Starting phenix.real_space_refine
on Wed Sep 17 09:33:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5h1c_9567/09_2025/5h1c_9567.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5h1c_9567/09_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_9567/09_2025/5h1c_9567.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5h1c_9567/09_2025/5h1c_9567.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5h1c_9567/09_2025/5h1c_9567.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5h1c_9567/09_2025/5h1c_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-2.0-5805/lib/python3.9/site-packages/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: 1.60, per 1000 atoms: 0.21
  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: 0.72
  Conformation dependent library (CDL) restraints added in 382.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.85
  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: 1.31

  Time building geometry restraints manager: 0.94 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:             1.550
  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:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.920
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.120
-------------------------------------------------------------------------------
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 : 41.53
  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 aren 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
  covalent geometry    : bond        0.00894 ( 7750)
  covalent geometry    : angle       1.29694 (10552)
  hydrogen bonds       : bond        0.15777 (  329)
  hydrogen bonds       : angle       9.91949 (  891)
  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  : 0.277 
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: 0.7212 (mp)
REVERT: A  205 TYR cc_start: 0.6809 (m-80) cc_final: 0.6555 (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: 0.1227
  time to fit residues: 14.0612
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  : 0.291 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 74 optimal weight:    7.9990
   overall best weight:    5.1990

-------------------------------------------------------------------------------
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 200 GLN
B 313 GLN
C  47 HIS
C 138 HIS
C 200 GLN
C 313 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.032655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2644 r_free = 0.2644 target = 0.026120 restraints weight = 78039.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2683 r_free = 0.2683 target = 0.026945 restraints weight = 44377.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2708 r_free = 0.2708 target = 0.027516 restraints weight = 30092.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.027922 restraints weight = 22889.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2735 r_free = 0.2735 target = 0.028160 restraints weight = 18744.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.3431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   7752  Z= 0.212
  Angle     :  0.735   6.300  10552  Z= 0.397
  Chirality :  0.042   0.147   1203
  Planarity :  0.006   0.053   1296
  Dihedral  : 17.687 172.742   1323
  Min Nonbonded Distance : 1.868

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  3.58 %
    Favored  : 95.44 %
  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 aren not related in a simple way.
  whole: -0.81 (0.26), residues: 921
  helix: -0.33 (0.22), residues: 426
  sheet: -1.11 (0.44), residues: 126
  loop : -0.31 (0.34), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 130 
 TYR   0.023   0.002   TYR B 315 
 PHE   0.024   0.003   PHE B 259 
 HIS   0.013   0.002   HIS C 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 7750)
  covalent geometry    : angle       0.73470 (10552)
  hydrogen bonds       : bond        0.04429 (  329)
  hydrogen bonds       : angle       5.61399 (  891)
  Misc. bond           : bond        0.00644 (    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
  41 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0751
  time to fit residues: 4.5266
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  : 0.247 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 90 optimal weight:   20.0000
   chunk 20 optimal weight:    4.9990
   chunk 58 optimal weight:    5.9990
   chunk 4 optimal weight:    9.9990
   chunk 15 optimal weight:    5.9990
   chunk 66 optimal weight:    0.0670
   chunk 45 optimal weight:    9.9990
   chunk 42 optimal weight:    4.9990
   chunk 54 optimal weight:    9.9990
   overall best weight:    4.4126

-------------------------------------------------------------------------------
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 = 0.2885 r_free = 0.2885 target = 0.032227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2619 r_free = 0.2619 target = 0.025839 restraints weight = 79321.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.026597 restraints weight = 46291.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2678 r_free = 0.2678 target = 0.027124 restraints weight = 32214.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.027491 restraints weight = 24955.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.027704 restraints weight = 20862.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.2692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.4285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7752  Z= 0.176
  Angle     :  0.623   6.018  10552  Z= 0.335
  Chirality :  0.039   0.136   1203
  Planarity :  0.004   0.045   1296
  Dihedral  : 17.026 168.114   1323
  Min Nonbonded Distance : 1.870

