Starting phenix.real_space_refine
on Fri Sep 11 04:44:07 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/5h1c_9567/09_2026/5h1c_9567.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5h1c_9567/09_2026/5h1c_9567.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/5h1c_9567/09_2026/5h1c_9567.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5h1c_9567/09_2026/5h1c_9567.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/5h1c_9567/09_2026/5h1c_9567.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5h1c_9567/09_2026/5h1c_9567.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/5h1c_9567/09_2026/5h1c_9567.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/5h1c_9567/09_2026/5h1c_9567.cif"
  }
  resolution = 4.5
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      27      5.49       5
     Mg      3      5.21       5
     S      39      5.16       5
     C    4677      2.51       5
     N    1341      2.21       5
     O    1515      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7602
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2379
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 311, 2379
          Classifications: {'peptide': 311}
          Link IDs: {'CIS': 3, 'PTRANS': 9, 'TRANS': 298}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2379
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 311, 2379
          Classifications: {'peptide': 311}
          Link IDs: {'CIS': 3, 'PTRANS': 9, 'TRANS': 298}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2379
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 311, 2379
          Classifications: {'peptide': 311}
          Link IDs: {'CIS': 3, 'PTRANS': 9, 'TRANS': 298}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 180
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 180
          Classifications: {'DNA': 9}
          Link IDs: {'rna3p': 8}
    Chain: "E"
      Number of atoms: 189
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 189
          Classifications: {'DNA': 9}
          Link IDs: {'rna3p': 8}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.73, per 1000 atoms: 0.23
  Number of scatterers: 7602
  At special positions: 0
  Unit cell: (104.48, 82.278, 114.928, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      39     16.00
     P      27     15.00
     Mg      3     11.99
     O    1515      8.00
     N    1341      7.00
     C    4677      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.66
  Conformation dependent library (CDL) restraints added in 352.0 milliseconds
  

