Starting phenix.real_space_refine
on Sun May 11 12:51:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lgm_63068/05_2025/9lgm_63068.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lgm_63068/05_2025/9lgm_63068.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lgm_63068/05_2025/9lgm_63068.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lgm_63068/05_2025/9lgm_63068.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lgm_63068/05_2025/9lgm_63068.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lgm_63068/05_2025/9lgm_63068.cif"
  }
  resolution = 2.84
  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=   0.001 sd=   0.019
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: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    5107      2.51       5
     N    1395      2.21       5
     O    1509      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8061
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1919
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1919
          Classifications: {'peptide': 239}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 6, 'TRANS': 232}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 67
          Unresolved non-hydrogen angles: 75
          Unresolved non-hydrogen dihedrals: 59
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 32
    Chain: "B"
      Number of atoms: 2533
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2533
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 67
          Unresolved non-hydrogen angles: 79
          Unresolved non-hydrogen dihedrals: 55
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 8, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 55
    Chain: "C"
      Number of atoms: 393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 393
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 27
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "N"
      Number of atoms: 963
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 963
          Classifications: {'peptide': 127}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "R"
      Number of atoms: 2253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2253
          Classifications: {'peptide': 289}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 12, 'TRANS': 276}
          Unresolved non-hydrogen bonds: 89
          Unresolved non-hydrogen angles: 110
          Unresolved non-hydrogen dihedrals: 81
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 6, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 65
  Time building chain proxies: 4.62, per 1000 atoms: 0.57
  Number of scatterers: 8061
  At special positions: 0
  Unit cell: (75.92, 100.88, 131.04, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      50     16.00
     O    1509      8.00
     N    1395      7.00
     C    5107      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  90 " - pdb=" SG  CYS R 168 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.70
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1968

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 11 sheets defined
      44.5% alpha, 20.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 39
    Processing helix  chain 'A' and resid 52 through 60
      removed outlier: 3.514A  pdb=" N   MET A  60 " --> pdb=" O   ILE A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 238
      removed outlier: 3.510A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 269
    Processing helix  chain 'A' and resid 283 through 294
    Processing helix  chain 'A' and resid 297 through 302
      removed outlier: 4.175A  pdb=" N   TYR A 301 " --> pdb=" O   LYS A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 308
      removed outlier: 3.550A  pdb=" N   ALA A 306 " --> pdb=" O   PRO A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 342
      removed outlier: 3.502A  pdb=" N   PHE A 335 " --> pdb=" O   ILE A 331 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   SER A 342 " --> pdb=" O   ILE A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 381
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.501A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 7 through 24
      removed outlier: 3.600A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 45 through 48
    Processing helix  chain 'C' and resid 55 through 59
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.712A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 18 through 48
      removed outlier: 3.746A  pdb=" N   LEU R  32 " --> pdb=" O   ILE R  28 " (cutoff:3.500A)
      Proline residue:  R  33  - end of helix
    Processing helix  chain 'R' and resid 50 through 80
      removed outlier: 4.070A  pdb=" N   VAL R  54 " --> pdb=" O   ASN R  50 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   TYR R  55 " --> pdb=" O   GLU R  51 " (cutoff:3.500A)
      Proline residue:  R  71  - end of helix
    Processing helix  chain 'R' and resid 86 through 121
      removed outlier: 5.027A  pdb=" N   ILE R 101 " --> pdb=" O   PHE R  97 " (cutoff:3.500A)
      removed outlier: 5.072A  pdb=" N   TYR R 102 " --> pdb=" O   TYR R  98 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 130 through 150
    Processing helix  chain 'R' and resid 150 through 155
    Processing helix  chain 'R' and resid 155 through 163
    Processing helix  chain 'R' and resid 175 through 189
      removed outlier: 3.857A  pdb=" N   TRP R 180 " --> pdb=" O   GLY R 176 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 190 through 211
    Processing helix  chain 'R' and resid 215 through 254
      removed outlier: 3.777A  pdb=" N   VAL R 233 " --> pdb=" O   LEU R 229 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU R 234 " --> pdb=" O   ILE R 230 " (cutoff:3.500A)
      Proline residue:  R 239  - end of helix
    Processing helix  chain 'R' and resid 258 through 276
      removed outlier: 4.235A  pdb=" N   SER R 266 " --> pdb=" O   GLU R 262 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   ALA R 267 " --> pdb=" O   ARG R 263 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   SER R 276 " --> pdb=" O   LEU R 272 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 277 through 287
      Proline residue:  R 283  - end of helix
    Processing helix  chain 'R' and resid 290 through 300
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 4.482A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 7.644A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 9.443A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.690A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.199A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   PHE A 280 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 280 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   ASN A 282 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 282 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52
      removed outlier: 5.642A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.649A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.678A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.758A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.039A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.515A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 7.149A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.032A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 4.495A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.644A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.783A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.661A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12
      removed outlier: 6.865A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 18 through 19

    439 hydrogen bonds defined for protein.