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  3.69 %
    Favored  : 95.33 %
  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 aren not related in a simple way.
  whole:  0.03 (0.27), residues: 921
  helix:  0.84 (0.25), residues: 408
  sheet: -0.84 (0.45), residues: 126
  loop : -0.44 (0.32), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 235 
 TYR   0.014   0.002   TYR B 301 
 PHE   0.012   0.002   PHE C 126 
 HIS   0.007   0.001   HIS B 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 7750)
  covalent geometry    : angle       0.62332 (10552)
  hydrogen bonds       : bond        0.03610 (  329)
  hydrogen bonds       : angle       4.83281 (  891)
  Misc. bond           : bond        0.00355 (    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
  39 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.284 
Fit side-chains
REVERT: A   46 PHE cc_start: 0.8592 (m-10) cc_final: 0.8276 (m-80)
REVERT: C   84 MET cc_start: 0.7842 (mtm) cc_final: 0.7630 (mtm)
REVERT: C  158 MET cc_start: 0.8361 (mtm) cc_final: 0.7745 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.0844
  time to fit residues: 4.8816
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  : 0.286 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 82 optimal weight:    9.9990
   chunk 59 optimal weight:   20.0000
   chunk 83 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9980
   chunk 48 optimal weight:    4.9990
   chunk 70 optimal weight:    8.9990
   chunk 84 optimal weight:    1.9990
   chunk 62 optimal weight:   20.0000
   chunk 14 optimal weight:   20.0000
   chunk 35 optimal weight:    8.9990
   overall best weight:    3.0786

-------------------------------------------------------------------------------
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 = 0.2885 r_free = 0.2885 target = 0.032085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2609 r_free = 0.2609 target = 0.025526 restraints weight = 79602.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2646 r_free = 0.2646 target = 0.026316 restraints weight = 46290.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2671 r_free = 0.2671 target = 0.026882 restraints weight = 31814.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.027267 restraints weight = 24377.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.027510 restraints weight = 20213.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.2689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.4716

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= 0.138
  Angle     :  0.568   6.402  10552  Z= 0.304
  Chirality :  0.038   0.134   1203
  Planarity :  0.004   0.048   1296
  Dihedral  : 16.911 170.591   1323
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  3.15 %
    Favored  : 95.87 %
  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 aren not related in a simple way.
  whole:  0.44 (0.28), residues: 921
  helix:  1.26 (0.25), residues: 408
  sheet: -0.44 (0.48), residues: 126
  loop : -0.40 (0.32), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 170 
 TYR   0.012   0.001   TYR A 216 
 PHE   0.010   0.002   PHE B 129 
 HIS   0.004   0.001   HIS B 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 7750)
  covalent geometry    : angle       0.56836 (10552)
  hydrogen bonds       : bond        0.03176 (  329)
  hydrogen bonds       : angle       4.46029 (  891)
  Misc. bond           : bond        0.00295 (    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
  41 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A   46 PHE cc_start: 0.8576 (m-10) cc_final: 0.8315 (m-80)
REVERT: C  125 MET cc_start: 0.8992 (mmm) cc_final: 0.8754 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0634
  time to fit residues: 4.1790
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  : 0.214 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 15 optimal weight:    9.9990
   chunk 80 optimal weight:    8.9990
   chunk 1 optimal weight:    9.9990
   chunk 6 optimal weight:   20.0000
   chunk 24 optimal weight:    3.9990
   chunk 44 optimal weight:   30.0000
   chunk 20 optimal weight:    0.8980
   chunk 42 optimal weight:   20.0000
   chunk 64 optimal weight:    9.9990
   chunk 79 optimal weight:    6.9990
   overall best weight:    4.3788

-------------------------------------------------------------------------------
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 = 0.2859 r_free = 0.2859 target = 0.031578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2572 r_free = 0.2572 target = 0.024980 restraints weight = 80035.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2611 r_free = 0.2611 target = 0.025755 restraints weight = 46633.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2636 r_free = 0.2636 target = 0.026309 restraints weight = 32066.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2653 r_free = 0.2653 target = 0.026695 restraints weight = 24612.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.026931 restraints weight = 20301.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.2655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.5126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7752  Z= 0.169
  Angle     :  0.607   6.964  10552  Z= 0.321
  Chirality :  0.038   0.149   1203
  Planarity :  0.004   0.056   1296
  Dihedral  : 16.616 169.415   1323
  Min Nonbonded Distance : 1.862