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1704

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 9 sheets defined
      52.2% alpha, 11.8% beta
      9 base pairs and 12 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 29
    Processing helix  chain 'A' and resid 34 through 42
    Processing helix  chain 'A' and resid 43 through 45
      No H-bonds generated for 'chain 'A' and resid 43 through 45'
    Processing helix  chain 'A' and resid 48 through 54
    Processing helix  chain 'A' and resid 56 through 63
      removed outlier: 3.777A  pdb=" N   ILE A  63 " --> pdb=" O   GLU A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 82
    Processing helix  chain 'A' and resid 88 through 97
    Processing helix  chain 'A' and resid 106 through 113
    Processing helix  chain 'A' and resid 132 through 144
    Processing helix  chain 'A' and resid 145 through 146
      No H-bonds generated for 'chain 'A' and resid 145 through 146'
    Processing helix  chain 'A' and resid 147 through 151
    Processing helix  chain 'A' and resid 167 through 179
      removed outlier: 3.563A  pdb=" N   LEU A 171 " --> pdb=" O   ARG A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 188
      removed outlier: 3.855A  pdb=" N   ASN A 188 " --> pdb=" O   ASP A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 212
      removed outlier: 3.570A  pdb=" N   GLN A 202 " --> pdb=" O   ASP A 198 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   VAL A 212 " --> pdb=" O   SER A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 232
      removed outlier: 3.535A  pdb=" N   ARG A 229 " --> pdb=" O   THR A 225 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   THR A 230 " --> pdb=" O   ALA A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 260
      removed outlier: 3.961A  pdb=" N   ARG A 247 " --> pdb=" O   MET A 243 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLU A 258 " --> pdb=" O   ARG A 254 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLY A 260 " --> pdb=" O   ALA A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 296
      removed outlier: 3.923A  pdb=" N   ILE A 292 " --> pdb=" O   GLY A 288 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ALA A 293 " --> pdb=" O   GLY A 289 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ALA A 295 " --> pdb=" O   ILE A 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 34 through 42
    Processing helix  chain 'B' and resid 43 through 45
      No H-bonds generated for 'chain 'B' and resid 43 through 45'
    Processing helix  chain 'B' and resid 48 through 54
    Processing helix  chain 'B' and resid 56 through 63
      removed outlier: 3.777A  pdb=" N   ILE B  63 " --> pdb=" O   GLU B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 82
    Processing helix  chain 'B' and resid 89 through 97
    Processing helix  chain 'B' and resid 106 through 113
    Processing helix  chain 'B' and resid 132 through 144
    Processing helix  chain 'B' and resid 145 through 146
      No H-bonds generated for 'chain 'B' and resid 145 through 146'
    Processing helix  chain 'B' and resid 147 through 151
    Processing helix  chain 'B' and resid 167 through 179
      removed outlier: 3.563A  pdb=" N   LEU B 171 " --> pdb=" O   ARG B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 188
      removed outlier: 3.856A  pdb=" N   ASN B 188 " --> pdb=" O   ASP B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 212
      removed outlier: 3.571A  pdb=" N   GLN B 202 " --> pdb=" O   ASP B 198 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   VAL B 212 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 232
      removed outlier: 3.536A  pdb=" N   ARG B 229 " --> pdb=" O   THR B 225 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   THR B 230 " --> pdb=" O   ALA B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 260
      removed outlier: 3.960A  pdb=" N   ARG B 247 " --> pdb=" O   MET B 243 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLU B 258 " --> pdb=" O   ARG B 254 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLY B 260 " --> pdb=" O   ALA B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 296
      removed outlier: 3.923A  pdb=" N   ILE B 292 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ALA B 293 " --> pdb=" O   GLY B 289 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ALA B 295 " --> pdb=" O   ILE B 291 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 24 through 29
    Processing helix  chain 'C' and resid 34 through 42
    Processing helix  chain 'C' and resid 43 through 45
      No H-bonds generated for 'chain 'C' and resid 43 through 45'
    Processing helix  chain 'C' and resid 48 through 54
    Processing helix  chain 'C' and resid 56 through 63
      removed outlier: 3.777A  pdb=" N   ILE C  63 " --> pdb=" O   GLU C  59 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 82
    Processing helix  chain 'C' and resid 89 through 97
    Processing helix  chain 'C' and resid 106 through 113
    Processing helix  chain 'C' and resid 132 through 144
    Processing helix  chain 'C' and resid 145 through 146
      No H-bonds generated for 'chain 'C' and resid 145 through 146'
    Processing helix  chain 'C' and resid 147 through 151
    Processing helix  chain 'C' and resid 167 through 179
      removed outlier: 3.563A  pdb=" N   LEU C 171 " --> pdb=" O   ARG C 167 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 181 through 188
      removed outlier: 3.856A  pdb=" N   ASN C 188 " --> pdb=" O   ASP C 184 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 198 through 212
      removed outlier: 3.571A  pdb=" N   GLN C 202 " --> pdb=" O   ASP C 198 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   VAL C 212 " --> pdb=" O   SER C 208 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 225 through 232
      removed outlier: 3.536A  pdb=" N   ARG C 229 " --> pdb=" O   THR C 225 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   THR C 230 " --> pdb=" O   ALA C 226 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 238 through 260
      removed outlier: 3.960A  pdb=" N   ARG C 247 " --> pdb=" O   MET C 243 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLU C 258 " --> pdb=" O   ARG C 254 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLY C 260 " --> pdb=" O   ALA C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 288 through 296
      removed outlier: 3.924A  pdb=" N   ILE C 292 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ALA C 293 " --> pdb=" O   GLY C 289 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ALA C 295 " --> pdb=" O   ILE C 291 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 126
      removed outlier: 8.366A  pdb=" N   VAL A 264 " --> pdb=" O   ALA A 217 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   LEU A 219 " --> pdb=" O   VAL A 264 " (cutoff:3.500A)
      removed outlier: 8.491A  pdb=" N   THR A 266 " --> pdb=" O   LEU A 219 " (cutoff:3.500A)
      removed outlier: 7.378A  pdb=" N   VAL A 221 " --> pdb=" O   THR A 266 " (cutoff:3.500A)
      removed outlier: 7.063A  pdb=" N   LYS A 156 " --> pdb=" O   ALA A 217 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   LEU A 219 " --> pdb=" O   LYS A 156 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   MET A 158 " --> pdb=" O   LEU A 219 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   VAL A 221 " --> pdb=" O   MET A 158 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   ILE A 160 " --> pdb=" O   VAL A 221 " (cutoff:3.500A)
      removed outlier: 7.479A  pdb=" N   ALA A 157 " --> pdb=" O   ALA A 190 " (cutoff:3.500A)
      removed outlier: 7.973A  pdb=" N   ALA A 192 " --> pdb=" O   ALA A 157 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   TYR A 159 " --> pdb=" O   ALA A 192 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 299 through 304
    Processing sheet with id=AA3, first strand: chain 'A' and resid 329 through 330
    Processing sheet with id=AA4, first strand: chain 'B' and resid 122 through 126
      removed outlier: 8.366A  pdb=" N   VAL B 264 " --> pdb=" O   ALA B 217 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   LEU B 219 " --> pdb=" O   VAL B 264 " (cutoff:3.500A)
      removed outlier: 8.492A  pdb=" N   THR B 266 " --> pdb=" O   LEU B 219 " (cutoff:3.500A)
      removed outlier: 7.378A  pdb=" N   VAL B 221 " --> pdb=" O   THR B 266 " (cutoff:3.500A)
      removed outlier: 7.063A  pdb=" N   LYS B 156 " --> pdb=" O   ALA B 217 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   LEU B 219 " --> pdb=" O   LYS B 156 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   MET B 158 " --> pdb=" O   LEU B 219 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   VAL B 221 " --> pdb=" O   MET B 158 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   ILE B 160 " --> pdb=" O   VAL B 221 " (cutoff:3.500A)
      removed outlier: 7.479A  pdb=" N   ALA B 157 " --> pdb=" O   ALA B 190 " (cutoff:3.500A)
      removed outlier: 7.973A  pdb=" N   ALA B 192 " --> pdb=" O   ALA B 157 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   TYR B 159 " --> pdb=" O   ALA B 192 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 299 through 304
    Processing sheet with id=AA6, first strand: chain 'B' and resid 329 through 330
    Processing sheet with id=AA7, first strand: chain 'C' and resid 122 through 126
      removed outlier: 8.367A  pdb=" N   VAL C 264 " --> pdb=" O   ALA C 217 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   LEU C 219 " --> pdb=" O   VAL C 264 " (cutoff:3.500A)
      removed outlier: 8.492A  pdb=" N   THR C 266 " --> pdb=" O   LEU C 219 " (cutoff:3.500A)
      removed outlier: 7.378A  pdb=" N   VAL C 221 " --> pdb=" O   THR C 266 " (cutoff:3.500A)
      removed outlier: 7.063A  pdb=" N   LYS C 156 " --> pdb=" O   ALA C 217 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   LEU C 219 " --> pdb=" O   LYS C 156 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   MET C 158 " --> pdb=" O   LEU C 219 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   VAL C 221 " --> pdb=" O   MET C 158 " (cutoff:3.500A)
      removed outlier: 7.302A  pdb=" N   ILE C 160 " --> pdb=" O   VAL C 221 " (cutoff:3.500A)
      removed outlier: 7.479A  pdb=" N   ALA C 157 " --> pdb=" O   ALA C 190 " (cutoff:3.500A)
      removed outlier: 7.973A  pdb=" N   ALA C 192 " --> pdb=" O   ALA C 157 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   TYR C 159 " --> pdb=" O   ALA C 192 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 299 through 304
    Processing sheet with id=AA9, first strand: chain 'C' and resid 329 through 330