    1254 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.29

  Time building geometry restraints manager: 2.02 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2664
        1.34 -     1.46: 1586
        1.46 -     1.58: 3921
        1.58 -     1.69: 0
        1.69 -     1.81: 67
  Bond restraints: 8238
  Sorted by residual:
  bond pdb=" C   LEU R  70 "
       pdb=" N   PRO R  71 "
    ideal  model  delta    sigma   weight residual
    1.335  1.359 -0.025 1.28e-02 6.10e+03 3.71e+00
  bond pdb=" C   VAL R 188 "
       pdb=" O   VAL R 188 "
    ideal  model  delta    sigma   weight residual
    1.242  1.230  0.012 1.17e-02 7.31e+03 1.12e+00
  bond pdb=" CB  GLU A 289 "
       pdb=" CG  GLU A 289 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.031 3.00e-02 1.11e+03 1.07e+00
  bond pdb=" CG  ARG A  38 "
       pdb=" CD  ARG A  38 "
    ideal  model  delta    sigma   weight residual
    1.520  1.489  0.031 3.00e-02 1.11e+03 1.05e+00
  bond pdb=" N   PHE R 169 "
       pdb=" CA  PHE R 169 "
    ideal  model  delta    sigma   weight residual
    1.457  1.469 -0.012 1.29e-02 6.01e+03 8.73e-01
  ... (remaining 8233 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 10996
        1.79 -     3.59: 160
        3.59 -     5.38: 36
        5.38 -     7.17: 11
        7.17 -     8.97: 1
  Bond angle restraints: 11204
  Sorted by residual:
  angle pdb=" C   HIS R  80 "
        pdb=" CA  HIS R  80 "
        pdb=" CB  HIS R  80 "
      ideal   model   delta    sigma   weight residual
     115.79  109.09    6.70 1.19e+00 7.06e-01 3.17e+01
  angle pdb=" N   VAL R 280 "
        pdb=" CA  VAL R 280 "
        pdb=" C   VAL R 280 "
      ideal   model   delta    sigma   weight residual
     111.81  108.32    3.49 8.60e-01 1.35e+00 1.65e+01
  angle pdb=" N   ILE A  62 "
        pdb=" CA  ILE A  62 "
        pdb=" C   ILE A  62 "
      ideal   model   delta    sigma   weight residual
     112.96  109.49    3.47 1.00e+00 1.00e+00 1.21e+01
  angle pdb=" N   ARG A  38 "
        pdb=" CA  ARG A  38 "
        pdb=" CB  ARG A  38 "
      ideal   model   delta    sigma   weight residual
     110.16  114.57   -4.41 1.48e+00 4.57e-01 8.87e+00
  angle pdb=" C   PHE R 169 "
        pdb=" CA  PHE R 169 "
        pdb=" CB  PHE R 169 "
      ideal   model   delta    sigma   weight residual
     110.42  115.64   -5.22 1.99e+00 2.53e-01 6.89e+00
  ... (remaining 11199 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 4251
       17.92 -    35.85: 420
       35.85 -    53.77: 137
       53.77 -    71.70: 30
       71.70 -    89.62: 10
  Dihedral angle restraints: 4848
    sinusoidal: 1798
      harmonic: 3050
  Sorted by residual:
  dihedral pdb=" CB  CYS R  90 "
           pdb=" SG  CYS R  90 "
           pdb=" SG  CYS R 168 "
           pdb=" CB  CYS R 168 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -175.62   89.62     1      1.00e+01 1.00e-02 9.54e+01
  dihedral pdb=" CA  TRP B  82 "
           pdb=" C   TRP B  82 "
           pdb=" N   ASP B  83 "
           pdb=" CA  ASP B  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.72   18.28     0      5.00e+00 4.00e-02 1.34e+01
  dihedral pdb=" CA  PHE B 151 "
           pdb=" C   PHE B 151 "
           pdb=" N   LEU B 152 "
           pdb=" CA  LEU B 152 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.08   17.92     0      5.00e+00 4.00e-02 1.28e+01
  ... (remaining 4845 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 814
       0.034 -    0.067: 310
       0.067 -    0.101: 106
       0.101 -    0.135: 35
       0.135 -    0.169: 1
  Chirality restraints: 1266
  Sorted by residual:
  chirality pdb=" CB  ILE R 232 "
            pdb=" CA  ILE R 232 "
            pdb=" CG1 ILE R 232 "
            pdb=" CG2 ILE R 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.81   -0.17 2.00e-01 2.50e+01 7.11e-01
  chirality pdb=" CA  ILE B 273 "
            pdb=" N   ILE B 273 "
            pdb=" C   ILE B 273 "
            pdb=" CB  ILE B 273 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.24e-01
  chirality pdb=" CA  PRO B 236 "
            pdb=" N   PRO B 236 "
            pdb=" C   PRO B 236 "
            pdb=" CB  PRO B 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.22e-01
  ... (remaining 1263 not shown)

  Planarity restraints: 1444
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.035 5.00e-02 4.00e+02   5.31e-02 4.50e+00
        pdb=" N   PRO B 236 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 196 "    0.011 2.00e-02 2.50e+03   2.11e-02 4.46e+00
        pdb=" C   THR B 196 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   THR B 196 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ARG B 197 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R 159 "   -0.005 2.00e-02 2.50e+03   1.32e-02 3.05e+00
        pdb=" CG  PHE R 159 "    0.027 2.00e-02 2.50e+03
        pdb=" CD1 PHE R 159 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE R 159 "   -0.017 2.00e-02 2.50e+03
        pdb=" CE1 PHE R 159 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE R 159 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE R 159 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1441 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 80
        2.60 -     3.18: 7063
        3.18 -     3.75: 13399
        3.75 -     4.33: 18867
        4.33 -     4.90: 30843
  Nonbonded interactions: 70252
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B 313 "
            pdb=" N   ARG B 314 "
     model   vdw
     2.028 3.120
  nonbonded pdb=" OD1 ASN A 269 "
            pdb=" OD2 ASP N 106 "
     model   vdw
     2.135 3.040
  nonbonded pdb=" NH2 ARG A 232 "
            pdb=" OD1 ASP B 228 "
     model   vdw
     2.162 3.120
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" CD1 ILE R 101 "
            pdb=" CG2 THR R 275 "
     model   vdw
     2.224 3.880
  ... (remaining 70247 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.900
  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:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     19.770
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  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:10.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
