Starting phenix.real_space_refine
on Wed Feb  4 00:55:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hij_34818/02_2026/8hij_34818_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hij_34818/02_2026/8hij_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_34818/02_2026/8hij_34818.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hij_34818/02_2026/8hij_34818.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hij_34818/02_2026/8hij_34818_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hij_34818/02_2026/8hij_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-2.0-5952/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: 1.74, per 1000 atoms: 0.21
  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: 0.63
  Conformation dependent library (CDL) restraints added in 218.6 milliseconds
  

  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: 0.33
  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: 1.25

  Time building geometry restraints manager: 0.78 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:             1.880
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.670
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.880
-------------------------------------------------------------------------------
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 are 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  : 0.229 
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: 0.7705 (t) cc_final: 0.7474 (m)
REVERT: A  127 SER cc_start: 0.8833 (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  398 LEU cc_start: 0.8654 (tp) cc_final: 0.8454 (mm)
REVERT: A  405 PHE cc_start: 0.8106 (t80) cc_final: 0.7820 (t80)
REVERT: A  406 PHE cc_start: 0.7491 (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: 0.6919 (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: 0.8299 (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: 0.7950 (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: 0.8092 (p90) cc_final: 0.7848 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 280
  average time/residue: 0.0775
  time to fit residues: 29.6573
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  : 0.289 
-------------------------------------------------------------------------------
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
A  -3 ASN
A  63 GLN
A  66 ASN
A  99 GLN
A 172 GLN
A 293 ASN
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 = 0.4004 r_free = 0.4004 target = 0.154137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.133553 restraints weight = 14131.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.137811 restraints weight = 7112.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.140657 restraints weight = 4318.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.142557 restraints weight = 2972.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.143752 restraints weight = 2247.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6912
moved from start:          0.2361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8453  Z= 0.187
  Angle     :  0.639   8.237  11503  Z= 0.327
  Chirality :  0.043   0.196   1298
  Planarity :  0.005   0.048   1440
  Dihedral  :  5.605  52.206   1184
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  :  8.73 %
    Favored  : 88.91 %
  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 are not related in a simple way.
  whole: -2.02 (0.25), residues: 1045
  helix:  0.49 (0.25), residues: 382
  sheet: -2.50 (0.30), residues: 245
  loop : -2.27 (0.28), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A -21 
 TYR   0.024   0.002   TYR A 438 
 PHE   0.016   0.002   PHE A -18 
 TRP   0.035   0.002   TRP H 102 
 HIS   0.004   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 8448)
  covalent geometry    : angle       0.63765 (11493)
  SS BOND              : bond        0.00390 (    5)
  SS BOND              : angle       1.69595 (   10)
  hydrogen bonds       : bond        0.04239 (  384)
  hydrogen bonds       : angle       5.16192 ( 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: 21
    poor density    : 234
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: A  -70 ASN cc_start: 0.7457 (m110) cc_final: 0.7208 (m110)
REVERT: A  -55 ASP cc_start: 0.6760 (t0) cc_final: 0.6557 (t0)
REVERT: A  -51 LYS cc_start: 0.8725 (mttt) cc_final: 0.8435 (mttt)
REVERT: A    1 VAL cc_start: 0.8594 (m) cc_final: 0.8380 (p)
REVERT: A   11 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7059 (tm)
REVERT: A   22 TYR cc_start: 0.7419 (m-80) cc_final: 0.7214 (m-80)
REVERT: A   46 SER cc_start: 0.7583 (m) cc_final: 0.7140 (t)
REVERT: A  127 SER cc_start: 0.8690 (p) cc_final: 0.8231 (t)
REVERT: A  139 TYR cc_start: 0.7243 (t80) cc_final: 0.6983 (t80)
REVERT: A  162 LEU cc_start: 0.8100 (tp) cc_final: 0.7834 (tp)
REVERT: A  190 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8229 (tp)
REVERT: A  254 MET cc_start: 0.7553 (mtt) cc_final: 0.7132 (mtt)
REVERT: A  293 ASN cc_start: 0.7840 (OUTLIER) cc_final: 0.7591 (t0)
REVERT: A  310 ASP cc_start: 0.7562 (t0) cc_final: 0.7336 (t0)
REVERT: A  314 THR cc_start: 0.8184 (m) cc_final: 0.7894 (p)
REVERT: A  394 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7563 (mm-30)
REVERT: A  398 LEU cc_start: 0.8715 (tp) cc_final: 0.8503 (mm)
REVERT: A  405 PHE cc_start: 0.8213 (t80) cc_final: 0.7920 (t80)
REVERT: A  406 PHE cc_start: 0.7638 (m-80) cc_final: 0.7175 (m-10)
REVERT: A  445 ILE cc_start: 0.6733 (mt) cc_final: 0.6485 (mt)
REVERT: H   74 SER cc_start: 0.7688 (t) cc_final: 0.7211 (p)
REVERT: H   80 ASN cc_start: 0.8266 (t0) cc_final: 0.7948 (t0)
REVERT: H   98 TYR cc_start: 0.8544 (m-80) cc_final: 0.8246 (m-80)
REVERT: N   34 MET cc_start: 0.6854 (mtp) cc_final: 0.6411 (mtp)
REVERT: N   89 GLU cc_start: 0.7405 (mp0) cc_final: 0.7166 (mp0)
REVERT: L    4 GLN cc_start: 0.7218 (mm-40) cc_final: 0.6759 (mm-40)
REVERT: L   53 SER cc_start: 0.7959 (m) cc_final: 0.7722 (t)
REVERT: L   73 THR cc_start: 0.8057 (m) cc_final: 0.7701 (t)
REVERT: L   83 ASP cc_start: 0.7368 (m-30) cc_final: 0.7076 (m-30)
REVERT: L   91 GLN cc_start: 0.8409 (pp30) cc_final: 0.7989 (pp30)
REVERT: L   97 LEU cc_start: 0.8578 (mp) cc_final: 0.8342 (mt)
REVERT: L  120 PHE cc_start: 0.7847 (m-80) cc_final: 0.7459 (m-80)
REVERT: L  142 TYR cc_start: 0.8074 (t80) cc_final: 0.7747 (t80)
REVERT: L  145 GLU cc_start: 0.7577 (mp0) cc_final: 0.7144 (mp0)
REVERT: L  172 ASP cc_start: 0.8483 (p0) cc_final: 0.8193 (p0)
REVERT: L  190 LYS cc_start: 0.7572 (ttpp) cc_final: 0.7056 (ttpp)
REVERT: L  211 PHE cc_start: 0.8246 (p90) cc_final: 0.7903 (p90)
  outliers start: 21
  outliers final: 10
  residues processed: 247
  average time/residue: 0.0794
  time to fit residues: 26.6837
Evaluate side-chains
  242 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 229
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
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:    0.0970
   chunk 48 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 93 optimal weight:    0.2980
   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:    2.9990
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
A -61 ASN
A  99 GLN
H 178 HIS
** 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 = 0.3984 r_free = 0.3984 target = 0.152178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.131948 restraints weight = 13878.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.136082 restraints weight = 7019.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.138936 restraints weight = 4305.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.140819 restraints weight = 2969.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.141910 restraints weight = 2241.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6945
moved from start:          0.2912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8453  Z= 0.154
  Angle     :  0.589   7.689  11503  Z= 0.301
  Chirality :  0.042   0.154   1298
  Planarity :  0.004   0.038   1440
  Dihedral  :  5.411  48.859   1184
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 11.31 %
    Favored  : 85.89 %
  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 are not related in a simple way.
