Starting phenix.real_space_refine
on Sat Aug 23 06:19:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ub7_42077/08_2025/8ub7_42077.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ub7_42077/08_2025/8ub7_42077.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ub7_42077/08_2025/8ub7_42077.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ub7_42077/08_2025/8ub7_42077.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ub7_42077/08_2025/8ub7_42077.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ub7_42077/08_2025/8ub7_42077.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.029
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: 6
    Type Number    sf(0)   Gaussians
     P     151      5.49       5
     Mg      1      5.21       5
     S      36      5.16       5
     C    6073      2.51       5
     N    1871      2.21       5
     O    2267      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10399
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 2690
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 2690
          Classifications: {'peptide': 328}
          Link IDs: {'PTRANS': 12, 'TRANS': 315}
    Chain: "B"
      Number of atoms: 976
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 976
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 5, 'TRANS': 116}
    Chain: "C"
      Number of atoms: 888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 888
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 4, 'TRANS': 106}
    Chain: "D"
      Number of atoms: 888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 888
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 4, 'TRANS': 106}
    Chain: "E"
      Number of atoms: 876
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 876
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 4, 'TRANS': 105}
    Chain: "F"
      Number of atoms: 888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 888
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 4, 'TRANS': 106}
    Chain: "G"
      Number of atoms: 289
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 289
          Classifications: {'RNA': 13}
          Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 3}
          Link IDs: {'rna3p': 12}
    Chain: "H"
      Number of atoms: 270
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 270
          Classifications: {'RNA': 13}
          Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 8}
          Link IDs: {'rna3p': 12}
    Chain: "I"
      Number of atoms: 2605
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 2605
          Classifications: {'RNA': 122}
          Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 11, 'rna3p_pur': 51, 'rna3p_pyr': 48}
          Link IDs: {'rna2p': 23, 'rna3p': 98}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 29
          Unusual residues: {' MG': 1, 'DCP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.64, per 1000 atoms: 0.25
  Number of scatterers: 10399
  At special positions: 0
  Unit cell: (81, 105, 134, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      36     16.00
     P     151     15.00
     Mg      1     11.99
     O    2267      8.00
     N    1871      7.00
     C    6073      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: 1.49
  Conformation dependent library (CDL) restraints added in 279.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1676

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 3 sheets defined
      75.7% alpha, 2.6% beta
      48 base pairs and 88 stacking pairs defined.
    Time for finding SS restraints: 1.57
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 13
    Processing helix  chain 'A' and resid 14 through 27
      removed outlier: 3.556A  pdb=" N   ASP A  20 " --> pdb=" O   GLU A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 39
    Processing helix  chain 'A' and resid 41 through 54
      removed outlier: 3.503A  pdb=" N   ALA A  51 " --> pdb=" O   LEU A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 91
    Processing helix  chain 'A' and resid 94 through 99
    Processing helix  chain 'A' and resid 114 through 128
    Processing helix  chain 'A' and resid 129 through 131
      No H-bonds generated for 'chain 'A' and resid 129 through 131'
    Processing helix  chain 'A' and resid 142 through 146
    Processing helix  chain 'A' and resid 150 through 154
      removed outlier: 3.617A  pdb=" N   ALA A 153 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 172
    Processing helix  chain 'A' and resid 183 through 199
      removed outlier: 4.200A  pdb=" N   VAL A 197 " --> pdb=" O   TYR A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 241
    Processing helix  chain 'A' and resid 273 through 289
    Processing helix  chain 'A' and resid 294 through 307
      removed outlier: 3.931A  pdb=" N   ARG A 298 " --> pdb=" O   GLU A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 324
    Processing helix  chain 'B' and resid 10 through 32
      removed outlier: 3.726A  pdb=" N   ARG B  22 " --> pdb=" O   GLU B  18 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   VAL B  23 " --> pdb=" O   ARG B  19 " (cutoff:3.500A)
      Proline residue:  B  29  - end of helix
    Processing helix  chain 'B' and resid 38 through 50
    Processing helix  chain 'B' and resid 51 through 62
    Processing helix  chain 'B' and resid 64 through 88
      removed outlier: 3.537A  pdb=" N   LEU B  68 " --> pdb=" O   GLN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 122
    Processing helix  chain 'C' and resid 12 through 32
      removed outlier: 3.754A  pdb=" N   ARG C  22 " --> pdb=" O   GLU C  18 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   VAL C  23 " --> pdb=" O   ARG C  19 " (cutoff:3.500A)
      Proline residue:  C  29  - end of helix
    Processing helix  chain 'C' and resid 35 through 37
      No H-bonds generated for 'chain 'C' and resid 35 through 37'
    Processing helix  chain 'C' and resid 38 through 50
    Processing helix  chain 'C' and resid 51 through 60
      removed outlier: 3.507A  pdb=" N   LEU C  55 " --> pdb=" O   GLY C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 64 through 88
      removed outlier: 3.508A  pdb=" N   LEU C  68 " --> pdb=" O   GLN C  64 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 95 through 121
    Processing helix  chain 'D' and resid 14 through 32
      removed outlier: 3.775A  pdb=" N   ARG D  22 " --> pdb=" O   GLU D  18 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   VAL D  23 " --> pdb=" O   ARG D  19 " (cutoff:3.500A)
      Proline residue:  D  29  - end of helix
    Processing helix  chain 'D' and resid 35 through 37
      No H-bonds generated for 'chain 'D' and resid 35 through 37'
    Processing helix  chain 'D' and resid 38 through 50
    Processing helix  chain 'D' and resid 51 through 62
      removed outlier: 3.529A  pdb=" N   LEU D  55 " --> pdb=" O   GLY D  51 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 64 through 86
    Processing helix  chain 'D' and resid 95 through 121
    Processing helix  chain 'E' and resid 13 through 32
      removed outlier: 3.749A  pdb=" N   ARG E  22 " --> pdb=" O   GLU E  18 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   VAL E  23 " --> pdb=" O   ARG E  19 " (cutoff:3.500A)
      Proline residue:  E  29  - end of helix
    Processing helix  chain 'E' and resid 35 through 37
      No H-bonds generated for 'chain 'E' and resid 35 through 37'
    Processing helix  chain 'E' and resid 38 through 50
    Processing helix  chain 'E' and resid 51 through 61
    Processing helix  chain 'E' and resid 66 through 86
      removed outlier: 3.730A  pdb=" N   ASP E  72 " --> pdb=" O   LEU E  68 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 95 through 121
    Processing helix  chain 'F' and resid 14 through 34
      removed outlier: 4.579A  pdb=" N   ARG F  22 " --> pdb=" O   GLU F  18 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   VAL F  23 " --> pdb=" O   ARG F  19 " (cutoff:3.500A)
      Proline residue:  F  29  - end of helix
      removed outlier: 3.557A  pdb=" N   ILE F  34 " --> pdb=" O   ILE F  30 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 35 through 37
      No H-bonds generated for 'chain 'F' and resid 35 through 37'
    Processing helix  chain 'F' and resid 38 through 50
    Processing helix  chain 'F' and resid 51 through 61
    Processing helix  chain 'F' and resid 64 through 87
      removed outlier: 3.597A  pdb=" N   GLY F  87 " --> pdb=" O   ARG F  83 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 88 through 93
      Proline residue:  F  91  - end of helix
      No H-bonds generated for 'chain 'F' and resid 88 through 93'
    Processing helix  chain 'F' and resid 95 through 122
      removed outlier: 4.484A  pdb=" N   LEU F 105 " --> pdb=" O   THR F 101 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65
    Processing sheet with id=AA2, first strand: chain 'A' and resid 211 through 213
      removed outlier: 4.321A  pdb=" N   HIS A 248 " --> pdb=" O   ASP A 138 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 263 through 265

    474 hydrogen bonds defined for protein.