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      :  0.004   0.031   8239  Z= 0.176
  Angle     :  0.605   8.967  11206  Z= 0.327
  Chirality :  0.042   0.169   1266
  Planarity :  0.004   0.053   1444
  Dihedral  : 16.710  88.756   2877
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 13.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  : 26.43 %
    Favored  : 73.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.64 (0.27), residues: 1037
  helix:  1.91 (0.25), residues: 408
  sheet: -0.44 (0.35), residues: 231
  loop : -0.54 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 234 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.027   0.002   PHE R 159 
 TYR   0.009   0.001   TYR A 329 
 ARG   0.014   0.001   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18218 (  439)
  hydrogen bonds       : angle       6.52562 ( 1254)
  SS BOND              : bond        0.00048 (    1)
  SS BOND              : angle       0.74864 (    2)
  covalent geometry    : bond        0.00398 ( 8238)
  covalent geometry    : angle       0.60544 (11204)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 183
  time to evaluate  : 0.796 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.7101 (mpp80) cc_final: 0.6771 (mpp80)
REVERT: A  252 ASP cc_start: 0.8095 (t70) cc_final: 0.7834 (t70)
REVERT: A  312 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6911 (mm-30)
REVERT: R  209 ARG cc_start: 0.8064 (ttp80) cc_final: 0.7497 (ttp80)
REVERT: R  277 LEU cc_start: 0.8190 (mm) cc_final: 0.7892 (mt)
  outliers start: 2
  outliers final: 6
  residues processed: 185
  average time/residue: 1.2209
  time to fit residues: 238.5377
Evaluate side-chains
  179 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 173
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  313 ASN
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain R residue  101 ILE
Chi-restraints excluded: chain R residue  250 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 79 optimal weight:    0.3980
   chunk 30 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 91 optimal weight:    0.1980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 220 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 295 ASN
R  58 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.124510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.109185 restraints weight = 11301.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 1.74
r_work: 0.3276 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3131 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.1039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   8239  Z= 0.215
  Angle     :  0.582   6.805  11206  Z= 0.309
  Chirality :  0.044   0.164   1266
  Planarity :  0.004   0.054   1444
  Dihedral  :  5.295  53.805   1149
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 21.31 %
    Favored  : 73.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.68 (0.26), residues: 1037
  helix:  2.06 (0.25), residues: 413
  sheet: -0.74 (0.32), residues: 229
  loop : -0.46 (0.32), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 234 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.016   0.002   PHE R 107 
 TYR   0.014   0.001   TYR A 329 
 ARG   0.007   0.001   ARG A 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04825 (  439)
  hydrogen bonds       : angle       4.91756 ( 1254)
  SS BOND              : bond        0.00161 (    1)
  SS BOND              : angle       0.54413 (    2)
  covalent geometry    : bond        0.00500 ( 8238)
  covalent geometry    : angle       0.58219 (11204)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 204
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7275 (mp-120)
REVERT: A   34 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8186 (tttp)
REVERT: A  269 ASN cc_start: 0.8355 (t0) cc_final: 0.8074 (t160)
REVERT: A  312 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7217 (mm-30)
REVERT: A  368 ASP cc_start: 0.7986 (m-30) cc_final: 0.7755 (m-30)
REVERT: A  370 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7513 (ttp80)
REVERT: B   59 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.6888 (m-80)
REVERT: B  215 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6777 (mp0)
REVERT: N   39 GLN cc_start: 0.8616 (tt0) cc_final: 0.8332 (tp40)
REVERT: N  108 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.7209 (m-80)
REVERT: R   49 ARG cc_start: 0.7747 (mmp-170) cc_final: 0.7372 (mmp-170)
REVERT: R  174 MET cc_start: 0.6972 (tpt) cc_final: 0.6614 (mmm)
REVERT: R  209 ARG cc_start: 0.8398 (ttp80) cc_final: 0.7911 (ttp80)
REVERT: R  277 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8040 (mt)
  outliers start: 43
  outliers final: 16
  residues processed: 228
  average time/residue: 1.2098
  time to fit residues: 291.5355
Evaluate side-chains
  219 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 196
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  370 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain R residue   57 MET
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue  130 ARG
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  244 LEU
Chi-restraints excluded: chain R residue  275 THR
Chi-restraints excluded: chain R residue  277 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 59 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 84 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN
B 220 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.124694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.109720 restraints weight = 11439.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3400 rms_B_bonded: 1.64
r_work: 0.3294 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3157 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.1322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8239  Z= 0.188
  Angle     :  0.550   6.765  11206  Z= 0.291
  Chirality :  0.043   0.138   1266
  Planarity :  0.004   0.053   1444
  Dihedral  :  4.853  50.510   1141
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  6.07 %
