Starting phenix.real_space_refine
on Mon Apr 28 14:51:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5h1c_9567/04_2025/5h1c_9567.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5h1c_9567/04_2025/5h1c_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5h1c_9567/04_2025/5h1c_9567.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5h1c_9567/04_2025/5h1c_9567.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5h1c_9567/04_2025/5h1c_9567.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5h1c_9567/04_2025/5h1c_9567.cif"
  }
  resolution = 4.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7602
  Number of models: 1
  Model: ""
    Number of chains: 6
    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: "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}
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 4.75, per 1000 atoms: 0.62
  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: 1.94
  Conformation dependent library (CDL) restraints added in 977.4 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: 2.50
  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: 2.08

  Time building geometry restraints manager: 2.29 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: 10259
        3.18 -     6.37: 255
        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: 4529
       32.87 -    65.75: 173
       65.75 -    98.62: 11
       98.62 -   131.50: 0
      131.50 -   164.37: 3
  Dihedral angle restraints: 4716
    sinusoidal: 2055
      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 4713 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 992
       0.065 -    0.131: 201
       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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.980
  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:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     22.160
  Find NCS groups from input model:        0.320
  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:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6746
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= 0.665
  Angle     :  1.297  15.919  10552  Z= 0.838
  Chirality :  0.052   0.327   1203
  Planarity :  0.005   0.047   1296
  Dihedral  : 15.373 164.369   3012
  Min Nonbonded Distance : 1.454

Molprobity Statistics.
  All-atom Clashscore : 41.46
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.37 (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
 HIS   0.004   0.001   HIS B 138 
 PHE   0.019   0.002   PHE C 259 
 TYR   0.030   0.004   TYR A 315 
 ARG   0.007   0.001   ARG B 170 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15777 (  329)
  hydrogen bonds       : angle       9.91949 (  891)
  covalent geometry    : bond        0.00894 ( 7750)
  covalent geometry    : angle       1.29694 (10552)
  Misc. bond           : bond        0.23951 (    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  : 0.781 
Fit side-chains
   revert: symmetry clash
   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: 0.6554 (m-80)
REVERT: A  235 ARG cc_start: 0.5757 (OUTLIER) cc_final: 0.5355 (tmt170)
  outliers start: 33
  outliers final: 6
  residues processed: 91
  average time/residue: 0.2825
  time to fit residues: 32.5358
Evaluate side-chains
  43 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 35
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:    8.9990
   chunk 70 optimal weight:    9.9990
   chunk 39 optimal weight:   10.0000
   chunk 24 optimal weight:    8.9990
   chunk 47 optimal weight:    7.9990
   chunk 37 optimal weight:   20.0000
   chunk 72 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 84 optimal weight:    2.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  47 HIS
A 138 HIS
A 200 GLN
A 313 GLN
B  47 HIS
B 138 HIS
B 200 GLN
B 313 GLN
C  47 HIS
C 138 HIS
C 200 GLN
C 313 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.032884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.026455 restraints weight = 77337.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.027260 restraints weight = 44934.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.027829 restraints weight = 30959.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.2703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.3150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   7752  Z= 0.189
  Angle     :  0.706   6.053  10552  Z= 0.384
  Chirality :  0.041   0.150   1203
  Planarity :  0.006   0.054   1296
  Dihedral  : 17.637 176.481   1323
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  3.47 %
    Favored  : 95.55 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.27), residues: 921
  helix: -0.39 (0.22), residues: 423
  sheet: -1.02 (0.45), residues: 126
  loop : -0.32 (0.35), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.012   0.002   HIS B 294 
 PHE   0.023   0.003   PHE B 259 
 TYR   0.024   0.002   TYR C 315 
 ARG   0.005   0.001   ARG A 130 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04276 (  329)
  hydrogen bonds       : angle       5.78383 (  891)
  covalent geometry    : bond        0.00424 ( 7750)
  covalent geometry    : angle       0.70591 (10552)
  Misc. bond           : bond        0.00728 (    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
  46 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.779 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.1763
  time to fit residues: 11.9887
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  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 31 optimal weight:   20.0000
   chunk 57 optimal weight:    9.9990
   chunk 74 optimal weight:    6.9990
   chunk 62 optimal weight:   20.0000
   chunk 27 optimal weight:    8.9990
   chunk 3 optimal weight:    8.9990
   chunk 1 optimal weight:    4.9990
   chunk 78 optimal weight:    0.4980
   chunk 28 optimal weight:    8.9990
   chunk 61 optimal weight:    6.9990
   chunk 39 optimal weight:   10.0000
   overall best weight:    5.6988

