Starting phenix.real_space_refine
on Sat Aug 23 03:29:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k20_36808/08_2025/8k20_36808.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k20_36808/08_2025/8k20_36808.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k20_36808/08_2025/8k20_36808.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k20_36808/08_2025/8k20_36808.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k20_36808/08_2025/8k20_36808.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k20_36808/08_2025/8k20_36808.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Fe      1      7.16       5
     S      55      5.16       5
     C    5899      2.51       5
     N    1618      2.21       5
     O    1783      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9356
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2596
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2596
          Classifications: {'peptide': 337}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 321}
    Chain: "B"
      Number of atoms: 1618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 1618
          Classifications: {'peptide': 208}
          Link IDs: {'PTRANS': 3, 'TRANS': 204}
    Chain: "C"
      Number of atoms: 1312
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 171, 1312
          Classifications: {'peptide': 171}
          Link IDs: {'PTRANS': 3, 'TRANS': 167}
    Chain: "D"
      Number of atoms: 624
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 624
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "F"
      Number of atoms: 609
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 609
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 1, 'TRANS': 75}
    Chain: "E"
      Number of atoms: 2596
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2596
          Classifications: {'peptide': 337}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 321}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' FE': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.91, per 1000 atoms: 0.20
  Number of scatterers: 9356
  At special positions: 0
  Unit cell: (85.14, 96.32, 159.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      1     26.01
     S      55     16.00
     O    1783      8.00
     N    1618      7.00
     C    5899      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  19 " - pdb=" SG  CYS F  19 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.54
  Conformation dependent library (CDL) restraints added in 232.0 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2260

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 14 sheets defined
      55.0% alpha, 16.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 69
      removed outlier: 4.924A  pdb=" N   LEU A  58 " --> pdb=" O   LEU A  54 " (cutoff:3.500A)
      Proline residue:  A  59  - end of helix
    Processing helix  chain 'A' and resid 71 through 75
    Processing helix  chain 'A' and resid 86 through 105
      removed outlier: 3.757A  pdb=" N   LEU A  90 " --> pdb=" O   MET A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 126
    Processing helix  chain 'A' and resid 160 through 173
    Processing helix  chain 'A' and resid 179 through 189
    Processing helix  chain 'A' and resid 208 through 225
      removed outlier: 4.060A  pdb=" N   LYS A 224 " --> pdb=" O   GLU A 220 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ASN A 225 " --> pdb=" O   GLU A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 257
    Processing helix  chain 'A' and resid 265 through 270
    Processing helix  chain 'A' and resid 271 through 284
    Processing helix  chain 'A' and resid 299 through 314
      removed outlier: 4.443A  pdb=" N   ILE A 303 " --> pdb=" O   ASN A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 322
    Processing helix  chain 'A' and resid 335 through 340
      removed outlier: 3.924A  pdb=" N   GLU A 339 " --> pdb=" O   ALA A 335 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LYS A 340 " --> pdb=" O   VAL A 336 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 335 through 340'
    Processing helix  chain 'B' and resid 45 through 70
    Processing helix  chain 'B' and resid 97 through 108
    Processing helix  chain 'B' and resid 110 through 131
      removed outlier: 3.897A  pdb=" N   GLY B 131 " --> pdb=" O   LYS B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 183
      removed outlier: 3.809A  pdb=" N   LYS B 169 " --> pdb=" O   LEU B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 184 through 188
      removed outlier: 4.632A  pdb=" N   CYS B 187 " --> pdb=" O   HIS B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 202
    Processing helix  chain 'B' and resid 204 through 221
      removed outlier: 3.671A  pdb=" N   THR B 208 " --> pdb=" O   GLN B 204 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   LYS B 221 " --> pdb=" O   GLN B 217 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 7 through 9
      No H-bonds generated for 'chain 'C' and resid 7 through 9'
    Processing helix  chain 'C' and resid 22 through 33
    Processing helix  chain 'C' and resid 45 through 47
      No H-bonds generated for 'chain 'C' and resid 45 through 47'
    Processing helix  chain 'C' and resid 49 through 66
      removed outlier: 4.198A  pdb=" N   LEU C  53 " --> pdb=" O   ASP C  49 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 84
      removed outlier: 3.626A  pdb=" N   SER C  83 " --> pdb=" O   VAL C  79 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   GLY C  84 " --> pdb=" O   TYR C  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 87 through 95
    Processing helix  chain 'C' and resid 112 through 123
    Processing helix  chain 'C' and resid 132 through 137
    Processing helix  chain 'C' and resid 138 through 147
    Processing helix  chain 'C' and resid 149 through 154
    Processing helix  chain 'C' and resid 157 through 169
    Processing helix  chain 'C' and resid 170 through 172
      No H-bonds generated for 'chain 'C' and resid 170 through 172'
    Processing helix  chain 'D' and resid 27 through 40
      removed outlier: 3.734A  pdb=" N   ALA D  31 " --> pdb=" O   SER D  27 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 68 through 93
    Processing helix  chain 'F' and resid 27 through 39