    Allowed  : 21.19 %
    Favored  : 72.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.78 (0.26), residues: 1037
  helix:  2.13 (0.25), residues: 414
  sheet: -0.65 (0.33), residues: 226
  loop : -0.42 (0.32), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 234 
 HIS   0.010   0.001   HIS A 220 
 PHE   0.018   0.002   PHE R 159 
 TYR   0.016   0.001   TYR A 329 
 ARG   0.008   0.001   ARG A 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04328 (  439)
  hydrogen bonds       : angle       4.75779 ( 1254)
  SS BOND              : bond        0.00164 (    1)
  SS BOND              : angle       0.51461 (    2)
  covalent geometry    : bond        0.00440 ( 8238)
  covalent geometry    : angle       0.54997 (11204)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 203
  time to evaluate  : 0.880 
Fit side-chains
REVERT: A   31 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7344 (mp-120)
REVERT: A   34 LYS cc_start: 0.8428 (tptm) cc_final: 0.7286 (tttm)
REVERT: A  223 ASP cc_start: 0.8070 (t0) cc_final: 0.7769 (t70)
REVERT: A  269 ASN cc_start: 0.8332 (t0) cc_final: 0.8064 (t160)
REVERT: A  312 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7130 (mm-30)
REVERT: A  320 GLU cc_start: 0.8157 (tt0) cc_final: 0.7783 (tt0)
REVERT: A  328 LYS cc_start: 0.8336 (mtpt) cc_final: 0.8057 (mtmm)
REVERT: B   10 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7042 (tm-30)
REVERT: B   15 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7672 (mptp)
REVERT: B   59 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.7129 (m-80)
REVERT: B  215 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6827 (mp0)
REVERT: B  336 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8191 (mt)
REVERT: N  108 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.7174 (m-80)
REVERT: R  174 MET cc_start: 0.6908 (tpt) cc_final: 0.6618 (mmm)
REVERT: R  209 ARG cc_start: 0.8357 (ttp80) cc_final: 0.7903 (ttp80)
REVERT: R  277 LEU cc_start: 0.8283 (mm) cc_final: 0.8023 (mt)
  outliers start: 51
  outliers final: 23
  residues processed: 232
  average time/residue: 1.2155
  time to fit residues: 297.8430
Evaluate side-chains
  235 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 205
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ASP
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain R residue   51 GLU
Chi-restraints excluded: chain R residue   57 MET
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue  101 ILE
Chi-restraints excluded: chain R residue  130 ARG
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  275 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 79 optimal weight:    0.6980
   chunk 92 optimal weight:    0.5980
   chunk 63 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0980
   chunk 32 optimal weight:    1.9990
   chunk 75 optimal weight:    0.5980
   chunk 72 optimal weight:    0.6980
   chunk 27 optimal weight:    0.3980
   chunk 59 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 284 GLN
** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 220 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
N  31 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.125531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.110586 restraints weight = 11483.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 1.65
r_work: 0.3295 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.1557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8239  Z= 0.147
  Angle     :  0.530   6.735  11206  Z= 0.282
  Chirality :  0.041   0.132   1266
  Planarity :  0.004   0.052   1444
  Dihedral  :  4.712  46.981   1141
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  6.07 %
    Allowed  : 22.38 %
    Favored  : 71.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.85 (0.27), residues: 1037
  helix:  2.24 (0.25), residues: 413
  sheet: -0.67 (0.34), residues: 218
  loop : -0.41 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 234 
 HIS   0.009   0.001   HIS A 220 
 PHE   0.018   0.001   PHE R 159 
 TYR   0.016   0.001   TYR R 268 
 ARG   0.008   0.001   ARG R 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03976 (  439)
  hydrogen bonds       : angle       4.60525 ( 1254)
  SS BOND              : bond        0.00072 (    1)
  SS BOND              : angle       0.27383 (    2)
  covalent geometry    : bond        0.00340 ( 8238)
  covalent geometry    : angle       0.52957 (11204)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 199
  time to evaluate  : 0.901 
Fit side-chains
REVERT: A   31 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7253 (mp-120)
REVERT: A  223 ASP cc_start: 0.8071 (t0) cc_final: 0.7764 (t70)
REVERT: A  283 LYS cc_start: 0.8138 (mttt) cc_final: 0.7894 (mttt)
REVERT: A  312 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7132 (mm-30)
REVERT: A  328 LYS cc_start: 0.8327 (mtpt) cc_final: 0.8031 (mtmm)
REVERT: A  358 ASP cc_start: 0.8045 (t70) cc_final: 0.7768 (t0)
REVERT: B   15 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7656 (mptp)
REVERT: B   59 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.7078 (m-80)
REVERT: B  215 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6654 (mp0)
REVERT: B  336 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8153 (mt)
REVERT: N   39 GLN cc_start: 0.8553 (tt0) cc_final: 0.8299 (tp40)
REVERT: R   49 ARG cc_start: 0.7770 (mmp-170) cc_final: 0.7543 (mmp-170)
REVERT: R  170 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6598 (tm-30)
REVERT: R  174 MET cc_start: 0.6819 (tpt) cc_final: 0.6253 (mmm)
  outliers start: 51
  outliers final: 26
  residues processed: 223
  average time/residue: 1.2185
  time to fit residues: 287.0508
Evaluate side-chains
  232 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 200
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue   51 GLU
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   77 PHE
Chi-restraints excluded: chain R residue  101 ILE
Chi-restraints excluded: chain R residue  130 ARG
Chi-restraints excluded: chain R residue  170 GLU
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  272 LEU