  whole: -1.32 (0.25), residues: 1045
  helix:  1.06 (0.25), residues: 382
  sheet: -2.10 (0.31), residues: 233
  loop : -1.91 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  70 
 TYR   0.025   0.001   TYR A 286 
 PHE   0.013   0.001   PHE A 372 
 TRP   0.029   0.002   TRP A 292 
 HIS   0.004   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 8448)
  covalent geometry    : angle       0.58775 (11493)
  SS BOND              : bond        0.00368 (    5)
  SS BOND              : angle       1.56780 (   10)
  hydrogen bonds       : bond        0.03944 (  384)
  hydrogen bonds       : angle       4.84105 ( 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
  271 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 246
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -57 VAL cc_start: 0.6951 (m) cc_final: 0.6735 (p)
REVERT: A  -51 LYS cc_start: 0.8703 (mttt) cc_final: 0.8424 (mttt)
REVERT: A  -12 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7603 (tt0)
REVERT: A   -6 LYS cc_start: 0.8120 (ttpt) cc_final: 0.7883 (ttpt)
REVERT: A    1 VAL cc_start: 0.8626 (m) cc_final: 0.8418 (p)
REVERT: A   11 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7052 (tm)
REVERT: A   46 SER cc_start: 0.7520 (m) cc_final: 0.7177 (t)
REVERT: A   77 LEU cc_start: 0.8585 (tp) cc_final: 0.8245 (mt)
REVERT: A  112 LEU cc_start: 0.6928 (mt) cc_final: 0.6721 (mt)
REVERT: A  127 SER cc_start: 0.8703 (p) cc_final: 0.8183 (t)
REVERT: A  128 VAL cc_start: 0.8411 (OUTLIER) cc_final: 0.8142 (p)
REVERT: A  162 LEU cc_start: 0.8111 (tp) cc_final: 0.7850 (tp)
REVERT: A  190 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8182 (tp)
REVERT: A  254 MET cc_start: 0.7604 (mtt) cc_final: 0.7163 (mtt)
REVERT: A  310 ASP cc_start: 0.7465 (t0) cc_final: 0.7258 (t0)
REVERT: A  314 THR cc_start: 0.8179 (m) cc_final: 0.7892 (p)
REVERT: A  326 PHE cc_start: 0.6631 (m-10) cc_final: 0.6352 (m-10)
REVERT: A  394 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7576 (mm-30)
REVERT: A  398 LEU cc_start: 0.8705 (tp) cc_final: 0.8498 (mm)
REVERT: A  405 PHE cc_start: 0.8238 (t80) cc_final: 0.7953 (t80)
REVERT: A  406 PHE cc_start: 0.7581 (m-80) cc_final: 0.7133 (m-10)
REVERT: A  445 ILE cc_start: 0.6798 (mt) cc_final: 0.6544 (mt)
REVERT: H   15 VAL cc_start: 0.8234 (m) cc_final: 0.7977 (p)
REVERT: H   74 SER cc_start: 0.7866 (t) cc_final: 0.7322 (p)
REVERT: H   80 ASN cc_start: 0.8255 (t0) cc_final: 0.7920 (t0)
REVERT: H   98 TYR cc_start: 0.8569 (m-80) cc_final: 0.8254 (m-80)
REVERT: H  131 LYS cc_start: 0.7630 (ptmm) cc_final: 0.7338 (ptpp)
REVERT: H  138 LEU cc_start: 0.8325 (mt) cc_final: 0.8113 (mt)
REVERT: H  191 SER cc_start: 0.8322 (t) cc_final: 0.8019 (m)
REVERT: N   34 MET cc_start: 0.6851 (mtp) cc_final: 0.6403 (mtp)
REVERT: N   89 GLU cc_start: 0.7496 (mp0) cc_final: 0.7178 (mp0)
REVERT: L    4 GLN cc_start: 0.7216 (mm-40) cc_final: 0.6772 (mm-40)
REVERT: L   53 SER cc_start: 0.8067 (m) cc_final: 0.7853 (t)
REVERT: L   87 TYR cc_start: 0.8260 (m-80) cc_final: 0.7902 (m-80)
REVERT: L   97 LEU cc_start: 0.8587 (mp) cc_final: 0.8331 (mt)
REVERT: L  172 ASP cc_start: 0.8467 (p0) cc_final: 0.8198 (p0)
REVERT: L  211 PHE cc_start: 0.8256 (p90) cc_final: 0.7941 (p90)
  outliers start: 25
  outliers final: 15
  residues processed: 257
  average time/residue: 0.0843
  time to fit residues: 29.4003
Evaluate side-chains
  258 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 239
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue  -12 GLN
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue  128 VAL
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  190 LEU
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  451 MET
Chi-restraints excluded: chain H residue   56 SER
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 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:    0.7980
   chunk 40 optimal weight:    0.3980
   chunk 50 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 49 optimal weight:    0.4980
   chunk 16 optimal weight:    0.7980
   chunk 88 optimal weight:    2.9990
   chunk 95 optimal weight:    0.0770
   chunk 58 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.5138

-------------------------------------------------------------------------------
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**
A  66 ASN
A 277 ASN
A 289 HIS
** 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 ** both conformations clash, **PLEASE CHECK MANUALLY**
L 168 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.149892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.129114 restraints weight = 14069.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.133355 restraints weight = 7127.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.136249 restraints weight = 4385.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.138040 restraints weight = 3028.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.139408 restraints weight = 2317.342|
|-----------------------------------------------------------------------------|
r_work (final): 0.3804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6980
moved from start:          0.3387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8453  Z= 0.167
  Angle     :  0.605   8.210  11503  Z= 0.306
  Chirality :  0.042   0.162   1298
  Planarity :  0.004   0.043   1440
  Dihedral  :  5.245  46.242   1184
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 12.32 %
    Favored  : 83.65 %
  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 are not related in a simple way.
