optimal weight:   40.0000
   chunk 85 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 125 optimal weight:   10.0000
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** T  70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.051361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.037634 restraints weight = 289398.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.038133 restraints weight = 129732.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.038572 restraints weight = 87783.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.038791 restraints weight = 73667.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.038871 restraints weight = 68266.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.2958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  32987  Z= 0.102
  Angle     :  0.469   9.274  49558  Z= 0.241
  Chirality :  0.028   0.219   6408
  Planarity :  0.003   0.032   2468
  Dihedral  : 23.330 165.710  16959
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 12.73 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.19 (0.26), residues: 1050
  helix:  1.44 (0.27), residues: 372
  sheet:  0.13 (0.42), residues: 153
  loop : -0.84 (0.27), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG S 110 
 TYR   0.009   0.001   TYR E 101 
 PHE   0.007   0.001   PHE Q  56 
 TRP   0.004   0.000   TRP J  15 
 HIS   0.004   0.001   HIS R  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00188 (32987)
  covalent geometry    : angle       0.46937 (49558)
  hydrogen bonds       : bond        0.05050 ( 1193)
  hydrogen bonds       : angle       3.31645 ( 2359)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.491 
Fit side-chains
REVERT: L   95 LEU cc_start: 0.4159 (pt) cc_final: 0.3751 (tt)
REVERT: S    1 MET cc_start: 0.6506 (ttt) cc_final: 0.6037 (ttp)
  outliers start: 8
  outliers final: 8
  residues processed: 53
  average time/residue: 0.1476
  time to fit residues: 13.8646
Evaluate side-chains
  46 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Q residue    3 VAL
Chi-restraints excluded: chain R residue   40 MET
Chi-restraints excluded: chain R residue   75 VAL
Chi-restraints excluded: chain T residue   93 LEU
Chi-restraints excluded: chain U residue   67 SER
Chi-restraints excluded: chain Z residue   34 THR
Chi-restraints excluded: chain Z residue   53 MET
Chi-restraints excluded: chain Z residue   56 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 110 optimal weight:   10.0000
   chunk 63 optimal weight:    2.9990
   chunk 146 optimal weight:   10.0000
   chunk 82 optimal weight:    6.9990
   chunk 165 optimal weight:   10.0000
   chunk 197 optimal weight:   30.0000
   chunk 139 optimal weight:   40.0000
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 119 optimal weight:   10.0000
   chunk 22 optimal weight:    9.9990
   overall best weight:    4.3386

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

Flipped N/Q/H residues before XYZ refinement:
** T  70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.050742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.036640 restraints weight = 288054.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.037320 restraints weight = 127691.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.037735 restraints weight = 88095.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.037910 restraints weight = 74876.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 63)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.038059 restraints weight = 70157.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.3186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  32987  Z= 0.184
  Angle     :  0.516   9.148  49558  Z= 0.262
  Chirality :  0.030   0.208   6408
  Planarity :  0.004   0.032   2468
  Dihedral  : 23.337 172.844  16959
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 12.95 %
    Favored  : 85.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.01 (0.26), residues: 1050
  helix:  1.18 (0.26), residues: 379
  sheet:  0.08 (0.40), residues: 158
  loop : -0.93 (0.27), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Z  37 
 TYR   0.008   0.001   TYR S  38 
 PHE   0.016   0.001   PHE 2  18 
 TRP   0.003   0.001   TRP J  15 
 HIS   0.003   0.001   HIS E  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (32987)
  covalent geometry    : angle       0.51617 (49558)
  hydrogen bonds       : bond        0.05687 ( 1193)
  hydrogen bonds       : angle       3.36004 ( 2359)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 42
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
REVERT: L   95 LEU cc_start: 0.4263 (pt) cc_final: 0.3901 (tt)
REVERT: S    1 MET cc_start: 0.6441 (ttt) cc_final: 0.6028 (ttp)
  outliers start: 16
  outliers final: 14
  residues processed: 55
  average time/residue: 0.1542
  time to fit residues: 15.3211
Evaluate side-chains
  55 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 41
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   16 HIS
Chi-restraints excluded: chain E residue   31 VAL
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain Q residue    3 VAL
Chi-restraints excluded: chain Q residue   82 LEU
Chi-restraints excluded: chain R residue   75 VAL
Chi-restraints excluded: chain S residue    4 ILE
Chi-restraints excluded: chain S residue   66 ILE
Chi-restraints excluded: chain T residue   93 LEU
Chi-restraints excluded: chain U residue   67 SER
Chi-restraints excluded: chain U residue   71 ILE
Chi-restraints excluded: chain Z residue   50 VAL
Chi-restraints excluded: chain Z residue   53 MET
Chi-restraints excluded: chain Z residue   56 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 176 optimal weight:   20.0000
   chunk 91 optimal weight:    9.9990
   chunk 144 optimal weight:   10.0000
   chunk 117 optimal weight:   40.0000
   chunk 183 optimal weight:   20.0000
   chunk 70 optimal weight:    7.9990
   chunk 68 optimal weight:   10.0000
   chunk 119 optimal weight:   10.0000
   chunk 175 optimal weight:   30.0000
   chunk 64 optimal weight:    5.9990
   chunk 33 optimal weight:    8.9990
   overall best weight:    8.5992