      removed outlier: 3.674A  pdb=" N   ALA F  31 " --> pdb=" O   SER F  27 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 68 through 91
    Processing helix  chain 'E' and resid 45 through 69
      removed outlier: 4.593A  pdb=" N   LEU E  58 " --> pdb=" O   LEU E  54 " (cutoff:3.500A)
      Proline residue:  E  59  - end of helix
    Processing helix  chain 'E' and resid 86 through 105
    Processing helix  chain 'E' and resid 113 through 126
    Processing helix  chain 'E' and resid 160 through 172
    Processing helix  chain 'E' and resid 179 through 190
    Processing helix  chain 'E' and resid 208 through 226
    Processing helix  chain 'E' and resid 229 through 257
      removed outlier: 3.611A  pdb=" N   LEU E 233 " --> pdb=" O   THR E 229 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 266 through 269
    Processing helix  chain 'E' and resid 270 through 284
      removed outlier: 4.122A  pdb=" N   GLN E 274 " --> pdb=" O   ASN E 270 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 292 through 297
      removed outlier: 3.516A  pdb=" N   ILE E 297 " --> pdb=" O   ASP E 293 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 299 through 314
      removed outlier: 3.862A  pdb=" N   ILE E 303 " --> pdb=" O   ASN E 299 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   TYR E 305 " --> pdb=" O   ALA E 301 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   THR E 306 " --> pdb=" O   MET E 302 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ASN E 313 " --> pdb=" O   LEU E 309 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   GLY E 314 " --> pdb=" O   ALA E 310 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 318 through 322
      removed outlier: 3.856A  pdb=" N   SER E 322 " --> pdb=" O   ILE E 319 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 329 through 333
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30
      removed outlier: 7.224A  pdb=" N   ILE A  21 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 30
      removed outlier: 7.224A  pdb=" N   ILE A  21 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   ILE A   8 " --> pdb=" O   CYS A  79 " (cutoff:3.500A)
      removed outlier: 7.867A  pdb=" N   THR A  81 " --> pdb=" O   ILE A   8 " (cutoff:3.500A)
      removed outlier: 7.593A  pdb=" N   PHE A  10 " --> pdb=" O   THR A  81 " (cutoff:3.500A)
      removed outlier: 7.840A  pdb=" N   GLY A  83 " --> pdb=" O   PHE A  10 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   ILE A  78 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   VAL A 111 " --> pdb=" O   ILE A  78 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   TYR A  80 " --> pdb=" O   VAL A 111 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 149 through 155
      removed outlier: 6.464A  pdb=" N   VAL A 142 " --> pdb=" O   PHE A 153 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   GLU A 155 " --> pdb=" O   THR A 140 " (cutoff:3.500A)
      removed outlier: 7.832A  pdb=" N   THR A 140 " --> pdb=" O   GLU A 155 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   VAL A 131 " --> pdb=" O   LEU A 262 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   VAL A 264 " --> pdb=" O   VAL A 131 " (cutoff:3.500A)
      removed outlier: 6.053A  pdb=" N   LEU A 133 " --> pdb=" O   VAL A 264 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   VAL A 261 " --> pdb=" O   PHE A 289 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 201 through 202
    Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 17
      removed outlier: 3.607A  pdb=" N   LYS B  16 " --> pdb=" O   VAL B  23 " (cutoff:3.500A)
      removed outlier: 6.979A  pdb=" N   SER B  86 " --> pdb=" O   VAL B  80 " (cutoff:3.500A)
      removed outlier: 4.861A  pdb=" N   VAL B  80 " --> pdb=" O   SER B  86 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   THR B  88 " --> pdb=" O   TYR B  78 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 94 through 96
    Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 5
      removed outlier: 3.605A  pdb=" N   ALA C 107 " --> pdb=" O   SER C  40 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   SER C  40 " --> pdb=" O   ALA C 107 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 5
      removed outlier: 4.077A  pdb=" N   LEU C  16 " --> pdb=" O   ILE C 128 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 17 through 21
    Processing sheet with id=AB1, first strand: chain 'F' and resid 17 through 21
    Processing sheet with id=AB2, first strand: chain 'E' and resid 28 through 30
      removed outlier: 7.199A  pdb=" N   ILE E  21 " --> pdb=" O   LEU E  29 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 28 through 30
      removed outlier: 7.199A  pdb=" N   ILE E  21 " --> pdb=" O   LEU E  29 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   VAL E  22 " --> pdb=" O   ALA E   7 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   ALA E   7 " --> pdb=" O   VAL E  22 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   ILE E   6 " --> pdb=" O   ASP E  76 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   ILE E  78 " --> pdb=" O   ILE E   6 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   ILE E   8 " --> pdb=" O   ILE E  78 " (cutoff:3.500A)
      removed outlier: 5.394A  pdb=" N   TYR E  80 " --> pdb=" O   ILE E   8 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   PHE E  10 " --> pdb=" O   TYR E  80 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   LYS E  82 " --> pdb=" O   PHE E  10 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 149 through 155
      removed outlier: 5.065A  pdb=" N   TYR E 150 " --> pdb=" O   SER E 146 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   SER E 146 " --> pdb=" O   TYR E 150 " (cutoff:3.500A)
      removed outlier: 5.231A  pdb=" N   ILE E 152 " --> pdb=" O   ALA E 144 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   ALA E 144 " --> pdb=" O   ILE E 152 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   GLY E 154 " --> pdb=" O   VAL E 142 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   VAL E 131 " --> pdb=" O   LEU E 262 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   VAL E 264 " --> pdb=" O   VAL E 131 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   LEU E 133 " --> pdb=" O   VAL E 264 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 201 through 202

    549 hydrogen bonds defined for protein.
