Starting phenix.real_space_refine
on Tue May 27 18:12:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c98_16505/05_2025/8c98_16505.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c98_16505/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c98_16505/05_2025/8c98_16505.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c98_16505/05_2025/8c98_16505.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c98_16505/05_2025/8c98_16505.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c98_16505/05_2025/8c98_16505.cif"
  }
  resolution = 3.66
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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:plan2': 1, '  G:plan': 1}
          Unresolved non-hydrogen planarities: 14
  Time building chain proxies: 16.77, per 1000 atoms: 0.55
  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: 7.01
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  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: 13.99
  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: 19.78

  Time building geometry restraints manager: 8.39 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:             2.120
  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:             0.020
  Extract box with map and model:          1.160
  Check model and map are aligned:         0.210
  Set scattering table:                    0.290
  Process input model:                     78.260
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.080
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   85.050
-------------------------------------------------------------------------------
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 : 5.79
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.002   0.000   TRP R  92 
 HIS   0.005   0.001   HIS Y  41 
 PHE   0.005   0.001   PHE S  75 
 TYR   0.006   0.001   TYR T  84 
 ARG   0.002   0.000   ARG Q  27 

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

*********************** 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  : 1.575 
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: 0.4434
  time to fit residues: 48.2929
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  : 1.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 172 optimal weight:   20.0000
   chunk 154 optimal weight:   20.0000
   chunk 85 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9990
   chunk 104 optimal weight:   10.0000
   chunk 82 optimal weight:    9.9990
   chunk 159 optimal weight:   10.0000
   chunk 61 optimal weight:    5.9990
   chunk 97 optimal weight:   10.0000
   chunk 119 optimal weight:   10.0000
   chunk 185 optimal weight:   20.0000
   overall best weight:    6.3992

-------------------------------------------------------------------------------
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
S  61 ASN
Y  41 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.051043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.037145 restraints weight = 286669.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.037569 restraints weight = 127509.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 67)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.037977 restraints weight = 86816.027|
|-----------------------------------------------------------------------------|
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.2056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  32987  Z= 0.259
  Angle     :  0.626  10.722  49558  Z= 0.313
  Chirality :  0.033   0.217   6408
  Planarity :  0.004   0.045   2468
  Dihedral  : 23.437 175.147  16959
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  5.57 %
    Favored  : 93.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.26), residues: 1050
  helix:  1.39 (0.26), residues: 375
  sheet:  0.13 (0.44), residues: 145
  loop : -0.69 (0.28), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP Q  60 
 HIS   0.005   0.001   HIS Z  33 
 PHE   0.019   0.002   PHE 2  18 
 TYR   0.014   0.002   TYR J  53 
 ARG   0.008   0.001   ARG T   3 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07354 ( 1193)
  hydrogen bonds       : angle       3.71030 ( 2359)
  covalent geometry    : bond        0.00506 (32987)
  covalent geometry    : angle       0.62629 (49558)

*********************** 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
  54 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 1.555 
Fit side-chains
REVERT: L   95 LEU cc_start: 0.4257 (pt) cc_final: 0.3858 (tt)
REVERT: R   37 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7027 (tp30)
REVERT: R   53 PHE cc_start: 0.7757 (m-10) cc_final: 0.7506 (m-80)
REVERT: S    1 MET cc_start: 0.6558 (ttt) cc_final: 0.6276 (ttt)
  outliers start: 5
  outliers final: 4
  residues processed: 52
  average time/residue: 0.3876
  time to fit residues: 34.7016
Evaluate side-chains
  46 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 1.741 
-------------------------------------------------------------------------------
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 147 optimal weight:   10.0000
   chunk 149 optimal weight:   10.0000
   chunk 131 optimal weight:   10.0000
   chunk 179 optimal weight:   20.0000
   chunk 187 optimal weight:   10.0000
   chunk 117 optimal weight:   40.0000
   chunk 11 optimal weight:    0.9980
   chunk 171 optimal weight:   30.0000
   chunk 176 optimal weight:   20.0000
   chunk 75 optimal weight:    4.9990
   chunk 197 optimal weight:   20.0000
   overall best weight:    7.1994

