Starting phenix.real_space_refine
on Fri Jun  6 23:17:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hij_34818/06_2025/8hij_34818_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hij_34818/06_2025/8hij_34818.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hij_34818/06_2025/8hij_34818.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hij_34818/06_2025/8hij_34818.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hij_34818/06_2025/8hij_34818_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hij_34818/06_2025/8hij_34818_neut.cif"
  }
  resolution = 3.54
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.41, per 1000 atoms: 0.66
  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: 2.13
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 1.02
  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: 2.32

  Time building geometry restraints manager: 2.50 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:             2.420
  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:             0.000
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     22.290
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.120
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.037   0.002   TRP H 102 
 HIS   0.004   0.001   HIS H  38 
 PHE   0.033   0.002   PHE A 103 
 TYR   0.026   0.002   TYR A 435 
 ARG   0.004   0.000   ARG N  52 

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

*********************** 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  : 0.901 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -55 ASP cc_start: 0.6609 (t0) cc_final: 0.6405 (t0)
REVERT: A  -51 LYS cc_start: 0.8509 (mttt) cc_final: 0.8247 (mttt)
REVERT: A  -50 MET cc_start: 0.6978 (mmm) cc_final: 0.6731 (mmm)
REVERT: A  -16 ILE cc_start: 0.8500 (tp) cc_final: 0.8173 (mt)
REVERT: A    1 VAL cc_start: 0.8584 (m) cc_final: 0.8263 (p)
REVERT: A   46 SER cc_start: 0.7456 (m) cc_final: 0.6633 (t)
REVERT: A   81 VAL cc_start: 0.7706 (t) cc_final: 0.7475 (m)
REVERT: A  127 SER cc_start: 0.8834 (p) cc_final: 0.8229 (t)
REVERT: A  139 TYR cc_start: 0.7092 (t80) cc_final: 0.6886 (t80)
REVERT: A  149 TYR cc_start: 0.6915 (t80) cc_final: 0.6580 (t80)
REVERT: A  155 TYR cc_start: 0.6982 (m-80) cc_final: 0.6754 (m-80)
REVERT: A  162 LEU cc_start: 0.7897 (tp) cc_final: 0.7613 (tp)
REVERT: A  254 MET cc_start: 0.7477 (mtt) cc_final: 0.7163 (mtt)
REVERT: A  314 THR cc_start: 0.8067 (m) cc_final: 0.7829 (p)
REVERT: A  405 PHE cc_start: 0.8105 (t80) cc_final: 0.7820 (t80)
REVERT: A  406 PHE cc_start: 0.7492 (m-80) cc_final: 0.6995 (m-80)
REVERT: A  411 LYS cc_start: 0.8025 (ttpt) cc_final: 0.7746 (ttpt)
REVERT: H   37 LEU cc_start: 0.7269 (mt) cc_final: 0.6950 (mm)
REVERT: H   46 LYS cc_start: 0.8134 (mmtt) cc_final: 0.7788 (mmtt)
REVERT: H  152 LEU cc_start: 0.7479 (tp) cc_final: 0.7115 (tp)
REVERT: N   34 MET cc_start: 0.6920 (mtp) cc_final: 0.6480 (mtp)
REVERT: L    4 GLN cc_start: 0.7196 (mm-40) cc_final: 0.6633 (mm-40)
REVERT: L   38 GLN cc_start: 0.8298 (tt0) cc_final: 0.8093 (tt0)
REVERT: L   73 THR cc_start: 0.8035 (m) cc_final: 0.7832 (t)
REVERT: L   83 ASP cc_start: 0.6949 (m-30) cc_final: 0.6615 (m-30)
REVERT: L   93 LEU cc_start: 0.7949 (tp) cc_final: 0.7464 (tp)
REVERT: L   97 LEU cc_start: 0.8607 (mp) cc_final: 0.8387 (mt)
REVERT: L  104 THR cc_start: 0.8497 (p) cc_final: 0.8194 (t)
REVERT: L  142 TYR cc_start: 0.7731 (t80) cc_final: 0.7496 (t80)
REVERT: L  147 LYS cc_start: 0.7312 (ttmm) cc_final: 0.7103 (ttmm)
REVERT: L  211 PHE cc_start: 0.8091 (p90) cc_final: 0.7847 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 280
  average time/residue: 0.2017
  time to fit residues: 76.1104
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  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 78 optimal weight:    4.9990
   chunk 43 optimal weight:    0.0670
   chunk 26 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 81 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 49 optimal weight:    0.0370
   chunk 60 optimal weight:    0.4980
   chunk 94 optimal weight:    0.5980
   overall best weight:    0.3796

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
N  65 GLN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.157210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.136919 restraints weight = 14024.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.141213 restraints weight = 7079.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.144007 restraints weight = 4290.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6901
moved from start:          0.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8453  Z= 0.145
  Angle     :  0.624  10.504  11503  Z= 0.315
  Chirality :  0.043   0.241   1298
  Planarity :  0.004   0.047   1440
  Dihedral  :  5.514  51.851   1184
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  :  9.07 %
    Favored  : 88.69 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.13 (0.24), residues: 1045
  helix:  0.41 (0.25), residues: 381
  sheet: -2.49 (0.30), residues: 245
  loop : -2.40 (0.27), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP H 102 
 HIS   0.003   0.001   HIS A 355 
 PHE   0.017   0.002   PHE A 211 
 TYR   0.023   0.001   TYR A 438 
 ARG   0.007   0.000   ARG A -21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04154 (  384)
  hydrogen bonds       : angle       5.22323 ( 1149)
  SS BOND              : bond        0.00456 (    5)
  SS BOND              : angle       1.67353 (   10)
  covalent geometry    : bond        0.00308 ( 8448)
  covalent geometry    : angle       0.62274 (11493)

