Starting phenix.real_space_refine
on Fri Aug 22 22:13:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hij_34818/08_2025/8hij_34818_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hij_34818/08_2025/8hij_34818.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hij_34818/08_2025/8hij_34818.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hij_34818/08_2025/8hij_34818.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hij_34818/08_2025/8hij_34818_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hij_34818/08_2025/8hij_34818_neut.cif"
  }
  resolution = 3.54
  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=   0.001 sd=   0.018
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: 4
    Type Number    sf(0)   Gaussians
     S      26      5.16       5
     C    5304      2.51       5
     N    1379      2.21       5
     O    1536      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8245
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3969
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 498, 3969
          Classifications: {'peptide': 498}
          Link IDs: {'PTRANS': 17, 'TRANS': 480}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 1686
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1686
          Classifications: {'peptide': 225}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211}
    Chain: "N"
      Number of atoms: 925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 925
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
    Chain: "L"
      Number of atoms: 1632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1632
          Classifications: {'peptide': 212}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 201}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 33
          Unusual residues: {'THH': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.48, per 1000 atoms: 0.30
  Number of scatterers: 8245
  At special positions: 0
  Unit cell: (66.34, 101.65, 151.94, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      26     16.00
     O    1536      8.00
     N    1379      7.00
     C    5304      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 154 " - pdb=" SG  CYS H 210 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 136 " - pdb=" SG  CYS L 196 " distance=2.02

  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: 0.70
  Conformation dependent library (CDL) restraints added in 478.4 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue is complicated and confusing
        pdb=" CB  THH A 601 "
  Number of C-beta restraints generated:  1972

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 16 sheets defined
      40.2% alpha, 20.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid -80 through -64
      removed outlier: 3.713A  pdb=" N   LYS A -64 " --> pdb=" O   LYS A -68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid -57 through -43
    Processing helix  chain 'A' and resid -38 through -33
      removed outlier: 3.828A  pdb=" N   ASP A -33 " --> pdb=" O   PRO A -37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid -25 through -3
      removed outlier: 3.799A  pdb=" N   LEU A  -5 " --> pdb=" O   ASP A  -9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3 through 18
    Processing helix  chain 'A' and resid 27 through 39
    Processing helix  chain 'A' and resid 47 through 53
    Processing helix  chain 'A' and resid 60 through 66
    Processing helix  chain 'A' and resid 68 through 79
      removed outlier: 3.747A  pdb=" N   LEU A  77 " --> pdb=" O   SER A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 88
      removed outlier: 3.759A  pdb=" N   VAL A  83 " --> pdb=" O   VAL A  79 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   PHE A  84 " --> pdb=" O   LEU A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 112
      removed outlier: 3.617A  pdb=" N   LEU A  96 " --> pdb=" O   TYR A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 132
      removed outlier: 3.856A  pdb=" N   MET A 119 " --> pdb=" O   SER A 115 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   VAL A 128 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   THR A 129 " --> pdb=" O   PHE A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 144
    Processing helix  chain 'A' and resid 148 through 176
      removed outlier: 3.540A  pdb=" N   VAL A 152 " --> pdb=" O   ARG A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 202
    Processing helix  chain 'A' and resid 251 through 260
    Processing helix  chain 'A' and resid 264 through 296
      removed outlier: 3.512A  pdb=" N   ARG A 268 " --> pdb=" O   ARG A 264 " (cutoff:3.500A)
      removed outlier: 4.723A  pdb=" N   HIS A 289 " --> pdb=" O   VAL A 285 " (cutoff:3.500A)
      removed outlier: 5.118A  pdb=" N   ILE A 290 " --> pdb=" O   TYR A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 323
    Processing helix  chain 'A' and resid 335 through 355
      removed outlier: 3.936A  pdb=" N   ILE A 339 " --> pdb=" O   SER A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 360
      No H-bonds generated for 'chain 'A' and resid 358 through 360'
    Processing helix  chain 'A' and resid 361 through 378
      removed outlier: 3.672A  pdb=" N   PHE A 378 " --> pdb=" O   GLY A 374 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 389
    Processing helix  chain 'A' and resid 392 through 419
    Processing helix  chain 'A' and resid 427 through 451
      removed outlier: 3.988A  pdb=" N   MET A 451 " --> pdb=" O   PHE A 447 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 94
      removed outlier: 3.570A  pdb=" N   THR H  94 " --> pdb=" O   ALA H  91 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 107 through 112
      removed outlier: 3.763A  pdb=" N   TRP H 111 " --> pdb=" O   GLY H 107 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 170 through 172
      No H-bonds generated for 'chain 'H' and resid 170 through 172'
    Processing helix  chain 'H' and resid 201 through 203
      No H-bonds generated for 'chain 'H' and resid 201 through 203'
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 4.023A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 3.930A  pdb=" N   PHE L  84 " --> pdb=" O   PRO L  81 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10
      removed outlier: 3.689A  pdb=" N   GLN H   6 " --> pdb=" O   SER H  28 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   SER H  28 " --> pdb=" O   GLN H   6 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL H   8 " --> pdb=" O   ALA H  26 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   THR H  81 " --> pdb=" O   ASP H  76 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 14 through 15
    Processing sheet with id=AA3, first strand: chain 'H' and resid 20 through 22
    Processing sheet with id=AA4, first strand: chain 'H' and resid 48 through 54
      removed outlier: 6.919A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.931A  pdb=" N   TYR H  53 " --> pdb=" O   LEU H  37 " (cutoff:3.500A)
      removed outlier: 7.399A  pdb=" N   LEU H  37 " --> pdb=" O   TYR H  53 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 48 through 54
      removed outlier: 6.919A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.931A  pdb=" N   TYR H  53 " --> pdb=" O   LEU H  37 " (cutoff:3.500A)
      removed outlier: 7.399A  pdb=" N   LEU H  37 " --> pdb=" O   TYR H  53 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 134 through 138
      removed outlier: 3.680A  pdb=" N   LYS H 157 " --> pdb=" O   SER H 134 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   GLY H 153 " --> pdb=" O   LEU H 138 " (cutoff:3.500A)
      removed outlier: 6.115A  pdb=" N   TYR H 190 " --> pdb=" O   ASP H 158 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   VAL H 195 " --> pdb=" O   HIS H 178 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 134 through 138
      removed outlier: 3.680A  pdb=" N   LYS H 157 " --> pdb=" O   SER H 134 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   GLY H 153 " --> pdb=" O   LEU H 138 " (cutoff:3.500A)
      removed outlier: 6.115A  pdb=" N   TYR H 190 " --> pdb=" O   ASP H 158 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 164 through 168
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.671A  pdb=" N   GLN N   3 " --> pdb=" O   SER N  25 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   SER N  25 " --> pdb=" O   GLN N   3 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   SER N  21 " --> pdb=" O   SER N   7 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 3.923A  pdb=" N   THR N 118 " --> pdb=" O   GLY N  10 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   VAL N  12 " --> pdb=" O   THR N 118 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   GLN N  39 " --> pdb=" O   VAL N  93 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   MET N  34 " --> pdb=" O   VAL N  50 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   VAL N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12
      removed outlier: 3.923A  pdb=" N   THR N 118 " --> pdb=" O   GLY N  10 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   VAL N  12 " --> pdb=" O   THR N 118 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   GLN N  39 " --> pdb=" O   VAL N  93 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ALA N  97 " --> pdb=" O   SER N  35 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 11 through 13
      removed outlier: 3.567A  pdb=" N   LEU L  12 " --> pdb=" O   LYS L 105 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 20 through 25
      removed outlier: 3.785A  pdb=" N   VAL L  20 " --> pdb=" O   ILE L  76 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   THR L  75 " --> pdb=" O   SER L  64 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 54 through 55
      removed outlier: 6.567A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
      removed outlier: 4.731A  pdb=" N   TYR L  50 " --> pdb=" O   VAL L  34 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   VAL L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'L' and resid 118 through 120
      removed outlier: 3.894A  pdb=" N   VAL L 135 " --> pdb=" O   PHE L 120 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   VAL L 134 " --> pdb=" O   LEU L 181 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   TYR L 175 " --> pdb=" O   ASN L 140 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'L' and resid 147 through 151
      removed outlier: 3.634A  pdb=" N   LYS L 147 " --> pdb=" O   THR L 199 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ALA L 195 " --> pdb=" O   LYS L 151 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   TYR L 194 " --> pdb=" O   PHE L 211 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   CYS L 196 " --> pdb=" O   LYS L 209 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   LYS L 209 " --> pdb=" O   CYS L 196 " (cutoff:3.500A)

    404 hydrogen bonds defined for protein.
