Starting phenix.real_space_refine
on Tue Sep 24 09:34:38 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1c_9567/09_2024/5h1c_9567.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1c_9567/09_2024/5h1c_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1c_9567/09_2024/5h1c_9567.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1c_9567/09_2024/5h1c_9567.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1c_9567/09_2024/5h1c_9567.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1c_9567/09_2024/5h1c_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-5461/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: 4.95, per 1000 atoms: 0.65
  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: 2.15
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 2.62
  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: 2.24

  Time building geometry restraints manager: 2.49 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:             1.040
  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:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.900
  Find NCS groups from input model:        0.340
  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:   27.450
-------------------------------------------------------------------------------
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      :  0.009   0.149   7750  Z= 0.553
  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 

*********************** 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 fitting.
    rotamer outliers: 33
    poor density    : 64
  time to evaluate  : 0.935 
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: 0.2767
  time to fit residues: 31.9385
Evaluate side-chains
  43 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 35
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6851
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   7750  Z= 0.275
  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 

*********************** 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 fitting.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 1.074 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.1866
  time to fit residues: 12.6923
Evaluate side-chains
  31 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 46 optimal weight:    9.9990
   chunk 26 optimal weight:    5.9990
   chunk 70 optimal weight:   20.0000
   chunk 57 optimal weight:   10.0000
   chunk 23 optimal weight:    6.9990
   chunk 84 optimal weight:    5.9990
   chunk 91 optimal weight:    6.9990
   chunk 75 optimal weight:   20.0000
   chunk 83 optimal weight:    8.9990
   chunk 28 optimal weight:   10.0000
   chunk 67 optimal weight:    3.9990
   overall best weight:    5.9990

-------------------------------------------------------------------------------
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**
A 196 ASN
** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 196 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6999
moved from start:          0.4601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   7750  Z= 0.314
  Angle     :  0.690   7.368  10552  Z= 0.365
  Chirality :  0.040   0.141   1203
  Planarity :  0.005   0.042   1296
  Dihedral  : 17.042 164.913   1323
  Min Nonbonded Distance : 1.825

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.23 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.22 (0.27), residues: 921
  helix:  0.65 (0.25), residues: 408
  sheet: -0.89 (0.46), residues: 126
  loop : -0.62 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B 294 
 PHE   0.010   0.002   PHE C 126 
 TYR   0.013   0.002   TYR A 315 
 ARG   0.007   0.001   ARG B 235 

*********************** 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 fitting.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.1730
  time to fit residues: 9.7750
Evaluate side-chains
  27 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 83 optimal weight:    9.9990
   chunk 63 optimal weight:   20.0000
   chunk 43 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   chunk 40 optimal weight:   10.0000
   chunk 56 optimal weight:   20.0000
   chunk 84 optimal weight:    7.9990
   chunk 89 optimal weight:    6.9990
   chunk 44 optimal weight:    9.9990
   chunk 80 optimal weight:   10.0000
   chunk 24 optimal weight:   10.0000
   overall best weight:    7.5990

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7067
moved from start:          0.5156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   7750  Z= 0.359
  Angle     :  0.703   6.275  10552  Z= 0.371
  Chirality :  0.040   0.139   1203
  Planarity :  0.005   0.045   1296
  Dihedral  : 16.832 165.658   1323
  Min Nonbonded Distance : 1.810

Molprobity Statistics.
  All-atom Clashscore : 13.84
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.13 %
    Favored  : 94.90 %
  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: -0.14 (0.26), residues: 921
  helix:  0.82 (0.24), residues: 408
  sheet: -0.65 (0.49), residues: 123
  loop : -0.80 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.011   0.002   HIS C 294 
 PHE   0.014   0.002   PHE A 259 
 TYR   0.024   0.002   TYR B 216 
 ARG   0.011   0.001   ARG B 235 

*********************** 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
  32 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.780 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.1597
  time to fit residues: 8.2661
Evaluate side-chains
  27 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 74 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 76 optimal weight:    8.9990
   chunk 62 optimal weight:   20.0000
   chunk 0 optimal weight:    5.9990
   chunk 45 optimal weight:   20.0000
   chunk 80 optimal weight:    8.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    2.5988