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

Flipped N/Q/H residues before XYZ refinement:
S   7 HIS
T  59 ASN
** T  70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.049905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.035685 restraints weight = 290407.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.036310 restraints weight = 131419.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.036707 restraints weight = 90525.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.036872 restraints weight = 76910.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.037015 restraints weight = 72162.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.4029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057  32987  Z= 0.330
  Angle     :  0.685   9.269  49558  Z= 0.342
  Chirality :  0.036   0.219   6408
  Planarity :  0.005   0.047   2468
  Dihedral  : 23.685 175.947  16959
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.48 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 13.52 %
    Favored  : 83.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.66 (0.24), residues: 1050
  helix:  0.72 (0.26), residues: 380
  sheet: -0.26 (0.39), residues: 156
  loop : -1.40 (0.25), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG T  77 
 TYR   0.012   0.002   TYR Q  44 
 PHE   0.026   0.003   PHE 2  18 
 TRP   0.005   0.001   TRP Q  60 
 HIS   0.006   0.002   HIS E 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00643 (32987)
  covalent geometry    : angle       0.68542 (49558)
  hydrogen bonds       : bond        0.08007 ( 1193)
  hydrogen bonds       : angle       3.77358 ( 2359)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 41
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
REVERT: L   95 LEU cc_start: 0.4290 (pt) cc_final: 0.3801 (tt)
REVERT: S    1 MET cc_start: 0.6999 (ttt) cc_final: 0.6483 (ttp)
  outliers start: 26
  outliers final: 20
  residues processed: 64
  average time/residue: 0.1384
  time to fit residues: 15.9952
Evaluate side-chains
  60 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 40
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   16 HIS
Chi-restraints excluded: chain 2 residue   44 VAL
Chi-restraints excluded: chain E residue   31 VAL
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain J residue  103 ILE
Chi-restraints excluded: chain Q residue    3 VAL
Chi-restraints excluded: chain Q residue   82 LEU
Chi-restraints excluded: chain R residue   40 MET
Chi-restraints excluded: chain R residue   75 VAL
Chi-restraints excluded: chain S residue    4 ILE
Chi-restraints excluded: chain S residue   66 ILE
Chi-restraints excluded: chain S residue   74 ILE
Chi-restraints excluded: chain T residue   93 LEU
Chi-restraints excluded: chain U residue   67 SER
Chi-restraints excluded: chain U residue   71 ILE
Chi-restraints excluded: chain Z residue   31 ILE
Chi-restraints excluded: chain Z residue   50 VAL
Chi-restraints excluded: chain Z residue   51 SER
Chi-restraints excluded: chain Z residue   53 MET
Chi-restraints excluded: chain Z residue   56 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 84 optimal weight:    0.4980
   chunk 153 optimal weight:   10.0000
   chunk 175 optimal weight:   30.0000
   chunk 155 optimal weight:   10.0000
   chunk 203 optimal weight:   40.0000
   chunk 28 optimal weight:    8.9990
   chunk 128 optimal weight:   20.0000
   chunk 35 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   chunk 113 optimal weight:   10.0000
   chunk 150 optimal weight:   10.0000
   overall best weight:    6.0990