    1149 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.41

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1289
        1.31 -     1.44: 2457
        1.44 -     1.56: 4662
        1.56 -     1.69: 2
        1.69 -     1.81: 38
  Bond restraints: 8448
  Sorted by residual:
  bond pdb=" N   THH A 601 "
       pdb=" C   THH A 601 "
    ideal  model  delta    sigma   weight residual
    1.346  1.523 -0.177 2.00e-02 2.50e+03 7.80e+01
  bond pdb=" C4  THH A 601 "
       pdb=" O4  THH A 601 "
    ideal  model  delta    sigma   weight residual
    1.347  1.191  0.156 2.00e-02 2.50e+03 6.11e+01
  bond pdb=" C8A THH A 601 "
       pdb=" N8  THH A 601 "
    ideal  model  delta    sigma   weight residual
    1.351  1.499 -0.148 2.00e-02 2.50e+03 5.45e+01
  bond pdb=" C6  THH A 601 "
       pdb=" C9  THH A 601 "
    ideal  model  delta    sigma   weight residual
    1.542  1.645 -0.103 2.00e-02 2.50e+03 2.68e+01
  bond pdb=" C4A THH A 601 "
       pdb=" N5  THH A 601 "
    ideal  model  delta    sigma   weight residual
    1.419  1.517 -0.098 2.00e-02 2.50e+03 2.39e+01
  ... (remaining 8443 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 11100
        1.71 -     3.41: 295
        3.41 -     5.12: 59
        5.12 -     6.83: 27
        6.83 -     8.53: 12
  Bond angle restraints: 11493
  Sorted by residual:
  angle pdb=" N   THR A  69 "
        pdb=" CA  THR A  69 "
        pdb=" C   THR A  69 "
      ideal   model   delta    sigma   weight residual
     109.81  117.88   -8.07 2.21e+00 2.05e-01 1.33e+01
  angle pdb=" C   ASN L 212 "
        pdb=" N   ARG L 213 "
        pdb=" CA  ARG L 213 "
      ideal   model   delta    sigma   weight residual
     121.70  128.02   -6.32 1.80e+00 3.09e-01 1.23e+01
  angle pdb=" C   PHE N 103 "
        pdb=" N   TYR N 104 "
        pdb=" CA  TYR N 104 "
      ideal   model   delta    sigma   weight residual
     122.36  127.05   -4.69 1.42e+00 4.96e-01 1.09e+01
  angle pdb=" C   SER L  51 "
        pdb=" N   ALA L  52 "
        pdb=" CA  ALA L  52 "
      ideal   model   delta    sigma   weight residual
     121.54  127.64   -6.10 1.91e+00 2.74e-01 1.02e+01
  angle pdb=" CA  THR A  69 "
        pdb=" C   THR A  69 "
        pdb=" N   PRO A  70 "
      ideal   model   delta    sigma   weight residual
     118.44  122.82   -4.38 1.59e+00 3.96e-01 7.59e+00
  ... (remaining 11488 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.81: 4800
       15.81 -    31.62: 132
       31.62 -    47.43: 39
       47.43 -    63.24: 5
       63.24 -    79.05: 12
  Dihedral angle restraints: 4988
    sinusoidal: 1911
      harmonic: 3077
  Sorted by residual:
  dihedral pdb=" CB  CYS H 154 "
           pdb=" SG  CYS H 154 "
           pdb=" SG  CYS H 210 "
           pdb=" CB  CYS H 210 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  172.05  -79.05     1      1.00e+01 1.00e-02 7.78e+01
  dihedral pdb=" CA  ARG A  91 "
           pdb=" C   ARG A  91 "
           pdb=" N   TYR A  92 "
           pdb=" CA  TYR A  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.01   23.99     0      5.00e+00 4.00e-02 2.30e+01
  dihedral pdb=" CA  ALA A  17 "
           pdb=" C   ALA A  17 "
           pdb=" N   TYR A  18 "
           pdb=" CA  TYR A  18 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.52  -23.48     0      5.00e+00 4.00e-02 2.21e+01
  ... (remaining 4985 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 995
       0.050 -    0.101: 236
       0.101 -    0.151: 61
       0.151 -    0.201: 4
       0.201 -    0.252: 2
  Chirality restraints: 1298
  Sorted by residual:
  chirality pdb=" CA  THR A  69 "
            pdb=" N   THR A  69 "
            pdb=" C   THR A  69 "
            pdb=" CB  THR A  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.27    0.25 2.00e-01 2.50e+01 1.58e+00
  chirality pdb=" CB  THR A  69 "
            pdb=" CA  THR A  69 "
            pdb=" OG1 THR A  69 "
            pdb=" CG2 THR A  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.34    0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CA  TRP A 107 "
            pdb=" N   TRP A 107 "
            pdb=" C   TRP A 107 "
            pdb=" CB  TRP A 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.03e-01
  ... (remaining 1295 not shown)

  Planarity restraints: 1440
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H 102 "   -0.014 2.00e-02 2.50e+03   1.39e-02 4.81e+00
        pdb=" CG  TRP H 102 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP H 102 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP H 102 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP H 102 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP H 102 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP H 102 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H 102 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H 102 "   -0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP H 102 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 103 "    0.014 2.00e-02 2.50e+03   1.53e-02 4.09e+00
        pdb=" CG  PHE A 103 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 103 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 103 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 103 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 103 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 103 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 108 "   -0.033 5.00e-02 4.00e+02   4.83e-02 3.74e+00
        pdb=" N   PRO H 109 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO H 109 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO H 109 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 1437 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 2578
        2.83 -     3.35: 7065
        3.35 -     3.87: 13375
        3.87 -     4.38: 14375
        4.38 -     4.90: 25690
  Nonbonded interactions: 63083
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A  49 "
            pdb=" O4  THH A 601 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" O   ARG A  61 "
            pdb=" OG1 THR A  65 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" O   VAL A  83 "
            pdb=" OG1 THR A  87 "
     model   vdw
     2.337 3.040
  nonbonded pdb=" OG  SER L  64 "
            pdb=" OG1 THR L  75 "
     model   vdw
     2.341 3.040
  nonbonded pdb=" OD2 ASP H  76 "
            pdb=" OG  SER H  78 "
     model   vdw
     2.350 3.040
  ... (remaining 63078 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.080
  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:                    0.030
  Process input model:                     10.340
  Find NCS groups from input model:        0.040
  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:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6779
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      :  0.005   0.177   8453  Z= 0.266
  Angle     :  0.758   8.532  11503  Z= 0.389
  Chirality :  0.047   0.252   1298
  Planarity :  0.006   0.048   1440
  Dihedral  :  9.657  76.505   3001
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -3.81 (0.21), residues: 1045
  helix: -1.71 (0.19), residues: 384
  sheet: -3.00 (0.29), residues: 231
  loop : -2.88 (0.24), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG N  52 
 TYR   0.026   0.002   TYR A 435 
 PHE   0.033   0.002   PHE A 103 
 TRP   0.037   0.002   TRP H 102 
 HIS   0.004   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 ( 8448)
  covalent geometry    : angle       0.75815 (11493)
  SS BOND              : bond        0.00327 (    5)
  SS BOND              : angle       0.94301 (   10)
  hydrogen bonds       : bond        0.17072 (  384)
  hydrogen bonds       : angle       7.63783 ( 1149)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 280
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -55 ASP cc_start: 0.6609 (t0) cc_final: 0.6405 (t0)
REVERT: A  -51 LYS cc_start: 0.8509 (mttt) cc_final: 0.8247 (mttt)
REVERT: A  -50 MET cc_start: 0.6978 (mmm) cc_final: 0.6731 (mmm)
REVERT: A  -16 ILE cc_start: 0.8500 (tp) cc_final: 0.8173 (mt)
REVERT: A    1 VAL cc_start: 0.8584 (m) cc_final: 0.8263 (p)
REVERT: A   46 SER cc_start: 0.7456 (m) cc_final: 0.6633 (t)
REVERT: A   81 VAL cc_start: 0.7706 (t) cc_final: 0.7475 (m)
REVERT: A  127 SER cc_start: 0.8834 (p) cc_final: 0.8229 (t)
