Starting phenix.real_space_refine
on Mon Sep 14 05:13:00 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7oi0_12916/09_2026/7oi0_12916.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7oi0_12916/09_2026/7oi0_12916.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7oi0_12916/09_2026/7oi0_12916.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7oi0_12916/09_2026/7oi0_12916.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7oi0_12916/09_2026/7oi0_12916.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7oi0_12916/09_2026/7oi0_12916.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7oi0_12916/09_2026/7oi0_12916.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7oi0_12916/09_2026/7oi0_12916.cif"
  }
  resolution = 2.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.007 sd=   0.083
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     963      5.49       5
     S      30      5.16       5
     C   14335      2.51       5
     N    5400      2.21       5
     O    8527      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 29255
  Number of models: 1
  Model: ""
    Number of chains: 17
    Chain: "D"
      Number of atoms: 1643
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 205, 1643
          Classifications: {'peptide': 205}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 198}
    Chain: "F"
      Number of atoms: 817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 817
          Classifications: {'peptide': 100}
          Link IDs: {'PTRANS': 4, 'TRANS': 95}
    Chain: "H"
      Number of atoms: 979
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 979
          Classifications: {'peptide': 129}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 123}
    Chain: "K"
      Number of atoms: 702
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 702
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
    Chain: "L"
      Number of atoms: 955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 955
          Classifications: {'peptide': 123}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 115}
    Chain: "O"
      Number of atoms: 716
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 716
          Classifications: {'peptide': 88}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 87}
    Chain: "P"
      Number of atoms: 649
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 649
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 79}
    Chain: "Q"
      Number of atoms: 648
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 648
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 2, 'TRANS': 77}
    Chain: "R"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 407
          Classifications: {'peptide': 50}
          Link IDs: {'PTRANS': 2, 'TRANS': 47}
    Chain: "T"
      Number of atoms: 665
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 665
          Classifications: {'peptide': 85}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 83}
    Chain: "A"
      Number of atoms: 20700
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 963, 20700
          Classifications: {'RNAv2': 963}
          Modifications used: {'rna2p_pur': 74, 'rna2p_pyr': 44, 'rna3p_pur': 487, 'rna3p_pyr': 358}
          Link IDs: {'rna2p': 118, 'rna3p': 844}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Classifications: {'water': 6}
          Link IDs: {None: 5}
    Chain: "L"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
    Chain: "P"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 18
          Classifications: {'water': 18}
          Link IDs: {None: 17}
    Chain: "Q"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "T"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Classifications: {'water': 6}
          Link IDs: {None: 5}
    Chain: "A"
      Number of atoms: 337
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 337
          Classifications: {'water': 337}
          Link IDs: {None: 336}
  Time building chain proxies: 5.81, per 1000 atoms: 0.20
  Number of scatterers: 29255
  At special positions: 0
  Unit cell: (111.8, 155.66, 212.42, 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      30     16.00
     P     963     15.00
     O    8527      8.00
     N    5400      7.00
     C   14335      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.47
  Conformation dependent library (CDL) restraints added in 652.1 milliseconds
  

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1930

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 11 sheets defined
      39.9% alpha, 15.9% beta
      338 base pairs and 532 stacking pairs defined.
    Time for finding SS restraints: 4.84
  Creating SS restraints...
    Processing helix  chain 'D' and resid 6 through 14
      removed outlier: 3.928A  pdb=" N   LEU D  10 " --> pdb=" O   PRO D   6 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   SER D  11 " --> pdb=" O   LYS D   7 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   GLU D  14 " --> pdb=" O   LEU D  10 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 48 through 65
    Processing helix  chain 'D' and resid 67 through 81
    Processing helix  chain 'D' and resid 84 through 95
    Processing helix  chain 'D' and resid 96 through 104
    Processing helix  chain 'D' and resid 109 through 119
    Processing helix  chain 'D' and resid 146 through 149
    Processing helix  chain 'D' and resid 151 through 160
      removed outlier: 3.603A  pdb=" N   GLU D 159 " --> pdb=" O   LYS D 155 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU D 160 " --> pdb=" O   ALA D 156 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 195 through 203
      removed outlier: 4.030A  pdb=" N   ILE D 199 " --> pdb=" O   ASN D 195 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 14 through 16
      No H-bonds generated for 'chain 'F' and resid 14 through 16'
    Processing helix  chain 'F' and resid 17 through 32
    Processing helix  chain 'F' and resid 50 through 54
      removed outlier: 3.640A  pdb=" N   LYS F  53 " --> pdb=" O   PRO F  50 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LEU F  54 " --> pdb=" O   ILE F  51 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 50 through 54'