*********************** 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
  248 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 228
  time to evaluate  : 1.161 
Fit side-chains
   revert: symmetry clash
REVERT: A  -51 LYS cc_start: 0.8698 (mttt) cc_final: 0.8390 (mttt)
REVERT: A  -12 GLN cc_start: 0.7727 (mt0) cc_final: 0.7425 (tt0)
REVERT: A    1 VAL cc_start: 0.8588 (m) cc_final: 0.8363 (p)
REVERT: A   11 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.7017 (tm)
REVERT: A   46 SER cc_start: 0.7519 (m) cc_final: 0.7068 (t)
REVERT: A   76 TYR cc_start: 0.8667 (t80) cc_final: 0.8350 (t80)
REVERT: A  127 SER cc_start: 0.8729 (p) cc_final: 0.8194 (t)
REVERT: A  128 VAL cc_start: 0.8358 (t) cc_final: 0.8051 (p)
REVERT: A  162 LEU cc_start: 0.8068 (tp) cc_final: 0.7799 (tp)
REVERT: A  254 MET cc_start: 0.7539 (mtt) cc_final: 0.7125 (mtt)
REVERT: A  314 THR cc_start: 0.8178 (m) cc_final: 0.7895 (p)
REVERT: A  394 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7724 (mm-30)
REVERT: A  405 PHE cc_start: 0.8203 (t80) cc_final: 0.7883 (t80)
REVERT: A  406 PHE cc_start: 0.7616 (m-80) cc_final: 0.7124 (m-10)
REVERT: H   70 ARG cc_start: 0.8336 (ttp80) cc_final: 0.7964 (ttp80)
REVERT: H   80 ASN cc_start: 0.8243 (t0) cc_final: 0.7967 (t0)
REVERT: H   98 TYR cc_start: 0.8561 (m-80) cc_final: 0.8230 (m-80)
REVERT: H  152 LEU cc_start: 0.7651 (tp) cc_final: 0.7445 (tp)
REVERT: H  159 TYR cc_start: 0.7695 (p90) cc_final: 0.7077 (p90)
REVERT: N   34 MET cc_start: 0.6878 (mtp) cc_final: 0.6418 (mtp)
REVERT: N   89 GLU cc_start: 0.7407 (mp0) cc_final: 0.7058 (mp0)
REVERT: L    4 GLN cc_start: 0.7185 (mm-40) cc_final: 0.6684 (mm-40)
REVERT: L   73 THR cc_start: 0.8059 (m) cc_final: 0.7516 (p)
REVERT: L   83 ASP cc_start: 0.7309 (m-30) cc_final: 0.6967 (m-30)
REVERT: L   97 LEU cc_start: 0.8565 (mp) cc_final: 0.8356 (mt)
REVERT: L  120 PHE cc_start: 0.7812 (m-80) cc_final: 0.7585 (m-80)
REVERT: L  142 TYR cc_start: 0.8035 (t80) cc_final: 0.7743 (t80)
REVERT: L  145 GLU cc_start: 0.7499 (mp0) cc_final: 0.7099 (mp0)
REVERT: L  172 ASP cc_start: 0.8498 (p0) cc_final: 0.8200 (p0)
REVERT: L  190 LYS cc_start: 0.7473 (ttpp) cc_final: 0.6964 (ttpp)
REVERT: L  192 LYS cc_start: 0.4886 (tppt) cc_final: 0.4489 (tppt)
REVERT: L  211 PHE cc_start: 0.8321 (p90) cc_final: 0.7983 (p90)
  outliers start: 20
  outliers final: 9
  residues processed: 239
  average time/residue: 0.3145
  time to fit residues: 100.5864
Evaluate side-chains
  235 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 225
  time to evaluate  : 1.039 
-------------------------------------------------------------------------------
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  169 VAL
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain H residue  167 SER
Chi-restraints excluded: chain L residue  125 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    0.0470
   chunk 25 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0870
   chunk 33 optimal weight:    0.0980
   chunk 5 optimal weight:    0.8980
   chunk 32 optimal weight:    0.3980
   chunk 34 optimal weight:    0.0980
   chunk 8 optimal weight:    0.4980
   chunk 59 optimal weight:    0.6980
   chunk 87 optimal weight:    0.0050
   chunk 63 optimal weight:    3.9990
   overall best weight:    0.0670

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

Flipped N/Q/H residues before XYZ refinement:
A -61 ASN
A 186 ASN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.158970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.138774 restraints weight = 14245.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.143118 restraints weight = 7257.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.145983 restraints weight = 4416.938|
|-----------------------------------------------------------------------------|
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6867
moved from start:          0.2601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8453  Z= 0.104
  Angle     :  0.562   8.725  11503  Z= 0.279
  Chirality :  0.041   0.274   1298
  Planarity :  0.004   0.034   1440
  Dihedral  :  5.202  49.685   1184
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 11.53 %
    Favored  : 86.23 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.25), residues: 1045
  helix:  1.08 (0.25), residues: 382
  sheet: -2.19 (0.31), residues: 244
  loop : -2.04 (0.29), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 292 
 HIS   0.004   0.001   HIS A -20 
 PHE   0.013   0.001   PHE A 103 
 TYR   0.026   0.001   TYR A 286 
 ARG   0.003   0.000   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03575 (  384)
  hydrogen bonds       : angle       4.73521 ( 1149)
  SS BOND              : bond        0.00345 (    5)
  SS BOND              : angle       1.27006 (   10)
  covalent geometry    : bond        0.00215 ( 8448)
  covalent geometry    : angle       0.56055 (11493)

*********************** 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
  244 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 224
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -57 VAL cc_start: 0.6844 (m) cc_final: 0.6613 (p)
REVERT: A  -51 LYS cc_start: 0.8576 (mttt) cc_final: 0.8346 (mttt)
REVERT: A  -12 GLN cc_start: 0.7768 (mt0) cc_final: 0.7506 (tt0)
REVERT: A    1 VAL cc_start: 0.8596 (m) cc_final: 0.8384 (p)
REVERT: A   11 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.7021 (tm)
REVERT: A   46 SER cc_start: 0.7423 (m) cc_final: 0.7118 (t)
REVERT: A  127 SER cc_start: 0.8728 (p) cc_final: 0.8205 (t)
REVERT: A  128 VAL cc_start: 0.8341 (OUTLIER) cc_final: 0.8035 (p)
REVERT: A  162 LEU cc_start: 0.8039 (tp) cc_final: 0.7768 (tp)
REVERT: A  204 LYS cc_start: 0.7629 (tttt) cc_final: 0.7374 (tttt)
REVERT: A  254 MET cc_start: 0.7534 (mtt) cc_final: 0.7164 (mtt)
REVERT: A  273 TRP cc_start: 0.4927 (t60) cc_final: 0.4658 (t60)
REVERT: A  293 ASN cc_start: 0.7883 (t0) cc_final: 0.7683 (t0)
REVERT: A  314 THR cc_start: 0.7988 (m) cc_final: 0.7635 (p)
REVERT: A  373 ARG cc_start: 0.7416 (mtp-110) cc_final: 0.7110 (mtp-110)
REVERT: A  394 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7625 (mm-30)
REVERT: A  405 PHE cc_start: 0.8219 (t80) cc_final: 0.7902 (t80)
REVERT: A  406 PHE cc_start: 0.7623 (m-80) cc_final: 0.7103 (m-10)
REVERT: H   15 VAL cc_start: 0.8268 (m) cc_final: 0.8062 (p)
REVERT: H   70 ARG cc_start: 0.8248 (ttp80) cc_final: 0.7802 (ttp80)
REVERT: H   80 ASN cc_start: 0.8152 (t0) cc_final: 0.7871 (t0)
REVERT: H   98 TYR cc_start: 0.8511 (m-80) cc_final: 0.8244 (m-80)
REVERT: H  159 TYR cc_start: 0.7636 (p90) cc_final: 0.7405 (p90)
REVERT: H  191 SER cc_start: 0.8222 (t) cc_final: 0.7896 (m)
REVERT: N   34 MET cc_start: 0.6834 (mtp) cc_final: 0.6378 (mtp)
REVERT: N   89 GLU cc_start: 0.7385 (mp0) cc_final: 0.7040 (mp0)
REVERT: L    4 GLN cc_start: 0.7083 (mm-40) cc_final: 0.6588 (mm-40)
REVERT: L   73 THR cc_start: 0.8002 (m) cc_final: 0.7671 (t)
REVERT: L   94 TYR cc_start: 0.8228 (t80) cc_final: 0.8015 (t80)
REVERT: L   97 LEU cc_start: 0.8581 (mp) cc_final: 0.8378 (mt)
REVERT: L  120 PHE cc_start: 0.7813 (m-80) cc_final: 0.7368 (m-80)
REVERT: L  142 TYR cc_start: 0.8025 (t80) cc_final: 0.7773 (t80)
REVERT: L  145 GLU cc_start: 0.7513 (mp0) cc_final: 0.7109 (mp0)
REVERT: L  190 LYS cc_start: 0.7413 (ttpp) cc_final: 0.6910 (ttpp)
REVERT: L  211 PHE cc_start: 0.8263 (p90) cc_final: 0.7912 (p90)
  outliers start: 20
  outliers final: 12
  residues processed: 232
  average time/residue: 0.2337
  time to fit residues: 72.4118
Evaluate side-chains
  231 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 217
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
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   69 THR
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  186 ASN
Chi-restraints excluded: chain A residue  277 ASN
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  377 GLN
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain H residue  165 THR
Chi-restraints excluded: chain N residue    2 VAL
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 86 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 81 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 43 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0170
   chunk 65 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 79 optimal weight:    2.9990
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
** A -61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  99 GLN
A 277 ASN
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**
** L 160 ASN ** 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 = 0.3980 r_free = 0.3980 target = 0.152267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.131508 restraints weight = 13808.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.135789 restraints weight = 7069.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.138638 restraints weight = 4362.541|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6991
moved from start:          0.3167