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 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 = 0.2870 r_free = 0.2870 target = 0.031871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2594 r_free = 0.2594 target = 0.025322 restraints weight = 81885.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2631 r_free = 0.2631 target = 0.026100 restraints weight = 47076.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.026645 restraints weight = 32415.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.2644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.4395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   7752  Z= 0.215
  Angle     :  0.675   6.577  10552  Z= 0.359
  Chirality :  0.040   0.139   1203
  Planarity :  0.005   0.044   1296
  Dihedral  : 17.096 166.443   1323
  Min Nonbonded Distance : 1.833

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.23 %
    Favored  : 94.79 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.27), residues: 921
  helix:  0.71 (0.25), residues: 408
  sheet: -0.84 (0.46), residues: 126
  loop : -0.56 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS B 294 
 PHE   0.012   0.002   PHE C 126 
 TYR   0.017   0.002   TYR B 216 
 ARG   0.007   0.001   ARG B 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03883 (  329)
  hydrogen bonds       : angle       4.97887 (  891)
  covalent geometry    : bond        0.00460 ( 7750)
  covalent geometry    : angle       0.67504 (10552)
  Misc. bond           : bond        0.00388 (    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
  37 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
REVERT: B   46 PHE cc_start: 0.8528 (m-10) cc_final: 0.8305 (m-80)
REVERT: B  211 MET cc_start: 0.8656 (mmm) cc_final: 0.8431 (mmm)
REVERT: C  158 MET cc_start: 0.8546 (mtm) cc_final: 0.8005 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.1789
  time to fit residues: 10.1548
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  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 62 optimal weight:   20.0000
   chunk 20 optimal weight:    0.8980
   chunk 67 optimal weight:    6.9990
   chunk 28 optimal weight:   10.0000
   chunk 92 optimal weight:   30.0000
   chunk 56 optimal weight:   20.0000
   chunk 3 optimal weight:    3.9990
   chunk 4 optimal weight:    8.9990
   chunk 57 optimal weight:    0.6980
   chunk 39 optimal weight:   20.0000
   chunk 8 optimal weight:    5.9990
   overall best weight:    3.7186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.031876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2591 r_free = 0.2591 target = 0.025315 restraints weight = 79127.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2629 r_free = 0.2629 target = 0.026093 restraints weight = 45823.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.026659 restraints weight = 31596.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.4756

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= 0.152
  Angle     :  0.581   6.483  10552  Z= 0.311
  Chirality :  0.038   0.134   1203
  Planarity :  0.004   0.047   1296
  Dihedral  : 16.887 169.089   1323
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  3.47 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.27), residues: 921
  helix:  1.17 (0.25), residues: 408
  sheet: -0.50 (0.48), residues: 126
  loop : -0.50 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B 294 
 PHE   0.017   0.002   PHE C  86 
 TYR   0.012   0.001   TYR B 315 
 ARG   0.002   0.000   ARG B 130 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03314 (  329)
  hydrogen bonds       : angle       4.55142 (  891)
  covalent geometry    : bond        0.00339 ( 7750)
  covalent geometry    : angle       0.58059 (10552)
  Misc. bond           : bond        0.00310 (    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
  40 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.856 
Fit side-chains
   revert: symmetry clash
REVERT: A   46 PHE cc_start: 0.8616 (m-10) cc_final: 0.8355 (m-80)
REVERT: B  211 MET cc_start: 0.8794 (mmm) cc_final: 0.8521 (mmm)
REVERT: C  158 MET cc_start: 0.8640 (mtm) cc_final: 0.7980 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.1607
  time to fit residues: 10.1747
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  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 26 optimal weight:    0.0270
   chunk 39 optimal weight:   20.0000
   chunk 46 optimal weight:    9.9990
   chunk 76 optimal weight:   20.0000
   chunk 21 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9990
   chunk 87 optimal weight:   20.0000
   chunk 56 optimal weight:    8.9990
   chunk 74 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 75 optimal weight:   20.0000
   overall best weight:    3.4046