  whole: -0.97 (0.26), residues: 1045
  helix:  1.36 (0.25), residues: 382
  sheet: -1.89 (0.32), residues: 236
  loop : -1.72 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A -21 
 TYR   0.027   0.001   TYR A 286 
 PHE   0.011   0.001   PHE A 432 
 TRP   0.020   0.002   TRP H 102 
 HIS   0.005   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 8448)
  covalent geometry    : angle       0.60414 (11493)
  SS BOND              : bond        0.00375 (    5)
  SS BOND              : angle       1.47281 (   10)
  hydrogen bonds       : bond        0.03960 (  384)
  hydrogen bonds       : angle       4.71121 ( 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
  285 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 249
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -57 VAL cc_start: 0.6952 (m) cc_final: 0.6630 (p)
REVERT: A  -51 LYS cc_start: 0.8650 (mttt) cc_final: 0.8385 (mttt)
REVERT: A  -50 MET cc_start: 0.7807 (mtm) cc_final: 0.7593 (mtm)
REVERT: A   -6 LYS cc_start: 0.8175 (ttpt) cc_final: 0.7873 (ttpt)
REVERT: A   11 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7097 (tm)
REVERT: A   46 SER cc_start: 0.7496 (m) cc_final: 0.7162 (t)
REVERT: A   72 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.5681 (tt)
REVERT: A  127 SER cc_start: 0.8760 (p) cc_final: 0.8291 (t)
REVERT: A  128 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.8135 (p)
REVERT: A  162 LEU cc_start: 0.8136 (tp) cc_final: 0.7903 (tp)
REVERT: A  190 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8111 (tt)
REVERT: A  254 MET cc_start: 0.7627 (mtt) cc_final: 0.7169 (mtt)
REVERT: A  310 ASP cc_start: 0.7535 (t0) cc_final: 0.7262 (t0)
REVERT: A  314 THR cc_start: 0.8145 (m) cc_final: 0.7838 (p)
REVERT: A  326 PHE cc_start: 0.6688 (m-10) cc_final: 0.6405 (m-10)
REVERT: A  346 GLN cc_start: 0.7598 (mt0) cc_final: 0.7362 (mt0)
REVERT: A  394 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7634 (mm-30)
REVERT: A  405 PHE cc_start: 0.8278 (t80) cc_final: 0.7973 (t80)
REVERT: A  406 PHE cc_start: 0.7576 (m-80) cc_final: 0.7132 (m-10)
REVERT: A  445 ILE cc_start: 0.6881 (mt) cc_final: 0.6614 (mt)
REVERT: H   74 SER cc_start: 0.7923 (t) cc_final: 0.7388 (p)
REVERT: H   80 ASN cc_start: 0.8260 (t0) cc_final: 0.7950 (t0)
REVERT: H   98 TYR cc_start: 0.8557 (m-80) cc_final: 0.8197 (m-80)
REVERT: H  131 LYS cc_start: 0.7552 (ptmm) cc_final: 0.7236 (ptpp)
REVERT: H  191 SER cc_start: 0.8361 (t) cc_final: 0.7992 (m)
REVERT: N   34 MET cc_start: 0.6912 (mtp) cc_final: 0.6419 (mtp)
REVERT: N   89 GLU cc_start: 0.7577 (mp0) cc_final: 0.7164 (mp0)
REVERT: L    4 GLN cc_start: 0.7279 (mm-40) cc_final: 0.6836 (mm-40)
REVERT: L   53 SER cc_start: 0.8183 (m) cc_final: 0.7972 (t)
REVERT: L   68 SER cc_start: 0.8012 (m) cc_final: 0.7549 (p)
REVERT: L   87 TYR cc_start: 0.8332 (m-80) cc_final: 0.7845 (m-80)
REVERT: L   97 LEU cc_start: 0.8525 (mp) cc_final: 0.8260 (mt)
REVERT: L  145 GLU cc_start: 0.7607 (mp0) cc_final: 0.7172 (mp0)
REVERT: L  168 GLN cc_start: 0.7648 (tt0) cc_final: 0.7338 (mm-40)
REVERT: L  190 LYS cc_start: 0.7441 (ttpp) cc_final: 0.6893 (ttpp)
REVERT: L  211 PHE cc_start: 0.8326 (p90) cc_final: 0.7891 (p90)
  outliers start: 36
  outliers final: 24
  residues processed: 262
  average time/residue: 0.0909
  time to fit residues: 32.1091
Evaluate side-chains
  262 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 234
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
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   56 ASP
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  185 LEU
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  316 LEU
Chi-restraints excluded: chain A residue  353 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   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
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:    2.9990
   chunk 100 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 98 optimal weight:    0.0980
   chunk 18 optimal weight:    0.5980
   chunk 97 optimal weight:    0.5980
   chunk 103 optimal weight:    1.9990
   chunk 32 optimal weight:    0.2980
   chunk 55 optimal weight:    0.4980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
A -70 ASN
A 277 ASN
H 214 HIS
** L  91 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 = 0.3951 r_free = 0.3951 target = 0.150005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.129272 restraints weight = 13923.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.133541 restraints weight = 7034.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.136415 restraints weight = 4306.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.138348 restraints weight = 2981.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.139626 restraints weight = 2247.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6982
moved from start:          0.3733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8453  Z= 0.146
  Angle     :  0.626  13.034  11503  Z= 0.309
  Chirality :  0.043   0.262   1298
  Planarity :  0.004   0.040   1440
  Dihedral  :  5.144  46.188   1184
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 15.34 %
    Favored  : 81.30 %
  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 are not related in a simple way.