    1404 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      121 hydrogen bonds
      190 hydrogen bond angles
      0 basepair planarities
      48 basepair parallelities
      88 stacking parallelities
  Total time for adding SS restraints: 2.27

  Time building geometry restraints manager: 1.48 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1406
        1.32 -     1.45: 4069
        1.45 -     1.58: 5098
        1.58 -     1.71: 297
        1.71 -     1.84: 61
  Bond restraints: 10931
  Sorted by residual:
  bond pdb=" C3' DCP A 401 "
       pdb=" C4' DCP A 401 "
    ideal  model  delta    sigma   weight residual
    1.527  1.302  0.225 1.10e-02 8.26e+03 4.20e+02
  bond pdb=" C1' DCP A 401 "
       pdb=" C2' DCP A 401 "
    ideal  model  delta    sigma   weight residual
    1.521  1.356  0.165 1.20e-02 6.94e+03 1.90e+02
  bond pdb=" O3A DCP A 401 "
       pdb=" PB  DCP A 401 "
    ideal  model  delta    sigma   weight residual
    1.592  1.698 -0.106 1.10e-02 8.26e+03 9.25e+01
  bond pdb=" C4' DCP A 401 "
       pdb=" O4' DCP A 401 "
    ideal  model  delta    sigma   weight residual
    1.444  1.540 -0.096 1.00e-02 1.00e+04 9.21e+01
  bond pdb=" C2' DCP A 401 "
       pdb=" C3' DCP A 401 "
    ideal  model  delta    sigma   weight residual
    1.523  1.626 -0.103 1.30e-02 5.92e+03 6.31e+01
  ... (remaining 10926 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.34: 13723
        2.34 -     4.68: 1555
        4.68 -     7.02: 186
        7.02 -     9.35: 30
        9.35 -    11.69: 2
  Bond angle restraints: 15496
  Sorted by residual:
  angle pdb=" PB  DCP A 401 "
        pdb=" O3B DCP A 401 "
        pdb=" PG  DCP A 401 "
      ideal   model   delta    sigma   weight residual
     139.87  129.72   10.15 1.00e+00 1.00e+00 1.03e+02
  angle pdb=" C   ARG A   4 "
        pdb=" CA  ARG A   4 "
        pdb=" CB  ARG A   4 "
      ideal   model   delta    sigma   weight residual
     116.54  107.41    9.13 1.15e+00 7.56e-01 6.30e+01
  angle pdb=" C1' DCP A 401 "
        pdb=" O4' DCP A 401 "
        pdb=" C4' DCP A 401 "
      ideal   model   delta    sigma   weight residual
     109.55  100.73    8.82 1.31e+00 5.82e-01 4.52e+01
  angle pdb=" PA  DCP A 401 "
        pdb=" O3A DCP A 401 "
        pdb=" PB  DCP A 401 "
      ideal   model   delta    sigma   weight residual
     136.83  130.27    6.56 1.00e+00 1.00e+00 4.31e+01
  angle pdb=" N   ARG A   6 "
        pdb=" CA  ARG A   6 "
        pdb=" C   ARG A   6 "
      ideal   model   delta    sigma   weight residual
     111.55  120.36   -8.81 1.37e+00 5.33e-01 4.13e+01
  ... (remaining 15491 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.16: 5936
       35.16 -    70.32: 776
       70.32 -   105.48: 76
      105.48 -   140.64: 1
      140.64 -   175.80: 4
  Dihedral angle restraints: 6793
    sinusoidal: 4194
      harmonic: 2599
  Sorted by residual:
  dihedral pdb=" C5'   A I  56 "
           pdb=" C4'   A I  56 "
           pdb=" C3'   A I  56 "
           pdb=" O3'   A I  56 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   87.25   59.75     1      8.00e+00 1.56e-02 7.44e+01
  dihedral pdb=" O4'   U I  94 "
           pdb=" C1'   U I  94 "
           pdb=" N1    U I  94 "
           pdb=" C2    U I  94 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   46.18 -174.18     1      1.70e+01 3.46e-03 6.63e+01
  dihedral pdb=" O4'   C I  82 "
           pdb=" C1'   C I  82 "
           pdb=" N1    C I  82 "
           pdb=" C2    C I  82 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   61.10  170.90     1      1.70e+01 3.46e-03 6.60e+01
  ... (remaining 6790 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.120: 1492
       0.120 -    0.240: 303
       0.240 -    0.360: 32
       0.360 -    0.480: 6
       0.480 -    0.600: 4
  Chirality restraints: 1837
  Sorted by residual:
  chirality pdb=" P     G H 117 "
            pdb=" OP1   G H 117 "
            pdb=" OP2   G H 117 "
            pdb=" O5'   G H 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -3.01   -0.60 2.00e-01 2.50e+01 9.00e+00
  chirality pdb=" P     U I  47 "
            pdb=" OP1   U I  47 "
            pdb=" OP2   U I  47 "
            pdb=" O5'   U I  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.99   -0.58 2.00e-01 2.50e+01 8.48e+00
  chirality pdb=" P     G G 369 "
            pdb=" OP1   G G 369 "
            pdb=" OP2   G G 369 "
            pdb=" O5'   G G 369 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.99   -0.58 2.00e-01 2.50e+01 8.45e+00
  ... (remaining 1834 not shown)

  Planarity restraints: 1403
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C  28 "   -0.081 2.00e-02 2.50e+03   4.09e-02 3.34e+01
        pdb=" CG  TYR C  28 "    0.058 2.00e-02 2.50e+03
        pdb=" CD1 TYR C  28 "    0.030 2.00e-02 2.50e+03
        pdb=" CD2 TYR C  28 "    0.031 2.00e-02 2.50e+03
        pdb=" CE1 TYR C  28 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR C  28 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR C  28 "   -0.008 2.00e-02 2.50e+03
        pdb=" OH  TYR C  28 "   -0.039 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U I   7 "   -0.066 2.00e-02 2.50e+03   3.07e-02 2.12e+01
        pdb=" N1    U I   7 "    0.032 2.00e-02 2.50e+03
        pdb=" C2    U I   7 "    0.021 2.00e-02 2.50e+03
        pdb=" O2    U I   7 "    0.007 2.00e-02 2.50e+03
        pdb=" N3    U I   7 "    0.010 2.00e-02 2.50e+03
        pdb=" C4    U I   7 "   -0.013 2.00e-02 2.50e+03
        pdb=" O4    U I   7 "   -0.034 2.00e-02 2.50e+03
        pdb=" C5    U I   7 "    0.009 2.00e-02 2.50e+03
        pdb=" C6    U I   7 "    0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C  90 "   -0.070 5.00e-02 4.00e+02   1.05e-01 1.75e+01
        pdb=" N   PRO C  91 "    0.181 5.00e-02 4.00e+02
        pdb=" CA  PRO C  91 "   -0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO C  91 "   -0.056 5.00e-02 4.00e+02
  ... (remaining 1400 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1821
        2.76 -     3.30: 10122
        3.30 -     3.83: 21661
        3.83 -     4.37: 26817
        4.37 -     4.90: 37337
  Nonbonded interactions: 97758
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 215 "
            pdb="MG    MG A 402 "
     model   vdw
     2.230 2.170
  nonbonded pdb=" O   ILE A 159 "
            pdb=" N   CYS A 161 "
     model   vdw
     2.273 3.120
  nonbonded pdb=" OD1 ASP A 138 "