    Processing helix  chain 'F' and resid 69 through 81
      removed outlier: 4.153A  pdb=" N   GLU F  73 " --> pdb=" O   GLU F  69 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   LEU F  74 " --> pdb=" O   VAL F  70 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 4 through 19
      removed outlier: 3.694A  pdb=" N   MET H   9 " --> pdb=" O   PRO H   5 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 29 through 42
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'H' and resid 111 through 119
    Processing helix  chain 'K' and resid 58 through 72
    Processing helix  chain 'K' and resid 91 through 101
    Processing helix  chain 'L' and resid 2 through 9
    Processing helix  chain 'O' and resid 3 through 14
    Processing helix  chain 'O' and resid 23 through 46
      removed outlier: 4.111A  pdb=" N   ALA O  43 " --> pdb=" O   GLN O  39 " (cutoff:3.500A)
      removed outlier: 5.275A  pdb=" N   GLU O  44 " --> pdb=" O   GLY O  40 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   HIS O  45 " --> pdb=" O   HIS O  41 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 49 through 73
      removed outlier: 3.678A  pdb=" N   ARG O  53 " --> pdb=" O   HIS O  49 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   GLY O  54 " --> pdb=" O   HIS O  50 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU O  55 " --> pdb=" O   SER O  51 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 73 through 84
      removed outlier: 5.012A  pdb=" N   GLU O  82 " --> pdb=" O   THR O  78 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 53 through 63
      removed outlier: 3.845A  pdb=" N   ILE P  57 " --> pdb=" O   ASP P  53 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 68 through 82
    Processing helix  chain 'R' and resid 25 through 32
      removed outlier: 3.662A  pdb=" N   LYS R  29 " --> pdb=" O   ALA R  26 " (cutoff:3.500A)
      removed outlier: 5.355A  pdb=" N   ASN R  30 " --> pdb=" O   THR R  27 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 49 through 64
    Processing helix  chain 'T' and resid 3 through 39
    Processing helix  chain 'T' and resid 42 through 63
      Proline residue:  T  55  - end of helix
    Processing helix  chain 'T' and resid 67 through 86
    Processing sheet with id=AA1, first strand: chain 'D' and resid 127 through 128
    Processing sheet with id=AA2, first strand: chain 'F' and resid 2 through 3
    Processing sheet with id=AA3, first strand: chain 'F' and resid 40 through 46
      removed outlier: 3.736A  pdb=" N   GLU F  40 " --> pdb=" O   LEU F  61 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU F  61 " --> pdb=" O   GLU F  40 " (cutoff:3.500A)
      removed outlier: 5.233A  pdb=" N   TYR F  59 " --> pdb=" O   TRP F  42 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   ARG F  44 " --> pdb=" O   ALA F  57 " (cutoff:3.500A)
      removed outlier: 4.987A  pdb=" N   ALA F  57 " --> pdb=" O   ARG F  44 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 23 through 24
    Processing sheet with id=AA5, first strand: chain 'H' and resid 50 through 51
    Processing sheet with id=AA6, first strand: chain 'H' and resid 75 through 76
    Processing sheet with id=AA7, first strand: chain 'H' and resid 75 through 76
      removed outlier: 6.900A  pdb=" N   VAL H 102 " --> pdb=" O   ILE H 125 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'K' and resid 40 through 45
      removed outlier: 6.645A  pdb=" N   ILE K  33 " --> pdb=" O   LEU K  41 " (cutoff:3.500A)
      removed outlier: 5.036A  pdb=" N   TRP K  43 " --> pdb=" O   VAL K  31 " (cutoff:3.500A)
      removed outlier: 7.321A  pdb=" N   VAL K  31 " --> pdb=" O   TRP K  43 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 28 through 31
      removed outlier: 10.174A  pdb=" N   VAL L  92 " --> pdb=" O   GLU L  61 " (cutoff:3.500A)
      removed outlier: 8.037A  pdb=" N   THR L  63 " --> pdb=" O   VAL L  92 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   TYR L  94 " --> pdb=" O   THR L  63 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'P' and resid 50 through 51
      removed outlier: 4.865A  pdb=" N   VAL P  19 " --> pdb=" O   VAL P  36 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   PHE P  38 " --> pdb=" O   TYR P  17 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   TYR P  17 " --> pdb=" O   PHE P  38 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'Q' and resid 7 through 16
      removed outlier: 7.901A  pdb=" N   GLN Q   8 " --> pdb=" O   GLU Q  25 " (cutoff:3.500A)
      removed outlier: 5.223A  pdb=" N   GLU Q  25 " --> pdb=" O   GLN Q   8 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   VAL Q  21 " --> pdb=" O   VAL Q  12 " (cutoff:3.500A)
      removed outlier: 4.965A  pdb=" N   ASP Q  14 " --> pdb=" O   SER Q  19 " (cutoff:3.500A)
      removed outlier: 7.447A  pdb=" N   SER Q  19 " --> pdb=" O   ASP Q  14 " (cutoff:3.500A)
      removed outlier: 15.667A  pdb=" N   LYS Q  70 " --> pdb=" O   THR Q  40 " (cutoff:3.500A)
      removed outlier: 14.072A  pdb=" N   LYS Q  42 " --> pdb=" O   LYS Q  70 " (cutoff:3.500A)
      removed outlier: 9.785A  pdb=" N   TRP Q  72 " --> pdb=" O   LYS Q  42 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   HIS Q  44 " --> pdb=" O   TRP Q  72 " (cutoff:3.500A)
      removed outlier: 7.683A  pdb=" N   LEU Q  74 " --> pdb=" O   HIS Q  44 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   HIS Q  46 " --> pdb=" O   LEU Q  74 " (cutoff:3.500A)
      removed outlier: 8.720A  pdb=" N   ARG Q  76 " --> pdb=" O   HIS Q  46 " (cutoff:3.500A)
      removed outlier: 5.922A  pdb=" N   SER Q  71 " --> pdb=" O   CYS Q  63 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   GLU Q  59 " --> pdb=" O   VAL Q  75 " (cutoff:3.500A)
      removed outlier: 4.801A  pdb=" N   VAL Q  77 " --> pdb=" O   VAL Q  57 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   VAL Q  57 " --> pdb=" O   VAL Q  77 " (cutoff:3.500A)

    363 hydrogen bonds defined for protein.