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= 0.173
  Angle     :  0.599   8.031  11503  Z= 0.303
  Chirality :  0.043   0.238   1298
  Planarity :  0.005   0.084   1440
  Dihedral  :  5.164  46.783   1184
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 12.88 %
    Favored  : 84.32 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.26), residues: 1045
  helix:  1.38 (0.25), residues: 383
  sheet: -1.88 (0.32), residues: 233
  loop : -1.66 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP H 102 
 HIS   0.005   0.001   HIS A 355 
 PHE   0.011   0.001   PHE H 114 
 TYR   0.028   0.002   TYR A 286 
 ARG   0.007   0.000   ARG A -21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03950 (  384)
  hydrogen bonds       : angle       4.66199 ( 1149)
  SS BOND              : bond        0.00425 (    5)
  SS BOND              : angle       1.56961 (   10)
  covalent geometry    : bond        0.00373 ( 8448)
  covalent geometry    : angle       0.59784 (11493)

*********************** 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
  266 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 241
  time to evaluate  : 0.872 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -57 VAL cc_start: 0.6977 (m) cc_final: 0.6677 (p)
REVERT: A  -51 LYS cc_start: 0.8585 (mttt) cc_final: 0.8339 (mttt)
REVERT: A   -6 LYS cc_start: 0.8196 (ttpt) cc_final: 0.7863 (ttpt)
REVERT: A    1 VAL cc_start: 0.8677 (m) cc_final: 0.8463 (p)
REVERT: A   11 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7073 (tm)
REVERT: A   21 LYS cc_start: 0.8278 (tttm) cc_final: 0.8069 (tttm)
REVERT: A   46 SER cc_start: 0.7504 (m) cc_final: 0.7208 (t)
REVERT: A   72 LEU cc_start: 0.7252 (tp) cc_final: 0.5994 (tt)
REVERT: A  112 LEU cc_start: 0.7047 (mt) cc_final: 0.6843 (mt)
REVERT: A  123 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6669 (tm-30)
REVERT: A  127 SER cc_start: 0.8741 (p) cc_final: 0.8325 (t)
REVERT: A  128 VAL cc_start: 0.8468 (OUTLIER) cc_final: 0.8150 (p)
REVERT: A  162 LEU cc_start: 0.8128 (tp) cc_final: 0.7863 (tp)
REVERT: A  204 LYS cc_start: 0.7827 (tttt) cc_final: 0.7569 (tttt)
REVERT: A  254 MET cc_start: 0.7663 (mtt) cc_final: 0.7215 (mtt)
REVERT: A  293 ASN cc_start: 0.7926 (t0) cc_final: 0.7698 (t0)
REVERT: A  314 THR cc_start: 0.8164 (m) cc_final: 0.7869 (p)
REVERT: A  326 PHE cc_start: 0.6662 (m-10) cc_final: 0.6386 (m-10)
REVERT: A  346 GLN cc_start: 0.7722 (mt0) cc_final: 0.7463 (mt0)
REVERT: A  370 VAL cc_start: 0.8584 (t) cc_final: 0.8366 (p)
REVERT: A  386 GLN cc_start: 0.7707 (mm-40) cc_final: 0.7500 (mm110)
REVERT: A  394 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7709 (mm-30)
REVERT: A  405 PHE cc_start: 0.8277 (t80) cc_final: 0.7985 (t80)
REVERT: A  406 PHE cc_start: 0.7664 (m-80) cc_final: 0.7168 (m-10)
REVERT: A  445 ILE cc_start: 0.6745 (mt) cc_final: 0.6470 (mt)
REVERT: H   74 SER cc_start: 0.7858 (t) cc_final: 0.7278 (p)
REVERT: H   80 ASN cc_start: 0.8237 (t0) cc_final: 0.7908 (t0)
REVERT: H   98 TYR cc_start: 0.8592 (m-80) cc_final: 0.8292 (m-80)
REVERT: H  131 LYS cc_start: 0.7527 (ptmm) cc_final: 0.7208 (ptpp)
REVERT: H  191 SER cc_start: 0.8287 (t) cc_final: 0.7979 (m)
REVERT: N   34 MET cc_start: 0.6955 (mtp) cc_final: 0.6446 (mtp)
REVERT: N   89 GLU cc_start: 0.7516 (mp0) cc_final: 0.7063 (mp0)
REVERT: L    4 GLN cc_start: 0.7109 (mm-40) cc_final: 0.6642 (mm-40)
REVERT: L   68 SER cc_start: 0.7762 (m) cc_final: 0.7342 (p)
REVERT: L   91 GLN cc_start: 0.8378 (pp30) cc_final: 0.7987 (pp30)
REVERT: L   97 LEU cc_start: 0.8548 (mp) cc_final: 0.8295 (mt)
REVERT: L  142 TYR cc_start: 0.8023 (t80) cc_final: 0.7780 (t80)
REVERT: L  172 ASP cc_start: 0.8463 (p0) cc_final: 0.8245 (p0)
REVERT: L  175 TYR cc_start: 0.7847 (m-10) cc_final: 0.7237 (m-10)
REVERT: L  190 LYS cc_start: 0.7467 (ttpp) cc_final: 0.6882 (ttpp)
REVERT: L  211 PHE cc_start: 0.8297 (p90) cc_final: 0.7918 (p90)
  outliers start: 25
  outliers final: 16
  residues processed: 253
  average time/residue: 0.2256
  time to fit residues: 76.0565
Evaluate side-chains
  249 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 231
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
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   81 VAL
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  251 LEU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  451 MET
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  125 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 50 optimal weight:    0.0570
   chunk 14 optimal weight:    1.9990
   chunk 78 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 96 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
A -70 ASN
** A  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  99 GLN
A 186 ASN
A 277 ASN
** H 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 160 ASN
L 168 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.149350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.128654 restraints weight = 13692.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.132832 restraints weight = 7027.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.135668 restraints weight = 4327.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7044
moved from start:          0.3715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8453  Z= 0.189
  Angle     :  0.622   6.793  11503  Z= 0.315
  Chirality :  0.044   0.185   1298
  Planarity :  0.004   0.039   1440
  Dihedral  :  5.152  46.465   1184
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 15.12 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.65 (0.26), residues: 1045
  helix:  1.56 (0.25), residues: 383
  sheet: -1.73 (0.32), residues: 236
  loop : -1.47 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.002   TRP A 292 
 HIS   0.005   0.001   HIS A 355 
 PHE   0.012   0.001   PHE A -18 
 TYR   0.031   0.002   TYR A 286 
 ARG   0.007   0.000   ARG A -21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03980 (  384)
  hydrogen bonds       : angle       4.65787 ( 1149)
  SS BOND              : bond        0.00373 (    5)
  SS BOND              : angle       1.54746 (   10)
  covalent geometry    : bond        0.00405 ( 8448)
  covalent geometry    : angle       0.62070 (11493)