  whole: -0.73 (0.26), residues: 1045
  helix:  1.47 (0.25), residues: 380
  sheet: -1.67 (0.33), residues: 234
  loop : -1.53 (0.31), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A -21 
 TYR   0.031   0.001   TYR A 286 
 PHE   0.021   0.002   PHE A  37 
 TRP   0.024   0.002   TRP A 270 
 HIS   0.005   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8448)
  covalent geometry    : angle       0.62503 (11493)
  SS BOND              : bond        0.00318 (    5)
  SS BOND              : angle       1.44553 (   10)
  hydrogen bonds       : bond        0.03963 (  384)
  hydrogen bonds       : angle       4.62913 ( 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
  266 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 236
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -57 VAL cc_start: 0.6944 (m) cc_final: 0.6622 (p)
REVERT: A  -51 LYS cc_start: 0.8645 (mttt) cc_final: 0.8381 (mttt)
REVERT: A  -36 LYS cc_start: 0.8026 (mppt) cc_final: 0.7622 (ttmm)
REVERT: A   11 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7138 (tm)
REVERT: A   21 LYS cc_start: 0.8374 (tttm) cc_final: 0.8148 (tttm)
REVERT: A   46 SER cc_start: 0.7443 (m) cc_final: 0.7124 (t)
REVERT: A   65 THR cc_start: 0.8351 (t) cc_final: 0.8090 (t)
REVERT: A  123 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6319 (tm-30)
REVERT: A  127 SER cc_start: 0.8667 (p) cc_final: 0.8095 (t)
REVERT: A  128 VAL cc_start: 0.8372 (OUTLIER) cc_final: 0.8090 (p)
REVERT: A  162 LEU cc_start: 0.8126 (tp) cc_final: 0.7904 (tp)
REVERT: A  190 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8071 (tt)
REVERT: A  204 LYS cc_start: 0.7923 (tttt) cc_final: 0.7601 (tttt)
REVERT: A  211 PHE cc_start: 0.7735 (m-80) cc_final: 0.6806 (m-80)
REVERT: A  254 MET cc_start: 0.7652 (mtt) cc_final: 0.7162 (mtt)
REVERT: A  310 ASP cc_start: 0.7496 (t0) cc_final: 0.7274 (t0)
REVERT: A  326 PHE cc_start: 0.6660 (m-10) cc_final: 0.6393 (m-10)
REVERT: A  346 GLN cc_start: 0.7641 (mt0) cc_final: 0.7387 (mt0)
REVERT: A  394 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7456 (mm-30)
REVERT: A  405 PHE cc_start: 0.8265 (t80) cc_final: 0.7808 (t80)
REVERT: A  406 PHE cc_start: 0.7546 (m-80) cc_final: 0.7074 (m-10)
REVERT: A  408 THR cc_start: 0.8621 (m) cc_final: 0.8307 (p)
REVERT: A  445 ILE cc_start: 0.6790 (mt) cc_final: 0.6538 (mt)
REVERT: H   35 PHE cc_start: 0.6870 (m-80) cc_final: 0.6364 (m-80)
REVERT: H   74 SER cc_start: 0.7961 (t) cc_final: 0.7444 (p)
REVERT: H   98 TYR cc_start: 0.8579 (m-80) cc_final: 0.8150 (m-80)
REVERT: H  131 LYS cc_start: 0.7541 (ptmm) cc_final: 0.7224 (ptpp)
REVERT: H  191 SER cc_start: 0.8358 (t) cc_final: 0.8003 (m)
REVERT: N   34 MET cc_start: 0.6894 (mtp) cc_final: 0.6407 (mtp)
REVERT: N   89 GLU cc_start: 0.7592 (mp0) cc_final: 0.7172 (mp0)
REVERT: L    4 GLN cc_start: 0.7273 (mm-40) cc_final: 0.6839 (mm-40)
REVERT: L   68 SER cc_start: 0.8048 (m) cc_final: 0.7582 (p)
REVERT: L   83 ASP cc_start: 0.7467 (m-30) cc_final: 0.7256 (m-30)
REVERT: L   87 TYR cc_start: 0.8322 (m-80) cc_final: 0.7895 (m-80)
REVERT: L   97 LEU cc_start: 0.8444 (mp) cc_final: 0.8236 (mt)
REVERT: L  145 GLU cc_start: 0.7641 (mp0) cc_final: 0.7177 (mp0)
REVERT: L  148 VAL cc_start: 0.8582 (OUTLIER) cc_final: 0.8329 (m)
REVERT: L  168 GLN cc_start: 0.7657 (tt0) cc_final: 0.7195 (mm-40)
REVERT: L  175 TYR cc_start: 0.7873 (m-10) cc_final: 0.6683 (m-10)
REVERT: L  190 LYS cc_start: 0.7497 (ttpp) cc_final: 0.6904 (ttpp)
REVERT: L  211 PHE cc_start: 0.8325 (p90) cc_final: 0.7865 (p90)
  outliers start: 30
  outliers final: 18
  residues processed: 250
  average time/residue: 0.0938
  time to fit residues: 31.1911
Evaluate side-chains
  252 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 229
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
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  123 GLU
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  185 LEU
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  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  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
Chi-restraints excluded: chain L residue  148 VAL
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:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 47 optimal weight:    0.0470
   chunk 3 optimal weight:    0.5980
   chunk 38 optimal weight:    0.2980
   chunk 43 optimal weight:    2.9990
   chunk 86 optimal weight:    0.8980
   overall best weight:    0.4278

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

Flipped N/Q/H residues before XYZ refinement:
A -61 ASN
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 = 0.3939 r_free = 0.3939 target = 0.148958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.128196 restraints weight = 13795.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.132451 restraints weight = 6955.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.135271 restraints weight = 4236.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.137169 restraints weight = 2930.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.138448 restraints weight = 2218.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6991
moved from start:          0.4023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8453  Z= 0.146
  Angle     :  0.623   9.583  11503  Z= 0.310
  Chirality :  0.043   0.286   1298
  Planarity :  0.004   0.040   1440
  Dihedral  :  5.053  46.054   1184
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 15.45 %
    Favored  : 80.85 %
  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 are not related in a simple way.