    311 hydrogen bonds defined for protein.
    855 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      18 hydrogen bonds
      36 hydrogen bond angles
      0 basepair planarities
      9 basepair parallelities
      12 stacking parallelities
  Total time for adding SS restraints: 1.17

  Time building geometry restraints manager: 0.85 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2419
        1.33 -     1.45: 1181
        1.45 -     1.57: 4035
        1.57 -     1.69: 52
        1.69 -     1.81: 63
  Bond restraints: 7750
  Sorted by residual:
  bond pdb=" O3A ANP C 401 "
       pdb=" PB  ANP C 401 "
    ideal  model  delta    sigma   weight residual
    1.700  1.551  0.149 2.00e-02 2.50e+03 5.54e+01
  bond pdb=" O3A ANP B 602 "
       pdb=" PB  ANP B 602 "
    ideal  model  delta    sigma   weight residual
    1.700  1.552  0.148 2.00e-02 2.50e+03 5.51e+01
  bond pdb=" O3A ANP A 602 "
       pdb=" PB  ANP A 602 "
    ideal  model  delta    sigma   weight residual
    1.700  1.552  0.148 2.00e-02 2.50e+03 5.50e+01
  bond pdb=" C   MET A 158 "
       pdb=" N   TYR A 159 "
    ideal  model  delta    sigma   weight residual
    1.332  1.255  0.077 1.31e-02 5.83e+03 3.42e+01
  bond pdb=" C   MET C 158 "
       pdb=" N   TYR C 159 "
    ideal  model  delta    sigma   weight residual
    1.332  1.255  0.076 1.31e-02 5.83e+03 3.40e+01
  ... (remaining 7745 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.18: 10258
        3.18 -     6.37: 256
        6.37 -     9.55: 29
        9.55 -    12.74: 6
       12.74 -    15.92: 3
  Bond angle restraints: 10552
  Sorted by residual:
  angle pdb=" C   LYS A 285 "
        pdb=" N   PRO A 286 "
        pdb=" CA  PRO A 286 "
      ideal   model   delta    sigma   weight residual
     119.78  126.62   -6.84 1.03e+00 9.43e-01 4.42e+01
  angle pdb=" C   LYS C 285 "
        pdb=" N   PRO C 286 "
        pdb=" CA  PRO C 286 "
      ideal   model   delta    sigma   weight residual
     119.78  126.60   -6.82 1.03e+00 9.43e-01 4.38e+01
  angle pdb=" C   LYS B 285 "
        pdb=" N   PRO B 286 "
        pdb=" CA  PRO B 286 "
      ideal   model   delta    sigma   weight residual
     119.78  126.60   -6.82 1.03e+00 9.43e-01 4.38e+01
  angle pdb=" N   GLU C 124 "
        pdb=" CA  GLU C 124 "
        pdb=" C   GLU C 124 "
      ideal   model   delta    sigma   weight residual
     108.48  118.38   -9.90 1.80e+00 3.09e-01 3.03e+01
  angle pdb=" N   GLU A 124 "
        pdb=" CA  GLU A 124 "
        pdb=" C   GLU A 124 "
      ideal   model   delta    sigma   weight residual
     108.48  118.37   -9.89 1.80e+00 3.09e-01 3.02e+01
  ... (remaining 10547 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.87: 4457
       32.87 -    65.75: 161
       65.75 -    98.62: 11
       98.62 -   131.50: 0
      131.50 -   164.37: 3
  Dihedral angle restraints: 4632
    sinusoidal: 1971
      harmonic: 2661
  Sorted by residual:
  dihedral pdb=" CA  ILE C 314 "
           pdb=" C   ILE C 314 "
           pdb=" N   TYR C 315 "
           pdb=" CA  TYR C 315 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.42   23.58     0      5.00e+00 4.00e-02 2.22e+01
  dihedral pdb=" CA  ILE B 314 "
           pdb=" C   ILE B 314 "
           pdb=" N   TYR B 315 "
           pdb=" CA  TYR B 315 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.44   23.56     0      5.00e+00 4.00e-02 2.22e+01
  dihedral pdb=" CA  ILE A 314 "
           pdb=" C   ILE A 314 "
           pdb=" N   TYR A 315 "
           pdb=" CA  TYR A 315 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.44   23.56     0      5.00e+00 4.00e-02 2.22e+01
  ... (remaining 4629 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 983
       0.065 -    0.131: 210
       0.131 -    0.196: 4
       0.196 -    0.261: 3
       0.261 -    0.327: 3
  Chirality restraints: 1203
  Sorted by residual:
  chirality pdb=" C3' ANP C 401 "
            pdb=" C2' ANP C 401 "
            pdb=" C4' ANP C 401 "
            pdb=" O3' ANP C 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.68    0.33 2.00e-01 2.50e+01 2.67e+00
  chirality pdb=" C3' ANP B 602 "
            pdb=" C2' ANP B 602 "
            pdb=" C4' ANP B 602 "
            pdb=" O3' ANP B 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.68    0.33 2.00e-01 2.50e+01 2.66e+00
  chirality pdb=" C3' ANP A 602 "
            pdb=" C2' ANP A 602 "
            pdb=" C4' ANP A 602 "
            pdb=" O3' ANP A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.68    0.33 2.00e-01 2.50e+01 2.66e+00
  ... (remaining 1200 not shown)