Chi-restraints excluded: chain R residue  275 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 93 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 91 optimal weight:    0.7980
   chunk 73 optimal weight:    0.0020
   chunk 8 optimal weight:    0.6980
   chunk 90 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.6188

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
N  31 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.125194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.110034 restraints weight = 11341.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 1.69
r_work: 0.3292 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3152 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.1666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8239  Z= 0.169
  Angle     :  0.537   6.728  11206  Z= 0.283
  Chirality :  0.042   0.133   1266
  Planarity :  0.004   0.053   1444
  Dihedral  :  4.700  46.487   1141
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  5.95 %
    Allowed  : 23.21 %
    Favored  : 70.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.86 (0.27), residues: 1037
  helix:  2.24 (0.25), residues: 413
  sheet: -0.65 (0.34), residues: 218
  loop : -0.42 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 234 
 HIS   0.010   0.001   HIS A 220 
 PHE   0.024   0.002   PHE R 159 
 TYR   0.027   0.002   TYR R 268 
 ARG   0.005   0.000   ARG A 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03995 (  439)
  hydrogen bonds       : angle       4.55598 ( 1254)
  SS BOND              : bond        0.00105 (    1)
  SS BOND              : angle       0.31005 (    2)
  covalent geometry    : bond        0.00395 ( 8238)
  covalent geometry    : angle       0.53744 (11204)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 198
  time to evaluate  : 0.809 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7322 (mp-120)
REVERT: A  223 ASP cc_start: 0.8089 (t0) cc_final: 0.7798 (t70)
REVERT: A  283 LYS cc_start: 0.8164 (mttt) cc_final: 0.7911 (mttt)
REVERT: A  312 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7127 (mm-30)
REVERT: A  328 LYS cc_start: 0.8327 (mtpt) cc_final: 0.8021 (mtmm)
REVERT: A  358 ASP cc_start: 0.8035 (t70) cc_final: 0.7738 (t0)
REVERT: B   10 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6993 (tm-30)
REVERT: B   15 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7677 (mptp)
REVERT: B   57 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8442 (pttt)
REVERT: B   59 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.6884 (m-80)
REVERT: B   75 GLN cc_start: 0.8396 (mm-40) cc_final: 0.7837 (tp40)
REVERT: B  212 ASP cc_start: 0.8098 (t70) cc_final: 0.7076 (t70)
REVERT: B  215 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6784 (mp0)
REVERT: B  251 ARG cc_start: 0.8687 (mtt90) cc_final: 0.8457 (mtt180)
REVERT: B  336 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8284 (mt)
REVERT: N   39 GLN cc_start: 0.8576 (tt0) cc_final: 0.8326 (tp40)
REVERT: N  108 PHE cc_start: 0.7720 (OUTLIER) cc_final: 0.7367 (m-80)
REVERT: R  170 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6583 (tm-30)
  outliers start: 50
  outliers final: 25
  residues processed: 227
  average time/residue: 1.1865
  time to fit residues: 284.3333
Evaluate side-chains
  225 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 191
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue   51 GLU
Chi-restraints excluded: chain R residue   57 MET
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   77 PHE
Chi-restraints excluded: chain R residue  101 ILE
Chi-restraints excluded: chain R residue  130 ARG
Chi-restraints excluded: chain R residue  170 GLU
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  272 LEU
Chi-restraints excluded: chain R residue  275 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 57 optimal weight:    0.7980
   chunk 91 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   chunk 96 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 347 HIS
B 220 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN
R 290 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.124476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.109269 restraints weight = 11282.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 1.68
r_work: 0.3285 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3146 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.1733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8239  Z= 0.198
  Angle     :  0.556   6.748  11206  Z= 0.294
  Chirality :  0.043   0.138   1266
  Planarity :  0.004   0.053   1444
  Dihedral  :  4.752  45.179   1141
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  6.31 %
    Allowed  : 23.33 %
    Favored  : 70.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.81 (0.27), residues: 1037
  helix:  2.21 (0.25), residues: 413
  sheet: -0.76 (0.34), residues: 220
  loop : -0.41 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 234 
 HIS   0.009   0.001   HIS A 220 
 PHE   0.020   0.002   PHE R 159 
 TYR   0.025   0.002   TYR R 268 
 ARG   0.006   0.000   ARG A 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04087 (  439)
  hydrogen bonds       : angle       4.59434 ( 1254)
  SS BOND              : bond        0.00143 (    1)
  SS BOND              : angle       0.26794 (    2)
  covalent geometry    : bond        0.00464 ( 8238)
  covalent geometry    : angle       0.55605 (11204)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 198
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7343 (mp-120)
REVERT: A   34 LYS cc_start: 0.8475 (tttm) cc_final: 0.8175 (tttm)
REVERT: A  223 ASP cc_start: 0.8098 (t0) cc_final: 0.7791 (t70)
REVERT: A  312 GLU cc_start: 0.7360 (mm-30) cc_final: 0.7098 (mm-30)
REVERT: A  328 LYS cc_start: 0.8345 (mtpt) cc_final: 0.8034 (mtmm)
REVERT: A  358 ASP cc_start: 0.8055 (t70) cc_final: 0.7749 (t0)
REVERT: B   10 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.6996 (tm-30)
REVERT: B   15 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7667 (mptp)
REVERT: B   57 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8413 (pttt)
REVERT: B   59 TYR cc_start: 0.8446 (OUTLIER) cc_final: 0.6927 (m-80)