  whole: -0.52 (0.26), residues: 1045
  helix:  1.57 (0.25), residues: 385
  sheet: -1.49 (0.33), residues: 234
  loop : -1.42 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A -21 
 TYR   0.035   0.001   TYR A 149 
 PHE   0.026   0.002   PHE A  37 
 TRP   0.046   0.002   TRP A 292 
 HIS   0.005   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 8448)
  covalent geometry    : angle       0.62223 (11493)
  SS BOND              : bond        0.00341 (    5)
  SS BOND              : angle       1.40116 (   10)
  hydrogen bonds       : bond        0.03974 (  384)
  hydrogen bonds       : angle       4.58216 ( 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
  260 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 227
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -57 VAL cc_start: 0.6942 (m) cc_final: 0.6611 (p)
REVERT: A  -51 LYS cc_start: 0.8590 (mttt) cc_final: 0.8352 (mttt)
REVERT: A    3 GLU cc_start: 0.7500 (mp0) cc_final: 0.6881 (mp0)
REVERT: A   46 SER cc_start: 0.7436 (m) cc_final: 0.7142 (t)
REVERT: A  127 SER cc_start: 0.8613 (p) cc_final: 0.8110 (t)
REVERT: A  128 VAL cc_start: 0.8357 (OUTLIER) cc_final: 0.8095 (p)
REVERT: A  162 LEU cc_start: 0.8120 (tp) cc_final: 0.7901 (tp)
REVERT: A  172 GLN cc_start: 0.7924 (tp40) cc_final: 0.7671 (tm-30)
REVERT: A  176 THR cc_start: 0.8166 (t) cc_final: 0.7597 (p)
REVERT: A  204 LYS cc_start: 0.7967 (tttt) cc_final: 0.7650 (tttt)
REVERT: A  211 PHE cc_start: 0.7804 (m-80) cc_final: 0.7479 (m-80)
REVERT: A  254 MET cc_start: 0.7689 (mtt) cc_final: 0.7192 (mtt)
REVERT: A  310 ASP cc_start: 0.7410 (t0) cc_final: 0.7141 (t0)
REVERT: A  326 PHE cc_start: 0.6660 (m-10) cc_final: 0.6445 (m-10)
REVERT: A  346 GLN cc_start: 0.7726 (mt0) cc_final: 0.7398 (mt0)
REVERT: A  405 PHE cc_start: 0.8296 (t80) cc_final: 0.7843 (t80)
REVERT: A  408 THR cc_start: 0.8614 (m) cc_final: 0.8299 (p)
REVERT: A  445 ILE cc_start: 0.6922 (mt) cc_final: 0.6668 (mt)
REVERT: H   35 PHE cc_start: 0.6929 (m-80) cc_final: 0.6406 (m-80)
REVERT: H   70 ARG cc_start: 0.8551 (ttp80) cc_final: 0.8182 (ttp80)
REVERT: H   74 SER cc_start: 0.7982 (t) cc_final: 0.7474 (p)
REVERT: H   98 TYR cc_start: 0.8565 (m-80) cc_final: 0.8123 (m-80)
REVERT: H  131 LYS cc_start: 0.7555 (ptmm) cc_final: 0.7234 (ptpp)
REVERT: H  191 SER cc_start: 0.8334 (t) cc_final: 0.7978 (m)
REVERT: N   34 MET cc_start: 0.6917 (mtp) cc_final: 0.6424 (mtp)
REVERT: N   89 GLU cc_start: 0.7615 (mp0) cc_final: 0.7175 (mp0)
REVERT: L    4 GLN cc_start: 0.7273 (mm-40) cc_final: 0.6826 (mm-40)
REVERT: L   68 SER cc_start: 0.8117 (m) cc_final: 0.7663 (p)
REVERT: L   83 ASP cc_start: 0.7473 (m-30) cc_final: 0.7213 (m-30)
REVERT: L   87 TYR cc_start: 0.8310 (m-80) cc_final: 0.7846 (m-80)
REVERT: L  134 VAL cc_start: 0.7632 (p) cc_final: 0.7331 (m)
REVERT: L  145 GLU cc_start: 0.7630 (mp0) cc_final: 0.7175 (mp0)
REVERT: L  168 GLN cc_start: 0.7729 (tt0) cc_final: 0.7242 (mm-40)
REVERT: L  175 TYR cc_start: 0.7880 (m-10) cc_final: 0.6780 (m-10)
REVERT: L  190 LYS cc_start: 0.7451 (ttpp) cc_final: 0.6827 (ttpp)
REVERT: L  211 PHE cc_start: 0.8329 (p90) cc_final: 0.7902 (p90)
  outliers start: 33
  outliers final: 25
  residues processed: 246
  average time/residue: 0.0924
  time to fit residues: 30.1534
Evaluate side-chains
  249 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 223
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -18 PHE
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  128 VAL
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  185 LEU
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  316 LEU
Chi-restraints excluded: chain A residue  353 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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 80 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0020
   chunk 48 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 102 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 85 optimal weight:    1.9990
   chunk 99 optimal weight:    0.8980
   chunk 34 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 88 optimal weight:    1.9990
   overall best weight:    0.7190

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN
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 = 0.3892 r_free = 0.3892 target = 0.145146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.124829 restraints weight = 13910.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.128960 restraints weight = 6991.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.131800 restraints weight = 4268.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.133617 restraints weight = 2936.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.134921 restraints weight = 2218.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7056
moved from start:          0.4516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   8453  Z= 0.214
  Angle     :  0.661   7.734  11503  Z= 0.338
  Chirality :  0.044   0.189   1298
  Planarity :  0.004   0.050   1440
  Dihedral  :  5.254  46.813   1184
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 15.79 %
    Favored  : 80.18 %
  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 are not related in a simple way.
  whole: -0.50 (0.27), residues: 1045
  helix:  1.46 (0.25), residues: 383
  sheet: -1.44 (0.33), residues: 244
  loop : -1.27 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 145 
 TYR   0.038   0.002   TYR A 149 
 PHE   0.024   0.002   PHE L 100 
 TRP   0.042   0.003   TRP A 270 
 HIS   0.004   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 8448)
  covalent geometry    : angle       0.65947 (11493)
  SS BOND              : bond        0.00438 (    5)
  SS BOND              : angle       1.67488 (   10)
  hydrogen bonds       : bond        0.04431 (  384)
  hydrogen bonds       : angle       4.79248 ( 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
  259 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 223
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
REVERT: A  -51 LYS cc_start: 0.8624 (mttt) cc_final: 0.8387 (mttt)
REVERT: A  -12 GLN cc_start: 0.7936 (tt0) cc_final: 0.7733 (tt0)
REVERT: A   15 ARG cc_start: 0.6861 (tmm160) cc_final: 0.6571 (tmm160)
REVERT: A   23 LEU cc_start: 0.6431 (OUTLIER) cc_final: 0.6074 (tt)
REVERT: A   46 SER cc_start: 0.7445 (m) cc_final: 0.7138 (t)
REVERT: A  123 GLU cc_start: 0.6474 (tm-30) cc_final: 0.6192 (tm-30)
REVERT: A  127 SER cc_start: 0.8648 (p) cc_final: 0.8352 (t)
REVERT: A  162 LEU cc_start: 0.8166 (tp) cc_final: 0.7952 (tp)
REVERT: A  176 THR cc_start: 0.7999 (t) cc_final: 0.7317 (p)
REVERT: A  182 PHE cc_start: 0.7918 (OUTLIER) cc_final: 0.7644 (m-80)
REVERT: A  254 MET cc_start: 0.7724 (mtt) cc_final: 0.7260 (mtt)
REVERT: A  277 ASN cc_start: 0.8450 (m110) cc_final: 0.8163 (m110)
REVERT: A  310 ASP cc_start: 0.7440 (t0) cc_final: 0.7184 (t0)
REVERT: A  326 PHE cc_start: 0.6749 (m-10) cc_final: 0.6543 (m-10)
REVERT: A  372 PHE cc_start: 0.8402 (t80) cc_final: 0.8028 (t80)
REVERT: A  405 PHE cc_start: 0.8231 (t80) cc_final: 0.8024 (t80)
REVERT: A  408 THR cc_start: 0.8635 (m) cc_final: 0.8408 (t)
REVERT: A  428 VAL cc_start: 0.8552 (OUTLIER) cc_final: 0.7952 (m)
REVERT: A  445 ILE cc_start: 0.7036 (mt) cc_final: 0.6783 (mt)
REVERT: H   74 SER cc_start: 0.8052 (t) cc_final: 0.7534 (p)
REVERT: H  131 LYS cc_start: 0.7639 (ptmm) cc_final: 0.7298 (ptpp)
REVERT: H  191 SER cc_start: 0.8391 (t) cc_final: 0.8077 (m)
REVERT: H  195 VAL cc_start: 0.8421 (p) cc_final: 0.8147 (m)
REVERT: N   34 MET cc_start: 0.6947 (mtp) cc_final: 0.6440 (mtp)
REVERT: N   89 GLU cc_start: 0.7670 (mp0) cc_final: 0.7277 (mp0)
REVERT: L    4 GLN cc_start: 0.7238 (mm-40) cc_final: 0.6844 (mm-40)