  Planarity restraints: 1296
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET B 158 "   -0.015 2.00e-02 2.50e+03   3.01e-02 9.08e+00
        pdb=" C   MET B 158 "    0.052 2.00e-02 2.50e+03
        pdb=" O   MET B 158 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   TYR B 159 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 158 "   -0.015 2.00e-02 2.50e+03   3.01e-02 9.06e+00
        pdb=" C   MET A 158 "    0.052 2.00e-02 2.50e+03
        pdb=" O   MET A 158 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   TYR A 159 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET C 158 "   -0.015 2.00e-02 2.50e+03   2.99e-02 8.95e+00
        pdb=" C   MET C 158 "    0.052 2.00e-02 2.50e+03
        pdb=" O   MET C 158 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   TYR C 159 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1293 not shown)

  Histogram of nonbonded interaction distances:
        1.45 -     2.14: 66
        2.14 -     2.83: 2630
        2.83 -     3.52: 10835
        3.52 -     4.21: 17830
        4.21 -     4.90: 30286
  Nonbonded interactions: 61647
  Sorted by model distance:
  nonbonded pdb=" O   ALA C 217 "
            pdb=" CG1 VAL C 261 "
     model   vdw
     1.454 3.460
  nonbonded pdb=" O   ALA B 217 "
            pdb=" CG1 VAL B 261 "
     model   vdw
     1.454 3.460
  nonbonded pdb=" O   ALA A 217 "
            pdb=" CG1 VAL A 261 "
     model   vdw
     1.454 3.460
  nonbonded pdb=" CG2 VAL B 270 "
            pdb=" CG2 ILE B 287 "
     model   vdw
     1.579 3.880
  nonbonded pdb=" CG2 VAL C 270 "
            pdb=" CG2 ILE C 287 "
     model   vdw
     1.580 3.880
  ... (remaining 61642 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 22 through 336)
  selection = (chain 'B' and resid 22 through 336)
  selection = (chain 'C' and resid 22 through 336)
}

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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     8.800
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6639
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      :  0.010   0.242   7752  Z= 0.687
  Angle     :  1.303  15.919  10552  Z= 0.859
  Chirality :  0.052   0.327   1203
  Planarity :  0.005   0.047   1296
  Dihedral  : 15.190 164.369   2928
  Min Nonbonded Distance : 1.454

Molprobity Statistics.
  All-atom Clashscore : 41.53
  Ramachandran Plot:
    Outliers :  2.28 %
    Allowed  :  4.89 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  :  2.82 %
    Favored  : 92.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.37 (0.25), residues: 921
  helix: -2.32 (0.16), residues: 408
  sheet: -2.56 (0.46), residues: 114
  loop : -0.07 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 170 
 TYR   0.030   0.004   TYR A 315 
 PHE   0.019   0.002   PHE C 259 
 HIS   0.004   0.001   HIS B 138 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00896 /  0.57 ( 7750)
  covalent geometry    : angle       1.30303 /  0.86 (10552)
  hydrogen bonds       : bond        0.15777 / 10.73 (  329)
  hydrogen bonds       : angle       9.91949 /  7.20 (  891)
  Misc. bond           : bond        0.23951 / 16.53 (    2)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 64
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7213 (mp)
REVERT: A  205 TYR cc_start: 0.6809 (m-80) cc_final: 0.6556 (m-80)
REVERT: A  235 ARG cc_start: 0.5757 (OUTLIER) cc_final: 0.5356 (tmt170)
  outliers start: 33
  outliers final: 7
  residues processed: 91
  average time/residue: 0.1190
  time to fit residues: 13.8777
Evaluate side-chains
  44 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 35
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:   20.0000
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:   20.0000
   chunk 45 optimal weight:    5.9990
   chunk 74 optimal weight:    7.9990
   overall best weight:    4.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  47 HIS
A 138 HIS
** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 200 GLN
A 202 GLN
A 313 GLN
B  47 HIS
B  93 HIS
B 138 HIS
** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 200 GLN
B 202 GLN
B 313 GLN
C  47 HIS
C  93 HIS
C 138 HIS
** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 200 GLN
C 202 GLN
C 313 GLN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.032918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2661 r_free = 0.2661 target = 0.026461 restraints weight = 78294.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2701 r_free = 0.2701 target = 0.027295 restraints weight = 44788.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2727 r_free = 0.2727 target = 0.027880 restraints weight = 30555.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.028236 restraints weight = 23281.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.028516 restraints weight = 19362.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.2744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.2642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   7752  Z= 0.221
  Angle     :  0.853   7.459  10552  Z= 0.450
  Chirality :  0.046   0.168   1203
  Planarity :  0.006   0.065   1296
  Dihedral  : 17.345 179.250   1239
  Min Nonbonded Distance : 1.891