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

Flipped N/Q/H residues before XYZ refinement:
R  18 GLN
T  48 GLN
** T  70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
T  91 GLN
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.050464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.036914 restraints weight = 292181.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.037689 restraints weight = 139480.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.037536 restraints weight = 92763.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.3136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046  32987  Z= 0.283
  Angle     :  0.627   9.960  49558  Z= 0.316
  Chirality :  0.034   0.241   6408
  Planarity :  0.005   0.035   2468
  Dihedral  : 23.587 171.613  16959
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  :  9.09 %
    Favored  : 89.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.25), residues: 1050
  helix:  0.75 (0.26), residues: 380
  sheet: -0.04 (0.42), residues: 155
  loop : -1.01 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP J  15 
 HIS   0.006   0.002   HIS Z  33 
 PHE   0.022   0.002   PHE 2  18 
 TYR   0.010   0.002   TYR J  44 
 ARG   0.006   0.001   ARG Y  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07135 ( 1193)
  hydrogen bonds       : angle       3.74184 ( 2359)
  covalent geometry    : bond        0.00553 (32987)
  covalent geometry    : angle       0.62694 (49558)

*********************** 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
  62 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 46
  time to evaluate  : 1.561 
Fit side-chains
   revert: symmetry clash
REVERT: L   95 LEU cc_start: 0.4091 (pt) cc_final: 0.3494 (tt)
  outliers start: 16
  outliers final: 10
  residues processed: 60
  average time/residue: 0.3339
  time to fit residues: 36.6415
Evaluate side-chains
  50 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 40
  time to evaluate  : 1.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   64 VAL
Chi-restraints excluded: chain Q residue    3 VAL
Chi-restraints excluded: chain Q residue   82 LEU
Chi-restraints excluded: chain R residue   32 THR
Chi-restraints excluded: chain R residue   54 VAL
Chi-restraints excluded: chain T residue   91 GLN
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 153 optimal weight:   10.0000
   chunk 60 optimal weight:    9.9990
   chunk 142 optimal weight:   40.0000
   chunk 29 optimal weight:    9.9990
   chunk 191 optimal weight:   10.0000
   chunk 167 optimal weight:   10.0000
   chunk 66 optimal weight:    6.9990
   chunk 68 optimal weight:    3.9990
   chunk 170 optimal weight:   10.0000
   chunk 70 optimal weight:    7.9990
   chunk 124 optimal weight:   30.0000
   overall best weight:    7.7990

-------------------------------------------------------------------------------
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 = 0.3635 r_free = 0.3635 target = 0.050132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.036250 restraints weight = 291670.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.036651 restraints weight = 130952.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 75)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.037024 restraints weight = 88876.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.3777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  32987  Z= 0.305
  Angle     :  0.654  10.349  49558  Z= 0.331
  Chirality :  0.036   0.261   6408
  Planarity :  0.005   0.037   2468
  Dihedral  : 23.706 176.269  16959
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.19 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 11.14 %
    Favored  : 86.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.25), residues: 1050
  helix:  0.60 (0.26), residues: 378
  sheet: -0.12 (0.41), residues: 150
  loop : -1.25 (0.25), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP Q  60 
 HIS   0.006   0.002   HIS E 165 
 PHE   0.023   0.002   PHE 2  18 
 TYR   0.011   0.002   TYR J  44 
 ARG   0.006   0.001   ARG Q  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07475 ( 1193)
  hydrogen bonds       : angle       3.75597 ( 2359)
  covalent geometry    : bond        0.00595 (32987)
  covalent geometry    : angle       0.65364 (49558)

