Starting phenix.real_space_refine
on Wed Jan 15 16:27:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ykv_39373/01_2025/8ykv_39373_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ykv_39373/01_2025/8ykv_39373.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.48
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ykv_39373/01_2025/8ykv_39373.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ykv_39373/01_2025/8ykv_39373.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ykv_39373/01_2025/8ykv_39373_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ykv_39373/01_2025/8ykv_39373_neut.cif"
  }
  resolution = 2.48
  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=   0.099
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: 5
    Type Number    sf(0)   Gaussians
     S      55      5.16       5
     C    5535      2.51       5
     N    1466      2.21       5
     O    1606      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 8665
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1713
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1713
          Classifications: {'peptide': 213}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 210}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 2578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2578
          Classifications: {'peptide': 337}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "E"
      Number of atoms: 1729
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1729
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 37
    Chain: "G"
      Number of atoms: 443
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 443
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          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: 2174
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2174
          Classifications: {'peptide': 271}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 11, 'TRANS': 259}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 52
          Unresolved non-hydrogen dihedrals: 40
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'TRP:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 26
    Chain: "R"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'A1LYV': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.13, per 1000 atoms: 0.59
  Number of scatterers: 8665
  At special positions: 0
  Unit cell: (86.92, 118.08, 135.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      55     16.00
     F       3      9.00
     O    1606      8.00
     N    1466      7.00
     C    5535      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.18
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2082

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 14 sheets defined
      40.8% alpha, 24.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.97
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.663A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.677A  pdb=" N   ILE A  49 " --> pdb=" O   GLY A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.446A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.600A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 232
      removed outlier: 3.618A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 4.188A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 4.083A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 3.734A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 5 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'G' and resid 8 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'R' and resid 12 through 45
      removed outlier: 3.609A  pdb=" N   TYR R  25 " --> pdb=" O   LEU R  21 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   LEU R  26 " --> pdb=" O   GLU R  22 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 56 through 74
    Processing helix  chain 'R' and resid 75 through 86
      removed outlier: 4.321A  pdb=" N   LEU R  79 " --> pdb=" O   THR R  75 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 91 through 126
    Processing helix  chain 'R' and resid 131 through 134
    Processing helix  chain 'R' and resid 135 through 155
    Processing helix  chain 'R' and resid 156 through 158
      No H-bonds generated for 'chain 'R' and resid 156 through 158'
    Processing helix  chain 'R' and resid 174 through 178
    Processing helix  chain 'R' and resid 180 through 196
    Processing helix  chain 'R' and resid 196 through 217
    Processing helix  chain 'R' and resid 227 through 260
      removed outlier: 3.536A  pdb=" N   VAL R 238 " --> pdb=" O   VAL R 234 " (cutoff:3.500A)
      Proline residue:  R 247  - end of helix
    Processing helix  chain 'R' and resid 269 through 285
      Proline residue:  R 282  - end of helix
      removed outlier: 3.559A  pdb=" N   PHE R 285 " --> pdb=" O   ARG R 281 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 286 through 297
      Proline residue:  R 292  - end of helix
    Processing helix  chain 'R' and resid 299 through 309
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 3.730A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.162A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.182A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.779A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.543A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.778A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.005A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.754A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.976A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 5.906A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.034A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.611A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.207A  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: 6.671A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.298A  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: 6.430A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.696A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.211A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.489A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.211A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148
      removed outlier: 3.515A  pdb=" N   GLU E 246 " --> pdb=" O   VAL E 147 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   LEU E 174 " --> pdb=" O   TYR E 190 " (cutoff:3.500A)
      removed outlier: 4.686A  pdb=" N   TYR E 190 " --> pdb=" O   LEU E 174 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148
      removed outlier: 3.515A  pdb=" N   GLU E 246 " --> pdb=" O   VAL E 147 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   THR E 238 " --> pdb=" O   GLN E 231 " (cutoff:3.500A)

    479 hydrogen bonds defined for protein.
    1308 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: 2.60