Molprobity Statistics.
  All-atom Clashscore : 13.71
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.67 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.27), residues: 921
  helix: -0.56 (0.22), residues: 405
  sheet: -1.14 (0.47), residues: 126
  loop : -0.48 (0.34), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 130 
 TYR   0.029   0.002   TYR C 315 
 PHE   0.038   0.003   PHE B 126 
 HIS   0.010   0.002   HIS B 294 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00464 /  0.22 ( 7750)
  covalent geometry    : angle       0.85343 /  0.45 (10552)
  hydrogen bonds       : bond        0.04895 /  3.13 (  329)
  hydrogen bonds       : angle       6.50706 /  4.72 (  891)
  Misc. bond           : bond        0.01019 /  0.70 (    2)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.301 
Fit side-chains
REVERT: B   84 MET cc_start: 0.7812 (mtp) cc_final: 0.7574 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.0854
  time to fit residues: 5.5730
Evaluate side-chains
  30 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 64 optimal weight:   20.0000
   chunk 87 optimal weight:   30.0000
   chunk 90 optimal weight:   20.0000
   chunk 20 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   chunk 4 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 66 optimal weight:    0.4980
   chunk 45 optimal weight:    8.9990
   chunk 42 optimal weight:    0.3980
   chunk 54 optimal weight:    5.9990
   overall best weight:    1.5786

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.033071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2666 r_free = 0.2666 target = 0.026477 restraints weight = 76218.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2706 r_free = 0.2706 target = 0.027318 restraints weight = 43423.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.027931 restraints weight = 29439.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2751 r_free = 0.2751 target = 0.028359 restraints weight = 22316.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.028595 restraints weight = 18217.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.3258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   7752  Z= 0.133
  Angle     :  0.670   9.435  10552  Z= 0.356
  Chirality :  0.041   0.194   1203
  Planarity :  0.004   0.050   1296
  Dihedral  : 17.278 177.668   1239
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  3.80 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  0.67 %
    Favored  : 99.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.27), residues: 921
  helix:  0.38 (0.24), residues: 405
  sheet: -0.51 (0.50), residues: 126
  loop : -0.53 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 247 
 TYR   0.024   0.002   TYR C 315 
 PHE   0.016   0.002   PHE B 259 
 HIS   0.009   0.002   HIS C 294 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.13 ( 7750)
  covalent geometry    : angle       0.66950 /  0.36 (10552)
  hydrogen bonds       : bond        0.04096 /  2.62 (  329)
  hydrogen bonds       : angle       5.48302 /  4.00 (  891)
  Misc. bond           : bond        0.00111 /  0.08 (    2)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 45
  time to evaluate  : 0.307 
Fit side-chains
REVERT: A   46 PHE cc_start: 0.8571 (m-10) cc_final: 0.8291 (m-80)
REVERT: A   99 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8302 (mp)
REVERT: B   84 MET cc_start: 0.7777 (mtp) cc_final: 0.7476 (mmm)
REVERT: B  210 MET cc_start: 0.8301 (ttp) cc_final: 0.8055 (ttt)
REVERT: B  211 MET cc_start: 0.8385 (mmp) cc_final: 0.7933 (mmm)
  outliers start: 2
  outliers final: 0
  residues processed: 47
  average time/residue: 0.0650
  time to fit residues: 5.0153
Evaluate side-chains
  32 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 31
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 82 optimal weight:    5.9990
   chunk 59 optimal weight:   20.0000
   chunk 83 optimal weight:   10.0000
   chunk 4 optimal weight:   10.0000
   chunk 48 optimal weight:   10.0000
   chunk 70 optimal weight:    8.9990
   chunk 84 optimal weight:    6.9990
   chunk 62 optimal weight:   20.0000
   chunk 14 optimal weight:    9.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    6.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 188 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 = 0.2866 r_free = 0.2866 target = 0.031611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2585 r_free = 0.2585 target = 0.025041 restraints weight = 81333.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2626 r_free = 0.2626 target = 0.025841 restraints weight = 46800.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.026410 restraints weight = 32035.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.026788 restraints weight = 24501.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2680 r_free = 0.2680 target = 0.027057 restraints weight = 20324.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.3763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   7752  Z= 0.240
  Angle     :  0.754   6.352  10552  Z= 0.393
  Chirality :  0.042   0.148   1203
  Planarity :  0.005   0.040   1296
  Dihedral  : 17.246 178.628   1239
  Min Nonbonded Distance : 1.755