REVERT: A  139 TYR cc_start: 0.7092 (t80) cc_final: 0.6886 (t80)
REVERT: A  149 TYR cc_start: 0.6915 (t80) cc_final: 0.6580 (t80)
REVERT: A  155 TYR cc_start: 0.6982 (m-80) cc_final: 0.6754 (m-80)
REVERT: A  162 LEU cc_start: 0.7897 (tp) cc_final: 0.7613 (tp)
REVERT: A  254 MET cc_start: 0.7477 (mtt) cc_final: 0.7163 (mtt)
REVERT: A  314 THR cc_start: 0.8067 (m) cc_final: 0.7829 (p)
REVERT: A  405 PHE cc_start: 0.8105 (t80) cc_final: 0.7820 (t80)
REVERT: A  406 PHE cc_start: 0.7492 (m-80) cc_final: 0.6995 (m-80)
REVERT: A  411 LYS cc_start: 0.8025 (ttpt) cc_final: 0.7746 (ttpt)
REVERT: H   37 LEU cc_start: 0.7269 (mt) cc_final: 0.6950 (mm)
REVERT: H   46 LYS cc_start: 0.8134 (mmtt) cc_final: 0.7788 (mmtt)
REVERT: H  152 LEU cc_start: 0.7479 (tp) cc_final: 0.7115 (tp)
REVERT: N   34 MET cc_start: 0.6920 (mtp) cc_final: 0.6480 (mtp)
REVERT: L    4 GLN cc_start: 0.7196 (mm-40) cc_final: 0.6633 (mm-40)
REVERT: L   38 GLN cc_start: 0.8298 (tt0) cc_final: 0.8093 (tt0)
REVERT: L   73 THR cc_start: 0.8035 (m) cc_final: 0.7832 (t)
REVERT: L   83 ASP cc_start: 0.6949 (m-30) cc_final: 0.6615 (m-30)
REVERT: L   93 LEU cc_start: 0.7949 (tp) cc_final: 0.7464 (tp)
REVERT: L   97 LEU cc_start: 0.8607 (mp) cc_final: 0.8387 (mt)
REVERT: L  104 THR cc_start: 0.8497 (p) cc_final: 0.8194 (t)
REVERT: L  142 TYR cc_start: 0.7731 (t80) cc_final: 0.7496 (t80)
REVERT: L  147 LYS cc_start: 0.7312 (ttmm) cc_final: 0.7103 (ttmm)
REVERT: L  211 PHE cc_start: 0.8091 (p90) cc_final: 0.7847 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 280
  average time/residue: 0.1022
  time to fit residues: 38.8237
Evaluate side-chains
  223 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    0.0370
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
** A -61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  -3 ASN
A  63 GLN
A  66 ASN
A  99 GLN
A 172 GLN
A 293 ASN
H 178 HIS
N  65 GLN
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 168 GLN
L 191 HIS
L 200 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.153986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.133575 restraints weight = 14078.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.137795 restraints weight = 7115.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.140430 restraints weight = 4331.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.142416 restraints weight = 3026.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.143737 restraints weight = 2282.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6915
moved from start:          0.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8453  Z= 0.185
  Angle     :  0.648  10.629  11503  Z= 0.330
  Chirality :  0.043   0.219   1298
  Planarity :  0.005   0.047   1440
  Dihedral  :  5.623  52.066   1184
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  :  8.96 %
    Favored  : 88.58 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -2.06 (0.24), residues: 1045
  helix:  0.44 (0.25), residues: 383
  sheet: -2.51 (0.30), residues: 245
  loop : -2.28 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A -21 
 TYR   0.023   0.002   TYR A 438 
 PHE   0.015   0.002   PHE A -18 
 TRP   0.035   0.002   TRP H 102 
 HIS   0.004   0.001   HIS L 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 8448)
  covalent geometry    : angle       0.64621 (11493)
  SS BOND              : bond        0.00379 (    5)
  SS BOND              : angle       1.67324 (   10)
  hydrogen bonds       : bond        0.04222 (  384)
  hydrogen bonds       : angle       5.15037 ( 1149)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 233
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
REVERT: A  -70 ASN cc_start: 0.7416 (m110) cc_final: 0.7160 (m110)
REVERT: A  -55 ASP cc_start: 0.6762 (t0) cc_final: 0.6558 (t0)
REVERT: A  -51 LYS cc_start: 0.8732 (mttt) cc_final: 0.8437 (mttt)
REVERT: A    1 VAL cc_start: 0.8603 (m) cc_final: 0.8385 (p)
REVERT: A   11 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7057 (tm)
REVERT: A   46 SER cc_start: 0.7571 (m) cc_final: 0.7144 (t)
REVERT: A  127 SER cc_start: 0.8704 (p) cc_final: 0.8246 (t)
REVERT: A  162 LEU cc_start: 0.8106 (tp) cc_final: 0.7835 (tp)
REVERT: A  190 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8222 (tp)
REVERT: A  254 MET cc_start: 0.7506 (mtt) cc_final: 0.7102 (mtt)
REVERT: A  310 ASP cc_start: 0.7555 (t0) cc_final: 0.7336 (t0)
REVERT: A  314 THR cc_start: 0.8174 (m) cc_final: 0.7889 (p)
REVERT: A  394 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7585 (mm-30)
REVERT: A  405 PHE cc_start: 0.8214 (t80) cc_final: 0.7906 (t80)
REVERT: A  406 PHE cc_start: 0.7569 (m-80) cc_final: 0.7110 (m-10)
REVERT: A  445 ILE cc_start: 0.6725 (mt) cc_final: 0.6477 (mt)
REVERT: H   74 SER cc_start: 0.7747 (t) cc_final: 0.7232 (p)
REVERT: H   80 ASN cc_start: 0.8284 (t0) cc_final: 0.8008 (t0)
REVERT: H   98 TYR cc_start: 0.8570 (m-80) cc_final: 0.8303 (m-80)
REVERT: N   34 MET cc_start: 0.6831 (mtp) cc_final: 0.6396 (mtp)
REVERT: N   89 GLU cc_start: 0.7395 (mp0) cc_final: 0.7160 (mp0)
REVERT: L    4 GLN cc_start: 0.7214 (mm-40) cc_final: 0.6768 (mm-40)
REVERT: L   53 SER cc_start: 0.8007 (m) cc_final: 0.7777 (t)
REVERT: L   73 THR cc_start: 0.8078 (m) cc_final: 0.7721 (t)
REVERT: L   83 ASP cc_start: 0.7359 (m-30) cc_final: 0.7052 (m-30)
REVERT: L   91 GLN cc_start: 0.8445 (pp30) cc_final: 0.8243 (pp30)
REVERT: L   97 LEU cc_start: 0.8615 (mp) cc_final: 0.8381 (mt)
REVERT: L  120 PHE cc_start: 0.7853 (m-80) cc_final: 0.7395 (m-80)
REVERT: L  142 TYR cc_start: 0.8027 (t80) cc_final: 0.7701 (t80)
REVERT: L  145 GLU cc_start: 0.7582 (mp0) cc_final: 0.7160 (mp0)
REVERT: L  172 ASP cc_start: 0.8484 (p0) cc_final: 0.8200 (p0)
REVERT: L  190 LYS cc_start: 0.7552 (ttpp) cc_final: 0.7052 (ttpp)
REVERT: L  211 PHE cc_start: 0.8270 (p90) cc_final: 0.7970 (p90)
  outliers start: 22
  outliers final: 11
  residues processed: 246
  average time/residue: 0.1038
  time to fit residues: 34.4342
Evaluate side-chains
  238 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 225
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   14 THR
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  293 ASN
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain H residue  167 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 57 optimal weight:    0.1980
   chunk 52 optimal weight:    0.9980
   chunk 93 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 78 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A -61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  66 ASN
A  99 GLN
A 289 HIS
** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.150233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.129740 restraints weight = 13640.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.133913 restraints weight = 6939.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.136595 restraints weight = 4304.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.138597 restraints weight = 3046.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.139918 restraints weight = 2285.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6972
moved from start:          0.3124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8453  Z= 0.183
  Angle     :  0.610   8.038  11503  Z= 0.313
  Chirality :  0.043   0.198   1298
  Planarity :  0.004   0.038   1440
  Dihedral  :  5.480  48.434   1184
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 10.30 %
    Favored  : 86.45 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -1.36 (0.25), residues: 1045
  helix:  1.00 (0.25), residues: 382
  sheet: -2.10 (0.31), residues: 233
  loop : -1.90 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  70 
 TYR   0.026   0.002   TYR A 286 
 PHE   0.012   0.002   PHE A 372 
 TRP   0.036   0.002   TRP A 292 
 HIS   0.004   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 8448)
  covalent geometry    : angle       0.60808 (11493)
  SS BOND              : bond        0.00440 (    5)
  SS BOND              : angle       1.71675 (   10)
  hydrogen bonds       : bond        0.04199 (  384)
  hydrogen bonds       : angle       4.90650 ( 1149)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 245
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -57 VAL cc_start: 0.7034 (m) cc_final: 0.6762 (p)