*********************** 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
  268 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 238
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -57 VAL cc_start: 0.6979 (m) cc_final: 0.6754 (p)
REVERT: A  -36 LYS cc_start: 0.8119 (mppt) cc_final: 0.7635 (ttmm)
REVERT: A   -6 LYS cc_start: 0.8235 (ttpt) cc_final: 0.7864 (ttpt)
REVERT: A    1 VAL cc_start: 0.8692 (m) cc_final: 0.8421 (p)
REVERT: A   46 SER cc_start: 0.7461 (m) cc_final: 0.7205 (t)
REVERT: A   53 LEU cc_start: 0.7620 (mp) cc_final: 0.7322 (tp)
REVERT: A   72 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6338 (tt)
REVERT: A  127 SER cc_start: 0.8737 (p) cc_final: 0.8298 (t)
REVERT: A  128 VAL cc_start: 0.8460 (OUTLIER) cc_final: 0.8155 (p)
REVERT: A  162 LEU cc_start: 0.8181 (tp) cc_final: 0.7946 (tp)
REVERT: A  211 PHE cc_start: 0.7870 (m-80) cc_final: 0.7229 (m-80)
REVERT: A  254 MET cc_start: 0.7662 (mtt) cc_final: 0.7188 (mtt)
REVERT: A  314 THR cc_start: 0.8185 (m) cc_final: 0.7893 (p)
REVERT: A  326 PHE cc_start: 0.6766 (m-10) cc_final: 0.6466 (m-10)
REVERT: A  346 GLN cc_start: 0.7679 (mt0) cc_final: 0.7433 (mt0)
REVERT: A  370 VAL cc_start: 0.8645 (t) cc_final: 0.8438 (p)
REVERT: A  394 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7792 (mm-30)
REVERT: A  405 PHE cc_start: 0.8265 (t80) cc_final: 0.7947 (t80)
REVERT: A  445 ILE cc_start: 0.7005 (mt) cc_final: 0.6771 (mt)
REVERT: H   35 PHE cc_start: 0.6940 (m-80) cc_final: 0.6425 (m-80)
REVERT: H   74 SER cc_start: 0.7949 (t) cc_final: 0.7412 (p)
REVERT: H   98 TYR cc_start: 0.8604 (m-80) cc_final: 0.8257 (m-80)
REVERT: H  131 LYS cc_start: 0.7554 (ptmm) cc_final: 0.7234 (ptpp)
REVERT: H  191 SER cc_start: 0.8419 (t) cc_final: 0.8067 (m)
REVERT: N   34 MET cc_start: 0.6974 (mtp) cc_final: 0.6459 (mtp)
REVERT: N   60 TYR cc_start: 0.8396 (m-10) cc_final: 0.7892 (m-80)
REVERT: N   89 GLU cc_start: 0.7570 (mp0) cc_final: 0.7112 (mp0)
REVERT: L    4 GLN cc_start: 0.7136 (mm-40) cc_final: 0.6685 (mm-40)
REVERT: L   68 SER cc_start: 0.8057 (m) cc_final: 0.7592 (p)
REVERT: L   83 ASP cc_start: 0.7531 (m-30) cc_final: 0.7296 (m-30)
REVERT: L  142 TYR cc_start: 0.8040 (t80) cc_final: 0.7791 (t80)
REVERT: L  145 GLU cc_start: 0.7636 (mp0) cc_final: 0.7264 (mp0)
REVERT: L  190 LYS cc_start: 0.7360 (ttpp) cc_final: 0.6721 (ttpp)
  outliers start: 30
  outliers final: 20
  residues processed: 250
  average time/residue: 0.2184
  time to fit residues: 72.9194
Evaluate side-chains
  250 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 228
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
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   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  186 ASN
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  451 MET
Chi-restraints excluded: chain H residue  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  112 VAL
Chi-restraints excluded: chain L residue  125 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 53 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9980
   chunk 13 optimal weight:    0.3980
   chunk 64 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0970
   chunk 99 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 46 optimal weight:    3.9990
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
** A -61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  66 ASN
A 186 ASN
** H 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3925 r_free = 0.3925 target = 0.147731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.127181 restraints weight = 13707.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.131353 restraints weight = 6963.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.134200 restraints weight = 4256.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7050
moved from start:          0.4008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8453  Z= 0.163
  Angle     :  0.622   7.465  11503  Z= 0.310
  Chirality :  0.043   0.212   1298
  Planarity :  0.004   0.040   1440
  Dihedral  :  5.076  46.743   1184
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 9.98
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.27), residues: 1045
  helix:  1.65 (0.25), residues: 383
  sheet: -1.56 (0.33), residues: 237
  loop : -1.45 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP A 292 
 HIS   0.005   0.001   HIS A 355 
 PHE   0.019   0.001   PHE A  37 
 TYR   0.032   0.002   TYR A 286 
 ARG   0.010   0.000   ARG H  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04006 (  384)
  hydrogen bonds       : angle       4.58424 ( 1149)
  SS BOND              : bond        0.00324 (    5)
  SS BOND              : angle       1.47549 (   10)
  covalent geometry    : bond        0.00355 ( 8448)
  covalent geometry    : angle       0.62030 (11493)