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  3.58 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.28), residues: 921
  helix:  0.93 (0.24), residues: 429
  sheet: -0.42 (0.51), residues: 126
  loop : -0.48 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 241 
 TYR   0.016   0.002   TYR A 216 
 PHE   0.014   0.002   PHE C 126 
 HIS   0.004   0.001   HIS B 294 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00500 /  0.24 ( 7750)
  covalent geometry    : angle       0.75399 /  0.39 (10552)
  hydrogen bonds       : bond        0.04243 /  2.75 (  329)
  hydrogen bonds       : angle       5.30147 /  3.87 (  891)
  Misc. bond           : bond        0.00937 /  0.65 (    2)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.300 
Fit side-chains
REVERT: B  211 MET cc_start: 0.8405 (mmp) cc_final: 0.8141 (mmm)
REVERT: C  158 MET cc_start: 0.8267 (mpp) cc_final: 0.7737 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0631
  time to fit residues: 3.7103
Evaluate side-chains
  30 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 53 optimal weight:    6.9990
   chunk 15 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 6 optimal weight:   10.0000
   chunk 24 optimal weight:    6.9990
   chunk 44 optimal weight:   20.0000
   chunk 20 optimal weight:    5.9990
   chunk 42 optimal weight:    7.9990
   chunk 64 optimal weight:   10.0000
   chunk 79 optimal weight:    5.9990
   overall best weight:    4.9990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.031756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2592 r_free = 0.2592 target = 0.025194 restraints weight = 79892.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2631 r_free = 0.2631 target = 0.025978 restraints weight = 45814.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.026517 restraints weight = 31250.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.026929 restraints weight = 24141.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2682 r_free = 0.2682 target = 0.027148 restraints weight = 19962.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.4028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7752  Z= 0.180
  Angle     :  0.637   6.788  10552  Z= 0.344
  Chirality :  0.039   0.120   1203
  Planarity :  0.004   0.039   1296
  Dihedral  : 17.169 179.519   1239
  Min Nonbonded Distance : 1.894

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.56 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.28), residues: 921
  helix:  1.25 (0.25), residues: 408
  sheet: -0.39 (0.50), residues: 126
  loop : -0.51 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  27 
 TYR   0.018   0.002   TYR C 315 
 PHE   0.011   0.002   PHE B 259 
 HIS   0.004   0.001   HIS B 294 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00382 /  0.18 ( 7750)
  covalent geometry    : angle       0.63741 /  0.34 (10552)
  hydrogen bonds       : bond        0.03893 /  2.53 (  329)
  hydrogen bonds       : angle       5.04280 /  3.69 (  891)
  Misc. bond           : bond        0.00182 /  0.13 (    2)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.244 
Fit side-chains
REVERT: B  210 MET cc_start: 0.8554 (ttp) cc_final: 0.8280 (ttp)
REVERT: B  211 MET cc_start: 0.8532 (mmp) cc_final: 0.8200 (mmm)
REVERT: C  158 MET cc_start: 0.8575 (mpp) cc_final: 0.8263 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0584
  time to fit residues: 3.3778
Evaluate side-chains
  30 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 44 optimal weight:   20.0000
   chunk 12 optimal weight:    6.9990
   chunk 49 optimal weight:    7.9990
   chunk 58 optimal weight:    9.9990
   chunk 74 optimal weight:    6.9990
   chunk 39 optimal weight:   10.0000
   chunk 28 optimal weight:   20.0000
   chunk 46 optimal weight:    8.9990
   chunk 41 optimal weight:    1.9990
   chunk 13 optimal weight:    9.9990
   chunk 71 optimal weight:    7.9990
   overall best weight:    6.3990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.031108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2557 r_free = 0.2557 target = 0.024573 restraints weight = 81626.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2596 r_free = 0.2596 target = 0.025333 restraints weight = 47579.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2620 r_free = 0.2620 target = 0.025884 restraints weight = 32691.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2636 r_free = 0.2636 target = 0.026226 restraints weight = 25147.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2648 r_free = 0.2648 target = 0.026493 restraints weight = 21065.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.2638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.4386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   7752  Z= 0.229
  Angle     :  0.682   6.959  10552  Z= 0.360
  Chirality :  0.040   0.140   1203
  Planarity :  0.005   0.046   1296
  Dihedral  : 17.058 174.777   1239
  Min Nonbonded Distance : 1.791

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  3.58 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.27), residues: 921
  helix:  1.15 (0.24), residues: 429
  sheet: -0.79 (0.47), residues: 123
  loop : -0.63 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 170 
 TYR   0.016   0.002   TYR A 216 
 PHE   0.015   0.002   PHE B 259 
 HIS   0.003   0.001   HIS B 294 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00478 /  0.23 ( 7750)
  covalent geometry    : angle       0.68192 /  0.36 (10552)
  hydrogen bonds       : bond        0.03970 /  2.63 (  329)
  hydrogen bonds       : angle       5.01878 /  3.67 (  891)
  Misc. bond           : bond        0.00700 /  0.48 (    2)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.268 
Fit side-chains
REVERT: B  211 MET cc_start: 0.8566 (mmp) cc_final: 0.8298 (mmm)
REVERT: C  158 MET cc_start: 0.8436 (mpp) cc_final: 0.8048 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0669
  time to fit residues: 3.8978
Evaluate side-chains
  29 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 85 optimal weight:    0.7980
   chunk 52 optimal weight:   10.0000
   chunk 43 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 90 optimal weight:    5.9990
   chunk 75 optimal weight:   20.0000
   chunk 10 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   overall best weight:    2.5588