REVERT: L    5 MET cc_start: 0.6970 (ttm) cc_final: 0.6761 (ttt)
REVERT: L   43 LYS cc_start: 0.8745 (mtpp) cc_final: 0.8406 (mtmm)
REVERT: L   68 SER cc_start: 0.8248 (m) cc_final: 0.7733 (p)
REVERT: L   83 ASP cc_start: 0.7545 (m-30) cc_final: 0.7202 (m-30)
REVERT: L   87 TYR cc_start: 0.8396 (m-80) cc_final: 0.7804 (m-80)
REVERT: L  118 PHE cc_start: 0.7797 (m-80) cc_final: 0.7372 (m-80)
REVERT: L  145 GLU cc_start: 0.7610 (mp0) cc_final: 0.7121 (mp0)
REVERT: L  175 TYR cc_start: 0.8024 (m-10) cc_final: 0.7657 (m-10)
REVERT: L  190 LYS cc_start: 0.7467 (ttpp) cc_final: 0.6934 (ttpp)
REVERT: L  211 PHE cc_start: 0.8334 (p90) cc_final: 0.7906 (p90)
  outliers start: 36
  outliers final: 25
  residues processed: 245
  average time/residue: 0.0958
  time to fit residues: 31.3556
Evaluate side-chains
  244 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 216
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -18 PHE
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   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  251 LEU
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  353 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   77 THR
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 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   66 SER
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:    0.0470
   chunk 89 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 46 optimal weight:    0.2980
   chunk 75 optimal weight:    0.6980
   chunk 13 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0770
   chunk 23 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   overall best weight:    0.3436

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

Flipped N/Q/H residues before XYZ refinement:
A -77 ASN
H 169 ASN
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 149 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.148487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.128315 restraints weight = 13857.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.132570 restraints weight = 6879.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.135397 restraints weight = 4123.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.137195 restraints weight = 2810.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.138527 restraints weight = 2130.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7018
moved from start:          0.4603

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= 0.136
  Angle     :  0.627   7.454  11503  Z= 0.314
  Chirality :  0.043   0.153   1298
  Planarity :  0.004   0.042   1440
  Dihedral  :  4.968  45.718   1184
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 16.69 %
    Favored  : 79.73 %
  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 are not related in a simple way.
  whole: -0.26 (0.27), residues: 1045
  helix:  1.69 (0.25), residues: 384
  sheet: -1.24 (0.33), residues: 240
  loop : -1.24 (0.32), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG H  70 
 TYR   0.032   0.002   TYR A 286 
 PHE   0.022   0.002   PHE A  37 
 TRP   0.040   0.002   TRP A 292 
 HIS   0.006   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 8448)
  covalent geometry    : angle       0.62639 (11493)
  SS BOND              : bond        0.00266 (    5)
  SS BOND              : angle       1.40170 (   10)
  hydrogen bonds       : bond        0.03979 (  384)
  hydrogen bonds       : angle       4.55231 ( 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
  245 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 213
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
REVERT: A  -51 LYS cc_start: 0.8688 (mttt) cc_final: 0.8457 (mttt)
REVERT: A  -50 MET cc_start: 0.7725 (mtm) cc_final: 0.7395 (ttm)
REVERT: A  -12 GLN cc_start: 0.7877 (tt0) cc_final: 0.7647 (tt0)
REVERT: A    3 GLU cc_start: 0.7509 (mp0) cc_final: 0.7007 (mp0)
REVERT: A   46 SER cc_start: 0.7501 (m) cc_final: 0.7190 (t)
REVERT: A  123 GLU cc_start: 0.6338 (tm-30) cc_final: 0.6118 (tm-30)
REVERT: A  127 SER cc_start: 0.8472 (p) cc_final: 0.8263 (t)
REVERT: A  162 LEU cc_start: 0.8142 (tp) cc_final: 0.7935 (tp)
REVERT: A  176 THR cc_start: 0.8054 (t) cc_final: 0.7367 (p)
REVERT: A  182 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7547 (m-80)
REVERT: A  254 MET cc_start: 0.7697 (mtt) cc_final: 0.7211 (mtt)
REVERT: A  304 VAL cc_start: 0.8044 (t) cc_final: 0.7829 (p)
REVERT: A  310 ASP cc_start: 0.7378 (t0) cc_final: 0.7134 (t0)
REVERT: A  372 PHE cc_start: 0.8357 (t80) cc_final: 0.7945 (t80)
REVERT: A  405 PHE cc_start: 0.8231 (t80) cc_final: 0.8026 (t80)
REVERT: A  408 THR cc_start: 0.8652 (m) cc_final: 0.8390 (t)
REVERT: A  428 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.7927 (m)
REVERT: A  445 ILE cc_start: 0.6984 (mt) cc_final: 0.6737 (mt)
REVERT: H   74 SER cc_start: 0.8048 (t) cc_final: 0.7539 (p)
REVERT: H  131 LYS cc_start: 0.7583 (ptmm) cc_final: 0.7257 (ptpp)
REVERT: H  191 SER cc_start: 0.8342 (t) cc_final: 0.8012 (m)
REVERT: N   34 MET cc_start: 0.6889 (mtp) cc_final: 0.6400 (mtp)
REVERT: N   89 GLU cc_start: 0.7633 (mp0) cc_final: 0.7280 (mp0)
REVERT: L    4 GLN cc_start: 0.7185 (mm-40) cc_final: 0.6750 (mm-40)
REVERT: L   43 LYS cc_start: 0.8728 (mtpp) cc_final: 0.8362 (mtmm)
REVERT: L   68 SER cc_start: 0.8164 (m) cc_final: 0.7774 (p)
REVERT: L   83 ASP cc_start: 0.7573 (m-30) cc_final: 0.7325 (m-30)
REVERT: L   87 TYR cc_start: 0.8321 (m-80) cc_final: 0.7816 (m-80)
REVERT: L  134 VAL cc_start: 0.7562 (p) cc_final: 0.7247 (m)
REVERT: L  145 GLU cc_start: 0.7597 (mp0) cc_final: 0.7098 (mp0)
REVERT: L  175 TYR cc_start: 0.7964 (m-10) cc_final: 0.7492 (m-10)
REVERT: L  190 LYS cc_start: 0.7470 (ttpp) cc_final: 0.6863 (ttpp)
REVERT: L  211 PHE cc_start: 0.8340 (p90) cc_final: 0.7943 (p90)
  outliers start: 32
  outliers final: 22
  residues processed: 230
  average time/residue: 0.0920
  time to fit residues: 27.9241
Evaluate side-chains
  235 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 211
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -77 ASN
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue    1 VAL
Chi-restraints excluded: chain A residue   69 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  270 TRP
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  377 GLN
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 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  165 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 58 optimal weight:    0.5980
   chunk 53 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   chunk 60 optimal weight:    0.1980
   chunk 63 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A -70 ASN
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 149 GLN
L 168 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.146376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.126180 restraints weight = 14071.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.130386 restraints weight = 6890.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.133261 restraints weight = 4150.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.135129 restraints weight = 2833.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.136349 restraints weight = 2132.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7053
moved from start:          0.4813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8453  Z= 0.187
  Angle     :  0.668  11.150  11503  Z= 0.336
  Chirality :  0.044   0.215   1298
  Planarity :  0.005   0.051   1440
  Dihedral  :  5.106  46.500   1184
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 17.69 %
    Favored  : 78.95 %
  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 are not related in a simple way.