            pdb="MG    MG A 402 "
     model   vdw
     2.276 2.170
  nonbonded pdb=" O   ALA E 118 "
            pdb=" O   ASN E 121 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   PHE A 139 "
            pdb="MG    MG A 402 "
     model   vdw
     2.345 2.170
  ... (remaining 97753 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and resid 13 through 121)
  selection = (chain 'C' and resid 13 through 121)
  selection = (chain 'D' and resid 13 through 121)
  selection = (chain 'E' and resid 13 through 121)
  selection = (chain 'F' and resid 13 through 121)
}

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=0.99
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:             3.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     12.140
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.010
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7041
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      :  0.011   0.225  10931  Z= 0.679
  Angle     :  1.531  11.693  15496  Z= 0.957
  Chirality :  0.098   0.600   1837
  Planarity :  0.011   0.106   1403
  Dihedral  : 25.464 175.798   5117
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  2.27 %
    Allowed  :  9.08 %
    Favored  : 88.65 %
  Rotamer:
    Outliers : 20.48 %
    Allowed  : 13.92 %
    Favored  : 65.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.80 (0.24), residues: 881
  helix: -1.84 (0.17), residues: 663
  sheet: -4.83 (0.91), residues: 24
  loop : -3.99 (0.36), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.002   ARG B  22 
 TYR   0.081   0.008   TYR C  28 
 PHE   0.057   0.009   PHE A 231 
 TRP   0.040   0.008   TRP A  33 
 HIS   0.018   0.004   HIS A 133 

Details of bonding type rmsd
  covalent geometry    : bond        0.01091 (10931)
  covalent geometry    : angle       1.53067 (15496)
  hydrogen bonds       : bond        0.18109 (  595)
  hydrogen bonds       : angle       8.70736 ( 1594)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 153
    poor density    : 154
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7509 (ptm-80)
REVERT: A  112 ASP cc_start: 0.8266 (m-30) cc_final: 0.7874 (t70)
REVERT: A  222 ASP cc_start: 0.7857 (p0) cc_final: 0.7309 (t0)
REVERT: A  223 ASP cc_start: 0.8338 (t70) cc_final: 0.7797 (t0)
REVERT: B   75 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7236 (mt)
REVERT: B   90 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.6794 (tppt)
REVERT: B  108 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6985 (tt0)
REVERT: C   14 MET cc_start: 0.6230 (OUTLIER) cc_final: 0.5925 (ttt)
REVERT: C   90 LYS cc_start: 0.6946 (OUTLIER) cc_final: 0.6468 (mtpp)
REVERT: C   92 HIS cc_start: 0.7220 (OUTLIER) cc_final: 0.6862 (m170)
REVERT: D   15 LEU cc_start: 0.6127 (OUTLIER) cc_final: 0.5919 (tp)
REVERT: D   19 ARG cc_start: 0.7493 (mmt-90) cc_final: 0.7240 (mmp80)
REVERT: D   64 GLN cc_start: 0.6507 (OUTLIER) cc_final: 0.6029 (pm20)
REVERT: D  122 ARG cc_start: 0.4726 (OUTLIER) cc_final: 0.4464 (mmp-170)
REVERT: E   19 ARG cc_start: 0.7046 (mmm160) cc_final: 0.6777 (mmm160)
REVERT: E   50 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.6861 (mt)
REVERT: E   52 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.6770 (tp40)
REVERT: E   54 GLU cc_start: 0.7082 (tt0) cc_final: 0.6832 (tt0)
REVERT: E   63 ASN cc_start: 0.6692 (OUTLIER) cc_final: 0.6125 (t0)
REVERT: E   77 MET cc_start: 0.8196 (tpt) cc_final: 0.7619 (tpp)
REVERT: E   89 GLN cc_start: 0.6429 (OUTLIER) cc_final: 0.6151 (mt0)
REVERT: E   90 LYS cc_start: 0.6919 (OUTLIER) cc_final: 0.6484 (ttmm)
REVERT: E   94 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8362 (ttm)
REVERT: F   13 GLN cc_start: 0.4172 (OUTLIER) cc_final: 0.3437 (mt0)
REVERT: F   14 MET cc_start: 0.5244 (OUTLIER) cc_final: 0.3709 (ttp)
REVERT: F   19 ARG cc_start: 0.6747 (tpp80) cc_final: 0.6477 (mmm160)
REVERT: F   43 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6457 (mp0)
REVERT: F   65 VAL cc_start: 0.6832 (OUTLIER) cc_final: 0.6451 (t)
REVERT: F   77 MET cc_start: 0.7380 (tpt) cc_final: 0.6831 (tpt)
REVERT: F   90 LYS cc_start: 0.5191 (OUTLIER) cc_final: 0.4842 (mtpp)
REVERT: F  122 ARG cc_start: 0.5272 (OUTLIER) cc_final: 0.4648 (mtt-85)
REVERT: F  123 LYS cc_start: 0.3481 (OUTLIER) cc_final: 0.3246 (mttm)
  outliers start: 153
  outliers final: 45
  residues processed: 272
  average time/residue: 0.1456
  time to fit residues: 49.1188
Evaluate side-chains
  195 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 127
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   23 ARG
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   82 LYS
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  110 ARG
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  158 LYS
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  208 ARG
Chi-restraints excluded: chain A residue  216 ASP
Chi-restraints excluded: chain A residue  256 ARG
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  276 SER
Chi-restraints excluded: chain A residue  290 HIS
Chi-restraints excluded: chain A residue  298 ARG
Chi-restraints excluded: chain A residue  302 SER
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue   54 GLU
Chi-restraints excluded: chain B residue   64 GLN
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   75 LEU
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain B residue   90 LYS
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain B residue  108 GLU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain C residue   14 MET
Chi-restraints excluded: chain C residue   16 ILE
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   90 LYS
Chi-restraints excluded: chain C residue   91 PRO
Chi-restraints excluded: chain C residue   92 HIS
Chi-restraints excluded: chain C residue   94 MET
Chi-restraints excluded: chain D residue   15 LEU
Chi-restraints excluded: chain D residue   64 GLN
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue  122 ARG
Chi-restraints excluded: chain E residue   50 LEU
Chi-restraints excluded: chain E residue   52 GLN
Chi-restraints excluded: chain E residue   63 ASN
Chi-restraints excluded: chain E residue   67 LYS
Chi-restraints excluded: chain E residue   75 LEU
Chi-restraints excluded: chain E residue   85 LEU
Chi-restraints excluded: chain E residue   89 GLN
Chi-restraints excluded: chain E residue   90 LYS
Chi-restraints excluded: chain E residue   94 MET