*********************** 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
  67 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 44
  time to evaluate  : 1.518 
Fit side-chains
REVERT: L   95 LEU cc_start: 0.4388 (pt) cc_final: 0.3910 (tt)
REVERT: R   31 GLU cc_start: 0.8688 (pt0) cc_final: 0.7520 (pm20)
REVERT: R   34 GLU cc_start: 0.8161 (mp0) cc_final: 0.7738 (mp0)
REVERT: Z   36 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6819 (mm-30)
  outliers start: 23
  outliers final: 18
  residues processed: 64
  average time/residue: 0.3378
  time to fit residues: 38.9526
Evaluate side-chains
  58 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 40
  time to evaluate  : 1.523 
-------------------------------------------------------------------------------
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   64 VAL
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   54 VAL
Chi-restraints excluded: chain R residue   75 VAL
Chi-restraints excluded: chain R residue   98 ILE
Chi-restraints excluded: chain S residue    4 ILE
Chi-restraints excluded: chain S residue   74 ILE
Chi-restraints excluded: chain T residue   93 LEU
Chi-restraints excluded: chain U residue   71 ILE
Chi-restraints excluded: chain Z residue    4 ILE
Chi-restraints excluded: chain Z residue   34 THR
Chi-restraints excluded: chain Z residue   51 SER
Chi-restraints excluded: chain Z residue   56 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 22 optimal weight:    6.9990
   chunk 99 optimal weight:    9.9990
   chunk 3 optimal weight:    0.0170
   chunk 110 optimal weight:   10.0000
   chunk 89 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 116 optimal weight:   20.0000
   chunk 161 optimal weight:   10.0000
   chunk 101 optimal weight:    4.9990
   chunk 93 optimal weight:    9.9990
   chunk 185 optimal weight:   20.0000
   overall best weight:    3.2026

-------------------------------------------------------------------------------
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**
** T  91 GLN ** 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 = 0.3655 r_free = 0.3655 target = 0.050519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.036893 restraints weight = 290750.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.037299 restraints weight = 129439.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.037667 restraints weight = 88075.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.3617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  32987  Z= 0.150
  Angle     :  0.517   9.953  49558  Z= 0.266
  Chirality :  0.030   0.253   6408
  Planarity :  0.004   0.032   2468
  Dihedral  : 23.516 169.709  16959
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 12.27 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.25), residues: 1050
  helix:  1.01 (0.26), residues: 373
  sheet: -0.26 (0.40), residues: 158
  loop : -1.06 (0.27), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP J  15 
 HIS   0.004   0.001   HIS E  29 
 PHE   0.009   0.001   PHE 2  18 
 TYR   0.007   0.001   TYR S  38 
 ARG   0.003   0.000   ARG S 110 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05431 ( 1193)
  hydrogen bonds       : angle       3.50075 ( 2359)
  covalent geometry    : bond        0.00289 (32987)
  covalent geometry    : angle       0.51744 (49558)

*********************** 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
  65 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 46
  time to evaluate  : 1.777 
Fit side-chains
REVERT: L   95 LEU cc_start: 0.4176 (pt) cc_final: 0.3689 (tt)
  outliers start: 19
  outliers final: 12
  residues processed: 62
  average time/residue: 0.3668
  time to fit residues: 40.0311
Evaluate side-chains
  53 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 41
  time to evaluate  : 1.598 
-------------------------------------------------------------------------------
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   82 LEU
Chi-restraints excluded: chain R residue   54 VAL
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   31 ILE
Chi-restraints excluded: chain Z residue   34 THR
Chi-restraints excluded: chain Z residue   51 SER
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 121 optimal weight:   30.0000
   chunk 46 optimal weight:    0.9980
   chunk 122 optimal weight:   10.0000
   chunk 158 optimal weight:   10.0000
   chunk 188 optimal weight:   30.0000
   chunk 85 optimal weight:    2.9990
   chunk 177 optimal weight:   40.0000
   chunk 20 optimal weight:    5.9990
   chunk 14 optimal weight:    7.9990
   chunk 31 optimal weight:   10.0000
   chunk 38 optimal weight:    9.9990
   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 = 0.3645 r_free = 0.3645 target = 0.050268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.036552 restraints weight = 291104.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.036949 restraints weight = 129193.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.037318 restraints weight = 88427.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.3726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  32987  Z= 0.227
  Angle     :  0.564   9.362  49558  Z= 0.287
  Chirality :  0.032   0.270   6408
  Planarity :  0.004   0.031   2468
  Dihedral  : 23.505 172.653  16959
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 13.52 %
    Favored  : 84.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.25), residues: 1050
  helix:  0.82 (0.26), residues: 385
  sheet: -0.27 (0.39), residues: 158
  loop : -1.20 (0.26), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP Q  60 
 HIS   0.005   0.001   HIS Y  41 
 PHE   0.017   0.002   PHE R  53 
 TYR   0.008   0.002   TYR J  74 
 ARG   0.004   0.000   ARG Q  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06123 ( 1193)
  hydrogen bonds       : angle       3.51957 ( 2359)
  covalent geometry    : bond        0.00441 (32987)
  covalent geometry    : angle       0.56397 (49558)