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6984
moved from start:          0.5278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7750  Z= 0.190
  Angle     :  0.572   6.839  10552  Z= 0.303
  Chirality :  0.038   0.140   1203
  Planarity :  0.004   0.050   1296
  Dihedral  : 16.498 162.919   1323
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.02 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.23 (0.27), residues: 921
  helix:  1.25 (0.25), residues: 408
  sheet: -0.92 (0.52), residues: 111
  loop : -0.60 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 294 
 PHE   0.013   0.002   PHE B  86 
 TYR   0.026   0.002   TYR B 216 
 ARG   0.002   0.000   ARG A 247 

*********************** 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
  35 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.860 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.1656
  time to fit residues: 9.4838
Evaluate side-chains
  29 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 1.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 30 optimal weight:   20.0000
   chunk 80 optimal weight:    1.9990
   chunk 17 optimal weight:    9.9990
   chunk 52 optimal weight:    8.9990
   chunk 22 optimal weight:    6.9990
   chunk 89 optimal weight:    5.9990
   chunk 74 optimal weight:    9.9990
   chunk 41 optimal weight:    8.9990
   chunk 7 optimal weight:   10.0000
   chunk 29 optimal weight:    0.0970
   chunk 47 optimal weight:   10.0000
   overall best weight:    4.8186

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7033
moved from start:          0.5509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   7750  Z= 0.255
  Angle     :  0.615   6.662  10552  Z= 0.323
  Chirality :  0.039   0.148   1203
  Planarity :  0.004   0.050   1296
  Dihedral  : 16.564 167.189   1323
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.89 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  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:  0.12 (0.26), residues: 921
  helix:  1.26 (0.25), residues: 408
  sheet: -1.27 (0.49), residues: 111
  loop : -0.69 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 294 
 PHE   0.009   0.002   PHE B  86 
 TYR   0.025   0.001   TYR B 216 
 ARG   0.003   0.000   ARG A 235 

*********************** 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 fitting.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.871 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 MET cc_start: 0.8264 (mmm) cc_final: 0.5872 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.1578
  time to fit residues: 9.1990
Evaluate side-chains
  29 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 86 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 51 optimal weight:    7.9990
   chunk 65 optimal weight:    8.9990
   chunk 50 optimal weight:    5.9990
   chunk 75 optimal weight:    8.9990
   chunk 89 optimal weight:    5.9990
   chunk 56 optimal weight:   10.0000
   chunk 54 optimal weight:    6.9990
   chunk 41 optimal weight:    6.9990
   chunk 55 optimal weight:    8.9990
   overall best weight:    5.5990

-------------------------------------------------------------------------------
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 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7046
moved from start:          0.5724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   7750  Z= 0.271
  Angle     :  0.643   7.435  10552  Z= 0.334
  Chirality :  0.040   0.150   1203
  Planarity :  0.004   0.042   1296
  Dihedral  : 16.788 173.810   1323
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.67 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  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:  0.03 (0.26), residues: 921
  helix:  1.25 (0.25), residues: 408
  sheet: -1.52 (0.48), residues: 114
  loop : -0.72 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 294 
 PHE   0.007   0.002   PHE A 248 
 TYR   0.024   0.002   TYR B 216 
 ARG   0.003   0.000   ARG A 235 

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

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 1.033 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.1792
  time to fit residues: 10.2819
Evaluate side-chains
  30 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 27 optimal weight:    7.9990
   chunk 17 optimal weight:    9.9990
   chunk 56 optimal weight:   10.0000
   chunk 61 optimal weight:   30.0000
   chunk 44 optimal weight:    1.9990
   chunk 8 optimal weight:   10.0000
   chunk 70 optimal weight:    9.9990
   chunk 81 optimal weight:    0.9980
   chunk 85 optimal weight:    7.9990
   overall best weight:    4.1988

-------------------------------------------------------------------------------
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 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7015
moved from start:          0.5853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7750  Z= 0.223
  Angle     :  0.604   6.582  10552  Z= 0.316
  Chirality :  0.039   0.181   1203
  Planarity :  0.003   0.036   1296
  Dihedral  : 16.450 171.532   1323
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.67 %
    Favored  : 94.35 %
  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:  0.10 (0.27), residues: 921
  helix:  1.34 (0.25), residues: 408
  sheet: -1.61 (0.48), residues: 114
  loop : -0.69 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 199 
 PHE   0.007   0.001   PHE B 129 
 TYR   0.017   0.001   TYR B 216 
 ARG   0.002   0.000   ARG C 170 