Chi-restraints excluded: chain F residue   13 GLN
Chi-restraints excluded: chain F residue   14 MET
Chi-restraints excluded: chain F residue   15 LEU
Chi-restraints excluded: chain F residue   16 ILE
Chi-restraints excluded: chain F residue   27 LEU
Chi-restraints excluded: chain F residue   33 SER
Chi-restraints excluded: chain F residue   43 GLU
Chi-restraints excluded: chain F residue   54 GLU
Chi-restraints excluded: chain F residue   55 LEU
Chi-restraints excluded: chain F residue   65 VAL
Chi-restraints excluded: chain F residue   90 LYS
Chi-restraints excluded: chain F residue  113 LEU
Chi-restraints excluded: chain F residue  122 ARG
Chi-restraints excluded: chain F residue  123 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.6980
   chunk 100 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  87 GLN
** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  92 HIS
C  32 GLN
C  64 GLN
C 121 ASN
** E  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  52 GLN
F  13 GLN
** F  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.174465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.132682 restraints weight = 12485.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 1.21
r_work: 0.3337 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3187 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.2862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.096  10931  Z= 0.190
  Angle     :  0.685   8.543  15496  Z= 0.358
  Chirality :  0.040   0.296   1837
  Planarity :  0.007   0.127   1403
  Dihedral  : 23.979 177.019   3539
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.91 %
    Allowed  :  6.81 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  7.23 %
    Allowed  : 19.54 %
    Favored  : 73.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.28 (0.28), residues: 881
  helix:  0.02 (0.19), residues: 665
  sheet: -4.51 (0.77), residues: 28
  loop : -3.13 (0.42), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 122 
 TYR   0.015   0.002   TYR C  28 
 PHE   0.027   0.002   PHE A 231 
 TRP   0.013   0.002   TRP D 116 
 HIS   0.005   0.001   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 (10931)
  covalent geometry    : angle       0.68456 (15496)
  hydrogen bonds       : bond        0.05506 (  595)
  hydrogen bonds       : angle       4.43884 ( 1594)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 152
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 HIS cc_start: 0.7878 (m-70) cc_final: 0.7614 (m90)
REVERT: A  283 LYS cc_start: 0.8166 (mmtt) cc_final: 0.7956 (mttm)
REVERT: B    4 ILE cc_start: 0.8882 (mt) cc_final: 0.8663 (mt)
REVERT: C   14 MET cc_start: 0.7593 (tpt) cc_final: 0.7233 (ttt)
REVERT: C   33 SER cc_start: 0.8491 (p) cc_final: 0.8221 (m)
REVERT: E   22 ARG cc_start: 0.7729 (ttm110) cc_final: 0.7461 (mtm-85)
REVERT: E   50 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7617 (mt)
REVERT: E   54 GLU cc_start: 0.7568 (tt0) cc_final: 0.7251 (tt0)
REVERT: E  108 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7846 (tp30)
REVERT: F   13 GLN cc_start: 0.6034 (OUTLIER) cc_final: 0.5805 (tt0)
REVERT: F   14 MET cc_start: 0.5213 (mmp) cc_final: 0.4243 (ttm)
REVERT: F   43 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7677 (tp30)
REVERT: F   77 MET cc_start: 0.8103 (tpt) cc_final: 0.7761 (tpt)
REVERT: F  122 ARG cc_start: 0.4708 (OUTLIER) cc_final: 0.4009 (tmm160)
  outliers start: 54
  outliers final: 20
  residues processed: 196
  average time/residue: 0.1170
  time to fit residues: 29.4170
Evaluate side-chains
  151 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 127
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  290 HIS
Chi-restraints excluded: chain B residue   64 GLN
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue   95 THR
Chi-restraints excluded: chain C residue   90 LYS
Chi-restraints excluded: chain D residue  103 GLN
Chi-restraints excluded: chain E residue   16 ILE
Chi-restraints excluded: chain E residue   43 GLU
Chi-restraints excluded: chain E residue   50 LEU
Chi-restraints excluded: chain E residue   85 LEU
Chi-restraints excluded: chain F residue   13 GLN
Chi-restraints excluded: chain F residue   16 ILE
Chi-restraints excluded: chain F residue   27 LEU
Chi-restraints excluded: chain F residue   43 GLU
Chi-restraints excluded: chain F residue  113 LEU
Chi-restraints excluded: chain F residue  122 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 88 optimal weight:    8.9990
   chunk 51 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 98 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 290 HIS
B  38 HIS
C  13 GLN
C  92 HIS
** C  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  32 GLN
E  63 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.173372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.132042 restraints weight = 12879.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 1.26
r_work: 0.3262 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.3587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.077  10931  Z= 0.196
  Angle     :  0.650   9.525  15496  Z= 0.333
  Chirality :  0.038   0.184   1837
  Planarity :  0.006   0.130   1403
  Dihedral  : 23.339 179.500   3407
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.68 %
    Allowed  :  7.04 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 21.55 %
    Favored  : 73.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.68 (0.28), residues: 881
  helix:  0.38 (0.20), residues: 663
  sheet: -3.40 (0.99), residues: 24
  loop : -2.78 (0.42), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 122 
 TYR   0.014   0.002   TYR F  28 
 PHE   0.026   0.002   PHE B  80 
 TRP   0.011   0.002   TRP C  81 
 HIS   0.006   0.001   HIS C  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (10931)
  covalent geometry    : angle       0.64963 (15496)
  hydrogen bonds       : bond        0.05144 (  595)
  hydrogen bonds       : angle       4.17323 ( 1594)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 142
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
REVERT: A  223 ASP cc_start: 0.7676 (t0) cc_final: 0.7430 (t70)
REVERT: A  248 HIS cc_start: 0.7847 (m-70) cc_final: 0.7582 (m-70)
REVERT: A  256 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7349 (mtp-110)
REVERT: B    4 ILE cc_start: 0.8802 (mt) cc_final: 0.8600 (mt)
REVERT: C   14 MET cc_start: 0.7503 (tpt) cc_final: 0.7276 (ttt)