*********************** 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  : 0.850 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -57 VAL cc_start: 0.7055 (m) cc_final: 0.6826 (p)
REVERT: A   -6 LYS cc_start: 0.8158 (ttpt) cc_final: 0.7786 (ttpt)
REVERT: A    1 VAL cc_start: 0.8666 (m) cc_final: 0.8373 (p)
REVERT: A    3 GLU cc_start: 0.7545 (mp0) cc_final: 0.6904 (mp0)
REVERT: A   11 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7176 (tm)
REVERT: A   46 SER cc_start: 0.7459 (m) cc_final: 0.7156 (t)
REVERT: A  127 SER cc_start: 0.8771 (p) cc_final: 0.8285 (t)
REVERT: A  128 VAL cc_start: 0.8373 (t) cc_final: 0.8099 (p)
REVERT: A  162 LEU cc_start: 0.8171 (tp) cc_final: 0.7952 (tp)
REVERT: A  186 ASN cc_start: 0.7150 (OUTLIER) cc_final: 0.6863 (t0)
REVERT: A  211 PHE cc_start: 0.7835 (m-80) cc_final: 0.6682 (m-80)
REVERT: A  254 MET cc_start: 0.7729 (mtt) cc_final: 0.7228 (mtt)
REVERT: A  293 ASN cc_start: 0.8124 (t0) cc_final: 0.7771 (t0)
REVERT: A  326 PHE cc_start: 0.6753 (m-10) cc_final: 0.6507 (m-10)
REVERT: A  346 GLN cc_start: 0.7802 (mt0) cc_final: 0.7467 (mt0)
REVERT: A  394 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7639 (mm-30)
REVERT: A  405 PHE cc_start: 0.8271 (t80) cc_final: 0.7872 (t80)
REVERT: A  445 ILE cc_start: 0.6966 (mt) cc_final: 0.6710 (mt)
REVERT: H   35 PHE cc_start: 0.6999 (m-80) cc_final: 0.6493 (m-80)
REVERT: H   74 SER cc_start: 0.7964 (t) cc_final: 0.7431 (p)
REVERT: H   98 TYR cc_start: 0.8619 (m-80) cc_final: 0.8190 (m-80)
REVERT: H  131 LYS cc_start: 0.7545 (ptmm) cc_final: 0.7224 (ptpp)
REVERT: H  191 SER cc_start: 0.8360 (t) cc_final: 0.8010 (m)
REVERT: N   34 MET cc_start: 0.6957 (mtp) cc_final: 0.6436 (mtp)
REVERT: N   89 GLU cc_start: 0.7639 (mp0) cc_final: 0.7161 (mp0)
REVERT: L    4 GLN cc_start: 0.7080 (mm-40) cc_final: 0.6617 (mm-40)
REVERT: L   68 SER cc_start: 0.8103 (m) cc_final: 0.7619 (p)
REVERT: L   83 ASP cc_start: 0.7594 (m-30) cc_final: 0.7362 (m-30)
REVERT: L  120 PHE cc_start: 0.8019 (m-80) cc_final: 0.7763 (m-80)
REVERT: L  142 TYR cc_start: 0.8051 (t80) cc_final: 0.7799 (t80)
REVERT: L  145 GLU cc_start: 0.7617 (mp0) cc_final: 0.7257 (mp0)
REVERT: L  148 VAL cc_start: 0.8606 (OUTLIER) cc_final: 0.8349 (m)
REVERT: L  190 LYS cc_start: 0.7413 (ttpp) cc_final: 0.6799 (ttpp)
REVERT: L  192 LYS cc_start: 0.5381 (OUTLIER) cc_final: 0.5180 (tptt)
  outliers start: 33
  outliers final: 22
  residues processed: 241
  average time/residue: 0.2340
  time to fit residues: 75.4824
Evaluate side-chains
  245 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 219
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -50 MET
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  186 ASN
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  451 MET
Chi-restraints excluded: chain H residue  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  112 VAL
Chi-restraints excluded: chain L residue  125 SER
Chi-restraints excluded: chain L residue  148 VAL
Chi-restraints excluded: chain L residue  192 LYS
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 6 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 18 optimal weight:    0.5980
   chunk 82 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 43 optimal weight:    0.4980
   chunk 11 optimal weight:    0.3980
   chunk 62 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 186 ASN
A 277 ASN
** H 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3902 r_free = 0.3902 target = 0.146065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.125769 restraints weight = 13656.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.129953 restraints weight = 6935.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.132762 restraints weight = 4236.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7092
moved from start:          0.4386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8453  Z= 0.198
  Angle     :  0.653   7.336  11503  Z= 0.332
  Chirality :  0.044   0.210   1298
  Planarity :  0.004   0.041   1440
  Dihedral  :  5.183  47.540   1184
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 16.01 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.27), residues: 1045
  helix:  1.50 (0.26), residues: 384
  sheet: -1.45 (0.33), residues: 241
  loop : -1.28 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP A 292 
 HIS   0.004   0.001   HIS A 355 
 PHE   0.016   0.002   PHE A  37 
 TYR   0.029   0.002   TYR A 286 
 ARG   0.009   0.001   ARG A -21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04289 (  384)
  hydrogen bonds       : angle       4.74203 ( 1149)
  SS BOND              : bond        0.00376 (    5)
  SS BOND              : angle       1.58105 (   10)
  covalent geometry    : bond        0.00430 ( 8448)
  covalent geometry    : angle       0.65166 (11493)