    1023 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      840 hydrogen bonds
      1286 hydrogen bond angles
      0 basepair planarities
      338 basepair parallelities
      532 stacking parallelities
  Total time for adding SS restraints: 12.19

  Time building geometry restraints manager: 3.44 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 2788
        1.30 -     1.43: 14063
        1.43 -     1.56: 12652
        1.56 -     1.68: 1924
        1.68 -     1.81: 51
  Bond restraints: 31478
  Sorted by residual:
  bond pdb=" CB  VAL P  20 "
       pdb=" CG2 VAL P  20 "
    ideal  model  delta    sigma   weight residual
    1.521  1.404  0.117 3.30e-02 9.18e+02 1.25e+01
  bond pdb=" C5    G A 108 "
       pdb=" C6    G A 108 "
    ideal  model  delta    sigma   weight residual
    1.419  1.350  0.069 2.00e-02 2.50e+03 1.20e+01
  bond pdb=" N   ILE T  66 "
       pdb=" CA  ILE T  66 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.036 1.11e-02 8.12e+03 1.03e+01
  bond pdb=" N9    A A 452 "
       pdb=" C4    A A 452 "
    ideal  model  delta    sigma   weight residual
    1.374  1.310  0.064 2.00e-02 2.50e+03 1.02e+01
  bond pdb=" CD2 HIS P   9 "
       pdb=" NE2 HIS P   9 "
    ideal  model  delta    sigma   weight residual
    1.374  1.339  0.035 1.10e-02 8.26e+03 9.97e+00
  ... (remaining 31473 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.62: 44229
        2.62 -     5.24: 2757
        5.24 -     7.87: 283
        7.87 -    10.49: 23
       10.49 -    13.11: 4
  Bond angle restraints: 47296
  Sorted by residual:
  angle pdb=" C4'   G A 416 "
        pdb=" C3'   G A 416 "
        pdb=" O3'   G A 416 "
      ideal   model   delta    sigma   weight residual
     112.50  125.61  -13.11 2.00e+00 2.50e-01 4.30e+01
  angle pdb=" C3'   C A 328 "
        pdb=" O3'   C A 328 "
        pdb=" P     A A 329 "
      ideal   model   delta    sigma   weight residual
     119.70  127.55   -7.85 1.20e+00 6.94e-01 4.28e+01
  angle pdb=" C4'   A A 465 "
        pdb=" C3'   A A 465 "
        pdb=" O3'   A A 465 "
      ideal   model   delta    sigma   weight residual
     112.50  123.41  -10.91 2.00e+00 2.50e-01 2.98e+01
  angle pdb=" O2'   G A 416 "
        pdb=" C2'   G A 416 "
        pdb=" C1'   G A 416 "
      ideal   model   delta    sigma   weight residual
     108.20   97.74   10.46 2.00e+00 2.50e-01 2.74e+01
  angle pdb=" C3'   C A 183 "
        pdb=" O3'   C A 183 "
        pdb=" P     G A 184 "
      ideal   model   delta    sigma   weight residual
     119.70  125.82   -6.12 1.20e+00 6.94e-01 2.60e+01
  ... (remaining 47291 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.35: 14727
       35.35 -    70.70: 1862
       70.70 -   106.05: 112
      106.05 -   141.39: 2
      141.39 -   176.74: 6
  Dihedral angle restraints: 16709
    sinusoidal: 13723
      harmonic: 2986
  Sorted by residual:
  dihedral pdb=" C4'   A A1519 "
           pdb=" C3'   A A1519 "
           pdb=" C2'   A A1519 "
           pdb=" C1'   A A1519 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.35  -41.85   78.19     1      3.10e+00 1.04e-01 7.95e+02
  dihedral pdb=" C4'   U A 121 "
           pdb=" C3'   U A 121 "
           pdb=" C2'   U A 121 "
           pdb=" C1'   U A 121 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -41.55   77.90     1      3.10e+00 1.04e-01 7.90e+02
  dihedral pdb=" C4'   U A 244 "
           pdb=" C3'   U A 244 "
           pdb=" C2'   U A 244 "
           pdb=" C1'   U A 244 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.35  -40.78   77.12     1      3.10e+00 1.04e-01 7.76e+02
  ... (remaining 16706 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.142: 4819
       0.142 -    0.284: 1140
       0.284 -    0.426: 93
       0.426 -    0.568: 3
       0.568 -    0.710: 1
  Chirality restraints: 6056
  Sorted by residual:
  chirality pdb=" C3'   A A 465 "
            pdb=" C4'   A A 465 "
            pdb=" O3'   A A 465 "
            pdb=" C2'   A A 465 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -1.79   -0.71 2.00e-01 2.50e+01 1.26e+01
  chirality pdb=" P     G A 413 "
            pdb=" OP1   G A 413 "
            pdb=" OP2   G A 413 "
            pdb=" O5'   G A 413 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.71   -0.54 2.00e-01 2.50e+01 7.18e+00
  chirality pdb=" P     G A 416 "
            pdb=" OP1   G A 416 "
            pdb=" OP2   G A 416 "
            pdb=" O5'   G A 416 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.66   -0.48 2.00e-01 2.50e+01 5.82e+00
  ... (remaining 6053 not shown)

  Planarity restraints: 2401
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C A 335 "   -0.069 2.00e-02 2.50e+03   3.65e-02 3.00e+01
        pdb=" N1    C A 335 "    0.080 2.00e-02 2.50e+03
        pdb=" C2    C A 335 "    0.002 2.00e-02 2.50e+03
        pdb=" O2    C A 335 "    0.008 2.00e-02 2.50e+03
        pdb=" N3    C A 335 "   -0.008 2.00e-02 2.50e+03
        pdb=" C4    C A 335 "   -0.005 2.00e-02 2.50e+03
        pdb=" N4    C A 335 "   -0.018 2.00e-02 2.50e+03
        pdb=" C5    C A 335 "   -0.006 2.00e-02 2.50e+03
        pdb=" C6    C A 335 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A A 181 "   -0.069 2.00e-02 2.50e+03   3.16e-02 2.75e+01
        pdb=" N9    A A 181 "    0.072 2.00e-02 2.50e+03
        pdb=" C8    A A 181 "    0.012 2.00e-02 2.50e+03
        pdb=" N7    A A 181 "   -0.013 2.00e-02 2.50e+03
        pdb=" C5    A A 181 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    A A 181 "   -0.011 2.00e-02 2.50e+03
        pdb=" N6    A A 181 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1    A A 181 "   -0.014 2.00e-02 2.50e+03
        pdb=" C2    A A 181 "    0.009 2.00e-02 2.50e+03
        pdb=" N3    A A 181 "    0.009 2.00e-02 2.50e+03
        pdb=" C4    A A 181 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U A 438 "    0.064 2.00e-02 2.50e+03   3.21e-02 2.32e+01
        pdb=" N1    U A 438 "   -0.063 2.00e-02 2.50e+03
        pdb=" C2    U A 438 "   -0.014 2.00e-02 2.50e+03
        pdb=" O2    U A 438 "   -0.009 2.00e-02 2.50e+03
        pdb=" N3    U A 438 "    0.015 2.00e-02 2.50e+03
        pdb=" C4    U A 438 "    0.008 2.00e-02 2.50e+03