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.031758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2587 r_free = 0.2587 target = 0.025188 restraints weight = 78982.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2626 r_free = 0.2626 target = 0.025970 restraints weight = 45907.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.026530 restraints weight = 31461.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.026900 restraints weight = 24190.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.027136 restraints weight = 20109.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.2669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.4517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7752  Z= 0.129
  Angle     :  0.623   7.367  10552  Z= 0.326
  Chirality :  0.040   0.159   1203
  Planarity :  0.004   0.049   1296
  Dihedral  : 16.968 171.748   1239
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.02 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.47 (0.27), residues: 921
  helix:  1.42 (0.25), residues: 408
  sheet: -0.62 (0.47), residues: 126
  loop : -0.49 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 229 
 TYR   0.017   0.001   TYR B 216 
 PHE   0.010   0.002   PHE B 129 
 HIS   0.004   0.001   HIS B 294 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.13 ( 7750)
  covalent geometry    : angle       0.62275 /  0.33 (10552)
  hydrogen bonds       : bond        0.03415 /  2.27 (  329)
  hydrogen bonds       : angle       4.63920 /  3.39 (  891)
  Misc. bond           : bond        0.00246 /  0.17 (    2)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: A   46 PHE cc_start: 0.8556 (m-10) cc_final: 0.8308 (m-80)
REVERT: C  158 MET cc_start: 0.8315 (mpp) cc_final: 0.8091 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.0576
  time to fit residues: 3.4770
Evaluate side-chains
  31 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 60 optimal weight:   20.0000
   chunk 38 optimal weight:   20.0000
   chunk 25 optimal weight:    0.5980
   chunk 66 optimal weight:   20.0000
   chunk 3 optimal weight:    7.9990
   chunk 73 optimal weight:   10.0000
   chunk 82 optimal weight:    4.9990
   chunk 37 optimal weight:    0.4980
   chunk 84 optimal weight:    0.9980
   chunk 90 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    3.0184

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.031665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2581 r_free = 0.2581 target = 0.025052 restraints weight = 79330.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2620 r_free = 0.2620 target = 0.025845 restraints weight = 45933.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.2645 r_free = 0.2645 target = 0.026398 restraints weight = 31593.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2661 r_free = 0.2661 target = 0.026755 restraints weight = 24298.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.2673 r_free = 0.2673 target = 0.027026 restraints weight = 20256.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.2662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.4658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7752  Z= 0.140
  Angle     :  0.595   7.514  10552  Z= 0.315
  Chirality :  0.039   0.152   1203
  Planarity :  0.004   0.048   1296
  Dihedral  : 16.913 171.088   1239
  Min Nonbonded Distance : 1.860

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.02 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.27), residues: 921
  helix:  1.54 (0.25), residues: 408
  sheet: -0.45 (0.48), residues: 123
  loop : -0.52 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 229 
 TYR   0.011   0.001   TYR A 315 
 PHE   0.010   0.001   PHE A 259 
 HIS   0.003   0.001   HIS B 294 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.14 ( 7750)
  covalent geometry    : angle       0.59457 /  0.32 (10552)
  hydrogen bonds       : bond        0.03288 /  2.19 (  329)
  hydrogen bonds       : angle       4.54269 /  3.32 (  891)
  Misc. bond           : bond        0.00374 /  0.26 (    2)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A   46 PHE cc_start: 0.8574 (m-10) cc_final: 0.8342 (m-80)
REVERT: A   84 MET cc_start: 0.8608 (mmp) cc_final: 0.6314 (ttt)
REVERT: B  210 MET cc_start: 0.8690 (ttp) cc_final: 0.8343 (ttm)
REVERT: B  211 MET cc_start: 0.8729 (mmp) cc_final: 0.8305 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.0666
  time to fit residues: 4.0153
Evaluate side-chains
  31 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 60 optimal weight:    7.9990
   chunk 7 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 73 optimal weight:    0.8980
   chunk 15 optimal weight:    9.9990
   chunk 6 optimal weight:   20.0000
   chunk 45 optimal weight:   20.0000
   chunk 72 optimal weight:    2.9990
   chunk 70 optimal weight:   10.0000
   chunk 38 optimal weight:    9.9990
   chunk 28 optimal weight:   20.0000
   overall best weight:    2.7186