*********************** 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
  253 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 218
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -57 VAL cc_start: 0.7124 (m) cc_final: 0.6875 (p)
REVERT: A   -6 LYS cc_start: 0.8178 (ttpt) cc_final: 0.7774 (ttpt)
REVERT: A   -5 LEU cc_start: 0.8201 (mt) cc_final: 0.7951 (mp)
REVERT: A    1 VAL cc_start: 0.8668 (m) cc_final: 0.8359 (p)
REVERT: A    3 GLU cc_start: 0.7543 (mp0) cc_final: 0.6875 (mp0)
REVERT: A   11 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7266 (tm)
REVERT: A   46 SER cc_start: 0.7537 (m) cc_final: 0.7246 (t)
REVERT: A  123 GLU cc_start: 0.6790 (tm-30) cc_final: 0.6474 (tm-30)
REVERT: A  127 SER cc_start: 0.8691 (p) cc_final: 0.8274 (t)
REVERT: A  128 VAL cc_start: 0.8381 (OUTLIER) cc_final: 0.8122 (p)
REVERT: A  162 LEU cc_start: 0.8198 (tp) cc_final: 0.7978 (tp)
REVERT: A  172 GLN cc_start: 0.7964 (tp40) cc_final: 0.7696 (tm-30)
REVERT: A  176 THR cc_start: 0.8085 (t) cc_final: 0.7516 (p)
REVERT: A  182 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7011 (m-80)
REVERT: A  186 ASN cc_start: 0.7153 (OUTLIER) cc_final: 0.6823 (t0)
REVERT: A  211 PHE cc_start: 0.7827 (m-80) cc_final: 0.7067 (m-80)
REVERT: A  254 MET cc_start: 0.7766 (mtt) cc_final: 0.7244 (mtt)
REVERT: A  277 ASN cc_start: 0.8445 (m110) cc_final: 0.8131 (m110)
REVERT: A  293 ASN cc_start: 0.8103 (t0) cc_final: 0.7781 (t0)
REVERT: A  326 PHE cc_start: 0.6762 (m-10) cc_final: 0.6532 (m-10)
REVERT: A  394 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7686 (mm-30)
REVERT: A  400 PHE cc_start: 0.7709 (m-80) cc_final: 0.7308 (m-80)
REVERT: A  405 PHE cc_start: 0.8160 (t80) cc_final: 0.7816 (t80)
REVERT: A  445 ILE cc_start: 0.6988 (mt) cc_final: 0.6739 (mt)
REVERT: H   35 PHE cc_start: 0.7109 (m-80) cc_final: 0.6608 (m-80)
REVERT: H   74 SER cc_start: 0.8018 (t) cc_final: 0.7555 (p)
REVERT: H  131 LYS cc_start: 0.7575 (ptmm) cc_final: 0.7234 (ptpp)
REVERT: H  191 SER cc_start: 0.8390 (t) cc_final: 0.8051 (m)
REVERT: H  195 VAL cc_start: 0.8347 (p) cc_final: 0.8128 (m)
REVERT: N   34 MET cc_start: 0.6984 (mtp) cc_final: 0.6435 (mtp)
REVERT: N   89 GLU cc_start: 0.7702 (mp0) cc_final: 0.7252 (mp0)
REVERT: L    4 GLN cc_start: 0.7144 (mm-40) cc_final: 0.6746 (mm-40)
REVERT: L   43 LYS cc_start: 0.8697 (mtpp) cc_final: 0.8344 (mtmm)
REVERT: L   83 ASP cc_start: 0.7647 (m-30) cc_final: 0.7397 (m-30)
REVERT: L  142 TYR cc_start: 0.8069 (t80) cc_final: 0.7866 (t80)
REVERT: L  145 GLU cc_start: 0.7621 (mp0) cc_final: 0.7256 (mp0)
REVERT: L  190 LYS cc_start: 0.7528 (ttpp) cc_final: 0.6927 (ttpp)
  outliers start: 35
  outliers final: 21
  residues processed: 235
  average time/residue: 0.2316
  time to fit residues: 72.3895
Evaluate side-chains
  238 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 213
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -50 MET
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   60 THR
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  186 ASN
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  451 MET
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  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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 4 optimal weight:    0.0170
   chunk 68 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 88 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0670
   chunk 7 optimal weight:    0.8980
   chunk 101 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.4556

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

Flipped N/Q/H residues before XYZ refinement:
A 186 ASN
A 403 ASN
H 211 ASN
H 214 HIS
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.147150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.126895 restraints weight = 13906.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.130998 restraints weight = 6999.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.133885 restraints weight = 4267.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7075
moved from start:          0.4522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8453  Z= 0.157
  Angle     :  0.634   8.329  11503  Z= 0.319
  Chirality :  0.043   0.211   1298
  Planarity :  0.004   0.039   1440
  Dihedral  :  5.094  47.445   1184
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 16.24 %
    Favored  : 79.96 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.27), residues: 1045
  helix:  1.53 (0.26), residues: 386
  sheet: -1.23 (0.34), residues: 238
  loop : -1.27 (0.32), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP A 292 
 HIS   0.006   0.001   HIS A 355 
 PHE   0.017   0.001   PHE A  37 
 TYR   0.036   0.002   TYR A 149 
 ARG   0.007   0.000   ARG H  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04039 (  384)
  hydrogen bonds       : angle       4.67849 ( 1149)
  SS BOND              : bond        0.00300 (    5)
  SS BOND              : angle       1.39968 (   10)
  covalent geometry    : bond        0.00344 ( 8448)
  covalent geometry    : angle       0.63246 (11493)

*********************** 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
  236 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 202
  time to evaluate  : 0.833 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -12 GLN cc_start: 0.7922 (tt0) cc_final: 0.7697 (tt0)
REVERT: A   -6 LYS cc_start: 0.8168 (ttpt) cc_final: 0.7786 (ttpt)
REVERT: A   21 LYS cc_start: 0.8380 (tttm) cc_final: 0.8104 (tttm)
REVERT: A   46 SER cc_start: 0.7507 (m) cc_final: 0.7226 (t)
REVERT: A  123 GLU cc_start: 0.6810 (tm-30) cc_final: 0.6523 (tm-30)
REVERT: A  127 SER cc_start: 0.8675 (p) cc_final: 0.8235 (t)
REVERT: A  128 VAL cc_start: 0.8352 (OUTLIER) cc_final: 0.8057 (p)
REVERT: A  162 LEU cc_start: 0.8198 (tp) cc_final: 0.7976 (tp)
REVERT: A  172 GLN cc_start: 0.7906 (tp40) cc_final: 0.7698 (tm-30)
REVERT: A  176 THR cc_start: 0.8071 (t) cc_final: 0.7424 (p)
REVERT: A  211 PHE cc_start: 0.7780 (m-80) cc_final: 0.6933 (m-80)
REVERT: A  254 MET cc_start: 0.7748 (mtt) cc_final: 0.7288 (mtt)
REVERT: A  293 ASN cc_start: 0.8044 (t0) cc_final: 0.7790 (t0)
REVERT: A  326 PHE cc_start: 0.6713 (m-10) cc_final: 0.6495 (m-10)
REVERT: A  394 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7658 (mm-30)
REVERT: A  405 PHE cc_start: 0.8156 (t80) cc_final: 0.7821 (t80)
REVERT: A  445 ILE cc_start: 0.6976 (mt) cc_final: 0.6724 (mt)
REVERT: H   35 PHE cc_start: 0.7118 (m-80) cc_final: 0.6639 (m-80)
REVERT: H   74 SER cc_start: 0.8055 (t) cc_final: 0.7556 (p)
REVERT: H  131 LYS cc_start: 0.7557 (ptmm) cc_final: 0.7228 (ptpp)
REVERT: H  191 SER cc_start: 0.8344 (t) cc_final: 0.7991 (m)
REVERT: N   34 MET cc_start: 0.6940 (mtp) cc_final: 0.6401 (mtp)
REVERT: N   89 GLU cc_start: 0.7689 (mp0) cc_final: 0.7263 (mp0)
REVERT: L    4 GLN cc_start: 0.7146 (mm-40) cc_final: 0.6736 (mm-40)
REVERT: L   43 LYS cc_start: 0.8687 (mtpp) cc_final: 0.8335 (mtmm)
REVERT: L   83 ASP cc_start: 0.7628 (m-30) cc_final: 0.7387 (m-30)
REVERT: L  145 GLU cc_start: 0.7597 (mp0) cc_final: 0.7252 (mp0)
REVERT: L  162 GLN cc_start: 0.7974 (tp40) cc_final: 0.7758 (mm-40)
REVERT: L  190 LYS cc_start: 0.7491 (ttpp) cc_final: 0.6890 (ttpp)
REVERT: L  211 PHE cc_start: 0.8310 (p90) cc_final: 0.7909 (p90)
  outliers start: 34
  outliers final: 25
  residues processed: 220
  average time/residue: 0.2323
  time to fit residues: 67.5278
Evaluate side-chains
  223 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 197
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue  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  186 ASN
Chi-restraints excluded: chain A residue  190 LEU
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  398 LEU
Chi-restraints excluded: chain A residue  451 MET
Chi-restraints excluded: chain H residue   87 ASN
Chi-restraints excluded: chain H residue  165 THR
Chi-restraints excluded: chain H residue  203 LEU
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  125 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 84 optimal weight:    0.3980
   chunk 88 optimal weight:    1.9990
   chunk 13 optimal weight:    0.1980
   chunk 22 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9990
   chunk 91 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   chunk 86 optimal weight:    0.9990
   chunk 94 optimal weight:    0.6980
   chunk 3 optimal weight:    0.5980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A -61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 186 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 = 0.3902 r_free = 0.3902 target = 0.145970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.125723 restraints weight = 14069.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.129810 restraints weight = 7080.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.132703 restraints weight = 4314.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7094
moved from start:          0.4735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8453  Z= 0.173
  Angle     :  0.641   6.895  11503  Z= 0.325
  Chirality :  0.044   0.218   1298
  Planarity :  0.004   0.040   1440
  Dihedral  :  5.154  47.987   1184
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 16.80 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.27), residues: 1045
  helix:  1.49 (0.25), residues: 386
  sheet: -1.16 (0.34), residues: 243
  loop : -1.20 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A 292 
 HIS   0.004   0.001   HIS A 355 
 PHE   0.017   0.002   PHE A  37 
 TYR   0.028   0.002   TYR A 149 
 ARG   0.007   0.000   ARG H  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04133 (  384)
  hydrogen bonds       : angle       4.68032 ( 1149)
  SS BOND              : bond        0.00372 (    5)
  SS BOND              : angle       1.55899 (   10)
  covalent geometry    : bond        0.00382 ( 8448)
  covalent geometry    : angle       0.63958 (11493)