        pdb=" O4    U A 438 "    0.014 2.00e-02 2.50e+03
        pdb=" C5    U A 438 "    0.004 2.00e-02 2.50e+03
        pdb=" C6    U A 438 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 2398 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 729
        2.56 -     3.15: 23322
        3.15 -     3.73: 63512
        3.73 -     4.32: 87681
        4.32 -     4.90: 112427
  Nonbonded interactions: 287671
  Sorted by model distance:
  nonbonded pdb=" N2    G A 444 "
            pdb=" O2    C A 490 "
     model   vdw
     1.977 2.496
  nonbonded pdb=" N2    G A 457 "
            pdb=" O2    C A 475 "
     model   vdw
     1.982 2.496
  nonbonded pdb=" O6    G A 410 "
            pdb=" O2'   U A 429 "
     model   vdw
     1.983 3.040
  nonbonded pdb=" O2    C A 658 "
            pdb=" N2    G A 748 "
     model   vdw
     2.021 2.496
  nonbonded pdb=" OD1 ASP D  98 "
            pdb=" N   ASN D  99 "
     model   vdw
     2.025 3.120
  ... (remaining 287666 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.030
  Extract box with map and model:          0.730
  Check model and map are aligned:         0.100
  Set scattering table:                    0.080
  Process input model:                     35.350
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  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:7.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   50.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
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      :  0.014   0.117  31478  Z= 0.711
  Angle     :  1.314  13.109  47296  Z= 0.575
  Chirality :  0.113   0.710   6056
  Planarity :  0.007   0.062   2401
  Dihedral  : 22.117 176.743  14779
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 23.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.23 %
    Favored  : 89.77 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  0.23 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.50 (0.24), residues: 1017
  helix: -0.71 (0.26), residues: 379
  sheet: -2.44 (0.38), residues: 147
  loop : -2.14 (0.26), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.002   ARG P  14 
 TYR   0.027   0.003   TYR L 116 
 PHE   0.016   0.003   PHE P  39 
 TRP   0.016   0.002   TRP Q  72 
 HIS   0.013   0.002   HIS D 119 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01420 /  0.71 (31478)
  covalent geometry    : angle       1.31446 /  0.57 (47296)
  hydrogen bonds       : bond        0.16612 / 10.88 ( 1201)
  hydrogen bonds       : angle       5.63530 /  3.83 ( 2309)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 113
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 3
  residues processed: 115
  average time/residue: 0.7155
  time to fit residues: 96.2901
Evaluate side-chains
  105 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 102
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    8 LEU
Chi-restraints excluded: chain L residue   19 ASN
Chi-restraints excluded: chain O residue   67 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 194 optimal weight:   20.0000
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    0.5980
   chunk 124 optimal weight:    0.5980
   chunk 103 optimal weight:    0.5980
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    0.5980
   chunk 91 optimal weight:   20.0000
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  99 ASN
** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F   3 HIS
** F  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 100 ASN
L   4 ASN
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  95 HIS
** O  45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.162524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.142569 restraints weight = 51834.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.4263 rms_B_bonded: 0.46
r_work: 0.3950 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work: 0.3903 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  31478  Z= 0.210
  Angle     :  1.306  18.868  47296  Z= 0.524
  Chirality :  0.106   1.818   6056
  Planarity :  0.005   0.052   2401
  Dihedral  : 19.952 179.872  12718
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 10.26 %
    Favored  : 88.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.48 (0.25), residues: 1017
  helix:  0.50 (0.26), residues: 391
  sheet: -2.14 (0.38), residues: 159
  loop : -1.83 (0.27), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG Q  76 
 TYR   0.014   0.002   TYR F  59 
 PHE   0.010   0.001   PHE D 106 
 TRP   0.007   0.001   TRP P  60 
 HIS   0.009   0.002   HIS O  41 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00413 /  0.21 (31478)
  covalent geometry    : angle       1.30593 /  0.52 (47296)
  hydrogen bonds       : bond        0.10169 /  6.85 ( 1201)
  hydrogen bonds       : angle       3.73155 /  2.54 ( 2309)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.557 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F    9 MET cc_start: -0.2107 (pmt) cc_final: -0.2545 (pmm)
REVERT: F   21 MET cc_start: -0.0215 (OUTLIER) cc_final: -0.0419 (tpt)
  outliers start: 13
  outliers final: 2
  residues processed: 125
  average time/residue: 0.7016
  time to fit residues: 102.7279
Evaluate side-chains
  103 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 100
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue    3 HIS
Chi-restraints excluded: chain F residue   21 MET
Chi-restraints excluded: chain L residue   63 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 183 optimal weight:   20.0000
   chunk 179 optimal weight:   50.0000
   chunk 192 optimal weight:   50.0000
   chunk 103 optimal weight:    2.9990
   chunk 165 optimal weight:   10.0000
   chunk 149 optimal weight:    3.9990
   chunk 180 optimal weight:    9.9990
   chunk 18 optimal weight:    0.8980
   chunk 166 optimal weight:   20.0000
   chunk 82 optimal weight:    4.9990
   chunk 23 optimal weight:    7.9990
   overall best weight:    4.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  95 HIS