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.23 %
    Favored  : 94.79 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.48 (0.28), residues: 921
  helix:  1.40 (0.25), residues: 408
  sheet: -0.45 (0.49), residues: 126
  loop : -0.51 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 241 
 TYR   0.013   0.001   TYR B 315 
 PHE   0.013   0.002   PHE C  46 
 HIS   0.005   0.001   HIS B 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 7750)
  covalent geometry    : angle       0.60711 (10552)
  hydrogen bonds       : bond        0.03313 (  329)
  hydrogen bonds       : angle       4.49903 (  891)
  Misc. bond           : bond        0.00260 (    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
  38 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A   46 PHE cc_start: 0.8613 (m-10) cc_final: 0.8373 (m-80)
REVERT: A   84 MET cc_start: 0.8480 (mmp) cc_final: 0.6546 (ttt)
REVERT: A  125 MET cc_start: 0.9100 (mmm) cc_final: 0.8894 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.0632
  time to fit residues: 3.9005
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  : 0.276 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 58 optimal weight:    5.9990
   chunk 74 optimal weight:    0.6980
   chunk 39 optimal weight:    9.9990
   chunk 28 optimal weight:   20.0000
   chunk 46 optimal weight:   10.0000
   chunk 41 optimal weight:    4.9990
   chunk 13 optimal weight:   20.0000
   chunk 71 optimal weight:    9.9990
   overall best weight:    4.7388

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

Flipped N/Q/H residues before XYZ refinement:
C  93 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.031374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2564 r_free = 0.2564 target = 0.024852 restraints weight = 81411.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2602 r_free = 0.2602 target = 0.025613 restraints weight = 47694.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2627 r_free = 0.2627 target = 0.026147 restraints weight = 33016.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2644 r_free = 0.2644 target = 0.026534 restraints weight = 25335.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.026768 restraints weight = 21089.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.2646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.5355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7752  Z= 0.172
  Angle     :  0.609   6.476  10552  Z= 0.320
  Chirality :  0.039   0.152   1203
  Planarity :  0.004   0.049   1296
  Dihedral  : 16.458 167.827   1323
  Min Nonbonded Distance : 1.847

Molprobity Statistics.
  All-atom Clashscore : 11.31
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.27), residues: 921
  helix:  1.38 (0.25), residues: 408
  sheet: -0.93 (0.49), residues: 114
  loop : -0.44 (0.30), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 170 
 TYR   0.017   0.001   TYR B 216 
 PHE   0.008   0.002   PHE B 129 
 HIS   0.002   0.001   HIS B 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 7750)
  covalent geometry    : angle       0.60932 (10552)
  hydrogen bonds       : bond        0.03276 (  329)
  hydrogen bonds       : angle       4.44315 (  891)
  Misc. bond           : bond        0.00259 (    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
  37 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.300 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.0642
  time to fit residues: 3.8826
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  : 0.281 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 52 optimal weight:    7.9990
   chunk 43 optimal weight:    0.0970
   chunk 1 optimal weight:   10.0000
   chunk 22 optimal weight:    8.9990
   chunk 63 optimal weight:    8.9990
   chunk 7 optimal weight:   10.0000
   chunk 90 optimal weight:    7.9990
   chunk 75 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9990
   chunk 26 optimal weight:    8.9990
   overall best weight:    4.4186

-------------------------------------------------------------------------------
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 = 0.2853 r_free = 0.2853 target = 0.031473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2570 r_free = 0.2570 target = 0.024957 restraints weight = 79712.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2608 r_free = 0.2608 target = 0.025714 restraints weight = 47269.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2632 r_free = 0.2632 target = 0.026237 restraints weight = 32756.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.026640 restraints weight = 25151.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.026866 restraints weight = 20788.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.5558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7752  Z= 0.165
  Angle     :  0.617   7.152  10552  Z= 0.320
  Chirality :  0.039   0.151   1203
  Planarity :  0.004   0.050   1296
  Dihedral  : 16.084 169.014   1323
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 11.11
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.27), residues: 921
  helix:  1.35 (0.25), residues: 408
  sheet: -0.82 (0.49), residues: 111
  loop : -0.49 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 235 
 TYR   0.012   0.001   TYR A 216 
 PHE   0.008   0.002   PHE B 129 
 HIS   0.003   0.001   HIS A 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 7750)
  covalent geometry    : angle       0.61683 (10552)
  hydrogen bonds       : bond        0.03222 (  329)
  hydrogen bonds       : angle       4.44223 (  891)
  Misc. bond           : bond        0.00222 (    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
  40 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 MET cc_start: 0.8551 (mmp) cc_final: 0.6212 (ttt)
REVERT: C  125 MET cc_start: 0.8724 (mmm) cc_final: 0.8491 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.0710
  time to fit residues: 4.2934
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  : 0.287 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 38 optimal weight:   10.0000
   chunk 25 optimal weight:    8.9990
   chunk 66 optimal weight:    8.9990
   chunk 3 optimal weight:    0.9980
   chunk 73 optimal weight:    6.9990
   chunk 82 optimal weight:    0.4980
   chunk 37 optimal weight:    0.3980
   chunk 84 optimal weight:    5.9990
   chunk 90 optimal weight:    8.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    2.9784