  whole: -0.27 (0.27), residues: 1045
  helix:  1.57 (0.25), residues: 385
  sheet: -1.09 (0.34), residues: 242
  loop : -1.22 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG H  70 
 TYR   0.032   0.002   TYR A 286 
 PHE   0.024   0.002   PHE A  47 
 TRP   0.043   0.002   TRP A 292 
 HIS   0.004   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 8448)
  covalent geometry    : angle       0.66697 (11493)
  SS BOND              : bond        0.00334 (    5)
  SS BOND              : angle       1.48832 (   10)
  hydrogen bonds       : bond        0.04216 (  384)
  hydrogen bonds       : angle       4.65807 ( 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
  241 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 211
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -51 LYS cc_start: 0.8676 (mttt) cc_final: 0.8441 (mttt)
REVERT: A  -12 GLN cc_start: 0.7887 (tt0) cc_final: 0.7682 (tt0)
REVERT: A   -9 ASP cc_start: 0.8152 (t0) cc_final: 0.7648 (t0)
REVERT: A   -5 LEU cc_start: 0.8228 (mt) cc_final: 0.8005 (mp)
REVERT: A    3 GLU cc_start: 0.7562 (mp0) cc_final: 0.7007 (mp0)
REVERT: A   46 SER cc_start: 0.7540 (m) cc_final: 0.7268 (t)
REVERT: A  123 GLU cc_start: 0.6430 (tm-30) cc_final: 0.6206 (tm-30)
REVERT: A  127 SER cc_start: 0.8574 (p) cc_final: 0.8327 (t)
REVERT: A  162 LEU cc_start: 0.8186 (tp) cc_final: 0.7975 (tp)
REVERT: A  172 GLN cc_start: 0.8051 (tp-100) cc_final: 0.7768 (tm-30)
REVERT: A  176 THR cc_start: 0.8096 (t) cc_final: 0.7673 (p)
REVERT: A  254 MET cc_start: 0.7730 (mtt) cc_final: 0.7222 (mtt)
REVERT: A  304 VAL cc_start: 0.8071 (t) cc_final: 0.7847 (p)
REVERT: A  310 ASP cc_start: 0.7370 (t0) cc_final: 0.7120 (t0)
REVERT: A  372 PHE cc_start: 0.8385 (t80) cc_final: 0.8064 (t80)
REVERT: A  405 PHE cc_start: 0.8229 (t80) cc_final: 0.8020 (t80)
REVERT: A  408 THR cc_start: 0.8681 (m) cc_final: 0.8416 (t)
REVERT: A  428 VAL cc_start: 0.8577 (OUTLIER) cc_final: 0.8028 (m)
REVERT: A  445 ILE cc_start: 0.7059 (mt) cc_final: 0.6795 (mt)
REVERT: H   74 SER cc_start: 0.8040 (t) cc_final: 0.7563 (p)
REVERT: H  131 LYS cc_start: 0.7620 (ptmm) cc_final: 0.7280 (ptpp)
REVERT: H  191 SER cc_start: 0.8387 (t) cc_final: 0.8081 (m)
REVERT: H  195 VAL cc_start: 0.8325 (p) cc_final: 0.8071 (m)
REVERT: N   34 MET cc_start: 0.6907 (mtp) cc_final: 0.6420 (mtp)
REVERT: N   89 GLU cc_start: 0.7604 (mp0) cc_final: 0.7241 (mp0)
REVERT: L    4 GLN cc_start: 0.7278 (mm-40) cc_final: 0.6861 (mm-40)
REVERT: L    5 MET cc_start: 0.6988 (ttm) cc_final: 0.6779 (ttt)
REVERT: L   43 LYS cc_start: 0.8712 (mtpp) cc_final: 0.8354 (mtmm)
REVERT: L   68 SER cc_start: 0.8237 (m) cc_final: 0.7753 (p)
REVERT: L   83 ASP cc_start: 0.7587 (m-30) cc_final: 0.7349 (m-30)
REVERT: L  134 VAL cc_start: 0.7624 (p) cc_final: 0.7314 (m)
REVERT: L  145 GLU cc_start: 0.7600 (mp0) cc_final: 0.6965 (mp0)
REVERT: L  190 LYS cc_start: 0.7490 (ttpp) cc_final: 0.6918 (ttpp)
REVERT: L  211 PHE cc_start: 0.8323 (p90) cc_final: 0.7990 (p90)
  outliers start: 30
  outliers final: 26
  residues processed: 228
  average time/residue: 0.0993
  time to fit residues: 29.9664
Evaluate side-chains
  237 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 210
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -32 LYS
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue    1 VAL
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  270 TRP
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  353 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 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  149 GLN
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:    0.0020
   chunk 94 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0870
   chunk 17 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9980
   chunk 100 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.3966

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

Flipped N/Q/H residues before XYZ refinement:
A -70 ASN
H 169 ASN
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 149 GLN
L 168 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.147672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.127547 restraints weight = 14042.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.131839 restraints weight = 6885.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.134693 restraints weight = 4133.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.136430 restraints weight = 2815.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.137775 restraints weight = 2143.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7031
moved from start:          0.4884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8453  Z= 0.147
  Angle     :  0.661  10.608  11503  Z= 0.332
  Chirality :  0.044   0.190   1298
  Planarity :  0.004   0.048   1440
  Dihedral  :  5.027  45.940   1184
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 12.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 18.03 %
    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 are not related in a simple way.