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

Flipped N/Q/H residues before XYZ refinement:
J  58 ASN
J 128 ASN
** T  70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.050158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.036382 restraints weight = 291653.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.036836 restraints weight = 129089.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 63)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.037199 restraints weight = 87550.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.037353 restraints weight = 74771.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.037450 restraints weight = 70239.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.4076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  32987  Z= 0.244
  Angle     :  0.585   9.365  49558  Z= 0.298
  Chirality :  0.033   0.266   6408
  Planarity :  0.004   0.034   2468
  Dihedral  : 23.581 173.361  16959
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 14.32 %
    Favored  : 82.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.66 (0.25), residues: 1050
  helix:  0.72 (0.26), residues: 385
  sheet: -0.35 (0.38), residues: 158
  loop : -1.38 (0.25), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG Q  52 
 TYR   0.010   0.002   TYR J  44 
 PHE   0.016   0.002   PHE 2  18 
 TRP   0.003   0.001   TRP J  15 
 HIS   0.005   0.001   HIS E 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00474 (32987)
  covalent geometry    : angle       0.58534 (49558)
  hydrogen bonds       : bond        0.06318 ( 1193)
  hydrogen bonds       : angle       3.57696 ( 2359)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 40
  time to evaluate  : 0.531 
Fit side-chains
   revert: symmetry clash
REVERT: L   95 LEU cc_start: 0.4207 (pt) cc_final: 0.3773 (tt)
REVERT: S    1 MET cc_start: 0.7008 (ttt) cc_final: 0.6577 (ttp)
  outliers start: 24
  outliers final: 20
  residues processed: 60
  average time/residue: 0.1418
  time to fit residues: 15.6253
Evaluate side-chains
  59 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 39
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   16 HIS
Chi-restraints excluded: chain 2 residue   44 VAL
Chi-restraints excluded: chain E residue   31 VAL
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain J residue  103 ILE
Chi-restraints excluded: chain Q residue    3 VAL
Chi-restraints excluded: chain Q residue   82 LEU
Chi-restraints excluded: chain R residue   40 MET
Chi-restraints excluded: chain R residue   75 VAL
Chi-restraints excluded: chain S residue    4 ILE
Chi-restraints excluded: chain S residue   66 ILE
Chi-restraints excluded: chain S residue   74 ILE
Chi-restraints excluded: chain T residue   93 LEU
Chi-restraints excluded: chain U residue   67 SER
Chi-restraints excluded: chain U residue   71 ILE
Chi-restraints excluded: chain Z residue   31 ILE
Chi-restraints excluded: chain Z residue   50 VAL
Chi-restraints excluded: chain Z residue   51 SER
Chi-restraints excluded: chain Z residue   53 MET
Chi-restraints excluded: chain Z residue   56 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 179 optimal weight:   20.0000
   chunk 197 optimal weight:   30.0000
   chunk 20 optimal weight:    0.9990
   chunk 135 optimal weight:   10.0000
   chunk 100 optimal weight:    0.9980
   chunk 11 optimal weight:    6.9990
   chunk 42 optimal weight:    0.1980
   chunk 191 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9990
   chunk 188 optimal weight:   30.0000
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
** T  70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.050889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.037169 restraints weight = 288961.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 68)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.037669 restraints weight = 130160.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 67)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.038100 restraints weight = 88166.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.038274 restraints weight = 74170.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.038404 restraints weight = 69250.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.3867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  32987  Z= 0.119
  Angle     :  0.489   9.472  49558  Z= 0.251
  Chirality :  0.029   0.263   6408
  Planarity :  0.003   0.032   2468
  Dihedral  : 23.396 168.518  16959
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 15.68 %
    Favored  : 82.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.21 (0.25), residues: 1050
  helix:  1.17 (0.27), residues: 376
  sheet: -0.16 (0.39), residues: 153
  loop : -1.11 (0.26), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG S 110 
 TYR   0.009   0.001   TYR E 101 
 PHE   0.009   0.001   PHE 2  18 
 TRP   0.003   0.001   TRP J  15 
 HIS   0.003   0.001   HIS R  12 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (32987)
  covalent geometry    : angle       0.48937 (49558)
  hydrogen bonds       : bond        0.05110 ( 1193)
  hydrogen bonds       : angle       3.30735 ( 2359)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: J   92 MET cc_start: 0.7950 (ttt) cc_final: 0.7451 (tpt)
REVERT: L   95 LEU cc_start: 0.4031 (pt) cc_final: 0.3679 (tt)
REVERT: R   62 GLU cc_start: 0.7746 (tp30) cc_final: 0.7422 (tp30)
REVERT: S    1 MET cc_start: 0.6850 (ttt) cc_final: 0.6433 (ttp)
REVERT: T    1 MET cc_start: 0.3097 (pmm) cc_final: -0.0433 (tmm)
  outliers start: 12
  outliers final: 11
  residues processed: 52
  average time/residue: 0.1341
  time to fit residues: 12.6200
Evaluate side-chains
  51 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 40