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.031629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2581 r_free = 0.2581 target = 0.025067 restraints weight = 79418.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2620 r_free = 0.2620 target = 0.025842 restraints weight = 46224.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2644 r_free = 0.2644 target = 0.026386 restraints weight = 31899.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.2631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.5052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7752  Z= 0.142
  Angle     :  0.571   6.574  10552  Z= 0.303
  Chirality :  0.038   0.137   1203
  Planarity :  0.004   0.048   1296
  Dihedral  : 16.575 166.946   1323
  Min Nonbonded Distance : 1.879

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  3.80 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.27), residues: 921
  helix:  1.41 (0.25), residues: 408
  sheet: -0.60 (0.52), residues: 111
  loop : -0.45 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.001   HIS C 294 
 PHE   0.011   0.002   PHE B  86 
 TYR   0.016   0.001   TYR A 216 
 ARG   0.002   0.000   ARG C 170 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03065 (  329)
  hydrogen bonds       : angle       4.40314 (  891)
  covalent geometry    : bond        0.00315 ( 7750)
  covalent geometry    : angle       0.57058 (10552)
  Misc. bond           : bond        0.00285 (    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
  40 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.988 
Fit side-chains
   revert: symmetry clash
REVERT: A   46 PHE cc_start: 0.8591 (m-10) cc_final: 0.8368 (m-80)
REVERT: C  158 MET cc_start: 0.8706 (mtm) cc_final: 0.8189 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.1824
  time to fit residues: 11.5627
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  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 90 optimal weight:    7.9990
   chunk 12 optimal weight:    6.9990
   chunk 79 optimal weight:    0.8980
   chunk 23 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 14 optimal weight:   20.0000
   chunk 65 optimal weight:   20.0000
   chunk 13 optimal weight:   20.0000
   chunk 44 optimal weight:    7.9990
   chunk 18 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   overall best weight:    4.5788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.031350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2567 r_free = 0.2567 target = 0.024825 restraints weight = 80198.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2604 r_free = 0.2604 target = 0.025583 restraints weight = 46741.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2629 r_free = 0.2629 target = 0.026126 restraints weight = 32277.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.2618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.5322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7752  Z= 0.171
  Angle     :  0.602   6.577  10552  Z= 0.318
  Chirality :  0.039   0.160   1203
  Planarity :  0.004   0.049   1296
  Dihedral  : 16.588 168.931   1323
  Min Nonbonded Distance : 1.851

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.23 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.27), residues: 921
  helix:  1.36 (0.25), residues: 408
  sheet: -0.94 (0.49), residues: 114
  loop : -0.45 (0.30), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 294 
 PHE   0.013   0.002   PHE B  46 
 TYR   0.015   0.001   TYR B 216 
 ARG   0.002   0.000   ARG A 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03270 (  329)
  hydrogen bonds       : angle       4.40536 (  891)
  covalent geometry    : bond        0.00372 ( 7750)
  covalent geometry    : angle       0.60213 (10552)
  Misc. bond           : bond        0.00279 (    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  : 1.063 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 MET cc_start: 0.8589 (mmp) cc_final: 0.6422 (ttt)
REVERT: C  158 MET cc_start: 0.8305 (mtm) cc_final: 0.7982 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.1931
  time to fit residues: 11.2593
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  : 1.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 37 optimal weight:   20.0000
   chunk 43 optimal weight:    0.0670
   chunk 4 optimal weight:    6.9990
   chunk 20 optimal weight:   10.0000
   chunk 16 optimal weight:    7.9990
   chunk 35 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 47 optimal weight:    3.9990
   chunk 87 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 41 optimal weight:    6.9990
   overall best weight:    3.1924