*********************** 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
  234 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 199
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -12 GLN cc_start: 0.7912 (tt0) cc_final: 0.7679 (tt0)
REVERT: A   -9 ASP cc_start: 0.8087 (t0) cc_final: 0.7843 (t0)
REVERT: A   -6 LYS cc_start: 0.8129 (ttpt) cc_final: 0.7712 (ttpt)
REVERT: A    0 LYS cc_start: 0.8061 (mttm) cc_final: 0.7399 (mttm)
REVERT: A    3 GLU cc_start: 0.7595 (mp0) cc_final: 0.6916 (mp0)
REVERT: A   21 LYS cc_start: 0.8392 (tttm) cc_final: 0.8118 (tttm)
REVERT: A   23 LEU cc_start: 0.6336 (OUTLIER) cc_final: 0.5948 (tt)
REVERT: A   46 SER cc_start: 0.7494 (m) cc_final: 0.7218 (t)
REVERT: A  123 GLU cc_start: 0.6826 (tm-30) cc_final: 0.6575 (tm-30)
REVERT: A  127 SER cc_start: 0.8664 (p) cc_final: 0.8268 (t)
REVERT: A  162 LEU cc_start: 0.8216 (tp) cc_final: 0.7998 (tp)
REVERT: A  176 THR cc_start: 0.8079 (t) cc_final: 0.7367 (p)
REVERT: A  182 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.6950 (m-80)
REVERT: A  211 PHE cc_start: 0.7782 (m-80) cc_final: 0.6968 (m-80)
REVERT: A  254 MET cc_start: 0.7793 (mtt) cc_final: 0.7239 (mtt)
REVERT: A  293 ASN cc_start: 0.8066 (t0) cc_final: 0.7802 (t0)
REVERT: A  326 PHE cc_start: 0.6718 (m-10) cc_final: 0.6501 (m-10)
REVERT: A  394 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7662 (mm-30)
REVERT: A  400 PHE cc_start: 0.7859 (m-80) cc_final: 0.7584 (m-80)
REVERT: A  405 PHE cc_start: 0.8146 (t80) cc_final: 0.7810 (t80)
REVERT: A  445 ILE cc_start: 0.7064 (mt) cc_final: 0.6809 (mt)
REVERT: H   74 SER cc_start: 0.8072 (t) cc_final: 0.7593 (p)
REVERT: H  131 LYS cc_start: 0.7578 (ptmm) cc_final: 0.7246 (ptpp)
REVERT: H  191 SER cc_start: 0.8365 (t) cc_final: 0.8020 (m)
REVERT: N   34 MET cc_start: 0.6963 (mtp) cc_final: 0.6384 (mtp)
REVERT: N   60 TYR cc_start: 0.8464 (m-10) cc_final: 0.7994 (m-10)
REVERT: L    4 GLN cc_start: 0.7184 (mm-40) cc_final: 0.6756 (mm-40)
REVERT: L   43 LYS cc_start: 0.8737 (mtpp) cc_final: 0.8399 (mtmm)
REVERT: L   83 ASP cc_start: 0.7620 (m-30) cc_final: 0.7370 (m-30)
REVERT: L  145 GLU cc_start: 0.7619 (mp0) cc_final: 0.6940 (mp0)
REVERT: L  162 GLN cc_start: 0.7954 (tp40) cc_final: 0.7737 (mm-40)
REVERT: L  190 LYS cc_start: 0.7571 (ttpp) cc_final: 0.7014 (ttpp)
  outliers start: 35
  outliers final: 25
  residues processed: 220
  average time/residue: 0.2337
  time to fit residues: 67.4336
Evaluate side-chains
  223 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 196
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
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   23 LEU
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   60 THR
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  182 PHE
Chi-restraints excluded: chain A residue  186 ASN
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  451 MET
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue   87 ASN
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  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 59 optimal weight:    0.9980
   chunk 70 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 3 optimal weight:    0.7980
   chunk 72 optimal weight:    4.9990
   chunk 4 optimal weight:    0.0470
   chunk 38 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0670
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.4816