    1569 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.01

  Time building geometry restraints manager: 0.69 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3131
        1.35 -     1.47: 2075
        1.47 -     1.59: 4219
        1.59 -     1.72: 0
        1.72 -     1.84: 83
  Bond restraints: 9508
  Sorted by residual:
  bond pdb=" CB  PRO D  46 "
       pdb=" CG  PRO D  46 "
    ideal  model  delta    sigma   weight residual
    1.492  1.567 -0.075 5.00e-02 4.00e+02 2.26e+00
  bond pdb=" CG  PRO D  46 "
       pdb=" CD  PRO D  46 "
    ideal  model  delta    sigma   weight residual
    1.503  1.455  0.048 3.40e-02 8.65e+02 1.97e+00
  bond pdb=" CB  ARG A 167 "
       pdb=" CG  ARG A 167 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.16e-01
  bond pdb=" CB  CYS F  19 "
       pdb=" SG  CYS F  19 "
    ideal  model  delta    sigma   weight residual
    1.808  1.837 -0.029 3.30e-02 9.18e+02 7.85e-01
  bond pdb=" CB  MET E 302 "
       pdb=" CG  MET E 302 "
    ideal  model  delta    sigma   weight residual
    1.520  1.495  0.025 3.00e-02 1.11e+03 7.09e-01
  ... (remaining 9503 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.83: 12637
        1.83 -     3.66: 189
        3.66 -     5.49: 28
        5.49 -     7.32: 8
        7.32 -     9.15: 1
  Bond angle restraints: 12863
  Sorted by residual:
  angle pdb=" N   VAL E 336 "
        pdb=" CA  VAL E 336 "
        pdb=" C   VAL E 336 "
      ideal   model   delta    sigma   weight residual
     113.71  109.48    4.23 9.50e-01 1.11e+00 1.99e+01
  angle pdb=" CG  ARG A 167 "
        pdb=" CD  ARG A 167 "
        pdb=" NE  ARG A 167 "
      ideal   model   delta    sigma   weight residual
     112.00  121.15   -9.15 2.20e+00 2.07e-01 1.73e+01
  angle pdb=" CA  PRO D  46 "
        pdb=" N   PRO D  46 "
        pdb=" CD  PRO D  46 "
      ideal   model   delta    sigma   weight residual
     112.00  107.18    4.82 1.40e+00 5.10e-01 1.18e+01
  angle pdb=" C   CYS D  19 "
        pdb=" CA  CYS D  19 "
        pdb=" CB  CYS D  19 "
      ideal   model   delta    sigma   weight residual
     111.78  105.76    6.02 1.98e+00 2.55e-01 9.23e+00
  angle pdb=" C   ASP A 166 "
        pdb=" N   ARG A 167 "
        pdb=" CA  ARG A 167 "
      ideal   model   delta    sigma   weight residual
     121.14  115.92    5.22 1.75e+00 3.27e-01 8.91e+00
  ... (remaining 12858 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.38: 5037
       15.38 -    30.76: 574
       30.76 -    46.14: 124
       46.14 -    61.52: 29
       61.52 -    76.90: 11
  Dihedral angle restraints: 5775
    sinusoidal: 2279
      harmonic: 3496
  Sorted by residual:
  dihedral pdb=" CA  SER D  18 "
           pdb=" C   SER D  18 "
           pdb=" N   CYS D  19 "
           pdb=" CA  CYS D  19 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.66   27.34     0      5.00e+00 4.00e-02 2.99e+01
  dihedral pdb=" CA  TYR C 103 "
           pdb=" C   TYR C 103 "
           pdb=" N   ILE C 104 "
           pdb=" CA  ILE C 104 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.26  -19.74     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CA  ARG A 167 "
           pdb=" C   ARG A 167 "
           pdb=" N   PHE A 168 "
           pdb=" CA  PHE A 168 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.54   16.46     0      5.00e+00 4.00e-02 1.08e+01
  ... (remaining 5772 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1090
       0.042 -    0.085: 323
       0.085 -    0.127: 82
       0.127 -    0.169: 9
       0.169 -    0.211: 4
  Chirality restraints: 1508
  Sorted by residual:
  chirality pdb=" CB  ILE A  37 "
            pdb=" CA  ILE A  37 "
            pdb=" CG1 ILE A  37 "
            pdb=" CG2 ILE A  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CG  LEU F  21 "
            pdb=" CB  LEU F  21 "
            pdb=" CD1 LEU F  21 "
            pdb=" CD2 LEU F  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 9.18e-01
  chirality pdb=" CB  ILE A  17 "
            pdb=" CA  ILE A  17 "
            pdb=" CG1 ILE A  17 "
            pdb=" CG2 ILE A  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.36e-01
  ... (remaining 1505 not shown)

  Planarity restraints: 1651
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN D  45 "   -0.072 5.00e-02 4.00e+02   1.06e-01 1.81e+01
        pdb=" N   PRO D  46 "    0.184 5.00e-02 4.00e+02
        pdb=" CA  PRO D  46 "   -0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO D  46 "   -0.058 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN F  45 "    0.041 5.00e-02 4.00e+02   6.21e-02 6.17e+00
        pdb=" N   PRO F  46 "   -0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO F  46 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO F  46 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU E 273 "   -0.011 2.00e-02 2.50e+03   2.26e-02 5.12e+00
        pdb=" C   LEU E 273 "    0.039 2.00e-02 2.50e+03
        pdb=" O   LEU E 273 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   GLN E 274 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1648 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 183
        2.66 -     3.22: 9191
        3.22 -     3.78: 15442
        3.78 -     4.34: 19622
        4.34 -     4.90: 31867
  Nonbonded interactions: 76305
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 298 "
            pdb="FE    FE A 401 "
     model   vdw
     2.100 2.260
  nonbonded pdb=" OG  SER C  98 "
            pdb=" OD1 ASN C 100 "
     model   vdw
     2.160 3.040
  nonbonded pdb=" O   LEU A  24 "
            pdb=" OH  TYR A 305 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" N   ASP F  16 "
            pdb=" OE2 GLU F  65 "
     model   vdw
     2.225 3.120
  nonbonded pdb=" OG1 THR E  23 "
            pdb=" OD1 ASP E  25 "
     model   vdw
     2.240 3.040
  ... (remaining 76300 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 4 through 339)
  selection = (chain 'E' and resid 4 through 339)
}
ncs_group {
  reference = (chain 'D' and resid 16 through 92)
  selection = chain 'F'
}

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:             8.980