  Time building geometry restraints manager: 2.50 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1403
        1.29 -     1.43: 2352
        1.43 -     1.56: 5004
        1.56 -     1.69: 2
        1.69 -     1.82: 79
  Bond restraints: 8840
  Sorted by residual:
  bond pdb=" C07 A1LYV R 401 "
       pdb=" N09 A1LYV R 401 "
    ideal  model  delta    sigma   weight residual
    1.334  1.448 -0.114 2.00e-02 2.50e+03 3.23e+01
  bond pdb=" C   LEU R  79 "
       pdb=" O   LEU R  79 "
    ideal  model  delta    sigma   weight residual
    1.236  1.192  0.045 1.26e-02 6.30e+03 1.25e+01
  bond pdb=" C07 A1LYV R 401 "
       pdb=" O08 A1LYV R 401 "
    ideal  model  delta    sigma   weight residual
    1.228  1.162  0.066 2.00e-02 2.50e+03 1.08e+01
  bond pdb=" CA  ASP R 174 "
       pdb=" C   ASP R 174 "
    ideal  model  delta    sigma   weight residual
    1.525  1.460  0.065 2.10e-02 2.27e+03 9.62e+00
  bond pdb=" C   PHE R 175 "
       pdb=" O   PHE R 175 "
    ideal  model  delta    sigma   weight residual
    1.236  1.205  0.030 1.18e-02 7.18e+03 6.55e+00
  ... (remaining 8835 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 11713
        1.73 -     3.46: 202
        3.46 -     5.18: 49
        5.18 -     6.91: 10
        6.91 -     8.64: 4
  Bond angle restraints: 11978
  Sorted by residual:
  angle pdb=" N   PHE R 175 "
        pdb=" CA  PHE R 175 "
        pdb=" C   PHE R 175 "
      ideal   model   delta    sigma   weight residual
     111.37  118.40   -7.03 1.65e+00 3.67e-01 1.82e+01
  angle pdb=" N   MET E 192 "
        pdb=" CA  MET E 192 "
        pdb=" CB  MET E 192 "
      ideal   model   delta    sigma   weight residual
     114.17  109.40    4.77 1.14e+00 7.69e-01 1.75e+01
  angle pdb=" N   ASP A 229 "
        pdb=" CA  ASP A 229 "
        pdb=" C   ASP A 229 "
      ideal   model   delta    sigma   weight residual
     112.34  117.14   -4.80 1.30e+00 5.92e-01 1.36e+01
  angle pdb=" CA  LEU A 232 "
        pdb=" C   LEU A 232 "
        pdb=" O   LEU A 232 "
      ideal   model   delta    sigma   weight residual
     121.46  117.49    3.97 1.17e+00 7.31e-01 1.15e+01
  angle pdb=" N   ALA A 226 "
        pdb=" CA  ALA A 226 "
        pdb=" C   ALA A 226 "
      ideal   model   delta    sigma   weight residual
     109.96  105.17    4.79 1.50e+00 4.44e-01 1.02e+01
  ... (remaining 11973 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.90: 4660
       16.90 -    33.81: 392
       33.81 -    50.71: 135
       50.71 -    67.62: 35
       67.62 -    84.52: 12
  Dihedral angle restraints: 5234
    sinusoidal: 2011
      harmonic: 3223
  Sorted by residual:
  dihedral pdb=" CA  LYS B  78 "
           pdb=" C   LYS B  78 "
           pdb=" N   LEU B  79 "
           pdb=" CA  LEU B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.59   21.41     0      5.00e+00 4.00e-02 1.83e+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  162.90   17.10     0      5.00e+00 4.00e-02 1.17e+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  163.51   16.49     0      5.00e+00 4.00e-02 1.09e+01
  ... (remaining 5231 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1197
       0.060 -    0.120: 155
       0.120 -    0.180: 15
       0.180 -    0.241: 1
       0.241 -    0.301: 1
  Chirality restraints: 1369
  Sorted by residual:
  chirality pdb=" CA  PHE R 175 "
            pdb=" N   PHE R 175 "
            pdb=" C   PHE R 175 "
            pdb=" CB  PHE R 175 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.26e+00
  chirality pdb=" CA  LEU A 227 "
            pdb=" N   LEU A 227 "
            pdb=" C   LEU A 227 "
            pdb=" CB  LEU A 227 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.33e+00
  chirality pdb=" CA  ARG B 304 "
            pdb=" N   ARG B 304 "
            pdb=" C   ARG B 304 "
            pdb=" CB  ARG B 304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.75e-01
  ... (remaining 1366 not shown)