REVERT: C   33 SER cc_start: 0.8381 (p) cc_final: 0.8081 (m)
REVERT: C   47 LYS cc_start: 0.8471 (mttm) cc_final: 0.8259 (mtpt)
REVERT: C   92 HIS cc_start: 0.7325 (OUTLIER) cc_final: 0.6875 (m90)
REVERT: E   50 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7236 (mt)
REVERT: E   67 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8556 (mmtt)
REVERT: E  103 GLN cc_start: 0.8280 (mm-40) cc_final: 0.7985 (mm-40)
REVERT: F   14 MET cc_start: 0.4443 (mmp) cc_final: 0.4101 (ttm)
REVERT: F   43 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7570 (tp30)
REVERT: F   54 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.7070 (tm-30)
REVERT: F   77 MET cc_start: 0.7812 (tpt) cc_final: 0.7506 (tpt)
REVERT: F  122 ARG cc_start: 0.4568 (OUTLIER) cc_final: 0.4095 (tmm160)
  outliers start: 40
  outliers final: 23
  residues processed: 167
  average time/residue: 0.1244
  time to fit residues: 26.9194
Evaluate side-chains
  155 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 125
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  256 ARG
Chi-restraints excluded: chain A residue  290 HIS
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain C residue   11 TYR
Chi-restraints excluded: chain C residue   92 HIS
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain E residue   16 ILE
Chi-restraints excluded: chain E residue   43 GLU
Chi-restraints excluded: chain E residue   50 LEU
Chi-restraints excluded: chain E residue   67 LYS
Chi-restraints excluded: chain E residue   85 LEU
Chi-restraints excluded: chain E residue   89 GLN
Chi-restraints excluded: chain E residue   94 MET
Chi-restraints excluded: chain E residue  117 ILE
Chi-restraints excluded: chain F residue   16 ILE
Chi-restraints excluded: chain F residue   27 LEU
Chi-restraints excluded: chain F residue   43 GLU
Chi-restraints excluded: chain F residue   54 GLU
Chi-restraints excluded: chain F residue  113 LEU
Chi-restraints excluded: chain F residue  122 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 93 optimal weight:    7.9990
   chunk 58 optimal weight:    0.6980
   chunk 41 optimal weight:    0.5980
   chunk 60 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 99 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B  64 GLN
** F  98 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 = 0.4009 r_free = 0.4009 target = 0.175208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.133661 restraints weight = 12980.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 1.27
r_work: 0.3284 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.3887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081  10931  Z= 0.166
  Angle     :  0.618   8.119  15496  Z= 0.315
  Chirality :  0.037   0.175   1837
  Planarity :  0.006   0.127   1403
  Dihedral  : 23.071 178.635   3396
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.57 %
    Allowed  :  6.36 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 22.22 %
    Favored  : 72.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.45 (0.28), residues: 881
  helix:  0.58 (0.20), residues: 662
  sheet: -3.49 (0.96), residues: 28
  loop : -2.74 (0.43), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 122 
 TYR   0.011   0.001   TYR F  28 
 PHE   0.026   0.002   PHE B  80 
 TRP   0.008   0.001   TRP A 303 
 HIS   0.023   0.001   HIS C  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (10931)
  covalent geometry    : angle       0.61814 (15496)
  hydrogen bonds       : bond        0.04904 (  595)
  hydrogen bonds       : angle       4.05906 ( 1594)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 134
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 HIS cc_start: 0.7808 (m-70) cc_final: 0.7585 (m-70)
REVERT: B    4 ILE cc_start: 0.8753 (mt) cc_final: 0.8549 (mt)
REVERT: B   26 TYR cc_start: 0.8643 (t80) cc_final: 0.8399 (t80)
REVERT: C   14 MET cc_start: 0.7519 (tpt) cc_final: 0.7284 (ttt)
REVERT: C   33 SER cc_start: 0.8375 (p) cc_final: 0.7978 (m)
REVERT: D  103 GLN cc_start: 0.7971 (mt0) cc_final: 0.7748 (mm-40)
REVERT: E   50 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7256 (mt)
REVERT: F   54 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.7090 (tm-30)
REVERT: F   77 MET cc_start: 0.7836 (tpt) cc_final: 0.7516 (tpt)
REVERT: F  122 ARG cc_start: 0.4546 (OUTLIER) cc_final: 0.4203 (tmm160)
  outliers start: 38
  outliers final: 20
  residues processed: 159
  average time/residue: 0.1060
  time to fit residues: 22.2444
Evaluate side-chains
  149 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 126
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  290 HIS
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain C residue   11 TYR
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain E residue   16 ILE
Chi-restraints excluded: chain E residue   43 GLU
Chi-restraints excluded: chain E residue   50 LEU
Chi-restraints excluded: chain E residue   85 LEU
Chi-restraints excluded: chain E residue   94 MET
Chi-restraints excluded: chain F residue   16 ILE
Chi-restraints excluded: chain F residue   54 GLU
Chi-restraints excluded: chain F residue  113 LEU
Chi-restraints excluded: chain F residue  122 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 49 optimal weight:    0.3980
   chunk 22 optimal weight:    1.9990
   chunk 63 optimal weight:    0.0870
   chunk 70 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 94 optimal weight:    9.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.5760

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

Flipped N/Q/H residues before XYZ refinement:
B  64 GLN
C  98 GLN
D  92 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.176992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.136511 restraints weight = 12931.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 1.24
r_work: 0.3315 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.4247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.084  10931  Z= 0.149
  Angle     :  0.600   8.907  15496  Z= 0.306
  Chirality :  0.036   0.217   1837
  Planarity :  0.006   0.119   1403
  Dihedral  : 22.772 177.670   3389
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.68 %
    Allowed  :  6.47 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 22.89 %
    Favored  : 72.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.09 (0.29), residues: 881
  helix:  0.79 (0.20), residues: 667