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

Flipped N/Q/H residues before XYZ refinement:
** A 272 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 = 0.2862 r_free = 0.2862 target = 0.031506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2582 r_free = 0.2582 target = 0.025057 restraints weight = 80366.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2620 r_free = 0.2620 target = 0.025812 restraints weight = 46751.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2645 r_free = 0.2645 target = 0.026355 restraints weight = 32248.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.2634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.5466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7752  Z= 0.135
  Angle     :  0.591   7.130  10552  Z= 0.306
  Chirality :  0.038   0.140   1203
  Planarity :  0.004   0.051   1296
  Dihedral  : 16.451 167.976   1323
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.13 %
    Favored  : 94.90 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.27), residues: 921
  helix:  1.51 (0.25), residues: 408
  sheet: -0.93 (0.48), residues: 114
  loop : -0.40 (0.30), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C 294 
 PHE   0.007   0.001   PHE B 129 
 TYR   0.017   0.001   TYR B 216 
 ARG   0.002   0.000   ARG A 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02988 (  329)
  hydrogen bonds       : angle       4.28271 (  891)
  covalent geometry    : bond        0.00298 ( 7750)
  covalent geometry    : angle       0.59062 (10552)
  Misc. bond           : bond        0.00259 (    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
  42 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 PHE cc_start: 0.8601 (m-10) cc_final: 0.8326 (m-80)
REVERT: C  125 MET cc_start: 0.8766 (mmm) cc_final: 0.8495 (mmm)
REVERT: C  158 MET cc_start: 0.8341 (mtm) cc_final: 0.8042 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.1846
  time to fit residues: 11.9315
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  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 90 optimal weight:    6.9990
   chunk 47 optimal weight:    5.9990
   chunk 29 optimal weight:    0.0010
   chunk 16 optimal weight:    5.9990
   chunk 42 optimal weight:    0.7980
   chunk 45 optimal weight:    9.9990
   chunk 50 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 51 optimal weight:    5.9990
   chunk 84 optimal weight:    1.9990
   chunk 52 optimal weight:    5.9990
   overall best weight:    2.1592

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

Flipped N/Q/H residues before XYZ refinement:
A  30 GLN
** A 272 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 = 0.2881 r_free = 0.2881 target = 0.031982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2595 r_free = 0.2595 target = 0.025369 restraints weight = 80208.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2634 r_free = 0.2634 target = 0.026173 restraints weight = 46655.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.026722 restraints weight = 31971.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.2647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.5623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7752  Z= 0.119
  Angle     :  0.582   7.552  10552  Z= 0.302
  Chirality :  0.039   0.138   1203
  Planarity :  0.004   0.078   1296
  Dihedral  : 15.854 165.874   1323
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  3.80 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.27), residues: 921
  helix:  1.46 (0.25), residues: 408
  sheet: -0.58 (0.50), residues: 111
  loop : -0.33 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C 294 
 PHE   0.008   0.001   PHE B 129 
 TYR   0.015   0.001   TYR B 216 
 ARG   0.003   0.000   ARG B 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02971 (  329)
  hydrogen bonds       : angle       4.18550 (  891)
  covalent geometry    : bond        0.00253 ( 7750)
  covalent geometry    : angle       0.58164 (10552)
  Misc. bond           : bond        0.00736 (    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
  41 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.795 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 PHE cc_start: 0.8594 (m-10) cc_final: 0.8334 (m-80)
REVERT: A   84 MET cc_start: 0.8770 (mmm) cc_final: 0.6691 (ttt)
REVERT: C  125 MET cc_start: 0.8750 (mmm) cc_final: 0.8439 (mmm)
REVERT: C  158 MET cc_start: 0.8327 (mtm) cc_final: 0.8016 (mpp)
REVERT: C  211 MET cc_start: 0.8170 (ppp) cc_final: 0.7843 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.1487
  time to fit residues: 9.8246
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  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 77 optimal weight:    9.9990
   chunk 10 optimal weight:    0.8980
   chunk 9 optimal weight:    5.9990
   chunk 90 optimal weight:    0.6980
   chunk 68 optimal weight:    6.9990
   chunk 46 optimal weight:    9.9990
   chunk 53 optimal weight:    0.6980
   chunk 38 optimal weight:   10.0000
   chunk 41 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 267 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.032292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2612 r_free = 0.2612 target = 0.025591 restraints weight = 80164.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.026389 restraints weight = 46690.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2676 r_free = 0.2676 target = 0.026959 restraints weight = 32287.966|
|-----------------------------------------------------------------------------|
r_work (final): 0.2669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.5767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   7752  Z= 0.109
  Angle     :  0.584   9.195  10552  Z= 0.298
  Chirality :  0.039   0.138   1203
  Planarity :  0.003   0.048   1296
  Dihedral  : 15.877 170.615   1323
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  3.47 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.28), residues: 921
  helix:  1.51 (0.25), residues: 408
  sheet: -0.52 (0.50), residues: 111
  loop : -0.31 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 294 
 PHE   0.008   0.001   PHE B 129 
 TYR   0.016   0.001   TYR B 216 
 ARG   0.005   0.000   ARG C  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02675 (  329)
  hydrogen bonds       : angle       4.10048 (  891)
  covalent geometry    : bond        0.00236 ( 7750)
  covalent geometry    : angle       0.58418 (10552)
  Misc. bond           : bond        0.00524 (    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
  42 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 1.116 
Fit side-chains
   revert: symmetry clash
REVERT: A   46 PHE cc_start: 0.8586 (m-10) cc_final: 0.8349 (m-80)
REVERT: A   84 MET cc_start: 0.8755 (mmm) cc_final: 0.6706 (ttt)
REVERT: B  125 MET cc_start: 0.8735 (mmm) cc_final: 0.8458 (mmm)
REVERT: C  125 MET cc_start: 0.8752 (mmm) cc_final: 0.8442 (mmm)
REVERT: C  158 MET cc_start: 0.8432 (mtm) cc_final: 0.8182 (mpp)
REVERT: C  211 MET cc_start: 0.8172 (ppp) cc_final: 0.7852 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.1913
  time to fit residues: 12.6280
Evaluate side-chains
  33 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 79 optimal weight:    4.9990
   chunk 44 optimal weight:    0.2980
   chunk 89 optimal weight:   10.0000
   chunk 31 optimal weight:   20.0000
   chunk 75 optimal weight:   10.0000
   chunk 80 optimal weight:    4.9990
   chunk 3 optimal weight:   10.0000
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    9.9990
   chunk 36 optimal weight:   20.0000
   chunk 8 optimal weight:   10.0000
   overall best weight:    5.0588