REVERT: A  -51 LYS cc_start: 0.8710 (mttt) cc_final: 0.8432 (mttt)
REVERT: A   -6 LYS cc_start: 0.8184 (ttpt) cc_final: 0.7887 (ttpt)
REVERT: A    1 VAL cc_start: 0.8636 (m) cc_final: 0.8325 (p)
REVERT: A    3 GLU cc_start: 0.7487 (mp0) cc_final: 0.6814 (mp0)
REVERT: A   11 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7065 (tm)
REVERT: A   46 SER cc_start: 0.7522 (m) cc_final: 0.7152 (t)
REVERT: A  127 SER cc_start: 0.8691 (p) cc_final: 0.8168 (t)
REVERT: A  128 VAL cc_start: 0.8431 (OUTLIER) cc_final: 0.8144 (p)
REVERT: A  162 LEU cc_start: 0.8132 (tp) cc_final: 0.7879 (tp)
REVERT: A  190 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8197 (tp)
REVERT: A  254 MET cc_start: 0.7598 (mtt) cc_final: 0.7157 (mtt)
REVERT: A  310 ASP cc_start: 0.7513 (t0) cc_final: 0.7300 (t0)
REVERT: A  314 THR cc_start: 0.8194 (m) cc_final: 0.7876 (p)
REVERT: A  326 PHE cc_start: 0.6702 (m-10) cc_final: 0.6408 (m-10)
REVERT: A  394 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7588 (mm-30)
REVERT: A  405 PHE cc_start: 0.8294 (t80) cc_final: 0.7973 (t80)
REVERT: A  406 PHE cc_start: 0.7608 (m-80) cc_final: 0.7144 (m-10)
REVERT: A  445 ILE cc_start: 0.6859 (mt) cc_final: 0.6590 (mt)
REVERT: H   74 SER cc_start: 0.7910 (t) cc_final: 0.7372 (p)
REVERT: H   80 ASN cc_start: 0.8272 (t0) cc_final: 0.7933 (t0)
REVERT: H   98 TYR cc_start: 0.8594 (m-80) cc_final: 0.8287 (m-80)
REVERT: H  131 LYS cc_start: 0.7661 (ptmm) cc_final: 0.7358 (ptpp)
REVERT: H  138 LEU cc_start: 0.8272 (mt) cc_final: 0.8056 (mt)
REVERT: N   34 MET cc_start: 0.6900 (mtp) cc_final: 0.6433 (mtp)
REVERT: N   89 GLU cc_start: 0.7514 (mp0) cc_final: 0.7168 (mp0)
REVERT: L    4 GLN cc_start: 0.7270 (mm-40) cc_final: 0.6824 (mm-40)
REVERT: L   53 SER cc_start: 0.8172 (m) cc_final: 0.7940 (t)
REVERT: L   68 SER cc_start: 0.7899 (m) cc_final: 0.7445 (p)
REVERT: L   87 TYR cc_start: 0.8315 (m-80) cc_final: 0.7877 (m-80)
REVERT: L   97 LEU cc_start: 0.8612 (mp) cc_final: 0.8360 (mt)
REVERT: L  142 TYR cc_start: 0.7996 (t80) cc_final: 0.7712 (t80)
REVERT: L  172 ASP cc_start: 0.8428 (p0) cc_final: 0.8169 (p0)
REVERT: L  190 LYS cc_start: 0.7462 (ttpp) cc_final: 0.6950 (ttpp)
REVERT: L  211 PHE cc_start: 0.8267 (p90) cc_final: 0.7910 (p90)
  outliers start: 29
  outliers final: 20
  residues processed: 259
  average time/residue: 0.1045
  time to fit residues: 36.3565
Evaluate side-chains
  260 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 237
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  157 ARG
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  451 MET
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain H residue   77 THR
Chi-restraints excluded: chain H residue   87 ASN
Chi-restraints excluded: chain H residue  165 THR
Chi-restraints excluded: chain H residue  167 SER
Chi-restraints excluded: chain H residue  184 LEU
Chi-restraints excluded: chain H residue  219 THR
Chi-restraints excluded: chain N residue  104 TYR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue  125 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 100 optimal weight:    0.9980
   chunk 40 optimal weight:    0.1980
   chunk 50 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 88 optimal weight:    1.9990
   chunk 95 optimal weight:    0.0370
   chunk 58 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
A -70 ASN
** H 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 160 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.149004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.128459 restraints weight = 14010.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.132670 restraints weight = 7043.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.135557 restraints weight = 4318.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.137473 restraints weight = 2973.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.138673 restraints weight = 2239.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6996
moved from start:          0.3611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8453  Z= 0.167
  Angle     :  0.602   8.424  11503  Z= 0.304
  Chirality :  0.043   0.201   1298
  Planarity :  0.004   0.041   1440
  Dihedral  :  5.248  45.993   1184
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 12.54 %
    Favored  : 83.54 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -1.00 (0.26), residues: 1045
  helix:  1.30 (0.25), residues: 383
  sheet: -1.87 (0.32), residues: 236
  loop : -1.73 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A -21 
 TYR   0.027   0.002   TYR A 286 
 PHE   0.013   0.001   PHE L 100 
 TRP   0.019   0.002   TRP A 292 
 HIS   0.005   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 8448)
  covalent geometry    : angle       0.60070 (11493)
  SS BOND              : bond        0.00350 (    5)
  SS BOND              : angle       1.42724 (   10)
  hydrogen bonds       : bond        0.03972 (  384)
  hydrogen bonds       : angle       4.69946 ( 1149)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 249
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -57 VAL cc_start: 0.6953 (m) cc_final: 0.6662 (p)
REVERT: A  -51 LYS cc_start: 0.8650 (mttt) cc_final: 0.8399 (mttt)
REVERT: A  -50 MET cc_start: 0.7828 (mtm) cc_final: 0.7590 (mtm)
REVERT: A  -36 LYS cc_start: 0.8058 (mppt) cc_final: 0.7558 (ttmm)
REVERT: A    1 VAL cc_start: 0.8646 (m) cc_final: 0.8433 (p)
REVERT: A   11 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7091 (tm)
REVERT: A   46 SER cc_start: 0.7504 (m) cc_final: 0.7213 (t)
REVERT: A  127 SER cc_start: 0.8763 (p) cc_final: 0.8273 (t)
REVERT: A  128 VAL cc_start: 0.8372 (OUTLIER) cc_final: 0.8100 (p)
REVERT: A  162 LEU cc_start: 0.8145 (tp) cc_final: 0.7916 (tp)
REVERT: A  190 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8183 (tp)
REVERT: A  211 PHE cc_start: 0.7768 (m-80) cc_final: 0.6890 (m-80)
REVERT: A  254 MET cc_start: 0.7607 (mtt) cc_final: 0.7151 (mtt)
REVERT: A  310 ASP cc_start: 0.7535 (t0) cc_final: 0.7254 (t0)
REVERT: A  314 THR cc_start: 0.8169 (m) cc_final: 0.7831 (p)
REVERT: A  326 PHE cc_start: 0.6690 (m-10) cc_final: 0.6413 (m-10)
REVERT: A  346 GLN cc_start: 0.7688 (mt0) cc_final: 0.7460 (mt0)
REVERT: A  370 VAL cc_start: 0.8729 (t) cc_final: 0.8494 (p)
REVERT: A  394 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7723 (mm-30)
REVERT: A  405 PHE cc_start: 0.8279 (t80) cc_final: 0.7975 (t80)
REVERT: A  406 PHE cc_start: 0.7568 (m-80) cc_final: 0.7131 (m-10)
REVERT: A  445 ILE cc_start: 0.6980 (mt) cc_final: 0.6725 (mt)
REVERT: H   35 PHE cc_start: 0.6946 (m-80) cc_final: 0.6415 (m-80)
REVERT: H   74 SER cc_start: 0.7962 (t) cc_final: 0.7436 (p)
REVERT: H   80 ASN cc_start: 0.8259 (t0) cc_final: 0.7901 (t0)
REVERT: H   98 TYR cc_start: 0.8567 (m-80) cc_final: 0.8165 (m-80)
REVERT: H  131 LYS cc_start: 0.7540 (ptmm) cc_final: 0.7230 (ptpp)
REVERT: N   34 MET cc_start: 0.6920 (mtp) cc_final: 0.6446 (mtp)
REVERT: N   89 GLU cc_start: 0.7593 (mp0) cc_final: 0.7178 (mp0)
REVERT: L    4 GLN cc_start: 0.7298 (mm-40) cc_final: 0.6870 (mm-40)
REVERT: L   68 SER cc_start: 0.8051 (m) cc_final: 0.7569 (p)
REVERT: L   87 TYR cc_start: 0.8352 (m-80) cc_final: 0.7873 (m-80)
REVERT: L   90 GLN cc_start: 0.8352 (tm-30) cc_final: 0.7263 (tt0)
REVERT: L   97 LEU cc_start: 0.8526 (mp) cc_final: 0.8268 (mt)
REVERT: L  145 GLU cc_start: 0.7664 (mp0) cc_final: 0.7166 (mp0)
REVERT: L  175 TYR cc_start: 0.7933 (m-10) cc_final: 0.7603 (m-10)
REVERT: L  190 LYS cc_start: 0.7453 (ttpp) cc_final: 0.6874 (ttpp)
REVERT: L  211 PHE cc_start: 0.8325 (p90) cc_final: 0.7904 (p90)
  outliers start: 35
  outliers final: 21
  residues processed: 261
  average time/residue: 0.1105
  time to fit residues: 38.3705
Evaluate side-chains
  257 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 233
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  451 MET
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain H residue   87 ASN
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  165 THR
Chi-restraints excluded: chain H residue  167 SER
Chi-restraints excluded: chain H residue  184 LEU
Chi-restraints excluded: chain H residue  219 THR
Chi-restraints excluded: chain N residue  104 TYR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   66 SER
Chi-restraints excluded: chain L residue  125 SER