** O  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.155784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.139368 restraints weight = 48857.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.4232 rms_B_bonded: 0.63
r_work: 0.3886 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work: 0.3835 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.2252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.067  31478  Z= 0.497
  Angle     :  1.411  15.081  47296  Z= 0.569
  Chirality :  0.113   1.325   6056
  Planarity :  0.007   0.068   2401
  Dihedral  : 19.951 178.482  12712
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 14.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.57 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 12.94 %
    Favored  : 83.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.25), residues: 1017
  helix:  0.55 (0.25), residues: 386
  sheet: -2.18 (0.40), residues: 160
  loop : -1.79 (0.27), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG P  35 
 TYR   0.021   0.002   TYR L 116 
 PHE   0.016   0.002   PHE D 106 
 TRP   0.012   0.002   TRP Q  72 
 HIS   0.017   0.002   HIS O  41 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01012 /  0.50 (31478)
  covalent geometry    : angle       1.41140 /  0.57 (47296)
  hydrogen bonds       : bond        0.11392 /  7.71 ( 1201)
  hydrogen bonds       : angle       3.69129 /  2.49 ( 2309)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 98
  time to evaluate  : 0.567 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F    9 MET cc_start: -0.1785 (pmt) cc_final: -0.2322 (pmm)
REVERT: H   79 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8192 (ptm-80)
REVERT: Q   39 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7816 (mmp-170)
  outliers start: 27
  outliers final: 7
  residues processed: 115
  average time/residue: 0.7111
  time to fit residues: 95.6638
Evaluate side-chains
  102 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue    3 HIS
Chi-restraints excluded: chain H residue   60 LEU
Chi-restraints excluded: chain H residue   79 ARG
Chi-restraints excluded: chain H residue   84 ILE
Chi-restraints excluded: chain L residue   63 THR
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue  118 VAL
Chi-restraints excluded: chain Q residue   39 ARG
Chi-restraints excluded: chain T residue   85 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 16 optimal weight:   10.0000
   chunk 80 optimal weight:    1.9990
   chunk 135 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   chunk 149 optimal weight:    0.5980
   chunk 141 optimal weight:    4.9990
   chunk 156 optimal weight:    5.9990
   chunk 120 optimal weight:    9.9990
   chunk 3 optimal weight:    3.9990
   chunk 133 optimal weight:    2.9990
   overall best weight:    1.4384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F   3 HIS
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  95 HIS
** O  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q   8 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 = 0.4431 r_free = 0.4431 target = 0.157286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.133242 restraints weight = 49556.512|
|-----------------------------------------------------------------------------|
r_work (start): 0.4085 rms_B_bonded: 0.46
r_work: 0.3722 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3662 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.3176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  31478  Z= 0.227
  Angle     :  1.140  13.678  47296  Z= 0.459
  Chirality :  0.089   0.877   6056
  Planarity :  0.005   0.051   2401
  Dihedral  : 19.720 179.724  12712
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 15.27 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.11 (0.26), residues: 1017
  helix:  0.96 (0.26), residues: 386
  sheet: -2.25 (0.41), residues: 151
  loop : -1.64 (0.27), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H 116 
 TYR   0.011   0.002   TYR L 116 
 PHE   0.019   0.001   PHE O  42 
 TRP   0.005   0.001   TRP P  60 
 HIS   0.011   0.001   HIS O  41 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00456 /  0.23 (31478)
  covalent geometry    : angle       1.14046 /  0.46 (47296)
  hydrogen bonds       : bond        0.09443 /  6.38 ( 1201)
  hydrogen bonds       : angle       3.32806 /  2.24 ( 2309)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 0.557 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   88 MET cc_start: -0.0334 (mpt) cc_final: -0.3483 (tpp)
  outliers start: 27
  outliers final: 8
  residues processed: 125
  average time/residue: 0.6881
  time to fit residues: 100.3389
Evaluate side-chains
  103 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain F residue    3 HIS
Chi-restraints excluded: chain H residue   60 LEU
Chi-restraints excluded: chain L residue   19 ASN
Chi-restraints excluded: chain L residue   63 THR
Chi-restraints excluded: chain L residue  118 VAL
Chi-restraints excluded: chain P residue   20 VAL
Chi-restraints excluded: chain T residue   85 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 172 optimal weight:    9.9990
   chunk 170 optimal weight:   50.0000
   chunk 131 optimal weight:    2.9990
   chunk 106 optimal weight:    3.9990
   chunk 148 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 171 optimal weight:   20.0000
   chunk 179 optimal weight:   50.0000
   chunk 7 optimal weight:    0.9990
   chunk 89 optimal weight:    0.7980
   overall best weight:    1.5588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 151 GLN
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F   3 HIS
** F  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
O  41 HIS
** Q   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  44 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.156798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.133700 restraints weight = 49539.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.4094 rms_B_bonded: 0.43
r_work: 0.3733 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3660 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.3379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  31478  Z= 0.239
  Angle     :  1.132  13.303  47296  Z= 0.456
  Chirality :  0.088   0.848   6056
  Planarity :  0.005   0.040   2401
  Dihedral  : 19.638 179.946  12712