  sheet: -2.85 (1.15), residues: 24
  loop : -2.63 (0.44), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 122 
 TYR   0.011   0.001   TYR F  20 
 PHE   0.023   0.002   PHE B  80 
 TRP   0.007   0.001   TRP A 303 
 HIS   0.004   0.001   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (10931)
  covalent geometry    : angle       0.60000 (15496)
  hydrogen bonds       : bond        0.04807 (  595)
  hydrogen bonds       : angle       3.92886 ( 1594)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 139
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  223 ASP cc_start: 0.7563 (t70) cc_final: 0.7107 (t70)
REVERT: A  290 HIS cc_start: 0.6998 (OUTLIER) cc_final: 0.6305 (m-70)
REVERT: A  296 LEU cc_start: 0.6921 (tt) cc_final: 0.6674 (tt)
REVERT: C   14 MET cc_start: 0.7579 (tpt) cc_final: 0.7289 (ttt)
REVERT: C   33 SER cc_start: 0.8405 (p) cc_final: 0.7997 (m)
REVERT: D   47 LYS cc_start: 0.8893 (mttm) cc_final: 0.8687 (mttm)
REVERT: E   54 GLU cc_start: 0.7075 (tt0) cc_final: 0.6513 (tt0)
REVERT: E  103 GLN cc_start: 0.8221 (mm-40) cc_final: 0.7966 (mm-40)
REVERT: F   43 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7237 (tt0)
REVERT: F   54 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.7018 (tm-30)
REVERT: F   77 MET cc_start: 0.7778 (tpt) cc_final: 0.7488 (tpt)
REVERT: F  122 ARG cc_start: 0.4594 (OUTLIER) cc_final: 0.4349 (tmm160)
  outliers start: 34
  outliers final: 18
  residues processed: 166
  average time/residue: 0.1307
  time to fit residues: 28.0290
Evaluate side-chains
  148 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 126
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  290 HIS
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain C residue   11 TYR
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain E residue   43 GLU
Chi-restraints excluded: chain E residue   85 LEU
Chi-restraints excluded: chain E residue   88 ILE
Chi-restraints excluded: chain F residue   16 ILE
Chi-restraints excluded: chain F residue   43 GLU
Chi-restraints excluded: chain F residue   54 GLU
Chi-restraints excluded: chain F residue  113 LEU
Chi-restraints excluded: chain F residue  122 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 37 optimal weight:    0.2980
   chunk 43 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 26 optimal weight:    0.1980
   chunk 25 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0570
   chunk 99 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 78 optimal weight:    0.3980
   overall best weight:    0.3898

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

Flipped N/Q/H residues before XYZ refinement:
B  64 GLN
D  92 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.178430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.138410 restraints weight = 13016.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3577 rms_B_bonded: 1.17
r_work: 0.3364 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.4523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.085  10931  Z= 0.132
  Angle     :  0.596   9.508  15496  Z= 0.302
  Chirality :  0.036   0.182   1837
  Planarity :  0.006   0.117   1403
  Dihedral  : 22.643 177.573   3387
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.57 %
    Allowed  :  5.45 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 24.10 %
    Favored  : 72.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.29), residues: 881
  helix:  0.91 (0.20), residues: 668
  sheet: -2.73 (1.17), residues: 24
  loop : -2.45 (0.45), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 122 
 TYR   0.018   0.001   TYR F  20 
 PHE   0.022   0.002   PHE B  80 
 TRP   0.006   0.001   TRP A 303 
 HIS   0.003   0.001   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (10931)
  covalent geometry    : angle       0.59619 (15496)
  hydrogen bonds       : bond        0.04733 (  595)
  hydrogen bonds       : angle       3.84452 ( 1594)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 132
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  223 ASP cc_start: 0.7504 (t70) cc_final: 0.7093 (t70)
REVERT: A  290 HIS cc_start: 0.6926 (OUTLIER) cc_final: 0.6211 (m-70)
REVERT: C   14 MET cc_start: 0.7468 (tpt) cc_final: 0.7266 (ttt)
REVERT: C   33 SER cc_start: 0.8357 (p) cc_final: 0.8054 (p)
REVERT: E   54 GLU cc_start: 0.6888 (tt0) cc_final: 0.6350 (tt0)
REVERT: F   43 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7208 (tt0)
REVERT: F   77 MET cc_start: 0.7721 (tpt) cc_final: 0.7424 (tpt)
  outliers start: 28
  outliers final: 17
  residues processed: 153
  average time/residue: 0.1408
  time to fit residues: 27.5504
Evaluate side-chains
  141 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 122
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  290 HIS
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain C residue   11 TYR
Chi-restraints excluded: chain E residue   43 GLU
Chi-restraints excluded: chain E residue   85 LEU
Chi-restraints excluded: chain E residue   88 ILE
Chi-restraints excluded: chain F residue   15 LEU
Chi-restraints excluded: chain F residue   16 ILE
Chi-restraints excluded: chain F residue   43 GLU
Chi-restraints excluded: chain F residue  113 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 93 optimal weight:    7.9990
   chunk 1 optimal weight:    0.6980
   chunk 46 optimal weight:    0.7980
   chunk 91 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   chunk 40 optimal weight:    0.6980
   chunk 72 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  87 GLN
B  64 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.176156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.134837 restraints weight = 12843.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.3538 rms_B_bonded: 1.24
r_work: 0.3299 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.4569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083  10931  Z= 0.172
  Angle     :  0.614   9.577  15496  Z= 0.313
  Chirality :  0.036   0.172   1837
  Planarity :  0.006   0.119   1403
  Dihedral  : 22.529 176.932   3383
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.57 %
    Allowed  :  6.13 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 24.23 %
    Favored  : 72.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.28), residues: 881
  helix:  0.90 (0.20), residues: 663
  sheet: -2.98 (1.09), residues: 26
  loop : -2.21 (0.45), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 122 