Chi-restraints excluded: chain L residue  199 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 100 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   chunk 52 optimal weight:    0.7980
   chunk 98 optimal weight:    0.7980
   chunk 18 optimal weight:    0.3980
   chunk 97 optimal weight:    0.6980
   chunk 103 optimal weight:    0.3980
   chunk 32 optimal weight:    0.6980
   chunk 55 optimal weight:    0.0000
   overall best weight:    0.4384

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

Flipped N/Q/H residues before XYZ refinement:
A -70 ASN
H 214 HIS
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.148656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.128219 restraints weight = 13951.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.132460 restraints weight = 6964.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.135301 restraints weight = 4229.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.137153 restraints weight = 2908.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.138429 restraints weight = 2194.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6995
moved from start:          0.3912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8453  Z= 0.150
  Angle     :  0.606   7.503  11503  Z= 0.304
  Chirality :  0.043   0.202   1298
  Planarity :  0.004   0.039   1440
  Dihedral  :  5.111  45.734   1184
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 14.11 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -0.67 (0.26), residues: 1045
  helix:  1.55 (0.25), residues: 384
  sheet: -1.62 (0.32), residues: 237
  loop : -1.58 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  70 
 TYR   0.027   0.001   TYR A 286 
 PHE   0.019   0.001   PHE L 100 
 TRP   0.039   0.002   TRP A 292 
 HIS   0.004   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 8448)
  covalent geometry    : angle       0.60446 (11493)
  SS BOND              : bond        0.00311 (    5)
  SS BOND              : angle       1.46046 (   10)
  hydrogen bonds       : bond        0.03886 (  384)
  hydrogen bonds       : angle       4.57297 ( 1149)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 227
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -57 VAL cc_start: 0.6985 (m) cc_final: 0.6688 (p)
REVERT: A  -51 LYS cc_start: 0.8605 (mttt) cc_final: 0.8360 (mttt)
REVERT: A  -32 LYS cc_start: 0.6421 (pttt) cc_final: 0.5918 (pttt)
REVERT: A    2 LYS cc_start: 0.8024 (ptpt) cc_final: 0.7765 (ptpt)
REVERT: A   11 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7150 (tm)
REVERT: A   46 SER cc_start: 0.7553 (m) cc_final: 0.7243 (t)
REVERT: A  127 SER cc_start: 0.8708 (p) cc_final: 0.8288 (t)
REVERT: A  128 VAL cc_start: 0.8359 (t) cc_final: 0.8116 (p)
REVERT: A  162 LEU cc_start: 0.8145 (tp) cc_final: 0.7914 (tp)
REVERT: A  190 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8068 (tt)
REVERT: A  211 PHE cc_start: 0.7781 (m-80) cc_final: 0.6722 (m-80)
REVERT: A  254 MET cc_start: 0.7667 (mtt) cc_final: 0.7167 (mtt)
REVERT: A  310 ASP cc_start: 0.7434 (t0) cc_final: 0.7203 (t0)
REVERT: A  326 PHE cc_start: 0.6672 (m-10) cc_final: 0.6406 (m-10)
REVERT: A  346 GLN cc_start: 0.7704 (mt0) cc_final: 0.7442 (mt0)
REVERT: A  394 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7607 (mm-30)
REVERT: A  405 PHE cc_start: 0.8279 (t80) cc_final: 0.7833 (t80)
REVERT: A  408 THR cc_start: 0.8594 (m) cc_final: 0.8263 (p)
REVERT: A  446 TYR cc_start: 0.7333 (m-80) cc_final: 0.7097 (m-10)
REVERT: H   35 PHE cc_start: 0.6923 (m-80) cc_final: 0.6402 (m-80)
REVERT: H   74 SER cc_start: 0.7976 (t) cc_final: 0.7458 (p)
REVERT: H   98 TYR cc_start: 0.8577 (m-80) cc_final: 0.8100 (m-80)
REVERT: H  131 LYS cc_start: 0.7529 (ptmm) cc_final: 0.7219 (ptpp)
REVERT: N   34 MET cc_start: 0.6944 (mtp) cc_final: 0.6438 (mtp)
REVERT: N   89 GLU cc_start: 0.7615 (mp0) cc_final: 0.7192 (mp0)
REVERT: L    4 GLN cc_start: 0.7291 (mm-40) cc_final: 0.6846 (mm-40)
REVERT: L   50 TYR cc_start: 0.7858 (p90) cc_final: 0.7653 (p90)
REVERT: L   68 SER cc_start: 0.8094 (m) cc_final: 0.7622 (p)
REVERT: L   87 TYR cc_start: 0.8342 (m-80) cc_final: 0.7825 (m-80)
REVERT: L  148 VAL cc_start: 0.8571 (OUTLIER) cc_final: 0.8339 (m)
REVERT: L  175 TYR cc_start: 0.7864 (m-10) cc_final: 0.7555 (m-10)
REVERT: L  190 LYS cc_start: 0.7400 (ttpp) cc_final: 0.6768 (ttpp)
REVERT: L  211 PHE cc_start: 0.8320 (p90) cc_final: 0.7844 (p90)
  outliers start: 35
  outliers final: 27
  residues processed: 246
  average time/residue: 0.1102
  time to fit residues: 35.9269
Evaluate side-chains
  251 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 221
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  182 PHE
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  451 MET
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain H residue   87 ASN
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  165 THR
Chi-restraints excluded: chain H residue  184 LEU
Chi-restraints excluded: chain H residue  219 THR
Chi-restraints excluded: chain H residue  228 LYS
Chi-restraints excluded: chain N residue  104 TYR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   66 SER
Chi-restraints excluded: chain L residue  112 VAL
Chi-restraints excluded: chain L residue  125 SER
Chi-restraints excluded: chain L residue  148 VAL
Chi-restraints excluded: chain L residue  199 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 11 optimal weight:    0.5980
   chunk 80 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 53 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 47 optimal weight:    0.0070
   chunk 3 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0270
   chunk 86 optimal weight:    0.0570
   overall best weight:    0.2574

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

Flipped N/Q/H residues before XYZ refinement:
H 169 ASN
** L  91 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 = 0.3957 r_free = 0.3957 target = 0.150082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.129535 restraints weight = 13826.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.133796 restraints weight = 6914.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.136362 restraints weight = 4189.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.138411 restraints weight = 2944.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.139648 restraints weight = 2215.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6973
moved from start:          0.4117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8453  Z= 0.124
  Angle     :  0.614   7.354  11503  Z= 0.306
  Chirality :  0.042   0.207   1298
  Planarity :  0.004   0.037   1440
  Dihedral  :  4.920  45.287   1184
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 14.33 %
    Favored  : 81.75 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -0.46 (0.26), residues: 1045
  helix:  1.71 (0.25), residues: 383
  sheet: -1.50 (0.33), residues: 233
  loop : -1.45 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A -21 
 TYR   0.028   0.001   TYR A 149 
 PHE   0.016   0.001   PHE A  37 
 TRP   0.029   0.002   TRP A 270 
 HIS   0.004   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 8448)
  covalent geometry    : angle       0.61347 (11493)
  SS BOND              : bond        0.00294 (    5)
  SS BOND              : angle       1.33524 (   10)
  hydrogen bonds       : bond        0.03750 (  384)
  hydrogen bonds       : angle       4.45801 ( 1149)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 219
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -51 LYS cc_start: 0.8470 (mttt) cc_final: 0.8240 (mttt)
REVERT: A   -6 LYS cc_start: 0.8165 (ttpt) cc_final: 0.7908 (ttpt)
REVERT: A    2 LYS cc_start: 0.7924 (ptpt) cc_final: 0.7650 (ptpt)
REVERT: A   21 LYS cc_start: 0.8300 (tttm) cc_final: 0.8038 (tttm)
REVERT: A   23 LEU cc_start: 0.6218 (OUTLIER) cc_final: 0.5909 (tt)
REVERT: A   46 SER cc_start: 0.7497 (m) cc_final: 0.7207 (t)
REVERT: A  123 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.6153 (tm-30)
REVERT: A  127 SER cc_start: 0.8651 (p) cc_final: 0.8216 (t)
REVERT: A  128 VAL cc_start: 0.8316 (t) cc_final: 0.8067 (p)
REVERT: A  162 LEU cc_start: 0.8141 (tp) cc_final: 0.7924 (tp)
REVERT: A  172 GLN cc_start: 0.7881 (tp40) cc_final: 0.7609 (tm-30)
REVERT: A  176 THR cc_start: 0.8171 (t) cc_final: 0.7678 (p)
REVERT: A  204 LYS cc_start: 0.7942 (tttt) cc_final: 0.7634 (tttt)