  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:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.330
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6422
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      :  0.003   0.075   9509  Z= 0.127
  Angle     :  0.600   9.152  12865  Z= 0.328
  Chirality :  0.043   0.211   1508
  Planarity :  0.005   0.106   1651
  Dihedral  : 14.078  76.901   3512
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 14.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.24), residues: 1197
  helix:  1.67 (0.21), residues: 594
  sheet: -0.45 (0.37), residues: 189
  loop : -0.40 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 167 
 TYR   0.018   0.001   TYR C 103 
 PHE   0.017   0.001   PHE F  76 
 TRP   0.012   0.002   TRP E 104 
 HIS   0.004   0.001   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 9508)
  covalent geometry    : angle       0.59585 (12863)
  SS BOND              : bond        0.00267 (    1)
  SS BOND              : angle       5.65363 (    2)
  hydrogen bonds       : bond        0.12196 (  545)
  hydrogen bonds       : angle       5.61877 ( 1569)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 TRP cc_start: 0.4952 (m-10) cc_final: 0.4701 (m100)
REVERT: B  208 THR cc_start: 0.9039 (p) cc_final: 0.8563 (p)
REVERT: C   17 PHE cc_start: 0.8463 (m-80) cc_final: 0.7946 (m-80)
REVERT: C  105 LEU cc_start: 0.7598 (tp) cc_final: 0.7050 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.0633
  time to fit residues: 9.3449
Evaluate side-chains
  75 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    0.6980
   chunk 113 optimal weight:    0.0470
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    0.0980
   chunk 62 optimal weight:    0.0470
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    9.9990
   overall best weight:    0.3576

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 138 ASN
** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 163 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.089102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.074249 restraints weight = 53125.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.076234 restraints weight = 30082.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.077014 restraints weight = 19916.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.077283 restraints weight = 15639.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.077599 restraints weight = 14186.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6440
moved from start:          0.1091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9509  Z= 0.115
  Angle     :  0.548   7.996  12865  Z= 0.286
  Chirality :  0.043   0.159   1508
  Planarity :  0.004   0.069   1651
  Dihedral  :  4.162  20.896   1301
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  6.80 %
    Favored  : 92.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.25), residues: 1197
  helix:  1.59 (0.21), residues: 613
  sheet: -0.42 (0.36), residues: 194
  loop : -0.38 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  38 
 TYR   0.020   0.002   TYR C 103 
 PHE   0.016   0.001   PHE F  76 
 TRP   0.007   0.001   TRP A 337 
 HIS   0.004   0.001   HIS C  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 9508)
  covalent geometry    : angle       0.54718 (12863)
  SS BOND              : bond        0.00381 (    1)
  SS BOND              : angle       2.59916 (    2)
  hydrogen bonds       : bond        0.03825 (  545)
  hydrogen bonds       : angle       4.77688 ( 1569)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 88
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  152 LEU cc_start: 0.6091 (tp) cc_final: 0.5667 (pt)
REVERT: C   17 PHE cc_start: 0.8397 (m-80) cc_final: 0.7945 (m-80)
REVERT: C  116 MET cc_start: 0.7136 (mmm) cc_final: 0.6818 (mmm)
REVERT: E  276 MET cc_start: 0.7142 (ppp) cc_final: 0.6838 (ppp)
  outliers start: 3
  outliers final: 3
  residues processed: 90
  average time/residue: 0.0644
  time to fit residues: 8.7039
Evaluate side-chains
  80 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 77
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain D residue   19 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 110 optimal weight:    5.9990
   chunk 31 optimal weight:    0.0060
   chunk 90 optimal weight:    9.9990
   chunk 25 optimal weight:    0.0870
   chunk 52 optimal weight:    2.9990
   chunk 84 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    1.4178

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 274 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.086543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.070538 restraints weight = 53067.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.072289 restraints weight = 31541.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.073518 restraints weight = 22067.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.074361 restraints weight = 17117.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.074926 restraints weight = 14293.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6549
moved from start:          0.1486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9509  Z= 0.183
  Angle     :  0.595   7.352  12865  Z= 0.317
  Chirality :  0.044   0.162   1508
  Planarity :  0.004   0.059   1651
  Dihedral  :  4.372  21.153   1301
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 13.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 10.87 %
    Favored  : 87.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.55 (0.25), residues: 1197
  helix:  1.37 (0.21), residues: 612
  sheet: -0.84 (0.37), residues: 188
  loop : -0.48 (0.32), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 167 
 TYR   0.018   0.002   TYR E 305 
 PHE   0.011   0.002   PHE F  76 
 TRP   0.014   0.002   TRP E 104 
 HIS   0.007   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 9508)
  covalent geometry    : angle       0.59380 (12863)
  SS BOND              : bond        0.00586 (    1)
  SS BOND              : angle       2.50213 (    2)
  hydrogen bonds       : bond        0.04241 (  545)