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 17.02 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.99 (0.26), residues: 1017
  helix:  1.07 (0.26), residues: 388
  sheet: -2.13 (0.40), residues: 154
  loop : -1.61 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG T  28 
 TYR   0.021   0.002   TYR D  75 
 PHE   0.010   0.001   PHE P  32 
 TRP   0.006   0.001   TRP Q  72 
 HIS   0.019   0.002   HIS F   3 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00482 /  0.24 (31478)
  covalent geometry    : angle       1.13201 /  0.46 (47296)
  hydrogen bonds       : bond        0.09463 /  6.41 ( 1201)
  hydrogen bonds       : angle       3.27902 /  2.21 ( 2309)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F    9 MET cc_start: -0.2368 (pmt) cc_final: -0.2801 (pmm)
REVERT: F   88 MET cc_start: -0.0288 (mpt) cc_final: -0.3213 (tpp)
REVERT: P    4 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.9031 (mm)
  outliers start: 19
  outliers final: 10
  residues processed: 114
  average time/residue: 0.6907
  time to fit residues: 92.2076
Evaluate side-chains
  107 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  106 PHE
Chi-restraints excluded: chain H residue   60 LEU
Chi-restraints excluded: chain H residue   84 ILE
Chi-restraints excluded: chain L residue   19 ASN
Chi-restraints excluded: chain L residue   63 THR
Chi-restraints excluded: chain L residue   66 ILE
Chi-restraints excluded: chain L residue  118 VAL
Chi-restraints excluded: chain P residue    4 ILE
Chi-restraints excluded: chain P residue   20 VAL
Chi-restraints excluded: chain Q residue   32 ILE
Chi-restraints excluded: chain T residue   85 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 168 optimal weight:   50.0000
   chunk 64 optimal weight:    0.6980
   chunk 94 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 23 optimal weight:   20.0000
   chunk 178 optimal weight:   50.0000
   chunk 180 optimal weight:   10.0000
   chunk 121 optimal weight:    2.9990
   chunk 139 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.9386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  95 HIS
** Q   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
T  12 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.153951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.128083 restraints weight = 47462.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.3987 rms_B_bonded: 0.52
r_work: 0.3631 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3577 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.3484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  31478  Z= 0.270
  Angle     :  1.146  13.425  47296  Z= 0.461
  Chirality :  0.089   0.906   6056
  Planarity :  0.005   0.053   2401
  Dihedral  : 19.600 179.172  12712
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 18.76 %
    Favored  : 78.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.92 (0.26), residues: 1017
  helix:  1.09 (0.26), residues: 389
  sheet: -2.15 (0.41), residues: 145
  loop : -1.53 (0.27), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG H 116 
 TYR   0.015   0.002   TYR F  25 
 PHE   0.011   0.001   PHE P  32 
 TRP   0.007   0.001   TRP Q  72 
 HIS   0.007   0.001   HIS K  21 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00544 /  0.27 (31478)
  covalent geometry    : angle       1.14641 /  0.46 (47296)
  hydrogen bonds       : bond        0.09563 /  6.48 ( 1201)
  hydrogen bonds       : angle       3.25494 /  2.19 ( 2309)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F    9 MET cc_start: -0.2217 (pmt) cc_final: -0.2707 (pmm)
REVERT: F   88 MET cc_start: -0.0465 (mpt) cc_final: -0.3077 (tpp)
  outliers start: 22
  outliers final: 14
  residues processed: 113
  average time/residue: 0.7319
  time to fit residues: 96.6778
Evaluate side-chains
  110 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  106 PHE
Chi-restraints excluded: chain D residue  160 LEU
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain F residue   23 GLU
Chi-restraints excluded: chain H residue   60 LEU
Chi-restraints excluded: chain H residue   84 ILE
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   19 ASN
Chi-restraints excluded: chain L residue   63 THR
Chi-restraints excluded: chain L residue   66 ILE
Chi-restraints excluded: chain L residue  118 VAL
Chi-restraints excluded: chain P residue   20 VAL
Chi-restraints excluded: chain Q residue   32 ILE
Chi-restraints excluded: chain T residue   85 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 190 optimal weight:    9.9990
   chunk 57 optimal weight:    1.9990
   chunk 112 optimal weight:    2.9990
   chunk 45 optimal weight:   40.0000
   chunk 72 optimal weight:    0.5980
   chunk 171 optimal weight:   20.0000
   chunk 162 optimal weight:    3.9990
   chunk 156 optimal weight:    6.9990
   chunk 41 optimal weight:   30.0000
   chunk 86 optimal weight:    0.8980
   chunk 187 optimal weight:    3.9990
   overall best weight:    2.0986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  81 ASN
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.153508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.129444 restraints weight = 47779.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.4011 rms_B_bonded: 0.48
r_work: 0.3644 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3584 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.3582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  31478  Z= 0.284
  Angle     :  1.153  14.456  47296  Z= 0.465
  Chirality :  0.090   0.948   6056
  Planarity :  0.005   0.046   2401
  Dihedral  : 19.577 178.792  12712
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 18.88 %
    Favored  : 78.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.87 (0.26), residues: 1017
  helix:  1.11 (0.26), residues: 388
  sheet: -1.89 (0.41), residues: 149
  loop : -1.56 (0.27), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG H 116 
 TYR   0.019   0.002   TYR D  75 
 PHE   0.010   0.001   PHE P  32 
 TRP   0.008   0.001   TRP Q  72 
 HIS   0.005   0.001   HIS O  41 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00574 /  0.28 (31478)
  covalent geometry    : angle       1.15333 /  0.46 (47296)