REVERT: A  211 PHE cc_start: 0.7768 (m-80) cc_final: 0.6574 (m-80)
REVERT: A  254 MET cc_start: 0.7676 (mtt) cc_final: 0.7168 (mtt)
REVERT: A  310 ASP cc_start: 0.7416 (t0) cc_final: 0.7171 (t0)
REVERT: A  326 PHE cc_start: 0.6624 (m-10) cc_final: 0.6423 (m-10)
REVERT: A  346 GLN cc_start: 0.7690 (mt0) cc_final: 0.7375 (mt0)
REVERT: A  394 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7549 (mm-30)
REVERT: A  405 PHE cc_start: 0.8282 (t80) cc_final: 0.7825 (t80)
REVERT: A  408 THR cc_start: 0.8565 (m) cc_final: 0.8245 (p)
REVERT: A  428 VAL cc_start: 0.8289 (OUTLIER) cc_final: 0.7649 (m)
REVERT: H   35 PHE cc_start: 0.6925 (m-80) cc_final: 0.6424 (m-80)
REVERT: H   74 SER cc_start: 0.8027 (t) cc_final: 0.7499 (p)
REVERT: H   98 TYR cc_start: 0.8556 (m-80) cc_final: 0.8002 (m-80)
REVERT: H  131 LYS cc_start: 0.7518 (ptmm) cc_final: 0.7216 (ptpp)
REVERT: N   34 MET cc_start: 0.6918 (mtp) cc_final: 0.6427 (mtp)
REVERT: N   89 GLU cc_start: 0.7608 (mp0) cc_final: 0.7175 (mp0)
REVERT: N   90 ASP cc_start: 0.7684 (t0) cc_final: 0.7443 (t0)
REVERT: L    4 GLN cc_start: 0.7189 (mm-40) cc_final: 0.6738 (mm-40)
REVERT: L   43 LYS cc_start: 0.8743 (mtpp) cc_final: 0.8378 (mtmm)
REVERT: L   68 SER cc_start: 0.8074 (m) cc_final: 0.7719 (p)
REVERT: L   87 TYR cc_start: 0.8303 (m-80) cc_final: 0.7890 (m-80)
REVERT: L   90 GLN cc_start: 0.8514 (tm-30) cc_final: 0.7414 (tt0)
REVERT: L  134 VAL cc_start: 0.7606 (p) cc_final: 0.7328 (m)
REVERT: L  145 GLU cc_start: 0.7586 (mp0) cc_final: 0.6937 (mp0)
REVERT: L  148 VAL cc_start: 0.8552 (OUTLIER) cc_final: 0.8327 (m)
REVERT: L  175 TYR cc_start: 0.7830 (m-10) cc_final: 0.7524 (m-10)
REVERT: L  190 LYS cc_start: 0.7368 (ttpp) cc_final: 0.6709 (ttpp)
  outliers start: 35
  outliers final: 23
  residues processed: 239
  average time/residue: 0.1090
  time to fit residues: 34.5300
Evaluate side-chains
  243 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 216
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   56 ASP
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  182 PHE
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  451 MET
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  165 THR
Chi-restraints excluded: chain H residue  184 LEU
Chi-restraints excluded: chain H residue  223 LYS
Chi-restraints excluded: chain H residue  228 LYS
Chi-restraints excluded: chain N residue  104 TYR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   66 SER
Chi-restraints excluded: chain L residue  112 VAL
Chi-restraints excluded: chain L residue  148 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 80 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 102 optimal weight:    0.4980
   chunk 16 optimal weight:    0.9990
   chunk 85 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 88 optimal weight:    1.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A -70 ASN
** A -61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 169 ASN
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.144262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.124157 restraints weight = 13930.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.128423 restraints weight = 6845.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.131243 restraints weight = 4114.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.132972 restraints weight = 2810.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.134296 restraints weight = 2141.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7079
moved from start:          0.4708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8453  Z= 0.237
  Angle     :  0.696   8.009  11503  Z= 0.354
  Chirality :  0.046   0.236   1298
  Planarity :  0.005   0.042   1440
  Dihedral  :  5.375  47.365   1184
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 15.57 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -0.62 (0.27), residues: 1045
  helix:  1.41 (0.25), residues: 387
  sheet: -1.66 (0.32), residues: 262
  loop : -1.25 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG H  70 
 TYR   0.026   0.002   TYR A  35 
 PHE   0.017   0.002   PHE L 100 
 TRP   0.045   0.003   TRP A 273 
 HIS   0.004   0.001   HIS H 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00510 ( 8448)
  covalent geometry    : angle       0.69445 (11493)
  SS BOND              : bond        0.00476 (    5)
  SS BOND              : angle       1.88162 (   10)
  hydrogen bonds       : bond        0.04506 (  384)
  hydrogen bonds       : angle       4.78656 ( 1149)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 221
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 LYS cc_start: 0.8376 (tttm) cc_final: 0.7921 (tttm)
REVERT: A   22 TYR cc_start: 0.7570 (m-80) cc_final: 0.6697 (m-80)
REVERT: A   23 LEU cc_start: 0.6372 (OUTLIER) cc_final: 0.6020 (tt)
REVERT: A   46 SER cc_start: 0.7593 (m) cc_final: 0.7305 (t)
REVERT: A  123 GLU cc_start: 0.6600 (tm-30) cc_final: 0.6352 (tm-30)
REVERT: A  127 SER cc_start: 0.8667 (p) cc_final: 0.8167 (t)
REVERT: A  162 LEU cc_start: 0.8210 (tp) cc_final: 0.7990 (tp)
REVERT: A  176 THR cc_start: 0.7995 (t) cc_final: 0.7063 (p)
REVERT: A  182 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.6804 (m-10)
REVERT: A  211 PHE cc_start: 0.7853 (m-80) cc_final: 0.6878 (m-80)
REVERT: A  254 MET cc_start: 0.7666 (mtt) cc_final: 0.7201 (mtt)
REVERT: A  292 TRP cc_start: 0.6925 (m-10) cc_final: 0.6655 (m-10)
REVERT: A  310 ASP cc_start: 0.7589 (t0) cc_final: 0.7280 (t0)
REVERT: A  326 PHE cc_start: 0.6768 (m-10) cc_final: 0.6550 (m-10)
REVERT: A  394 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7577 (mm-30)
REVERT: A  400 PHE cc_start: 0.7677 (m-80) cc_final: 0.7317 (m-80)
REVERT: A  405 PHE cc_start: 0.8204 (t80) cc_final: 0.7837 (t80)
REVERT: A  428 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8018 (m)
REVERT: H   74 SER cc_start: 0.8056 (t) cc_final: 0.7591 (p)
REVERT: H  131 LYS cc_start: 0.7674 (ptmm) cc_final: 0.7352 (ptpp)
REVERT: H  195 VAL cc_start: 0.8476 (p) cc_final: 0.8182 (m)
REVERT: N   34 MET cc_start: 0.6924 (mtp) cc_final: 0.6429 (mtp)
REVERT: N   89 GLU cc_start: 0.7702 (mp0) cc_final: 0.7265 (mp0)
REVERT: N   90 ASP cc_start: 0.7969 (t0) cc_final: 0.7692 (t70)
REVERT: L    4 GLN cc_start: 0.7269 (mm-40) cc_final: 0.6894 (mm-40)
REVERT: L   43 LYS cc_start: 0.8761 (mtpp) cc_final: 0.8409 (mtmm)
REVERT: L   90 GLN cc_start: 0.8600 (tm-30) cc_final: 0.7800 (tt0)
REVERT: L  110 ARG cc_start: 0.8105 (ttt-90) cc_final: 0.7620 (ttp80)
REVERT: L  145 GLU cc_start: 0.7673 (mp0) cc_final: 0.7031 (mp0)
REVERT: L  162 GLN cc_start: 0.7981 (tp40) cc_final: 0.7771 (mm-40)
REVERT: L  190 LYS cc_start: 0.7556 (ttpp) cc_final: 0.7037 (ttpp)
REVERT: L  211 PHE cc_start: 0.8374 (p90) cc_final: 0.7947 (p90)
  outliers start: 36
  outliers final: 22
  residues processed: 239
  average time/residue: 0.1143
  time to fit residues: 35.7704
Evaluate side-chains
  239 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 214
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -26 GLU
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   56 ASP
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  182 PHE
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue  165 THR
Chi-restraints excluded: chain H residue  219 THR
Chi-restraints excluded: chain H residue  228 LYS
Chi-restraints excluded: chain N residue  104 TYR
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue  112 VAL
Chi-restraints excluded: chain L residue  125 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 77 optimal weight:    0.7980
   chunk 89 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   chunk 75 optimal weight:    0.8980
   chunk 13 optimal weight:    0.3980
   chunk 65 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 86 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 -77 ASN
A -70 ASN
A -61 ASN
** A -12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 403 ASN
H 169 ASN
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.145539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.125125 restraints weight = 13794.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.129185 restraints weight = 6795.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.131999 restraints weight = 4106.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.133775 restraints weight = 2814.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.135144 restraints weight = 2139.765|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7075