*********************** 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
  65 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 44
  time to evaluate  : 1.581 
Fit side-chains
   revert: symmetry clash
REVERT: L   95 LEU cc_start: 0.4110 (pt) cc_final: 0.3605 (tt)
REVERT: R    1 MET cc_start: 0.7590 (tpt) cc_final: 0.7247 (tpp)
REVERT: R   37 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7525 (mm-30)
REVERT: S    1 MET cc_start: 0.6891 (ttt) cc_final: 0.6456 (ttp)
  outliers start: 21
  outliers final: 18
  residues processed: 63
  average time/residue: 0.3382
  time to fit residues: 38.5768
Evaluate side-chains
  61 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 43
  time to evaluate  : 1.510 
-------------------------------------------------------------------------------
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 Q residue    3 VAL
Chi-restraints excluded: chain Q residue   82 LEU
Chi-restraints excluded: chain R residue   51 VAL
Chi-restraints excluded: chain R residue   54 VAL
Chi-restraints excluded: chain R residue   75 VAL
Chi-restraints excluded: chain S residue    4 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 Z residue   31 ILE
Chi-restraints excluded: chain Z residue   34 THR
Chi-restraints excluded: chain Z residue   50 VAL
Chi-restraints excluded: chain Z residue   51 SER
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 154 optimal weight:   10.0000
   chunk 94 optimal weight:    3.9990
   chunk 194 optimal weight:   10.0000
   chunk 105 optimal weight:   10.0000
   chunk 90 optimal weight:    6.9990
   chunk 109 optimal weight:   10.0000
   chunk 73 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 85 optimal weight:    6.9990
   chunk 122 optimal weight:   20.0000
   chunk 151 optimal weight:   10.0000
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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 = 0.3650 r_free = 0.3650 target = 0.050392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.036668 restraints weight = 290547.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.037087 restraints weight = 129485.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.037472 restraints weight = 88303.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.3844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  32987  Z= 0.187
  Angle     :  0.536   9.243  49558  Z= 0.274
  Chirality :  0.031   0.267   6408
  Planarity :  0.004   0.032   2468
  Dihedral  : 23.489 173.288  16959
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 15.00 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.25), residues: 1050
  helix:  0.97 (0.26), residues: 378
  sheet: -0.28 (0.39), residues: 158
  loop : -1.18 (0.26), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP Q  60 
 HIS   0.003   0.001   HIS Y  41 
 PHE   0.012   0.001   PHE 2  18 
 TYR   0.008   0.001   TYR S  38 
 ARG   0.004   0.000   ARG Q  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05749 ( 1193)
  hydrogen bonds       : angle       3.49784 ( 2359)
  covalent geometry    : bond        0.00362 (32987)
  covalent geometry    : angle       0.53567 (49558)

*********************** 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: 22
    poor density    : 45
  time to evaluate  : 1.552 
Fit side-chains
REVERT: L   95 LEU cc_start: 0.4209 (pt) cc_final: 0.3810 (tt)
REVERT: R   37 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7470 (mm-30)
REVERT: R   53 PHE cc_start: 0.7695 (m-80) cc_final: 0.7385 (m-80)
REVERT: S    1 MET cc_start: 0.6808 (ttt) cc_final: 0.6405 (ttp)
REVERT: Z   36 GLU cc_start: 0.6781 (mm-30) cc_final: 0.6575 (mm-30)
  outliers start: 22
  outliers final: 17
  residues processed: 66
  average time/residue: 0.3591
  time to fit residues: 41.5588
Evaluate side-chains
  57 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 40
  time to evaluate  : 1.526 
-------------------------------------------------------------------------------
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   75 VAL
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   34 THR
Chi-restraints excluded: chain Z residue   50 VAL
Chi-restraints excluded: chain Z residue   51 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 62 optimal weight:    6.9990
   chunk 106 optimal weight:   10.0000
   chunk 132 optimal weight:   10.0000
   chunk 60 optimal weight:    5.9990
   chunk 56 optimal weight:    0.9990
   chunk 78 optimal weight:    9.9990
   chunk 114 optimal weight:   10.0000
   chunk 180 optimal weight:   20.0000
   chunk 4 optimal weight:    4.9990
   chunk 108 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   overall best weight:    5.7990