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

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

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

  1842 Ramachandran restraints generated.
    921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 MET cc_start: 0.5956 (mmp) cc_final: 0.5219 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.1592
  time to fit residues: 9.1906
Evaluate side-chains
  30 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:   20.0000
   chunk 83 optimal weight:   10.0000
   chunk 85 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 36 optimal weight:    6.9990
   chunk 65 optimal weight:    5.9990
   chunk 25 optimal weight:   20.0000
   chunk 75 optimal weight:    0.0970
   chunk 79 optimal weight:    8.9990
   chunk 54 optimal weight:    6.9990
   chunk 88 optimal weight:    5.9990
   overall best weight:    4.2186

-------------------------------------------------------------------------------
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 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7022
moved from start:          0.5967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7750  Z= 0.230
  Angle     :  0.617   7.275  10552  Z= 0.320
  Chirality :  0.039   0.166   1203
  Planarity :  0.003   0.035   1296
  Dihedral  : 16.102 172.521   1323
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.45 %
    Favored  : 94.57 %
  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:  0.16 (0.27), residues: 921
  helix:  1.46 (0.25), residues: 402
  sheet: -1.67 (0.48), residues: 114
  loop : -0.69 (0.28), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 199 
 PHE   0.027   0.002   PHE A 259 
 TYR   0.019   0.001   TYR B 216 
 ARG   0.002   0.000   ARG C 170 

*********************** 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
  37 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 MET cc_start: 0.6046 (mmp) cc_final: 0.5332 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.1832
  time to fit residues: 10.3477
Evaluate side-chains
  29 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 41 optimal weight:    7.9990
   chunk 61 optimal weight:    9.9990
   chunk 92 optimal weight:    6.9990
   chunk 85 optimal weight:    0.8980
   chunk 73 optimal weight:    4.9990
   chunk 7 optimal weight:    9.9990
   chunk 56 optimal weight:   20.0000
   chunk 45 optimal weight:   10.0000
   chunk 58 optimal weight:    3.9990
   chunk 78 optimal weight:    9.9990
   overall best weight:    3.7788

-------------------------------------------------------------------------------
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 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7008
moved from start:          0.6050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7750  Z= 0.218
  Angle     :  0.604  11.190  10552  Z= 0.314
  Chirality :  0.039   0.167   1203
  Planarity :  0.003   0.034   1296
  Dihedral  : 16.141 174.803   1323
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  4.78 %
    Favored  : 94.25 %
  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:  0.16 (0.27), residues: 921
  helix:  1.46 (0.25), residues: 402
  sheet: -1.75 (0.41), residues: 162
  loop : -0.42 (0.30), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 199 
 PHE   0.007   0.001   PHE A 248 
 TYR   0.018   0.001   TYR B 216 
 ARG   0.003   0.000   ARG C 310 

********************** 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
  35 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 MET cc_start: 0.5927 (mmp) cc_final: 0.5153 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.1743
  time to fit residues: 9.6887
Evaluate side-chains
  29 residues out of total 744 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 22 optimal weight:    7.9990
   chunk 68 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    7.9990
   chunk 73 optimal weight:    5.9990
   chunk 30 optimal weight:    7.9990
   chunk 75 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0470
   chunk 64 optimal weight:    2.9990
   chunk 4 optimal weight:   20.0000
   overall best weight:    1.8086

-------------------------------------------------------------------------------
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 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 = 0.2879 r_free = 0.2879 target = 0.032064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2605 r_free = 0.2605 target = 0.025497 restraints weight = 80950.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.026256 restraints weight = 48343.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2665 r_free = 0.2665 target = 0.026794 restraints weight = 34002.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.6169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7750  Z= 0.166
  Angle     :  0.598  10.340  10552  Z= 0.304
  Chirality :  0.039   0.131   1203
  Planarity :  0.003   0.033   1296
  Dihedral  : 16.078 175.826   1323
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  3.91 %
    Favored  : 95.11 %
  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:  0.26 (0.27), residues: 921
  helix:  1.40 (0.25), residues: 420
  sheet: -1.56 (0.50), residues: 111
  loop : -0.58 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 199 
 PHE   0.013   0.001   PHE B 259 
 TYR   0.014   0.001   TYR C 315 
 ARG   0.002   0.000   ARG B 310 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1284.90 seconds
wall clock time: 24 minutes 12.49 seconds (1452.49 seconds total)