 TYR   0.016   0.001   TYR F  20 
 PHE   0.025   0.002   PHE B  80 
 TRP   0.007   0.001   TRP C  81 
 HIS   0.004   0.001   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 (10931)
  covalent geometry    : angle       0.61427 (15496)
  hydrogen bonds       : bond        0.04905 (  595)
  hydrogen bonds       : angle       3.92803 ( 1594)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 135
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 TYR cc_start: 0.8730 (t80) cc_final: 0.8421 (t80)
REVERT: A  290 HIS cc_start: 0.7101 (OUTLIER) cc_final: 0.6358 (m-70)
REVERT: C   14 MET cc_start: 0.7645 (tpt) cc_final: 0.7336 (ttt)
REVERT: C   33 SER cc_start: 0.8354 (p) cc_final: 0.7991 (m)
REVERT: F   43 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7294 (tt0)
REVERT: F   77 MET cc_start: 0.7795 (tpt) cc_final: 0.7457 (tpt)
  outliers start: 28
  outliers final: 20
  residues processed: 153
  average time/residue: 0.1231
  time to fit residues: 24.4871
Evaluate side-chains
  155 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 133
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  290 HIS
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain C residue   11 TYR
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain E residue   43 GLU
Chi-restraints excluded: chain E residue   85 LEU
Chi-restraints excluded: chain E residue   88 ILE
Chi-restraints excluded: chain E residue  117 ILE
Chi-restraints excluded: chain F residue   15 LEU
Chi-restraints excluded: chain F residue   43 GLU
Chi-restraints excluded: chain F residue  113 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 64 optimal weight:    0.7980
   chunk 71 optimal weight:    8.9990
   chunk 19 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 67 optimal weight:    0.0870
   chunk 56 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
D  92 HIS
F  98 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.188186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.148411 restraints weight = 12900.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3725 rms_B_bonded: 1.21
r_work: 0.3543 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3378 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.4644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083  10931  Z= 0.163
  Angle     :  0.607   8.286  15496  Z= 0.308
  Chirality :  0.036   0.175   1837
  Planarity :  0.006   0.119   1403
  Dihedral  : 22.475 177.192   3381
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.57 %
    Allowed  :  5.56 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 23.83 %
    Favored  : 72.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.28), residues: 881
  helix:  0.90 (0.20), residues: 664
  sheet: -3.24 (1.01), residues: 28
  loop : -2.18 (0.45), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 122 
 TYR   0.014   0.001   TYR F  20 
 PHE   0.026   0.002   PHE B  80 
 TRP   0.006   0.001   TRP A 249 
 HIS   0.004   0.001   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (10931)
  covalent geometry    : angle       0.60671 (15496)
  hydrogen bonds       : bond        0.04893 (  595)
  hydrogen bonds       : angle       3.94029 ( 1594)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 133
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 TYR cc_start: 0.8765 (t80) cc_final: 0.8446 (t80)
REVERT: A  290 HIS cc_start: 0.7187 (OUTLIER) cc_final: 0.6430 (m-70)
REVERT: C   14 MET cc_start: 0.7729 (tpt) cc_final: 0.7408 (ttt)
REVERT: C   33 SER cc_start: 0.8526 (p) cc_final: 0.8182 (m)
REVERT: F   43 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7683 (tt0)
REVERT: F   77 MET cc_start: 0.7916 (tpt) cc_final: 0.7551 (tpt)
  outliers start: 30
  outliers final: 24
  residues processed: 151
  average time/residue: 0.1193
  time to fit residues: 23.2678
Evaluate side-chains
  154 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 128
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  290 HIS
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain C residue   11 TYR
Chi-restraints excluded: chain C residue   90 LYS
Chi-restraints excluded: chain C residue   92 HIS
Chi-restraints excluded: chain C residue   94 MET
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain E residue   43 GLU
Chi-restraints excluded: chain E residue   85 LEU
Chi-restraints excluded: chain E residue   88 ILE
Chi-restraints excluded: chain E residue  117 ILE
Chi-restraints excluded: chain F residue   15 LEU
Chi-restraints excluded: chain F residue   43 GLU
Chi-restraints excluded: chain F residue  113 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 87 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9980
   chunk 98 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 51 optimal weight:    0.0670
   chunk 18 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 81 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
D  92 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.188806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.149316 restraints weight = 12915.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 1.16
r_work: 0.3542 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3386 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.4724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.084  10931  Z= 0.153
  Angle     :  0.602   8.198  15496  Z= 0.306
  Chirality :  0.036   0.178   1837
  Planarity :  0.006   0.118   1403
  Dihedral  : 22.418 177.863   3381
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.57 %
    Allowed  :  6.13 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 23.29 %
    Favored  : 72.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.28), residues: 881
  helix:  0.90 (0.19), residues: 667
  sheet: -3.26 (1.00), residues: 28
  loop : -2.23 (0.46), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 122 
 TYR   0.016   0.001   TYR F  20 
 PHE   0.026   0.002   PHE B  80 
 TRP   0.007   0.001   TRP A 210 
 HIS   0.003   0.001   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (10931)
  covalent geometry    : angle       0.60179 (15496)
  hydrogen bonds       : bond        0.04862 (  595)
  hydrogen bonds       : angle       3.96343 ( 1594)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 130
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 TYR cc_start: 0.8784 (t80) cc_final: 0.8466 (t80)