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

Flipped N/Q/H residues before XYZ refinement:
A 196 ASN
** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 196 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.031578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2577 r_free = 0.2577 target = 0.024954 restraints weight = 80219.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2615 r_free = 0.2615 target = 0.025728 restraints weight = 46900.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2640 r_free = 0.2640 target = 0.026279 restraints weight = 32505.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.2628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.5863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7752  Z= 0.185
  Angle     :  0.642  11.194  10552  Z= 0.330
  Chirality :  0.040   0.172   1203
  Planarity :  0.004   0.049   1296
  Dihedral  : 16.039 174.426   1323
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 12.11
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.27), residues: 921
  helix:  1.45 (0.25), residues: 408
  sheet: -1.08 (0.49), residues: 114
  loop : -0.41 (0.30), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 294 
 PHE   0.008   0.002   PHE B 248 
 TYR   0.013   0.001   TYR B 216 
 ARG   0.002   0.000   ARG A 235 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03287 (  329)
  hydrogen bonds       : angle       4.24374 (  891)
  covalent geometry    : bond        0.00398 ( 7750)
  covalent geometry    : angle       0.64222 (10552)
  Misc. bond           : bond        0.00459 (    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
  33 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 1.417 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 MET cc_start: 0.8661 (mmm) cc_final: 0.6753 (ttt)
REVERT: C  125 MET cc_start: 0.8785 (mmm) cc_final: 0.8487 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.2182
  time to fit residues: 11.7548
Evaluate side-chains
  28 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 1.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 89 optimal weight:    5.9990
   chunk 58 optimal weight:    7.9990
   chunk 64 optimal weight:   10.0000
   chunk 56 optimal weight:   20.0000
   chunk 33 optimal weight:   20.0000
   chunk 18 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0970
   chunk 43 optimal weight:    1.9990
   chunk 65 optimal weight:    7.9990
   chunk 37 optimal weight:    6.9990
   overall best weight:    2.8186

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

Flipped N/Q/H residues before XYZ refinement:
** A 272 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 = 0.2878 r_free = 0.2878 target = 0.031973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2602 r_free = 0.2602 target = 0.025439 restraints weight = 81544.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2639 r_free = 0.2639 target = 0.026206 restraints weight = 47955.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.026748 restraints weight = 33522.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.2649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.5970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7752  Z= 0.128
  Angle     :  0.581   9.343  10552  Z= 0.301
  Chirality :  0.039   0.138   1203
  Planarity :  0.003   0.036   1296
  Dihedral  : 16.009 175.523   1323
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  3.26 %
    Favored  : 95.77 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.27), residues: 921
  helix:  1.48 (0.25), residues: 408
  sheet: -0.93 (0.51), residues: 111
  loop : -0.43 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 294 
 PHE   0.007   0.001   PHE B 129 
 TYR   0.013   0.001   TYR B 216 
 ARG   0.002   0.000   ARG C 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02911 (  329)
  hydrogen bonds       : angle       4.03885 (  891)
  covalent geometry    : bond        0.00279 ( 7750)
  covalent geometry    : angle       0.58095 (10552)
  Misc. bond           : bond        0.00439 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2262.32 seconds
wall clock time: 41 minutes 51.34 seconds (2511.34 seconds total)