REVERT: B   75 GLN cc_start: 0.8437 (mm-40) cc_final: 0.7862 (tp40)
REVERT: B  212 ASP cc_start: 0.8115 (t70) cc_final: 0.7111 (t70)
REVERT: B  215 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6806 (mp0)
REVERT: B  336 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8278 (mt)
REVERT: N  108 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.7351 (m-80)
REVERT: R  170 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6600 (tm-30)
  outliers start: 53
  outliers final: 27
  residues processed: 229
  average time/residue: 1.1925
  time to fit residues: 288.3076
Evaluate side-chains
  229 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 193
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue   51 GLU
Chi-restraints excluded: chain R residue   57 MET
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   77 PHE
Chi-restraints excluded: chain R residue  101 ILE
Chi-restraints excluded: chain R residue  130 ARG
Chi-restraints excluded: chain R residue  170 GLU
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  272 LEU
Chi-restraints excluded: chain R residue  275 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.5980
   chunk 7 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 68 optimal weight:    0.8980
   chunk 88 optimal weight:    0.9980
   chunk 92 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 96 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 347 HIS
B 220 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.124470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.109582 restraints weight = 11366.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 1.64
r_work: 0.3287 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3150 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8239  Z= 0.194
  Angle     :  0.557   7.989  11206  Z= 0.293
  Chirality :  0.042   0.138   1266
  Planarity :  0.004   0.053   1444
  Dihedral  :  4.742  44.226   1141
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 24.40 %
    Favored  : 70.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.75 (0.27), residues: 1037
  helix:  2.10 (0.25), residues: 416
  sheet: -0.78 (0.34), residues: 220
  loop : -0.38 (0.33), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 234 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.025   0.002   PHE R 159 
 TYR   0.023   0.002   TYR R 268 
 ARG   0.006   0.000   ARG A 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04060 (  439)
  hydrogen bonds       : angle       4.58895 ( 1254)
  SS BOND              : bond        0.00097 (    1)
  SS BOND              : angle       0.31736 (    2)
  covalent geometry    : bond        0.00457 ( 8238)
  covalent geometry    : angle       0.55728 (11204)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 196
  time to evaluate  : 0.808 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7364 (mp-120)
REVERT: A   34 LYS cc_start: 0.8499 (tttm) cc_final: 0.8211 (tttm)
REVERT: A  223 ASP cc_start: 0.8064 (t0) cc_final: 0.7764 (t70)
REVERT: A  283 LYS cc_start: 0.8221 (mttt) cc_final: 0.7884 (mtpt)
REVERT: A  312 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7094 (mm-30)
REVERT: A  328 LYS cc_start: 0.8352 (mtpt) cc_final: 0.8041 (mtmm)
REVERT: A  358 ASP cc_start: 0.8013 (t70) cc_final: 0.7720 (t0)
REVERT: B   10 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7023 (tm-30)
REVERT: B   15 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7657 (mptp)
REVERT: B   59 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.6898 (m-80)
REVERT: B   75 GLN cc_start: 0.8431 (mm-40) cc_final: 0.7846 (tp40)
REVERT: B  215 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6655 (mp0)
REVERT: B  336 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8303 (mt)
REVERT: N   39 GLN cc_start: 0.8590 (tt0) cc_final: 0.8356 (tp40)
REVERT: N  108 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.7487 (m-80)
  outliers start: 47
  outliers final: 25
  residues processed: 220
  average time/residue: 1.2402
  time to fit residues: 287.6259
Evaluate side-chains
  226 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 194
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue   51 GLU
Chi-restraints excluded: chain R residue   57 MET
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   77 PHE
Chi-restraints excluded: chain R residue  101 ILE
Chi-restraints excluded: chain R residue  130 ARG
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  272 LEU
Chi-restraints excluded: chain R residue  275 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 46 optimal weight:    0.1980
   chunk 76 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 64 optimal weight:    0.8980
   chunk 68 optimal weight:    0.6980
   chunk 72 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   chunk 83 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 347 HIS
B  88 ASN
B 220 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
N  31 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.125199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.110298 restraints weight = 11479.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 1.65
r_work: 0.3295 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.1857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8239  Z= 0.164
  Angle     :  0.547   8.356  11206  Z= 0.288
  Chirality :  0.042   0.133   1266
  Planarity :  0.004   0.051   1444
  Dihedral  :  4.661  43.236   1141
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 24.52 %
    Favored  : 69.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.80 (0.27), residues: 1037
  helix:  2.17 (0.25), residues: 416
  sheet: -0.76 (0.34), residues: 220
  loop : -0.38 (0.33), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 234 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.016   0.002   PHE R 159 
 TYR   0.022   0.002   TYR R 268 
 ARG   0.006   0.000   ARG A 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03923 (  439)
  hydrogen bonds       : angle       4.52978 ( 1254)
  SS BOND              : bond        0.00076 (    1)
  SS BOND              : angle       0.07707 (    2)