REVERT: A  290 HIS cc_start: 0.7178 (OUTLIER) cc_final: 0.6410 (m-70)
REVERT: C   14 MET cc_start: 0.7901 (tpt) cc_final: 0.7416 (ttt)
REVERT: C   33 SER cc_start: 0.8555 (p) cc_final: 0.8222 (m)
REVERT: D   18 GLU cc_start: 0.7308 (mp0) cc_final: 0.7100 (mp0)
REVERT: E   50 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7385 (mt)
REVERT: F   43 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7665 (tt0)
REVERT: F   77 MET cc_start: 0.7930 (tpt) cc_final: 0.7528 (tpt)
  outliers start: 34
  outliers final: 26
  residues processed: 151
  average time/residue: 0.1126
  time to fit residues: 22.1538
Evaluate side-chains
  155 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 126
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  290 HIS
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain C residue   11 TYR
Chi-restraints excluded: chain C residue   90 LYS
Chi-restraints excluded: chain C residue   92 HIS
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain E residue   43 GLU
Chi-restraints excluded: chain E residue   50 LEU
Chi-restraints excluded: chain E residue   85 LEU
Chi-restraints excluded: chain E residue   88 ILE
Chi-restraints excluded: chain E residue  117 ILE
Chi-restraints excluded: chain F residue   15 LEU
Chi-restraints excluded: chain F residue   16 ILE
Chi-restraints excluded: chain F residue   43 GLU
Chi-restraints excluded: chain F residue  113 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 95 optimal weight:    6.9990
   chunk 25 optimal weight:    0.0770
   chunk 29 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 76 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 97 optimal weight:    4.9990
   chunk 90 optimal weight:    5.9990
   overall best weight:    1.1542

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

Flipped N/Q/H residues before XYZ refinement:
C  92 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.174282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.134141 restraints weight = 12749.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 1.14
r_work: 0.3328 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.4608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.089  10931  Z= 0.222
  Angle     :  0.659   8.067  15496  Z= 0.335
  Chirality :  0.038   0.179   1837
  Planarity :  0.006   0.119   1403
  Dihedral  : 22.415 178.947   3381
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.57 %
    Allowed  :  6.24 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 23.83 %
    Favored  : 72.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.09 (0.28), residues: 881
  helix:  0.72 (0.19), residues: 669
  sheet: -3.27 (1.01), residues: 28
  loop : -2.26 (0.45), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 122 
 TYR   0.018   0.002   TYR F  20 
 PHE   0.029   0.002   PHE B  80 
 TRP   0.011   0.002   TRP A 210 
 HIS   0.004   0.001   HIS F  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00519 (10931)
  covalent geometry    : angle       0.65893 (15496)
  hydrogen bonds       : bond        0.05178 (  595)
  hydrogen bonds       : angle       4.14113 ( 1594)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 129
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 TYR cc_start: 0.8826 (t80) cc_final: 0.8517 (t80)
REVERT: A  290 HIS cc_start: 0.7259 (OUTLIER) cc_final: 0.6557 (m-70)
REVERT: B   26 TYR cc_start: 0.8901 (t80) cc_final: 0.8552 (t80)
REVERT: C   14 MET cc_start: 0.7893 (tpt) cc_final: 0.7438 (ttt)
REVERT: C   33 SER cc_start: 0.8507 (p) cc_final: 0.8223 (m)
REVERT: E   50 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7440 (mt)
REVERT: F   43 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7511 (tt0)
REVERT: F   77 MET cc_start: 0.7997 (tpt) cc_final: 0.7620 (tpt)
  outliers start: 31
  outliers final: 23
  residues processed: 149
  average time/residue: 0.1263
  time to fit residues: 24.5857
Evaluate side-chains
  151 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 125
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  290 HIS
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain C residue   11 TYR
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain E residue   43 GLU
Chi-restraints excluded: chain E residue   50 LEU
Chi-restraints excluded: chain E residue   85 LEU
Chi-restraints excluded: chain E residue   88 ILE
Chi-restraints excluded: chain E residue  117 ILE
Chi-restraints excluded: chain F residue   43 GLU
Chi-restraints excluded: chain F residue  113 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 23 optimal weight:    0.3980
   chunk 43 optimal weight:    1.9990
   chunk 81 optimal weight:    0.2980
   chunk 97 optimal weight:    4.9990
   chunk 71 optimal weight:    0.1980
   chunk 56 optimal weight:    0.5980
   chunk 79 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 8 optimal weight:    0.3980
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.3780

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

Flipped N/Q/H residues before XYZ refinement:
C  92 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.179967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.140091 restraints weight = 12821.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3594 rms_B_bonded: 1.13
r_work: 0.3392 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.5070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.088  10931  Z= 0.131
  Angle     :  0.590   8.173  15496  Z= 0.301
  Chirality :  0.035   0.198   1837
  Planarity :  0.006   0.117   1403
  Dihedral  : 22.243 179.938   3381
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.57 %
    Allowed  :  5.68 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 24.77 %
    Favored  : 72.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.33 (0.28), residues: 881
  helix:  1.02 (0.19), residues: 669
  sheet: -2.69 (1.13), residues: 24
  loop : -2.20 (0.46), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 122 
 TYR   0.021   0.001   TYR F  20 
 PHE   0.022   0.002   PHE B  80 
 TRP   0.011   0.001   TRP A 210 
 HIS   0.004   0.001   HIS C  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (10931)
  covalent geometry    : angle       0.58957 (15496)
  hydrogen bonds       : bond        0.04870 (  595)
  hydrogen bonds       : angle       3.88704 ( 1594)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2119.34 seconds
wall clock time: 37 minutes 20.41 seconds (2240.41 seconds total)