-------------------------------------------------------------------------------
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  30 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.031759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2587 r_free = 0.2587 target = 0.025247 restraints weight = 79373.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2623 r_free = 0.2623 target = 0.026006 restraints weight = 46907.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2648 r_free = 0.2648 target = 0.026552 restraints weight = 32768.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2665 r_free = 0.2665 target = 0.026930 restraints weight = 25147.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2675 r_free = 0.2675 target = 0.027180 restraints weight = 20808.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.5699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7752  Z= 0.131
  Angle     :  0.582   6.676  10552  Z= 0.304
  Chirality :  0.039   0.147   1203
  Planarity :  0.004   0.048   1296
  Dihedral  : 15.983 173.659   1323
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.02 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  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 aren not related in a simple way.
  whole:  0.48 (0.27), residues: 921
  helix:  1.42 (0.25), residues: 408
  sheet: -0.62 (0.49), residues: 108
  loop : -0.48 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 170 
 TYR   0.014   0.001   TYR B 216 
 PHE   0.008   0.001   PHE A 129 
 HIS   0.003   0.001   HIS A 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 7750)
  covalent geometry    : angle       0.58161 (10552)
  hydrogen bonds       : bond        0.03062 (  329)
  hydrogen bonds       : angle       4.29524 (  891)
  Misc. bond           : bond        0.00496 (    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
  38 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 MET cc_start: 0.8488 (mmp) cc_final: 0.6235 (ttt)
REVERT: C  125 MET cc_start: 0.8782 (mmm) cc_final: 0.8494 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.0687
  time to fit residues: 4.1061
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  : 0.263 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 12 optimal weight:    6.9990
   chunk 73 optimal weight:    9.9990
   chunk 15 optimal weight:    7.9990
   chunk 6 optimal weight:    9.9990
   chunk 45 optimal weight:    7.9990
   chunk 72 optimal weight:    7.9990
   chunk 70 optimal weight:   10.0000
   chunk 38 optimal weight:    5.9990
   chunk 28 optimal weight:   20.0000
   overall best weight:    6.1990

-------------------------------------------------------------------------------
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**
B  93 HIS
** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 267 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.031269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2563 r_free = 0.2563 target = 0.024777 restraints weight = 80287.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2600 r_free = 0.2600 target = 0.025549 restraints weight = 47658.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2625 r_free = 0.2625 target = 0.026089 restraints weight = 32859.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.026464 restraints weight = 25244.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.026699 restraints weight = 20861.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.2641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.5871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   7752  Z= 0.215
  Angle     :  0.660   7.592  10552  Z= 0.343
  Chirality :  0.040   0.186   1203
  Planarity :  0.004   0.037   1296
  Dihedral  : 16.189 177.206   1323
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  5.65 %
    Favored  : 93.38 %
  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 aren not related in a simple way.
  whole:  0.19 (0.27), residues: 921
  helix:  1.22 (0.25), residues: 408
  sheet: -1.07 (0.50), residues: 111
  loop : -0.58 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 235 
 TYR   0.014   0.001   TYR B 216 
 PHE   0.008   0.002   PHE B 248 
 HIS   0.003   0.001   HIS C  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 7750)
  covalent geometry    : angle       0.65994 (10552)
  hydrogen bonds       : bond        0.03595 (  329)
  hydrogen bonds       : angle       4.55713 (  891)
  Misc. bond           : bond        0.00672 (    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
  34 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.285 
Fit side-chains
REVERT: A   31 CYS cc_start: 0.8067 (m) cc_final: 0.7666 (m)
REVERT: A  210 MET cc_start: 0.9297 (ttp) cc_final: 0.9085 (ptm)
REVERT: C  125 MET cc_start: 0.8760 (mmm) cc_final: 0.8517 (mmm)
REVERT: C  326 MET cc_start: 0.8613 (tmm) cc_final: 0.8383 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0617
  time to fit residues: 3.4559
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  : 0.279 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 3 optimal weight:    3.9990
   chunk 14 optimal weight:   20.0000
   chunk 35 optimal weight:    3.9990
   chunk 13 optimal weight:    9.9990
   chunk 15 optimal weight:    9.9990
   chunk 86 optimal weight:    6.9990
   chunk 77 optimal weight:    7.9990
   chunk 33 optimal weight:    7.9990
   chunk 30 optimal weight:    0.4980
   chunk 48 optimal weight:   10.0000
   overall best weight:    4.4988