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Q residue    3 VAL
Chi-restraints excluded: chain Q residue   82 LEU
Chi-restraints excluded: chain R residue   40 MET
Chi-restraints excluded: chain R residue   75 VAL
Chi-restraints excluded: chain S residue    4 ILE
Chi-restraints excluded: chain S residue   66 ILE
Chi-restraints excluded: chain T residue   93 LEU
Chi-restraints excluded: chain U residue   67 SER
Chi-restraints excluded: chain Z residue   31 ILE
Chi-restraints excluded: chain Z residue   50 VAL
Chi-restraints excluded: chain Z residue   56 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 172 optimal weight:   20.0000
   chunk 7 optimal weight:    0.8980
   chunk 60 optimal weight:   20.0000
   chunk 187 optimal weight:   10.0000
   chunk 19 optimal weight:    7.9990
   chunk 61 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9990
   chunk 100 optimal weight:   20.0000
   chunk 59 optimal weight:    5.9990
   chunk 6 optimal weight:    6.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
** T  70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.050675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.036949 restraints weight = 288863.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.037436 restraints weight = 130065.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.037847 restraints weight = 87773.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.038022 restraints weight = 74445.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.038204 restraints weight = 69419.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.3877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  32987  Z= 0.143
  Angle     :  0.502  10.469  49558  Z= 0.257
  Chirality :  0.029   0.263   6408
  Planarity :  0.003   0.033   2468
  Dihedral  : 23.376 170.535  16959
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 16.14 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.19 (0.25), residues: 1050
  helix:  1.24 (0.27), residues: 372
  sheet: -0.22 (0.39), residues: 159
  loop : -1.12 (0.26), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG Q  63 
 TYR   0.009   0.001   TYR S  38 
 PHE   0.013   0.001   PHE 2  18 
 TRP   0.002   0.001   TRP Q  60 
 HIS   0.004   0.001   HIS S  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (32987)
  covalent geometry    : angle       0.50248 (49558)
  hydrogen bonds       : bond        0.05194 ( 1193)
  hydrogen bonds       : angle       3.28866 ( 2359)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 40
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
REVERT: L   95 LEU cc_start: 0.4068 (pt) cc_final: 0.3715 (tt)
REVERT: S    1 MET cc_start: 0.6891 (ttt) cc_final: 0.6490 (ttp)
REVERT: T    1 MET cc_start: 0.2851 (pmm) cc_final: -0.0510 (tmm)
  outliers start: 11
  outliers final: 11
  residues processed: 51
  average time/residue: 0.1633
  time to fit residues: 15.0350
Evaluate side-chains
  50 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 39
  time to evaluate  : 0.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   31 VAL
Chi-restraints excluded: chain Q residue    3 VAL
Chi-restraints excluded: chain Q residue   82 LEU
Chi-restraints excluded: chain R residue   75 VAL
Chi-restraints excluded: chain S residue    4 ILE
Chi-restraints excluded: chain S residue   66 ILE
Chi-restraints excluded: chain T residue   93 LEU
Chi-restraints excluded: chain U residue   67 SER
Chi-restraints excluded: chain Z residue   31 ILE
Chi-restraints excluded: chain Z residue   50 VAL
Chi-restraints excluded: chain Z residue   56 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 178 optimal weight:   40.0000
   chunk 0 optimal weight:   20.0000
   chunk 92 optimal weight:    9.9990
   chunk 107 optimal weight:   10.0000
   chunk 50 optimal weight:    6.9990
   chunk 159 optimal weight:   10.0000
   chunk 75 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 174 optimal weight:   30.0000
   chunk 200 optimal weight:   50.0000
   overall best weight:    5.5988

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

Flipped N/Q/H residues before XYZ refinement:
** T  70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.050369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.036363 restraints weight = 290225.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.037000 restraints weight = 128913.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.037365 restraints weight = 88508.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.037626 restraints weight = 76429.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.037723 restraints weight = 70097.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.4007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  32987  Z= 0.216
  Angle     :  0.557   9.412  49558  Z= 0.282
  Chirality :  0.031   0.256   6408
  Planarity :  0.004   0.033   2468
  Dihedral  : 23.405 174.077  16959
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 16.14 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.44 (0.25), residues: 1050
  helix:  0.92 (0.26), residues: 384
  sheet: -0.30 (0.38), residues: 158
  loop : -1.24 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Y  52 
 TYR   0.009   0.002   TYR J  44 
 PHE   0.019   0.002   PHE 2  18 
 TRP   0.003   0.001   TRP Q  60 
 HIS   0.009   0.001   HIS Z  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 (32987)
  covalent geometry    : angle       0.55725 (49558)
  hydrogen bonds       : bond        0.06008 ( 1193)
  hydrogen bonds       : angle       3.41924 ( 2359)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4873.70 seconds
wall clock time: 84 minutes 56.77 seconds (5096.77 seconds total)