  covalent geometry    : bond        0.00385 ( 8238)
  covalent geometry    : angle       0.54690 (11204)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 193
  time to evaluate  : 0.850 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7434 (mp-120)
REVERT: A   34 LYS cc_start: 0.8503 (tttm) cc_final: 0.8224 (tttm)
REVERT: A  223 ASP cc_start: 0.8080 (t0) cc_final: 0.7750 (t70)
REVERT: A  245 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8137 (mp)
REVERT: A  312 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7095 (mm-30)
REVERT: A  328 LYS cc_start: 0.8330 (mtpt) cc_final: 0.8019 (mtmm)
REVERT: A  358 ASP cc_start: 0.8028 (t70) cc_final: 0.7721 (t0)
REVERT: B   10 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7041 (tm-30)
REVERT: B   15 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7665 (mptp)
REVERT: B   59 TYR cc_start: 0.8442 (OUTLIER) cc_final: 0.6907 (m-80)
REVERT: B   75 GLN cc_start: 0.8444 (mm-40) cc_final: 0.7857 (tp40)
REVERT: B  212 ASP cc_start: 0.8061 (t70) cc_final: 0.6999 (t70)
REVERT: B  215 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6631 (mp0)
REVERT: B  258 ASP cc_start: 0.7538 (t0) cc_final: 0.7167 (t0)
REVERT: B  336 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8283 (mt)
REVERT: N   39 GLN cc_start: 0.8581 (tt0) cc_final: 0.8365 (tp40)
REVERT: N  108 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.7167 (m-80)
REVERT: R  170 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6678 (tm-30)
REVERT: R  174 MET cc_start: 0.6624 (mmt) cc_final: 0.6297 (mmm)
REVERT: R  232 ILE cc_start: 0.8391 (tt) cc_final: 0.8181 (tt)
  outliers start: 47
  outliers final: 24
  residues processed: 217
  average time/residue: 1.2826
  time to fit residues: 293.8836
Evaluate side-chains
  220 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 187
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue   51 GLU
Chi-restraints excluded: chain R residue   57 MET
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   77 PHE
Chi-restraints excluded: chain R residue  101 ILE
Chi-restraints excluded: chain R residue  130 ARG
Chi-restraints excluded: chain R residue  170 GLU
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  272 LEU
Chi-restraints excluded: chain R residue  275 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 95 optimal weight:    0.9980
   chunk 54 optimal weight:    0.8980
   chunk 62 optimal weight:    0.2980
   chunk 5 optimal weight:    0.5980
   chunk 99 optimal weight:    0.6980
   chunk 97 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9980
   chunk 88 optimal weight:    5.9990
   chunk 73 optimal weight:    0.0980
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN
R  85 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.125460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.110662 restraints weight = 11616.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 1.67
r_work: 0.3300 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8239  Z= 0.147
  Angle     :  0.533   6.671  11206  Z= 0.282
  Chirality :  0.041   0.128   1266
  Planarity :  0.004   0.051   1444
  Dihedral  :  4.580  41.801   1141
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 24.52 %
    Favored  : 69.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.86 (0.27), residues: 1037
  helix:  2.24 (0.25), residues: 416
  sheet: -0.73 (0.34), residues: 220
  loop : -0.38 (0.33), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 234 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.025   0.002   PHE R 159 
 TYR   0.020   0.001   TYR R 268 
 ARG   0.006   0.000   ARG A 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03818 (  439)
  hydrogen bonds       : angle       4.48456 ( 1254)
  SS BOND              : bond        0.00008 (    1)
  SS BOND              : angle       0.57993 (    2)
  covalent geometry    : bond        0.00341 ( 8238)
  covalent geometry    : angle       0.53345 (11204)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 196
  time to evaluate  : 0.991 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7425 (mp-120)
REVERT: A   33 ASP cc_start: 0.7757 (t0) cc_final: 0.7460 (t0)
REVERT: A   34 LYS cc_start: 0.8536 (tttm) cc_final: 0.8238 (tttm)
REVERT: A  223 ASP cc_start: 0.8100 (t0) cc_final: 0.7770 (t70)
REVERT: A  245 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8139 (mp)
REVERT: A  312 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7089 (mm-30)
REVERT: A  328 LYS cc_start: 0.8347 (mtpt) cc_final: 0.8032 (mtmm)
REVERT: A  358 ASP cc_start: 0.7996 (t70) cc_final: 0.7708 (t0)
REVERT: B   10 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7062 (tm-30)
REVERT: B   15 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7691 (mptp)
REVERT: B   59 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.6935 (m-80)
REVERT: B   75 GLN cc_start: 0.8432 (mm-40) cc_final: 0.7847 (tp40)
REVERT: B  215 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6635 (mp0)
REVERT: B  258 ASP cc_start: 0.7545 (t0) cc_final: 0.7214 (t0)
REVERT: B  336 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8308 (mt)
REVERT: N   39 GLN cc_start: 0.8578 (tt0) cc_final: 0.8375 (tp40)
REVERT: R  170 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6621 (tm-30)
REVERT: R  174 MET cc_start: 0.6652 (mmt) cc_final: 0.6351 (mmm)
REVERT: R  232 ILE cc_start: 0.8386 (tt) cc_final: 0.8186 (tt)
  outliers start: 47
  outliers final: 27
  residues processed: 221
  average time/residue: 1.2302
  time to fit residues: 287.2130
Evaluate side-chains
  231 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 196
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue   51 GLU
Chi-restraints excluded: chain R residue   57 MET
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   77 PHE
Chi-restraints excluded: chain R residue  101 ILE
Chi-restraints excluded: chain R residue  130 ARG
Chi-restraints excluded: chain R residue  170 GLU
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  250 ILE
Chi-restraints excluded: chain R residue  272 LEU
Chi-restraints excluded: chain R residue  275 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 82 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   chunk 67 optimal weight:    0.5980