  hydrogen bonds       : bond        0.09631 /  6.52 ( 1201)
  hydrogen bonds       : angle       3.25875 /  2.19 ( 2309)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 96
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F    9 MET cc_start: -0.2074 (pmt) cc_final: -0.2641 (pmm)
REVERT: F   88 MET cc_start: -0.0352 (mpt) cc_final: -0.2973 (tpp)
REVERT: H   79 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8214 (ptm-80)
REVERT: P    5 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.7816 (ptp-170)
  outliers start: 24
  outliers final: 15
  residues processed: 113
  average time/residue: 0.6879
  time to fit residues: 91.5263
Evaluate side-chains
  110 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  106 PHE
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain F residue   23 GLU
Chi-restraints excluded: chain H residue   60 LEU
Chi-restraints excluded: chain H residue   79 ARG
Chi-restraints excluded: chain H residue   84 ILE
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   19 ASN
Chi-restraints excluded: chain L residue   38 THR
Chi-restraints excluded: chain L residue   51 VAL
Chi-restraints excluded: chain L residue   63 THR
Chi-restraints excluded: chain L residue   66 ILE
Chi-restraints excluded: chain L residue  118 VAL
Chi-restraints excluded: chain P residue    5 ARG
Chi-restraints excluded: chain P residue   20 VAL
Chi-restraints excluded: chain Q residue   32 ILE
Chi-restraints excluded: chain T residue   85 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0030
   chunk 28 optimal weight:    1.9990
   chunk 135 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 4 optimal weight:    6.9990
   chunk 16 optimal weight:   10.0000
   chunk 147 optimal weight:    2.9990
   chunk 79 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 162 optimal weight:    3.9990
   overall best weight:    0.8592

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 100 ASN
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.156067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.130633 restraints weight = 48134.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.4028 rms_B_bonded: 0.50
r_work: 0.3677 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3619 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.3978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  31478  Z= 0.182
  Angle     :  1.077  17.346  47296  Z= 0.433
  Chirality :  0.083   0.831   6056
  Planarity :  0.005   0.049   2401
  Dihedral  : 19.532 178.559  12712
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 19.58 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.67 (0.26), residues: 1017
  helix:  1.27 (0.26), residues: 389
  sheet: -1.73 (0.44), residues: 140
  loop : -1.49 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG H 116 
 TYR   0.016   0.001   TYR F  25 
 PHE   0.008   0.001   PHE P  32 
 TRP   0.007   0.001   TRP K  43 
 HIS   0.005   0.001   HIS O  41 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00366 /  0.18 (31478)
  covalent geometry    : angle       1.07711 /  0.43 (47296)
  hydrogen bonds       : bond        0.09117 /  6.13 ( 1201)
  hydrogen bonds       : angle       3.15860 /  2.13 ( 2309)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.554 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   67 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8559 (mp)
REVERT: F    9 MET cc_start: -0.2271 (pmt) cc_final: -0.2808 (pmm)
REVERT: F   88 MET cc_start: -0.0582 (mpt) cc_final: -0.3055 (tpp)
REVERT: P    5 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.7869 (ptp-170)
  outliers start: 22
  outliers final: 13
  residues processed: 113
  average time/residue: 0.6506
  time to fit residues: 86.1606
Evaluate side-chains
  107 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  106 PHE
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain F residue   23 GLU
Chi-restraints excluded: chain H residue   60 LEU
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   19 ASN
Chi-restraints excluded: chain L residue   51 VAL
Chi-restraints excluded: chain L residue   63 THR
Chi-restraints excluded: chain L residue  118 VAL
Chi-restraints excluded: chain P residue    5 ARG
Chi-restraints excluded: chain P residue   20 VAL
Chi-restraints excluded: chain Q residue   32 ILE
Chi-restraints excluded: chain Q residue   66 LEU
Chi-restraints excluded: chain T residue   85 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 96 optimal weight:    1.9990
   chunk 91 optimal weight:   40.0000
   chunk 78 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 188 optimal weight:   10.0000
   chunk 68 optimal weight:    9.9990
   chunk 85 optimal weight:    0.7980
   chunk 95 optimal weight:    0.0050
   chunk 167 optimal weight:   40.0000
   overall best weight:    0.9396

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4457 r_free = 0.4457 target = 0.158706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.135268 restraints weight = 50154.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.4124 rms_B_bonded: 0.47
r_work: 0.3770 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3717 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.4111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  31478  Z= 0.184
  Angle     :  1.070  18.742  47296  Z= 0.431
  Chirality :  0.082   0.807   6056
  Planarity :  0.005   0.055   2401
  Dihedral  : 19.478 179.868  12712
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 20.16 %
    Favored  : 77.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.56 (0.26), residues: 1017
  helix:  1.40 (0.26), residues: 384
  sheet: -1.61 (0.40), residues: 160
  loop : -1.43 (0.28), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG H 116 
 TYR   0.021   0.001   TYR D  75 
 PHE   0.010   0.001   PHE P  32 
 TRP   0.008   0.001   TRP K  43 
 HIS   0.005   0.001   HIS O  41 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00370 /  0.18 (31478)
  covalent geometry    : angle       1.06980 /  0.43 (47296)
  hydrogen bonds       : bond        0.09131 /  6.14 ( 1201)