  hydrogen bonds       : angle       4.96463 ( 1569)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   17 PHE cc_start: 0.8106 (m-80) cc_final: 0.7727 (m-80)
REVERT: C  116 MET cc_start: 0.7335 (mmm) cc_final: 0.7068 (mmm)
REVERT: E  276 MET cc_start: 0.7166 (ppp) cc_final: 0.6924 (ppp)
  outliers start: 17
  outliers final: 11
  residues processed: 88
  average time/residue: 0.0689
  time to fit residues: 8.7951
Evaluate side-chains
  78 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  209 PHE
Chi-restraints excluded: chain C residue    5 ASN
Chi-restraints excluded: chain D residue   19 CYS
Chi-restraints excluded: chain D residue   53 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 71 optimal weight:    4.9990
   chunk 103 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 80 optimal weight:    1.9990
   chunk 63 optimal weight:    4.9990
   chunk 11 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 116 optimal weight:    0.0020
   chunk 62 optimal weight:    9.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.6390

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 313 ASN
** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.087609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.071545 restraints weight = 53657.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.073388 restraints weight = 31899.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.074687 restraints weight = 22238.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.075568 restraints weight = 17124.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.076043 restraints weight = 14204.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6500
moved from start:          0.1594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9509  Z= 0.121
  Angle     :  0.542   7.419  12865  Z= 0.283
  Chirality :  0.042   0.148   1508
  Planarity :  0.003   0.053   1651
  Dihedral  :  4.220  20.745   1301
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 13.88 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.25), residues: 1197
  helix:  1.48 (0.21), residues: 613
  sheet: -0.88 (0.37), residues: 188
  loop : -0.43 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  88 
 TYR   0.016   0.001   TYR C 103 
 PHE   0.010   0.001   PHE F  76 
 TRP   0.007   0.001   TRP A 337 
 HIS   0.004   0.001   HIS C  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 9508)
  covalent geometry    : angle       0.54094 (12863)
  SS BOND              : bond        0.00309 (    1)
  SS BOND              : angle       2.41831 (    2)
  hydrogen bonds       : bond        0.03771 (  545)
  hydrogen bonds       : angle       4.75584 ( 1569)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  152 LEU cc_start: 0.6234 (tp) cc_final: 0.5806 (pt)
REVERT: C   17 PHE cc_start: 0.8119 (m-80) cc_final: 0.7756 (m-80)
REVERT: C  116 MET cc_start: 0.7301 (mmm) cc_final: 0.7016 (mmm)
REVERT: E    5 MET cc_start: 0.2933 (ptm) cc_final: 0.1995 (ptm)
REVERT: E  276 MET cc_start: 0.7089 (ppp) cc_final: 0.6882 (ppp)
  outliers start: 15
  outliers final: 9
  residues processed: 86
  average time/residue: 0.0566
  time to fit residues: 7.3349
Evaluate side-chains
  75 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain C residue    5 ASN
Chi-restraints excluded: chain D residue   19 CYS
Chi-restraints excluded: chain D residue   53 MET
Chi-restraints excluded: chain E residue   19 VAL
Chi-restraints excluded: chain E residue  142 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 96 optimal weight:    0.6980
   chunk 102 optimal weight:   10.0000
   chunk 116 optimal weight:    8.9990
   chunk 101 optimal weight:    5.9990
   chunk 81 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   chunk 85 optimal weight:    8.9990
   chunk 19 optimal weight:    2.9990
   chunk 43 optimal weight:    6.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    1.3388

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 135 HIS
B 210 ASN
** C  10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  30 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.086147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.069907 restraints weight = 54014.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.071627 restraints weight = 32343.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.072833 restraints weight = 22827.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.073698 restraints weight = 17798.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.074164 restraints weight = 14845.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6596
moved from start:          0.1912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9509  Z= 0.179
  Angle     :  0.595   7.413  12865  Z= 0.316
  Chirality :  0.044   0.178   1508
  Planarity :  0.004   0.054   1651
  Dihedral  :  4.395  20.225   1301
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 14.27 %
    Favored  : 83.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.25), residues: 1197
  helix:  1.31 (0.21), residues: 610
  sheet: -1.26 (0.36), residues: 196
  loop : -0.60 (0.33), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 167 
 TYR   0.016   0.002   TYR E 305 
 PHE   0.013   0.002   PHE A 208 
 TRP   0.010   0.002   TRP E 104 
 HIS   0.006   0.001   HIS E 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 9508)
  covalent geometry    : angle       0.59437 (12863)
  SS BOND              : bond        0.00528 (    1)
  SS BOND              : angle       2.25268 (    2)
  hydrogen bonds       : bond        0.04172 (  545)
  hydrogen bonds       : angle       4.98284 ( 1569)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 71
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 ASP cc_start: 0.8126 (t70) cc_final: 0.7705 (t70)
REVERT: B  183 MET cc_start: 0.8792 (ppp) cc_final: 0.8546 (ppp)
REVERT: C   17 PHE cc_start: 0.8138 (m-80) cc_final: 0.7743 (m-80)
REVERT: E    5 MET cc_start: 0.3165 (ptm) cc_final: 0.2147 (ptm)
REVERT: E  253 MET cc_start: 0.1881 (tpt) cc_final: 0.1639 (tpt)
  outliers start: 28
  outliers final: 15
  residues processed: 92
  average time/residue: 0.0545
  time to fit residues: 7.7985