-------------------------------------------------------------------------------
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 = 0.3643 r_free = 0.3643 target = 0.050235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.036494 restraints weight = 291334.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.036920 restraints weight = 131545.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.037300 restraints weight = 88492.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.3909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  32987  Z= 0.234
  Angle     :  0.568   9.005  49558  Z= 0.288
  Chirality :  0.032   0.266   6408
  Planarity :  0.004   0.033   2468
  Dihedral  : 23.479 173.510  16959
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 15.23 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.25), residues: 1050
  helix:  0.95 (0.26), residues: 378
  sheet: -0.28 (0.39), residues: 158
  loop : -1.25 (0.26), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP Q  60 
 HIS   0.005   0.001   HIS Y  41 
 PHE   0.016   0.002   PHE 2  18 
 TYR   0.008   0.002   TYR J  44 
 ARG   0.011   0.001   ARG J  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06131 ( 1193)
  hydrogen bonds       : angle       3.52319 ( 2359)
  covalent geometry    : bond        0.00456 (32987)
  covalent geometry    : angle       0.56811 (49558)

*********************** 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
  70 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 42
  time to evaluate  : 1.572 
Fit side-chains
REVERT: J   92 MET cc_start: 0.7124 (ttp) cc_final: 0.6532 (tpt)
REVERT: L   95 LEU cc_start: 0.4299 (pt) cc_final: 0.3831 (tt)
REVERT: R   37 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7479 (mm-30)
REVERT: R   53 PHE cc_start: 0.7705 (m-80) cc_final: 0.7385 (m-80)
REVERT: S    1 MET cc_start: 0.6847 (ttt) cc_final: 0.6443 (ttp)
  outliers start: 28
  outliers final: 22
  residues processed: 68
  average time/residue: 0.3341
  time to fit residues: 41.0000
Evaluate side-chains
  63 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 41
  time to evaluate  : 1.516 
-------------------------------------------------------------------------------
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   32 THR
Chi-restraints excluded: chain R residue   51 VAL
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   34 THR
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 76 optimal weight:   20.0000
   chunk 82 optimal weight:    0.9990
   chunk 157 optimal weight:   10.0000
   chunk 79 optimal weight:   40.0000
   chunk 10 optimal weight:    0.6980
   chunk 169 optimal weight:   10.0000
   chunk 203 optimal weight:   40.0000
   chunk 71 optimal weight:    6.9990
   chunk 191 optimal weight:   10.0000
   chunk 196 optimal weight:   10.0000
   chunk 156 optimal weight:   10.0000
   overall best weight:    5.7392

-------------------------------------------------------------------------------
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 = 0.3642 r_free = 0.3642 target = 0.050229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.036515 restraints weight = 289877.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.036907 restraints weight = 130021.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.037302 restraints weight = 88665.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.3973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  32987  Z= 0.229
  Angle     :  0.568   9.331  49558  Z= 0.288
  Chirality :  0.032   0.268   6408
  Planarity :  0.004   0.033   2468
  Dihedral  : 23.504 173.962  16959
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.71 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 16.48 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.51 (0.25), residues: 1050
  helix:  0.86 (0.26), residues: 384
  sheet: -0.29 (0.39), residues: 158
  loop : -1.29 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP Q  60 
 HIS   0.004   0.001   HIS Z  33 
 PHE   0.016   0.002   PHE 2  18 
 TYR   0.007   0.002   TYR S  38 
 ARG   0.003   0.000   ARG Q  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06211 ( 1193)
  hydrogen bonds       : angle       3.55070 ( 2359)
  covalent geometry    : bond        0.00445 (32987)
  covalent geometry    : angle       0.56786 (49558)

*********************** 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
  63 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 43
  time to evaluate  : 1.865 
Fit side-chains
   revert: symmetry clash
REVERT: J   92 MET cc_start: 0.7017 (ttp) cc_final: 0.6603 (tpt)
REVERT: L   95 LEU cc_start: 0.4171 (pt) cc_final: 0.3718 (tt)
REVERT: R   37 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7493 (mm-30)
REVERT: R   53 PHE cc_start: 0.7696 (m-80) cc_final: 0.7379 (m-80)
REVERT: S    1 MET cc_start: 0.6897 (ttt) cc_final: 0.6518 (ttp)
  outliers start: 20
  outliers final: 19
  residues processed: 62
  average time/residue: 0.3499
  time to fit residues: 39.1606
Evaluate side-chains
  59 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 40
  time to evaluate  : 1.541 
-------------------------------------------------------------------------------
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   51 VAL
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   56 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 33 optimal weight:    0.0870
   chunk 122 optimal weight:   20.0000
   chunk 70 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 75 optimal weight:    5.9990
   chunk 135 optimal weight:   10.0000
   chunk 47 optimal weight:    3.9990
   chunk 153 optimal weight:   10.0000
   chunk 121 optimal weight:   30.0000
   overall best weight:    3.2166