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

Flipped N/Q/H residues before XYZ refinement:
A 172 GLN
A 186 ASN
H 169 ASN
** 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 = 0.3915 r_free = 0.3915 target = 0.146277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.126160 restraints weight = 13830.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.130364 restraints weight = 6843.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.133184 restraints weight = 4110.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7087
moved from start:          0.4834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8453  Z= 0.163
  Angle     :  0.656  11.105  11503  Z= 0.330
  Chirality :  0.044   0.211   1298
  Planarity :  0.004   0.040   1440
  Dihedral  :  5.146  48.042   1184
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 18.03 %
    Favored  : 78.61 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.27), residues: 1045
  helix:  1.50 (0.25), residues: 387
  sheet: -1.03 (0.35), residues: 238
  loop : -1.20 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP A 292 
 HIS   0.004   0.001   HIS A 355 
 PHE   0.016   0.001   PHE A  37 
 TYR   0.027   0.002   TYR A 286 
 ARG   0.008   0.000   ARG H  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04087 (  384)
  hydrogen bonds       : angle       4.67121 ( 1149)
  SS BOND              : bond        0.00343 (    5)
  SS BOND              : angle       1.47939 (   10)
  covalent geometry    : bond        0.00358 ( 8448)
  covalent geometry    : angle       0.65502 (11493)

********************** 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
  231 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 201
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -12 GLN cc_start: 0.7877 (tt0) cc_final: 0.7594 (tt0)
REVERT: A   -9 ASP cc_start: 0.8078 (t0) cc_final: 0.7845 (t0)
REVERT: A   -6 LYS cc_start: 0.8151 (ttpt) cc_final: 0.7726 (ttpt)
REVERT: A    0 LYS cc_start: 0.8039 (mttm) cc_final: 0.7380 (mttm)
REVERT: A    3 GLU cc_start: 0.7614 (mp0) cc_final: 0.6959 (mp0)
REVERT: A   21 LYS cc_start: 0.8405 (tttm) cc_final: 0.8129 (tttm)
REVERT: A   46 SER cc_start: 0.7476 (m) cc_final: 0.7161 (t)
REVERT: A   53 LEU cc_start: 0.7724 (mp) cc_final: 0.7414 (tp)
REVERT: A  123 GLU cc_start: 0.6824 (tm-30) cc_final: 0.6597 (tm-30)
REVERT: A  127 SER cc_start: 0.8581 (p) cc_final: 0.8241 (t)
REVERT: A  176 THR cc_start: 0.8001 (t) cc_final: 0.7501 (p)
REVERT: A  204 LYS cc_start: 0.7943 (tttt) cc_final: 0.7668 (tttt)
REVERT: A  211 PHE cc_start: 0.7804 (m-80) cc_final: 0.7143 (m-80)
REVERT: A  254 MET cc_start: 0.7780 (mtt) cc_final: 0.7232 (mtt)
REVERT: A  326 PHE cc_start: 0.6710 (m-10) cc_final: 0.6504 (m-10)
REVERT: A  372 PHE cc_start: 0.8367 (t80) cc_final: 0.8063 (t80)
REVERT: A  394 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7805 (mm-30)
REVERT: A  405 PHE cc_start: 0.8156 (t80) cc_final: 0.7951 (t80)
REVERT: A  445 ILE cc_start: 0.7084 (mt) cc_final: 0.6834 (mt)
REVERT: H   74 SER cc_start: 0.8075 (t) cc_final: 0.7606 (p)
REVERT: H  131 LYS cc_start: 0.7550 (ptmm) cc_final: 0.7225 (ptpp)
REVERT: H  191 SER cc_start: 0.8380 (t) cc_final: 0.8024 (m)
REVERT: N   34 MET cc_start: 0.6931 (mtp) cc_final: 0.6374 (mtp)
REVERT: N   60 TYR cc_start: 0.8467 (m-10) cc_final: 0.7997 (m-10)
REVERT: L    4 GLN cc_start: 0.7185 (mm-40) cc_final: 0.6783 (mm-40)
REVERT: L    5 MET cc_start: 0.7154 (ttt) cc_final: 0.6777 (ttt)
REVERT: L   43 LYS cc_start: 0.8719 (mtpp) cc_final: 0.8382 (mtmm)
REVERT: L   79 LEU cc_start: 0.8436 (mt) cc_final: 0.8180 (mp)
REVERT: L   83 ASP cc_start: 0.7613 (m-30) cc_final: 0.7356 (m-30)
REVERT: L  134 VAL cc_start: 0.7686 (p) cc_final: 0.7380 (m)
REVERT: L  145 GLU cc_start: 0.7601 (mp0) cc_final: 0.6961 (mp0)
REVERT: L  162 GLN cc_start: 0.7932 (tp40) cc_final: 0.7720 (mm-40)
REVERT: L  190 LYS cc_start: 0.7521 (ttpp) cc_final: 0.6972 (ttpp)
  outliers start: 30
  outliers final: 30
  residues processed: 219
  average time/residue: 0.2362
  time to fit residues: 68.1732
Evaluate side-chains
  229 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 199
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
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   60 THR
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  182 PHE
Chi-restraints excluded: chain A residue  186 ASN
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  398 LEU
Chi-restraints excluded: chain A residue  451 MET
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue   87 ASN
Chi-restraints excluded: chain H residue  165 THR
Chi-restraints excluded: chain H residue  203 LEU
Chi-restraints excluded: chain H residue  219 THR
Chi-restraints excluded: chain H residue  221 VAL
Chi-restraints excluded: chain H residue  223 LYS
Chi-restraints excluded: chain N residue  104 TYR
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   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 82 optimal weight:    0.9980
   chunk 2 optimal weight:    0.0040
   chunk 3 optimal weight:    0.6980
   chunk 44 optimal weight:    3.9990
   chunk 14 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 99 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 92 optimal weight:    0.6980
   chunk 89 optimal weight:    1.9990
   overall best weight:    0.6192

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

Flipped N/Q/H residues before XYZ refinement:
A -70 ASN
A 186 ASN
H 169 ASN
** 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 = 0.3898 r_free = 0.3898 target = 0.144693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.124349 restraints weight = 14040.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.128599 restraints weight = 6959.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.131417 restraints weight = 4196.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7114
moved from start:          0.4981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8453  Z= 0.189
  Angle     :  0.675  10.658  11503  Z= 0.341
  Chirality :  0.045   0.208   1298
  Planarity :  0.004   0.040   1440
  Dihedral  :  5.232  48.515   1184
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 18.37 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.27), residues: 1045
  helix:  1.44 (0.25), residues: 387
  sheet: -1.03 (0.35), residues: 241
  loop : -1.11 (0.33), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP A 292 
 HIS   0.003   0.001   HIS A 355 
 PHE   0.016   0.002   PHE L 100 
 TYR   0.026   0.002   TYR A 286 
 ARG   0.008   0.001   ARG H  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04224 (  384)
  hydrogen bonds       : angle       4.74689 ( 1149)
  SS BOND              : bond        0.00364 (    5)
  SS BOND              : angle       1.54655 (   10)
  covalent geometry    : bond        0.00413 ( 8448)
  covalent geometry    : angle       0.67348 (11493)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3218.95 seconds
wall clock time: 57 minutes 27.93 seconds (3447.93 seconds total)