Evaluate side-chains
  79 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain C residue    5 ASN
Chi-restraints excluded: chain D residue   19 CYS
Chi-restraints excluded: chain D residue   53 MET
Chi-restraints excluded: chain E residue   19 VAL
Chi-restraints excluded: chain E residue  142 VAL
Chi-restraints excluded: chain E residue  299 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 113 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 67 optimal weight:    2.9990
   chunk 52 optimal weight:    5.9990
   chunk 107 optimal weight:   10.0000
   chunk 29 optimal weight:    0.7980
   chunk 109 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0970
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.087145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.071008 restraints weight = 53977.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.072820 restraints weight = 32164.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.074086 restraints weight = 22573.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.074902 restraints weight = 17507.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.075530 restraints weight = 14608.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.3952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6518
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9509  Z= 0.124
  Angle     :  0.563   7.802  12865  Z= 0.293
  Chirality :  0.043   0.157   1508
  Planarity :  0.003   0.051   1651
  Dihedral  :  4.240  20.365   1301
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 16.50 %
    Favored  : 81.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.25), residues: 1197
  helix:  1.43 (0.21), residues: 611
  sheet: -1.13 (0.37), residues: 187
  loop : -0.51 (0.33), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 278 
 TYR   0.015   0.001   TYR C 103 
 PHE   0.012   0.002   PHE D  64 
 TRP   0.006   0.001   TRP A 337 
 HIS   0.004   0.001   HIS C  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 9508)
  covalent geometry    : angle       0.56260 (12863)
  SS BOND              : bond        0.00361 (    1)
  SS BOND              : angle       2.29048 (    2)
  hydrogen bonds       : bond        0.03847 (  545)
  hydrogen bonds       : angle       4.78820 ( 1569)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  152 LEU cc_start: 0.6249 (tp) cc_final: 0.5812 (pt)
REVERT: C   17 PHE cc_start: 0.8106 (m-80) cc_final: 0.7738 (m-80)
REVERT: C  116 MET cc_start: 0.6904 (mmm) cc_final: 0.6627 (mmm)
REVERT: E    5 MET cc_start: 0.2873 (ptm) cc_final: 0.1953 (ptm)
  outliers start: 17
  outliers final: 10
  residues processed: 87
  average time/residue: 0.0637
  time to fit residues: 8.4524
Evaluate side-chains
  75 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  217 GLN
Chi-restraints excluded: chain C residue    5 ASN
Chi-restraints excluded: chain F residue   19 CYS
Chi-restraints excluded: chain E residue   19 VAL
Chi-restraints excluded: chain E residue   54 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 33 optimal weight:   10.0000
   chunk 8 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   chunk 42 optimal weight:    8.9990
   chunk 24 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 84 optimal weight:    4.9990
   chunk 115 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.087143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.070996 restraints weight = 53509.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.072723 restraints weight = 31983.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.073952 restraints weight = 22518.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.074836 restraints weight = 17486.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.075298 restraints weight = 14545.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6535
moved from start:          0.2074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9509  Z= 0.132
  Angle     :  0.603  11.775  12865  Z= 0.307
  Chirality :  0.045   0.396   1508
  Planarity :  0.003   0.053   1651
  Dihedral  :  4.278  20.425   1301
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 17.38 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.25), residues: 1197
  helix:  1.44 (0.21), residues: 610
  sheet: -1.10 (0.38), residues: 181
  loop : -0.55 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  32 
 TYR   0.014   0.001   TYR C 103 
 PHE   0.025   0.002   PHE D  79 
 TRP   0.006   0.001   TRP A 337 
 HIS   0.004   0.001   HIS F  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 9508)
  covalent geometry    : angle       0.60137 (12863)
  SS BOND              : bond        0.00682 (    1)
  SS BOND              : angle       3.21460 (    2)
  hydrogen bonds       : bond        0.03876 (  545)
  hydrogen bonds       : angle       4.82593 ( 1569)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 67
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  152 LEU cc_start: 0.6277 (tp) cc_final: 0.5842 (pt)
REVERT: C   17 PHE cc_start: 0.8129 (m-80) cc_final: 0.7739 (m-80)
REVERT: C  116 MET cc_start: 0.7011 (mmm) cc_final: 0.6652 (mmm)
REVERT: E    5 MET cc_start: 0.2820 (ptm) cc_final: 0.1907 (ptm)
REVERT: E  100 LEU cc_start: 0.4157 (OUTLIER) cc_final: 0.3760 (mm)
REVERT: E  253 MET cc_start: 0.1739 (tpt) cc_final: 0.1519 (tpt)
REVERT: E  276 MET cc_start: 0.7416 (ppp) cc_final: 0.6514 (ppp)
REVERT: E  299 ASN cc_start: 0.4357 (OUTLIER) cc_final: 0.3163 (t0)
REVERT: E  302 MET cc_start: 0.4527 (tpp) cc_final: 0.4039 (tpp)
  outliers start: 20
  outliers final: 16
  residues processed: 82
  average time/residue: 0.0489
  time to fit residues: 6.4308
Evaluate side-chains
  82 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 64
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  217 GLN
Chi-restraints excluded: chain C residue    5 ASN
Chi-restraints excluded: chain C residue   14 VAL
Chi-restraints excluded: chain F residue   19 CYS
Chi-restraints excluded: chain E residue   19 VAL
Chi-restraints excluded: chain E residue   54 LEU
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain E residue  115 VAL