-------------------------------------------------------------------------------
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 = 0.3658 r_free = 0.3658 target = 0.050546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.036822 restraints weight = 290784.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.037264 restraints weight = 132563.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.037669 restraints weight = 89329.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.3940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  32987  Z= 0.153
  Angle     :  0.510  13.307  49558  Z= 0.261
  Chirality :  0.030   0.263   6408
  Planarity :  0.003   0.033   2468
  Dihedral  : 23.431 170.328  16959
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 17.39 %
    Favored  : 80.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.25), residues: 1050
  helix:  1.05 (0.27), residues: 381
  sheet: -0.22 (0.39), residues: 158
  loop : -1.17 (0.26), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP Q  60 
 HIS   0.004   0.001   HIS R  12 
 PHE   0.011   0.001   PHE 2  18 
 TYR   0.007   0.001   TYR J  74 
 ARG   0.003   0.000   ARG R  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05291 ( 1193)
  hydrogen bonds       : angle       3.40805 ( 2359)
  covalent geometry    : bond        0.00295 (32987)
  covalent geometry    : angle       0.50974 (49558)

********************** 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
  58 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 43
  time to evaluate  : 1.633 
Fit side-chains
   revert: symmetry clash
REVERT: J   92 MET cc_start: 0.7225 (ttp) cc_final: 0.6733 (tpt)
REVERT: L   95 LEU cc_start: 0.4034 (pt) cc_final: 0.3695 (tt)
REVERT: S    1 MET cc_start: 0.6840 (ttt) cc_final: 0.6442 (ttp)
  outliers start: 15
  outliers final: 15
  residues processed: 57
  average time/residue: 0.3613
  time to fit residues: 37.2772
Evaluate side-chains
  56 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 41
  time to evaluate  : 1.804 
-------------------------------------------------------------------------------
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 Q residue    3 VAL
Chi-restraints excluded: chain Q residue   82 LEU
Chi-restraints excluded: chain R residue   51 VAL
Chi-restraints excluded: chain R residue   75 VAL
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   51 SER
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 18 optimal weight:    0.5980
   chunk 180 optimal weight:   20.0000
   chunk 4 optimal weight:    1.9990
   chunk 185 optimal weight:   30.0000
   chunk 142 optimal weight:   40.0000
   chunk 129 optimal weight:   40.0000
   chunk 96 optimal weight:   10.0000
   chunk 203 optimal weight:   40.0000
   chunk 200 optimal weight:   50.0000
   chunk 186 optimal weight:   10.0000
   chunk 151 optimal weight:   10.0000
   overall best weight:    6.5194

-------------------------------------------------------------------------------
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 = 0.3639 r_free = 0.3639 target = 0.050148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.036379 restraints weight = 290490.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.036791 restraints weight = 133185.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.037148 restraints weight = 89534.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.4143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  32987  Z= 0.254
  Angle     :  0.588  12.753  49558  Z= 0.297
  Chirality :  0.033   0.266   6408
  Planarity :  0.004   0.034   2468
  Dihedral  : 23.488 174.796  16959
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 17.27 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.25), residues: 1050
  helix:  0.83 (0.26), residues: 385
  sheet: -0.34 (0.39), residues: 157
  loop : -1.36 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP J  15 
 HIS   0.004   0.001   HIS E 165 
 PHE   0.019   0.002   PHE 2  18 
 TYR   0.008   0.002   TYR J  44 
 ARG   0.004   0.001   ARG J  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06581 ( 1193)
  hydrogen bonds       : angle       3.56530 ( 2359)
  covalent geometry    : bond        0.00494 (32987)
  covalent geometry    : angle       0.58791 (49558)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8428.20 seconds
wall clock time: 149 minutes 21.51 seconds (8961.51 seconds total)