  whole: -0.22 (0.27), residues: 1045
  helix:  1.55 (0.25), residues: 385
  sheet: -0.97 (0.34), residues: 240
  loop : -1.20 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG H  70 
 TYR   0.053   0.002   TYR A 286 
 PHE   0.026   0.002   PHE A  47 
 TRP   0.044   0.002   TRP A 292 
 HIS   0.004   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 8448)
  covalent geometry    : angle       0.65990 (11493)
  SS BOND              : bond        0.00289 (    5)
  SS BOND              : angle       1.41355 (   10)
  hydrogen bonds       : bond        0.04139 (  384)
  hydrogen bonds       : angle       4.60245 ( 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
  237 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 205
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -51 LYS cc_start: 0.8713 (mttt) cc_final: 0.8459 (mttt)
REVERT: A  -12 GLN cc_start: 0.7865 (tt0) cc_final: 0.7632 (tt0)
REVERT: A   -9 ASP cc_start: 0.8155 (t0) cc_final: 0.7667 (t0)
REVERT: A   -5 LEU cc_start: 0.8228 (mt) cc_final: 0.8009 (mp)
REVERT: A    3 GLU cc_start: 0.7595 (mp0) cc_final: 0.7075 (mp0)
REVERT: A   11 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7194 (tm)
REVERT: A   23 LEU cc_start: 0.6294 (OUTLIER) cc_final: 0.5905 (tt)
REVERT: A   46 SER cc_start: 0.7551 (m) cc_final: 0.7342 (t)
REVERT: A  123 GLU cc_start: 0.6380 (tm-30) cc_final: 0.6177 (tm-30)
REVERT: A  127 SER cc_start: 0.8567 (p) cc_final: 0.8316 (t)
REVERT: A  162 LEU cc_start: 0.8204 (tp) cc_final: 0.7992 (tp)
REVERT: A  172 GLN cc_start: 0.8016 (tp-100) cc_final: 0.7787 (tm-30)
REVERT: A  176 THR cc_start: 0.8052 (t) cc_final: 0.7568 (p)
REVERT: A  182 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.7614 (m-80)
REVERT: A  254 MET cc_start: 0.7693 (mtt) cc_final: 0.7188 (mtt)
REVERT: A  304 VAL cc_start: 0.8063 (t) cc_final: 0.7849 (p)
REVERT: A  310 ASP cc_start: 0.7342 (t0) cc_final: 0.7092 (t0)
REVERT: A  372 PHE cc_start: 0.8377 (t80) cc_final: 0.8003 (t80)
REVERT: A  405 PHE cc_start: 0.8209 (t80) cc_final: 0.7997 (t80)
REVERT: A  408 THR cc_start: 0.8659 (m) cc_final: 0.8404 (t)
REVERT: A  428 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8047 (m)
REVERT: A  445 ILE cc_start: 0.7021 (mt) cc_final: 0.6769 (mt)
REVERT: H   70 ARG cc_start: 0.8603 (ttp80) cc_final: 0.7860 (ttp-170)
REVERT: H   74 SER cc_start: 0.8032 (t) cc_final: 0.7554 (p)
REVERT: H  131 LYS cc_start: 0.7574 (ptmm) cc_final: 0.7246 (ptpp)
REVERT: H  191 SER cc_start: 0.8358 (t) cc_final: 0.8046 (m)
REVERT: N   34 MET cc_start: 0.6877 (mtp) cc_final: 0.6395 (mtp)
REVERT: L    4 GLN cc_start: 0.7223 (mm-40) cc_final: 0.6833 (mm-40)
REVERT: L    5 MET cc_start: 0.6835 (ttm) cc_final: 0.6609 (ttt)
REVERT: L   43 LYS cc_start: 0.8698 (mtpp) cc_final: 0.8345 (mtmm)
REVERT: L   68 SER cc_start: 0.8211 (m) cc_final: 0.7827 (p)
REVERT: L   83 ASP cc_start: 0.7576 (m-30) cc_final: 0.7349 (m-30)
REVERT: L   91 GLN cc_start: 0.8469 (pp30) cc_final: 0.7842 (pp30)
REVERT: L  134 VAL cc_start: 0.7598 (p) cc_final: 0.7282 (m)
REVERT: L  145 GLU cc_start: 0.7556 (mp0) cc_final: 0.6929 (mp0)
REVERT: L  190 LYS cc_start: 0.7504 (ttpp) cc_final: 0.6884 (ttpp)
REVERT: L  198 VAL cc_start: 0.7807 (p) cc_final: 0.7513 (m)
REVERT: L  211 PHE cc_start: 0.8298 (p90) cc_final: 0.7934 (p90)
  outliers start: 32
  outliers final: 23
  residues processed: 225
  average time/residue: 0.0877
  time to fit residues: 26.1175
Evaluate side-chains
  233 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 206
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -32 LYS
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue    1 VAL
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   69 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  270 TRP
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  353 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 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  165 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 100 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0070
   chunk 73 optimal weight:    5.9990
   chunk 96 optimal weight:    0.8980
   chunk 89 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 58 optimal weight:    0.7980
   chunk 66 optimal weight:    0.0770
   chunk 86 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0970
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.3354

-------------------------------------------------------------------------------
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**
L 168 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.147969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.127903 restraints weight = 14054.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.132127 restraints weight = 6990.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.134978 restraints weight = 4179.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.136851 restraints weight = 2840.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.138022 restraints weight = 2131.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7023
moved from start:          0.4934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8453  Z= 0.136
  Angle     :  0.645  10.189  11503  Z= 0.322
  Chirality :  0.043   0.179   1298
  Planarity :  0.004   0.045   1440
  Dihedral  :  4.950  45.519   1184
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 18.48 %
    Favored  : 78.28 %
  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 are not related in a simple way.
  whole: -0.14 (0.27), residues: 1045
  helix:  1.58 (0.25), residues: 386
  sheet: -0.90 (0.34), residues: 242
  loop : -1.14 (0.33), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A  15 
 TYR   0.051   0.002   TYR A 286 
 PHE   0.020   0.001   PHE A  47 
 TRP   0.043   0.002   TRP A 292 
 HIS   0.003   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 8448)
  covalent geometry    : angle       0.64407 (11493)
  SS BOND              : bond        0.00259 (    5)
  SS BOND              : angle       1.35946 (   10)
  hydrogen bonds       : bond        0.03990 (  384)
  hydrogen bonds       : angle       4.57707 ( 1149)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1378.64 seconds
wall clock time: 24 minutes 32.37 seconds (1472.37 seconds total)