Chi-restraints excluded: chain E residue  299 ASN
Chi-restraints excluded: chain E residue  315 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   chunk 108 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 99 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0980
   chunk 114 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.086594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.070395 restraints weight = 53606.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.072163 restraints weight = 32157.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.073398 restraints weight = 22624.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.074266 restraints weight = 17590.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.074733 restraints weight = 14639.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6562
moved from start:          0.2196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9509  Z= 0.147
  Angle     :  0.595   8.610  12865  Z= 0.307
  Chirality :  0.044   0.294   1508
  Planarity :  0.003   0.049   1651
  Dihedral  :  4.323  20.295   1301
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 17.77 %
    Favored  : 79.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.40 (0.25), residues: 1197
  helix:  1.35 (0.21), residues: 609
  sheet: -1.10 (0.39), residues: 178
  loop : -0.63 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 272 
 TYR   0.014   0.002   TYR C 103 
 PHE   0.014   0.002   PHE D  79 
 TRP   0.007   0.001   TRP B 205 
 HIS   0.004   0.001   HIS D  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 9508)
  covalent geometry    : angle       0.59362 (12863)
  SS BOND              : bond        0.00993 (    1)
  SS BOND              : angle       2.79445 (    2)
  hydrogen bonds       : bond        0.03986 (  545)
  hydrogen bonds       : angle       4.90475 ( 1569)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 67
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
REVERT: B  205 TRP cc_start: 0.9022 (p-90) cc_final: 0.8771 (p-90)
REVERT: C   17 PHE cc_start: 0.8133 (m-80) cc_final: 0.7715 (m-80)
REVERT: C  116 MET cc_start: 0.7236 (mmm) cc_final: 0.6853 (mmm)
REVERT: D   38 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6764 (tt)
REVERT: E    5 MET cc_start: 0.2862 (ptm) cc_final: 0.2001 (ptm)
REVERT: E  100 LEU cc_start: 0.4187 (OUTLIER) cc_final: 0.3786 (mm)
REVERT: E  253 MET cc_start: 0.1789 (tpt) cc_final: 0.1564 (tpt)
REVERT: E  276 MET cc_start: 0.7538 (ppp) cc_final: 0.6650 (ppp)
REVERT: E  299 ASN cc_start: 0.4427 (OUTLIER) cc_final: 0.3146 (t0)
REVERT: E  302 MET cc_start: 0.4492 (tpp) cc_final: 0.3922 (tpp)
  outliers start: 24
  outliers final: 18
  residues processed: 84
  average time/residue: 0.0613
  time to fit residues: 7.9187
Evaluate side-chains
  87 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 66
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  217 GLN
Chi-restraints excluded: chain C residue    5 ASN
Chi-restraints excluded: chain C residue   14 VAL
Chi-restraints excluded: chain D residue   19 CYS
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain F residue   19 CYS
Chi-restraints excluded: chain E residue   19 VAL
Chi-restraints excluded: chain E residue   54 LEU
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain E residue  115 VAL
Chi-restraints excluded: chain E residue  163 ASN
Chi-restraints excluded: chain E residue  299 ASN
Chi-restraints excluded: chain E residue  315 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 45 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   chunk 39 optimal weight:    0.3980
   chunk 2 optimal weight:    2.9990
   chunk 22 optimal weight:    9.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.085315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.069063 restraints weight = 53957.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.070770 restraints weight = 32568.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.071978 restraints weight = 23019.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.072770 restraints weight = 17938.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.073368 restraints weight = 15074.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6630
moved from start:          0.2452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9509  Z= 0.191
  Angle     :  0.645   7.581  12865  Z= 0.338
  Chirality :  0.045   0.242   1508
  Planarity :  0.004   0.042   1651
  Dihedral  :  4.608  20.133   1301
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 15.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 18.25 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.03 (0.25), residues: 1197
  helix:  1.10 (0.21), residues: 604
  sheet: -1.37 (0.40), residues: 161
  loop : -0.99 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG E 278 
 TYR   0.019   0.002   TYR E 295 
 PHE   0.020   0.002   PHE A 208 
 TRP   0.012   0.002   TRP B 205 
 HIS   0.007   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 9508)
  covalent geometry    : angle       0.64400 (12863)
  SS BOND              : bond        0.00663 (    1)
  SS BOND              : angle       2.66351 (    2)
  hydrogen bonds       : bond        0.04417 (  545)
  hydrogen bonds       : angle       5.16449 ( 1569)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 67
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
REVERT: B  205 TRP cc_start: 0.9128 (p-90) cc_final: 0.8908 (p-90)
REVERT: C  116 MET cc_start: 0.7241 (mmm) cc_final: 0.6926 (mmm)
REVERT: E    5 MET cc_start: 0.3008 (ptm) cc_final: 0.2162 (ptm)
REVERT: E  100 LEU cc_start: 0.4338 (OUTLIER) cc_final: 0.3852 (mm)
REVERT: E  253 MET cc_start: 0.1932 (tpt) cc_final: 0.1688 (tpt)
REVERT: E  276 MET cc_start: 0.7567 (ppp) cc_final: 0.6513 (ppp)
REVERT: E  299 ASN cc_start: 0.4441 (OUTLIER) cc_final: 0.3035 (t0)
REVERT: E  302 MET cc_start: 0.4527 (tpp) cc_final: 0.4013 (tpp)
  outliers start: 24
  outliers final: 20
  residues processed: 85
  average time/residue: 0.0641
  time to fit residues: 8.2407
Evaluate side-chains
  87 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 65