moved from start:          0.4903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   8453  Z= 0.200
  Angle     :  0.668   7.702  11503  Z= 0.338
  Chirality :  0.045   0.222   1298
  Planarity :  0.005   0.064   1440
  Dihedral  :  5.246  47.419   1184
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 12.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 16.46 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -0.51 (0.27), residues: 1045
  helix:  1.39 (0.26), residues: 386
  sheet: -1.41 (0.33), residues: 257
  loop : -1.23 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A  61 
 TYR   0.034   0.002   TYR A 286 
 PHE   0.014   0.001   PHE A  37 
 TRP   0.025   0.002   TRP A 273 
 HIS   0.004   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 8448)
  covalent geometry    : angle       0.66647 (11493)
  SS BOND              : bond        0.00366 (    5)
  SS BOND              : angle       1.52469 (   10)
  hydrogen bonds       : bond        0.04254 (  384)
  hydrogen bonds       : angle       4.73560 ( 1149)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 219
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -12 GLN cc_start: 0.7873 (tt0) cc_final: 0.7412 (tt0)
REVERT: A   -9 ASP cc_start: 0.8100 (t0) cc_final: 0.7857 (t0)
REVERT: A   -6 LYS cc_start: 0.8168 (ttpt) cc_final: 0.7843 (ttpt)
REVERT: A    3 GLU cc_start: 0.7560 (mp0) cc_final: 0.7030 (mp0)
REVERT: A   23 LEU cc_start: 0.6304 (OUTLIER) cc_final: 0.5948 (tt)
REVERT: A   46 SER cc_start: 0.7603 (m) cc_final: 0.7321 (t)
REVERT: A  119 MET cc_start: 0.5442 (mmm) cc_final: 0.5174 (mmm)
REVERT: A  139 TYR cc_start: 0.7289 (t80) cc_final: 0.7084 (t80)
REVERT: A  162 LEU cc_start: 0.8185 (tp) cc_final: 0.7976 (tp)
REVERT: A  176 THR cc_start: 0.8074 (t) cc_final: 0.7594 (p)
REVERT: A  211 PHE cc_start: 0.7758 (m-80) cc_final: 0.6851 (m-80)
REVERT: A  254 MET cc_start: 0.7729 (mtt) cc_final: 0.7214 (mtt)
REVERT: A  310 ASP cc_start: 0.7670 (t0) cc_final: 0.7335 (t0)
REVERT: A  326 PHE cc_start: 0.6744 (m-10) cc_final: 0.6528 (m-10)
REVERT: A  394 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7593 (mm-30)
REVERT: A  400 PHE cc_start: 0.7825 (m-80) cc_final: 0.7482 (m-80)
REVERT: A  405 PHE cc_start: 0.8144 (t80) cc_final: 0.7819 (t80)
REVERT: A  428 VAL cc_start: 0.8654 (OUTLIER) cc_final: 0.8111 (m)
REVERT: H   74 SER cc_start: 0.8047 (t) cc_final: 0.7562 (p)
REVERT: H  131 LYS cc_start: 0.7600 (ptmm) cc_final: 0.7269 (ptpp)
REVERT: H  195 VAL cc_start: 0.8380 (p) cc_final: 0.8107 (m)
REVERT: N   34 MET cc_start: 0.6921 (mtp) cc_final: 0.6403 (mtp)
REVERT: N   89 GLU cc_start: 0.7724 (mp0) cc_final: 0.7341 (mp0)
REVERT: N   90 ASP cc_start: 0.7984 (t0) cc_final: 0.7624 (t0)
REVERT: L    4 GLN cc_start: 0.7343 (mm-40) cc_final: 0.6961 (mm-40)
REVERT: L   43 LYS cc_start: 0.8739 (mtpp) cc_final: 0.8396 (mtmm)
REVERT: L   90 GLN cc_start: 0.8588 (tm-30) cc_final: 0.7904 (tt0)
REVERT: L  134 VAL cc_start: 0.7673 (p) cc_final: 0.7338 (m)
REVERT: L  145 GLU cc_start: 0.7618 (mp0) cc_final: 0.6983 (mp0)
REVERT: L  162 GLN cc_start: 0.7994 (tp40) cc_final: 0.7772 (mm-40)
REVERT: L  190 LYS cc_start: 0.7574 (ttpp) cc_final: 0.7023 (ttpp)
REVERT: L  211 PHE cc_start: 0.8363 (p90) cc_final: 0.7994 (p90)
  outliers start: 33
  outliers final: 24
  residues processed: 237
  average time/residue: 0.1113
  time to fit residues: 34.8277
Evaluate side-chains
  240 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 214
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 VAL
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  182 PHE
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain H residue  165 THR
Chi-restraints excluded: chain H residue  219 THR
Chi-restraints excluded: chain H residue  228 LYS
Chi-restraints excluded: chain N residue  104 TYR
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   99 THR
Chi-restraints excluded: chain L residue  112 VAL
Chi-restraints excluded: chain L residue  125 SER
Chi-restraints excluded: chain L residue  165 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 16 optimal weight:    0.1980
   chunk 58 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0470
   chunk 8 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   chunk 63 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 55 optimal weight:    0.0470
   overall best weight:    0.3576

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

Flipped N/Q/H residues before XYZ refinement:
H 169 ASN
H 211 ASN
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.147316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.127070 restraints weight = 13775.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.131261 restraints weight = 6776.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.134016 restraints weight = 4041.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.135747 restraints weight = 2751.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.137152 restraints weight = 2083.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7043
moved from start:          0.4945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8453  Z= 0.144
  Angle     :  0.672  10.758  11503  Z= 0.333
  Chirality :  0.044   0.218   1298
  Planarity :  0.004   0.049   1440
  Dihedral  :  5.111  46.575   1184
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 17.25 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -0.39 (0.27), residues: 1045
  helix:  1.45 (0.25), residues: 386
  sheet: -1.28 (0.33), residues: 257
  loop : -1.16 (0.33), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A  61 
 TYR   0.030   0.002   TYR A 286 
 PHE   0.013   0.001   PHE A  37 
 TRP   0.063   0.002   TRP A 292 
 HIS   0.004   0.001   HIS H 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 8448)
  covalent geometry    : angle       0.67126 (11493)
  SS BOND              : bond        0.00265 (    5)
  SS BOND              : angle       1.34866 (   10)
  hydrogen bonds       : bond        0.04104 (  384)
  hydrogen bonds       : angle       4.65366 ( 1149)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 222
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -12 GLN cc_start: 0.7861 (tt0) cc_final: 0.7369 (tt0)
REVERT: A   -9 ASP cc_start: 0.8115 (t0) cc_final: 0.7835 (t0)
REVERT: A   -6 LYS cc_start: 0.8132 (ttpt) cc_final: 0.7907 (ttpt)
REVERT: A    3 GLU cc_start: 0.7536 (mp0) cc_final: 0.7044 (mp0)
REVERT: A   23 LEU cc_start: 0.6231 (OUTLIER) cc_final: 0.5878 (tt)
REVERT: A   46 SER cc_start: 0.7577 (m) cc_final: 0.7296 (t)
REVERT: A  139 TYR cc_start: 0.7241 (t80) cc_final: 0.7037 (t80)
REVERT: A  162 LEU cc_start: 0.8176 (tp) cc_final: 0.7974 (tp)
REVERT: A  176 THR cc_start: 0.8057 (t) cc_final: 0.7566 (p)
REVERT: A  211 PHE cc_start: 0.7738 (m-80) cc_final: 0.6869 (m-80)
REVERT: A  254 MET cc_start: 0.7632 (mtt) cc_final: 0.7154 (mtt)
REVERT: A  310 ASP cc_start: 0.7501 (t0) cc_final: 0.7270 (t0)
REVERT: A  394 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7567 (mm-30)
REVERT: A  405 PHE cc_start: 0.8132 (t80) cc_final: 0.7795 (t80)
REVERT: A  428 VAL cc_start: 0.8667 (OUTLIER) cc_final: 0.8149 (m)
REVERT: H   74 SER cc_start: 0.8047 (t) cc_final: 0.7565 (p)
REVERT: H  131 LYS cc_start: 0.7549 (ptmm) cc_final: 0.7223 (ptpp)
REVERT: H  195 VAL cc_start: 0.8307 (p) cc_final: 0.8042 (m)
REVERT: N    2 VAL cc_start: 0.7310 (t) cc_final: 0.7100 (m)
REVERT: N   34 MET cc_start: 0.6889 (mtp) cc_final: 0.6363 (mtp)
REVERT: N   89 GLU cc_start: 0.7694 (mp0) cc_final: 0.7315 (mp0)
REVERT: N   90 ASP cc_start: 0.7938 (t0) cc_final: 0.7694 (t0)
REVERT: L    4 GLN cc_start: 0.7316 (mm-40) cc_final: 0.6935 (mm-40)
REVERT: L   37 TYR cc_start: 0.8570 (m-80) cc_final: 0.8149 (m-80)
REVERT: L   43 LYS cc_start: 0.8697 (mtpp) cc_final: 0.8367 (mtmm)
REVERT: L   87 TYR cc_start: 0.8317 (m-80) cc_final: 0.7839 (m-80)
REVERT: L   90 GLN cc_start: 0.8546 (tm-30) cc_final: 0.7723 (tt0)
REVERT: L  120 PHE cc_start: 0.7902 (m-10) cc_final: 0.7624 (m-80)
REVERT: L  134 VAL cc_start: 0.7704 (p) cc_final: 0.7360 (m)
REVERT: L  145 GLU cc_start: 0.7583 (mp0) cc_final: 0.6964 (mp0)