-------------------------------------------------------------------------------
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 = 0.2856 r_free = 0.2856 target = 0.031524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2577 r_free = 0.2577 target = 0.024984 restraints weight = 82117.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2614 r_free = 0.2614 target = 0.025742 restraints weight = 48915.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2638 r_free = 0.2638 target = 0.026273 restraints weight = 34095.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.026651 restraints weight = 26379.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.026874 restraints weight = 21990.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.2660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.5955

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= 0.170
  Angle     :  0.637  11.996  10552  Z= 0.327
  Chirality :  0.040   0.168   1203
  Planarity :  0.003   0.036   1296
  Dihedral  : 16.218 177.397   1323
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.34 %
    Favored  : 94.68 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.19 (0.27), residues: 921
  helix:  1.26 (0.25), residues: 408
  sheet: -1.14 (0.50), residues: 108
  loop : -0.61 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 235 
 TYR   0.014   0.001   TYR B 216 
 PHE   0.008   0.002   PHE C 126 
 HIS   0.002   0.001   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 7750)
  covalent geometry    : angle       0.63734 (10552)
  hydrogen bonds       : bond        0.03287 (  329)
  hydrogen bonds       : angle       4.36791 (  891)
  Misc. bond           : bond        0.00577 (    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
  34 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 MET cc_start: 0.8744 (mmm) cc_final: 0.6415 (ttt)
REVERT: C  125 MET cc_start: 0.8711 (mmm) cc_final: 0.8482 (mmm)
REVERT: C  326 MET cc_start: 0.8581 (tmm) cc_final: 0.8343 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0656
  time to fit residues: 3.7413
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  : 0.225 
-------------------------------------------------------------------------------
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:    0.0770
   chunk 44 optimal weight:    5.9990
   chunk 82 optimal weight:    0.9980
   chunk 39 optimal weight:   20.0000
   chunk 37 optimal weight:    2.9990
   chunk 21 optimal weight:    9.9990
   chunk 16 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 20 optimal weight:   10.0000
   chunk 55 optimal weight:    6.9990
   chunk 43 optimal weight:   20.0000
   overall best weight:    1.5542

-------------------------------------------------------------------------------
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 = 0.2899 r_free = 0.2899 target = 0.032493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.025943 restraints weight = 80929.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2659 r_free = 0.2659 target = 0.026729 restraints weight = 47825.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2685 r_free = 0.2685 target = 0.027292 restraints weight = 33312.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.027641 restraints weight = 25695.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.027910 restraints weight = 21543.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.6105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7752  Z= 0.110
  Angle     :  0.583   8.940  10552  Z= 0.299
  Chirality :  0.039   0.131   1203
  Planarity :  0.003   0.034   1296
  Dihedral  : 16.013 175.298   1323
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  3.58 %
    Favored  : 95.44 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.48 (0.28), residues: 921
  helix:  1.43 (0.25), residues: 420
  sheet: -0.86 (0.53), residues: 108
  loop : -0.48 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 170 
 TYR   0.008   0.001   TYR C 301 
 PHE   0.010   0.001   PHE B 129 
 HIS   0.003   0.001   HIS A 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 7750)
  covalent geometry    : angle       0.58317 (10552)
  hydrogen bonds       : bond        0.02754 (  329)
  hydrogen bonds       : angle       4.03539 (  891)
  Misc. bond           : bond        0.00488 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1020.65 seconds
wall clock time: 18 minutes 34.44 seconds (1114.44 seconds total)