  hydrogen bonds       : angle       3.14696 /  2.12 ( 2309)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   67 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8580 (mp)
REVERT: F    9 MET cc_start: -0.2319 (pmt) cc_final: -0.2857 (pmm)
REVERT: F   88 MET cc_start: -0.0489 (mpt) cc_final: -0.3031 (tpp)
REVERT: H   79 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8100 (ptm-80)
REVERT: P    5 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.7700 (ptp-170)
  outliers start: 21
  outliers final: 14
  residues processed: 110
  average time/residue: 0.6824
  time to fit residues: 87.7313
Evaluate side-chains
  111 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  106 PHE
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain F residue   23 GLU
Chi-restraints excluded: chain H residue   60 LEU
Chi-restraints excluded: chain H residue   61 THR
Chi-restraints excluded: chain H residue   79 ARG
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   19 ASN
Chi-restraints excluded: chain L residue   51 VAL
Chi-restraints excluded: chain L residue   63 THR
Chi-restraints excluded: chain L residue   66 ILE
Chi-restraints excluded: chain L residue  118 VAL
Chi-restraints excluded: chain P residue    5 ARG
Chi-restraints excluded: chain P residue   20 VAL
Chi-restraints excluded: chain Q residue   32 ILE
Chi-restraints excluded: chain T residue   85 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 155 optimal weight:    8.9990
   chunk 195 optimal weight:   30.0000
   chunk 19 optimal weight:    2.9990
   chunk 109 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 127 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 67 optimal weight:    3.9990
   chunk 140 optimal weight:    4.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 197 HIS
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.155424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.130976 restraints weight = 49205.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.4065 rms_B_bonded: 0.54
r_work: 0.3693 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3645 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.3764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.056  31478  Z= 0.332
  Angle     :  1.193  20.376  47296  Z= 0.481
  Chirality :  0.092   0.997   6056
  Planarity :  0.005   0.049   2401
  Dihedral  : 19.518 179.756  12712
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 20.16 %
    Favored  : 77.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.74 (0.26), residues: 1017
  helix:  1.20 (0.26), residues: 388
  sheet: -1.83 (0.41), residues: 147
  loop : -1.47 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG H 116 
 TYR   0.020   0.002   TYR F  25 
 PHE   0.009   0.001   PHE P  32 
 TRP   0.009   0.002   TRP Q  72 
 HIS   0.006   0.001   HIS P   9 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00673 /  0.33 (31478)
  covalent geometry    : angle       1.19261 /  0.48 (47296)
  hydrogen bonds       : bond        0.09949 /  6.71 ( 1201)
  hydrogen bonds       : angle       3.27846 /  2.21 ( 2309)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   67 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8660 (mp)
REVERT: F    9 MET cc_start: -0.2018 (pmt) cc_final: -0.2613 (pmm)
REVERT: F   88 MET cc_start: -0.0279 (mpt) cc_final: -0.2916 (tpp)
REVERT: H   79 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8281 (ptm-80)
REVERT: P    5 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.7844 (ptp-170)
  outliers start: 21
  outliers final: 13
  residues processed: 110
  average time/residue: 0.6857
  time to fit residues: 88.3910
Evaluate side-chains
  113 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  106 PHE
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain F residue   23 GLU
Chi-restraints excluded: chain H residue   60 LEU
Chi-restraints excluded: chain H residue   79 ARG
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   38 THR
Chi-restraints excluded: chain L residue   63 THR
Chi-restraints excluded: chain L residue   66 ILE
Chi-restraints excluded: chain L residue  118 VAL
Chi-restraints excluded: chain P residue    5 ARG
Chi-restraints excluded: chain P residue   20 VAL
Chi-restraints excluded: chain Q residue   32 ILE
Chi-restraints excluded: chain Q residue   66 LEU
Chi-restraints excluded: chain T residue   85 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 111 optimal weight:    1.9990
   chunk 69 optimal weight:   10.0000
   chunk 97 optimal weight:    0.6980
   chunk 56 optimal weight:    1.9990
   chunk 113 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   chunk 144 optimal weight:    1.9990
   chunk 20 optimal weight:   50.0000
   chunk 35 optimal weight:    8.9990
   chunk 7 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   overall best weight:    1.2584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.156889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.131907 restraints weight = 49869.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.4077 rms_B_bonded: 0.49
r_work: 0.3666 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3544 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.3892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  31478  Z= 0.217
  Angle     :  1.129  20.140  47296  Z= 0.455
  Chirality :  0.088   0.931   6056
  Planarity :  0.005   0.053   2401
  Dihedral  : 19.535 178.282  12712
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 20.16 %
    Favored  : 77.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.62 (0.26), residues: 1017
  helix:  1.32 (0.26), residues: 382
  sheet: -1.84 (0.41), residues: 149
  loop : -1.35 (0.28), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG H 116 
 TYR   0.044   0.002   TYR D  75 
 PHE   0.015   0.001   PHE H  44 
 TRP   0.008   0.001   TRP Q  72 
 HIS   0.006   0.001   HIS O  41 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00437 /  0.22 (31478)
  covalent geometry    : angle       1.12938 /  0.46 (47296)
  hydrogen bonds       : bond        0.09597 /  6.46 ( 1201)
  hydrogen bonds       : angle       3.25705 /  2.20 ( 2309)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8248.32 seconds
wall clock time: 142 minutes 8.64 seconds (8528.64 seconds total)