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.031890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2585 r_free = 0.2585 target = 0.025243 restraints weight = 79363.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2624 r_free = 0.2624 target = 0.026022 restraints weight = 46037.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.026574 restraints weight = 31683.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2665 r_free = 0.2665 target = 0.026931 restraints weight = 24405.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2677 r_free = 0.2677 target = 0.027211 restraints weight = 20415.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.4783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7752  Z= 0.127
  Angle     :  0.592   8.537  10552  Z= 0.312
  Chirality :  0.039   0.149   1203
  Planarity :  0.004   0.050   1296
  Dihedral  : 16.901 171.802   1239
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.34 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.62 (0.28), residues: 921
  helix:  1.58 (0.25), residues: 408
  sheet: -0.56 (0.47), residues: 126
  loop : -0.44 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 310 
 TYR   0.012   0.001   TYR B 216 
 PHE   0.014   0.002   PHE B 126 
 HIS   0.003   0.001   HIS B 294 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.13 ( 7750)
  covalent geometry    : angle       0.59154 /  0.31 (10552)
  hydrogen bonds       : bond        0.03118 /  2.08 (  329)
  hydrogen bonds       : angle       4.40606 /  3.21 (  891)
  Misc. bond           : bond        0.00254 /  0.18 (    2)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: A   46 PHE cc_start: 0.8572 (m-10) cc_final: 0.8324 (m-80)
REVERT: A   84 MET cc_start: 0.8566 (mmp) cc_final: 0.6294 (ttt)
REVERT: A  211 MET cc_start: 0.8864 (mmm) cc_final: 0.8316 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.0651
  time to fit residues: 4.2332
Evaluate side-chains
  31 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 43 optimal weight:    9.9990
   chunk 3 optimal weight:   10.0000
   chunk 14 optimal weight:   20.0000
   chunk 35 optimal weight:    8.9990
   chunk 13 optimal weight:    0.0870
   chunk 15 optimal weight:    6.9990
   chunk 86 optimal weight:    5.9990
   chunk 77 optimal weight:   20.0000
   chunk 33 optimal weight:    2.9990
   chunk 30 optimal weight:   20.0000
   chunk 48 optimal weight:    4.9990
   overall best weight:    4.2166

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.031728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2577 r_free = 0.2577 target = 0.025058 restraints weight = 80504.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2615 r_free = 0.2615 target = 0.025835 restraints weight = 46751.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.026404 restraints weight = 32330.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.026790 restraints weight = 24810.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.027018 restraints weight = 20570.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.2659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.4862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   7752  Z= 0.165
  Angle     :  0.638   9.173  10552  Z= 0.332
  Chirality :  0.039   0.143   1203
  Planarity :  0.004   0.048   1296
  Dihedral  : 16.896 171.438   1239
  Min Nonbonded Distance : 1.836

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.13 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.28), residues: 921
  helix:  1.57 (0.25), residues: 408
  sheet: -0.62 (0.48), residues: 126
  loop : -0.48 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 310 
 TYR   0.023   0.002   TYR A 216 
 PHE   0.013   0.002   PHE B  86 
 HIS   0.003   0.001   HIS B 294 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.16 ( 7750)
  covalent geometry    : angle       0.63848 /  0.33 (10552)
  hydrogen bonds       : bond        0.03386 /  2.24 (  329)
  hydrogen bonds       : angle       4.51910 /  3.33 (  891)
  Misc. bond           : bond        0.00314 /  0.22 (    2)

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 PHE cc_start: 0.8603 (m-10) cc_final: 0.8314 (m-80)
REVERT: A   84 MET cc_start: 0.8569 (mmp) cc_final: 0.6327 (ttt)
REVERT: C  125 MET cc_start: 0.8845 (mmm) cc_final: 0.8573 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.0604
  time to fit residues: 3.7435
Evaluate side-chains
  32 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 41 optimal weight:    9.9990
   chunk 44 optimal weight:   20.0000
   chunk 82 optimal weight:   20.0000
   chunk 39 optimal weight:    6.9990
   chunk 37 optimal weight:    7.9990
   chunk 21 optimal weight:    0.0970
   chunk 16 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 55 optimal weight:    8.9990
   chunk 43 optimal weight:    8.9990
   overall best weight:    3.6186

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.031877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2583 r_free = 0.2583 target = 0.025218 restraints weight = 80402.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2621 r_free = 0.2621 target = 0.025992 restraints weight = 46582.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2646 r_free = 0.2646 target = 0.026532 restraints weight = 32315.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.026885 restraints weight = 25025.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.2674 r_free = 0.2674 target = 0.027169 restraints weight = 20995.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.4944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.099   7752  Z= 0.160
  Angle     :  0.630  10.139  10552  Z= 0.328
  Chirality :  0.039   0.152   1203
  Planarity :  0.004   0.046   1296
  Dihedral  : 16.911 171.906   1239
  Min Nonbonded Distance : 1.853

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.13 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.61 (0.28), residues: 921
  helix:  1.56 (0.25), residues: 408
  sheet: -0.55 (0.48), residues: 126
  loop : -0.46 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 306 
 TYR   0.018   0.001   TYR C 315 
 PHE   0.011   0.001   PHE C 259 
 HIS   0.003   0.001   HIS B 294 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.16 ( 7750)
  covalent geometry    : angle       0.63014 /  0.33 (10552)
  hydrogen bonds       : bond        0.03331 /  2.29 (  329)
  hydrogen bonds       : angle       4.45905 /  3.28 (  891)
  Misc. bond           : bond        0.00304 /  0.21 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1028.07 seconds
wall clock time: 18 minutes 36.26 seconds (1116.26 seconds total)