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  217 GLN
Chi-restraints excluded: chain C residue    5 ASN
Chi-restraints excluded: chain C residue   14 VAL
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain D residue   19 CYS
Chi-restraints excluded: chain D residue   53 MET
Chi-restraints excluded: chain F residue   19 CYS
Chi-restraints excluded: chain E residue   19 VAL
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain E residue  115 VAL
Chi-restraints excluded: chain E residue  163 ASN
Chi-restraints excluded: chain E residue  299 ASN
Chi-restraints excluded: chain E residue  315 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 77 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 116 optimal weight:    0.9990
   chunk 82 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 102 optimal weight:   10.0000
   chunk 109 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 96 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.086553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.070432 restraints weight = 53371.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.072188 restraints weight = 32040.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.073422 restraints weight = 22596.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.074257 restraints weight = 17585.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.074667 restraints weight = 14709.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6568
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9509  Z= 0.131
  Angle     :  0.600   9.509  12865  Z= 0.307
  Chirality :  0.044   0.293   1508
  Planarity :  0.003   0.048   1651
  Dihedral  :  4.415  20.522   1301
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 18.74 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.25), residues: 1197
  helix:  1.24 (0.21), residues: 607
  sheet: -1.35 (0.40), residues: 163
  loop : -0.84 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  73 
 TYR   0.015   0.001   TYR C 103 
 PHE   0.011   0.001   PHE A 242 
 TRP   0.007   0.001   TRP B 205 
 HIS   0.004   0.001   HIS C  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 9508)
  covalent geometry    : angle       0.59867 (12863)
  SS BOND              : bond        0.00624 (    1)
  SS BOND              : angle       2.98694 (    2)
  hydrogen bonds       : bond        0.03983 (  545)
  hydrogen bonds       : angle       4.95070 ( 1569)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 71
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 MET cc_start: 0.7480 (pmm) cc_final: 0.6967 (pmm)
REVERT: A  166 ASP cc_start: 0.8073 (t70) cc_final: 0.7622 (t70)
REVERT: B  152 LEU cc_start: 0.6230 (tp) cc_final: 0.5812 (pt)
REVERT: B  205 TRP cc_start: 0.9097 (p-90) cc_final: 0.8839 (p90)
REVERT: C   17 PHE cc_start: 0.8334 (m-80) cc_final: 0.7872 (m-80)
REVERT: C  116 MET cc_start: 0.7174 (mmm) cc_final: 0.6752 (mmm)
REVERT: D   46 PRO cc_start: 0.8573 (Cg_exo) cc_final: 0.8298 (Cg_endo)
REVERT: E    5 MET cc_start: 0.2807 (ptm) cc_final: 0.2009 (ptm)
REVERT: E  100 LEU cc_start: 0.4251 (OUTLIER) cc_final: 0.3773 (mm)
REVERT: E  276 MET cc_start: 0.7523 (ppp) cc_final: 0.6569 (ppp)
REVERT: E  299 ASN cc_start: 0.4485 (OUTLIER) cc_final: 0.3238 (t0)
REVERT: E  302 MET cc_start: 0.4404 (tpp) cc_final: 0.3825 (tpp)
  outliers start: 21
  outliers final: 18
  residues processed: 85
  average time/residue: 0.0614
  time to fit residues: 8.1209
Evaluate side-chains
  87 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 67
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  217 GLN
Chi-restraints excluded: chain C residue    5 ASN
Chi-restraints excluded: chain C residue   14 VAL
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain D residue   19 CYS
Chi-restraints excluded: chain F residue   19 CYS
Chi-restraints excluded: chain E residue   19 VAL
Chi-restraints excluded: chain E residue   54 LEU
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain E residue  115 VAL
Chi-restraints excluded: chain E residue  163 ASN
Chi-restraints excluded: chain E residue  299 ASN
Chi-restraints excluded: chain E residue  315 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   chunk 96 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0050
   chunk 42 optimal weight:    4.9990
   chunk 70 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9990
   overall best weight:    0.6796

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.086846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.070781 restraints weight = 53118.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.072570 restraints weight = 31811.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.073745 restraints weight = 22345.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 63)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.074623 restraints weight = 17444.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.075182 restraints weight = 14530.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6546
moved from start:          0.2429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9509  Z= 0.125
  Angle     :  0.588   8.865  12865  Z= 0.302
  Chirality :  0.044   0.273   1508
  Planarity :  0.003   0.047   1651
  Dihedral  :  4.319  20.798   1301
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 19.51 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.34 (0.25), residues: 1197
  helix:  1.40 (0.21), residues: 600
  sheet: -1.29 (0.39), residues: 166
  loop : -0.74 (0.31), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  70 
 TYR   0.014   0.001   TYR C 103 
 PHE   0.012   0.001   PHE A 242 
 TRP   0.006   0.001   TRP B 205 
 HIS   0.004   0.001   HIS F  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 9508)
  covalent geometry    : angle       0.58659 (12863)
  SS BOND              : bond        0.00549 (    1)
  SS BOND              : angle       2.89511 (    2)
  hydrogen bonds       : bond        0.03901 (  545)
  hydrogen bonds       : angle       4.86839 ( 1569)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1703.01 seconds
wall clock time: 30 minutes 7.71 seconds (1807.71 seconds total)