   chunk 64 optimal weight:    0.6980
   chunk 4 optimal weight:    0.1980
   chunk 78 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0870
   chunk 89 optimal weight:    2.9990
   chunk 73 optimal weight:    0.0370
   chunk 3 optimal weight:    0.4980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.2836

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
B 295 ASN
N  31 ASN
R 290 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.127007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.112265 restraints weight = 11369.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3433 rms_B_bonded: 1.68
r_work: 0.3327 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3192 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.2137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   8239  Z= 0.122
  Angle     :  0.531   9.100  11206  Z= 0.277
  Chirality :  0.041   0.152   1266
  Planarity :  0.004   0.050   1444
  Dihedral  :  4.458  40.211   1141
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 25.71 %
    Favored  : 69.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.96 (0.27), residues: 1037
  helix:  2.35 (0.25), residues: 415
  sheet: -0.62 (0.33), residues: 220
  loop : -0.39 (0.33), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 234 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.014   0.001   PHE R 159 
 TYR   0.016   0.001   TYR A 329 
 ARG   0.006   0.000   ARG A 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03636 (  439)
  hydrogen bonds       : angle       4.40576 ( 1254)
  SS BOND              : bond        0.00037 (    1)
  SS BOND              : angle       0.41884 (    2)
  covalent geometry    : bond        0.00284 ( 8238)
  covalent geometry    : angle       0.53058 (11204)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 203
  time to evaluate  : 0.905 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7424 (mp-120)
REVERT: A   33 ASP cc_start: 0.7793 (t0) cc_final: 0.7444 (t0)
REVERT: A   34 LYS cc_start: 0.8516 (tttm) cc_final: 0.8208 (tttm)
REVERT: A  223 ASP cc_start: 0.8059 (t0) cc_final: 0.7722 (t70)
REVERT: A  229 ASP cc_start: 0.7714 (p0) cc_final: 0.7496 (p0)
REVERT: A  245 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8111 (mp)
REVERT: A  312 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7118 (mm-30)
REVERT: A  334 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7573 (OUTLIER)
REVERT: A  358 ASP cc_start: 0.7992 (t70) cc_final: 0.7733 (t0)
REVERT: B   10 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7083 (tm-30)
REVERT: B   15 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7647 (mptp)
REVERT: B   59 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.6879 (m-80)
REVERT: B   75 GLN cc_start: 0.8388 (mm-40) cc_final: 0.7839 (tp40)
REVERT: B  186 ASP cc_start: 0.6935 (m-30) cc_final: 0.6593 (t0)
REVERT: B  212 ASP cc_start: 0.8011 (t70) cc_final: 0.7353 (t70)
REVERT: B  215 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6734 (mp0)
REVERT: B  251 ARG cc_start: 0.8536 (mtt90) cc_final: 0.8279 (mtt180)
REVERT: B  285 LEU cc_start: 0.8448 (tp) cc_final: 0.8246 (tp)
REVERT: B  313 ASN cc_start: 0.8639 (t0) cc_final: 0.8260 (t0)
REVERT: B  336 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8285 (mt)
REVERT: R  170 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6485 (tm-30)
REVERT: R  174 MET cc_start: 0.6600 (mmt) cc_final: 0.6251 (mmt)
REVERT: R  232 ILE cc_start: 0.8385 (tt) cc_final: 0.8185 (tt)
  outliers start: 38
  outliers final: 22
  residues processed: 226
  average time/residue: 1.1937
  time to fit residues: 285.0938
Evaluate side-chains
  227 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 198
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue   51 GLU
Chi-restraints excluded: chain R residue   57 MET
Chi-restraints excluded: chain R residue   77 PHE
Chi-restraints excluded: chain R residue  101 ILE
Chi-restraints excluded: chain R residue  130 ARG
Chi-restraints excluded: chain R residue  170 GLU
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  275 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 81 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 77 optimal weight:    0.7980
   chunk 92 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 93 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 347 HIS
** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  13 GLN
B  17 GLN
B 125 ASN
B 220 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
B 239 ASN
B 259 GLN
B 266 HIS
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN
R 290 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.124645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.109705 restraints weight = 11465.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 1.69
r_work: 0.3285 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3145 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.2005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.089   8239  Z= 0.212
  Angle     :  0.586  10.082  11206  Z= 0.307
  Chirality :  0.044   0.148   1266
  Planarity :  0.004   0.054   1444
  Dihedral  :  4.409  35.274   1139
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 25.95 %
    Favored  : 69.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.79 (0.27), residues: 1037
  helix:  2.11 (0.25), residues: 421
  sheet: -0.77 (0.34), residues: 221
  loop : -0.35 (0.33), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 234 
 HIS   0.009   0.001   HIS A 220 
 PHE   0.026   0.002   PHE R 159 
 TYR   0.017   0.002   TYR B 264 
 ARG   0.007   0.001   ARG N  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04147 (  439)
  hydrogen bonds       : angle       4.61388 ( 1254)
  SS BOND              : bond        0.00014 (    1)
  SS BOND              : angle       0.83088 (    2)
  covalent geometry    : bond        0.00506 ( 8238)
  covalent geometry    : angle       0.58615 (11204)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6750.86 seconds
wall clock time: 116 minutes 40.97 seconds (7000.97 seconds total)