REVERT: L  162 GLN cc_start: 0.7978 (tp40) cc_final: 0.7764 (mm-40)
REVERT: L  175 TYR cc_start: 0.7970 (m-10) cc_final: 0.7651 (m-10)
REVERT: L  190 LYS cc_start: 0.7507 (ttpp) cc_final: 0.7003 (ttpp)
REVERT: L  211 PHE cc_start: 0.8314 (p90) cc_final: 0.7903 (p90)
  outliers start: 31
  outliers final: 25
  residues processed: 240
  average time/residue: 0.1054
  time to fit residues: 33.8105
Evaluate side-chains
  243 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 216
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -50 MET
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  182 PHE
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  165 THR
Chi-restraints excluded: chain H residue  219 THR
Chi-restraints excluded: chain H residue  228 LYS
Chi-restraints excluded: chain N residue  104 TYR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   99 THR
Chi-restraints excluded: chain L residue  112 VAL
Chi-restraints excluded: chain L residue  165 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 77 optimal weight:    0.0670
   chunk 94 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 56 optimal weight:    0.7980
   chunk 62 optimal weight:    0.3980
   chunk 17 optimal weight:    0.9990
   chunk 40 optimal weight:    0.5980
   chunk 13 optimal weight:    0.1980
   chunk 76 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.3718

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.147830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.127868 restraints weight = 13733.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.131995 restraints weight = 6753.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.134725 restraints weight = 4025.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.136623 restraints weight = 2731.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.137800 restraints weight = 2030.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7038
moved from start:          0.5049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8453  Z= 0.144
  Angle     :  0.672   9.908  11503  Z= 0.333
  Chirality :  0.044   0.220   1298
  Planarity :  0.004   0.049   1440
  Dihedral  :  5.053  46.520   1184
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 17.81 %
    Favored  : 78.61 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -0.37 (0.27), residues: 1045
  helix:  1.40 (0.25), residues: 386
  sheet: -1.22 (0.33), residues: 257
  loop : -1.11 (0.33), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG H  70 
 TYR   0.028   0.002   TYR A 286 
 PHE   0.014   0.001   PHE A  37 
 TRP   0.052   0.002   TRP A 292 
 HIS   0.003   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 8448)
  covalent geometry    : angle       0.67093 (11493)
  SS BOND              : bond        0.00310 (    5)
  SS BOND              : angle       1.45437 (   10)
  hydrogen bonds       : bond        0.04043 (  384)
  hydrogen bonds       : angle       4.58184 ( 1149)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 215
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -12 GLN cc_start: 0.7875 (tt0) cc_final: 0.7377 (tt0)
REVERT: A   -9 ASP cc_start: 0.8094 (t0) cc_final: 0.7832 (t0)
REVERT: A    3 GLU cc_start: 0.7561 (mp0) cc_final: 0.7057 (mp0)
REVERT: A   15 ARG cc_start: 0.7710 (ttp80) cc_final: 0.7340 (ttp80)
REVERT: A   23 LEU cc_start: 0.6179 (OUTLIER) cc_final: 0.5844 (tt)
REVERT: A   46 SER cc_start: 0.7591 (m) cc_final: 0.7320 (t)
REVERT: A  139 TYR cc_start: 0.7241 (t80) cc_final: 0.7013 (t80)
REVERT: A  162 LEU cc_start: 0.8200 (tp) cc_final: 0.7997 (tp)
REVERT: A  176 THR cc_start: 0.8055 (t) cc_final: 0.7564 (p)
REVERT: A  211 PHE cc_start: 0.7741 (m-80) cc_final: 0.6921 (m-80)
REVERT: A  254 MET cc_start: 0.7646 (mtt) cc_final: 0.7168 (mtt)
REVERT: A  310 ASP cc_start: 0.7464 (t0) cc_final: 0.7240 (t0)
REVERT: A  394 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7653 (mm-30)
REVERT: A  405 PHE cc_start: 0.8146 (t80) cc_final: 0.7807 (t80)
REVERT: A  428 VAL cc_start: 0.8663 (OUTLIER) cc_final: 0.8154 (m)
REVERT: H   70 ARG cc_start: 0.8611 (ttp80) cc_final: 0.8389 (ttp80)
REVERT: H   74 SER cc_start: 0.8061 (t) cc_final: 0.7570 (p)
REVERT: H   92 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7387 (tm-30)
REVERT: H  131 LYS cc_start: 0.7540 (ptmm) cc_final: 0.7217 (ptpp)
REVERT: N    2 VAL cc_start: 0.7325 (t) cc_final: 0.7110 (m)
REVERT: N   34 MET cc_start: 0.6886 (mtp) cc_final: 0.6337 (mtp)
REVERT: N   60 TYR cc_start: 0.8397 (m-10) cc_final: 0.7945 (m-10)
REVERT: N   89 GLU cc_start: 0.7697 (mp0) cc_final: 0.7320 (mp0)
REVERT: N   90 ASP cc_start: 0.7926 (t0) cc_final: 0.7655 (t0)
REVERT: L    4 GLN cc_start: 0.7214 (mm-40) cc_final: 0.6904 (mm-40)
REVERT: L   37 TYR cc_start: 0.8580 (m-80) cc_final: 0.8216 (m-80)
REVERT: L   43 LYS cc_start: 0.8670 (mtpp) cc_final: 0.8325 (mtmm)
REVERT: L   87 TYR cc_start: 0.8334 (m-80) cc_final: 0.7880 (m-80)
REVERT: L   90 GLN cc_start: 0.8365 (tm-30) cc_final: 0.7776 (tt0)
REVERT: L  120 PHE cc_start: 0.7910 (m-10) cc_final: 0.7647 (m-80)
REVERT: L  134 VAL cc_start: 0.7670 (p) cc_final: 0.7330 (m)
REVERT: L  162 GLN cc_start: 0.7963 (tp40) cc_final: 0.7761 (mm-40)
REVERT: L  175 TYR cc_start: 0.7968 (m-10) cc_final: 0.7630 (m-10)
REVERT: L  190 LYS cc_start: 0.7557 (ttpp) cc_final: 0.7047 (ttpp)
REVERT: L  198 VAL cc_start: 0.7885 (p) cc_final: 0.7593 (m)
REVERT: L  211 PHE cc_start: 0.8305 (p90) cc_final: 0.7960 (p90)
  outliers start: 32
  outliers final: 27
  residues processed: 234
  average time/residue: 0.1080
  time to fit residues: 33.6923
Evaluate side-chains
  235 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 206
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -50 MET
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  182 PHE
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  165 THR
Chi-restraints excluded: chain H residue  219 THR
Chi-restraints excluded: chain H residue  228 LYS
Chi-restraints excluded: chain N residue  104 TYR
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   99 THR
Chi-restraints excluded: chain L residue  112 VAL
Chi-restraints excluded: chain L residue  125 SER
Chi-restraints excluded: chain L residue  165 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 100 optimal weight:    0.6980
   chunk 50 optimal weight:    0.0980
   chunk 73 optimal weight:    2.9990
   chunk 96 optimal weight:    1.9990
   chunk 89 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0980
   chunk 66 optimal weight:    0.6980
   chunk 86 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.4180

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.147781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.127502 restraints weight = 13788.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.131707 restraints weight = 6783.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.134511 restraints weight = 4051.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.136448 restraints weight = 2746.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.137666 restraints weight = 2045.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7039
moved from start:          0.5114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8453  Z= 0.149
  Angle     :  0.663   9.731  11503  Z= 0.333
  Chirality :  0.044   0.215   1298
  Planarity :  0.004   0.047   1440
  Dihedral  :  5.075  46.655   1184
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 18.48 %
    Favored  : 78.39 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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: -0.36 (0.27), residues: 1045
  helix:  1.39 (0.25), residues: 387
  sheet: -1.20 (0.33), residues: 257
  loop : -1.12 (0.33), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 148 
 TYR   0.027   0.002   TYR A 286 
 PHE   0.013   0.001   PHE A  37 
 TRP   0.048   0.002   TRP A 292 
 HIS   0.003   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 8448)
  covalent geometry    : angle       0.66193 (11493)
  SS BOND              : bond        0.00306 (    5)
  SS BOND              : angle       1.42929 (   10)
  hydrogen bonds       : bond        0.04090 (  384)
  hydrogen bonds       : angle       4.55670 ( 1149)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1701.91 seconds
wall clock time: 30 minutes 13.10 seconds (1813.10 seconds total)