  Planarity restraints: 1511
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 223 "    0.010 2.00e-02 2.50e+03   1.91e-02 3.64e+00
        pdb=" C   PHE A 223 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   PHE A 223 "    0.012 2.00e-02 2.50e+03
        pdb=" N   CYS A 224 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 281 "    0.027 5.00e-02 4.00e+02   4.02e-02 2.58e+00
        pdb=" N   PRO A 282 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 282 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 282 "    0.022 5.00e-02 4.00e+02
                                   delta    sigma   weight rms_deltas residual
  plane pdb=" C05 A1LYV R 401 "   -0.009 2.00e-02 2.50e+03   1.42e-02 2.53e+00
        pdb=" C07 A1LYV R 401 "    0.025 2.00e-02 2.50e+03
        pdb=" C10 A1LYV R 401 "    0.005 2.00e-02 2.50e+03
        pdb=" N09 A1LYV R 401 "   -0.015 2.00e-02 2.50e+03
        pdb=" O08 A1LYV R 401 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1508 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 56
        2.58 -     3.16: 7248
        3.16 -     3.74: 13755
        3.74 -     4.32: 20012
        4.32 -     4.90: 33455
  Nonbonded interactions: 74526
  Sorted by model distance:
  nonbonded pdb=" C22 A1LYV R 401 "
            pdb=" F28 A1LYV R 401 "
     model   vdw
     1.997 3.290
  nonbonded pdb=" O   THR B  86 "
            pdb=" OG1 THR B  87 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" O   ASP B 195 "
            pdb=" OG1 THR B 196 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" O   GLY E 112 "
            pdb=" OG  SER E 184 "
     model   vdw
     2.322 3.040
  ... (remaining 74521 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:             0.700
  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:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.670
  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:12.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
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   0.114   8840  Z= 0.251
  Angle     :  0.630   8.638  11978  Z= 0.349
  Chirality :  0.042   0.301   1369
  Planarity :  0.004   0.049   1511
  Dihedral  : 15.419  84.523   3152
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 2.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 13.87 %
    Favored  : 85.59 %
  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:  1.66 (0.26), residues: 1084
  helix:  2.48 (0.26), residues: 379
  sheet:  0.67 (0.31), residues: 271
  loop :  0.22 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.012   0.001   PHE R 115 
 TYR   0.015   0.001   TYR R  83 
 ARG   0.006   0.000   ARG R 303 

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 142
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
REVERT: A  208 ARG cc_start: 0.8382 (ttm-80) cc_final: 0.8131 (ttp-110)
REVERT: B  197 ARG cc_start: 0.8186 (mmt90) cc_final: 0.7814 (mmm160)
REVERT: B  217 MET cc_start: 0.7266 (mmm) cc_final: 0.7017 (mpm)
REVERT: R  203 MET cc_start: 0.8086 (ttm) cc_final: 0.7791 (ttt)
REVERT: R  296 PHE cc_start: 0.6817 (t80) cc_final: 0.5101 (m-80)
  outliers start: 5
  outliers final: 1
  residues processed: 145
  average time/residue: 1.5632
  time to fit residues: 239.1144
Evaluate side-chains
  127 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  294 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    0.6980
   chunk 82 optimal weight:    3.9990
   chunk 45 optimal weight:    0.3980
   chunk 28 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 85 optimal weight:    9.9990
   chunk 33 optimal weight:    0.8980
   chunk 51 optimal weight:    7.9990
   chunk 63 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9990
   overall best weight:    0.7382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.159746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.105520 restraints weight = 9439.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 2.16
r_work: 0.3113 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.1215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8840  Z= 0.173
  Angle     :  0.542   6.401  11978  Z= 0.292
  Chirality :  0.042   0.195   1369
  Planarity :  0.004   0.034   1511
  Dihedral  :  6.637  58.435   1215
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 12.37 %
    Favored  : 84.84 %
  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:  1.81 (0.26), residues: 1084
  helix:  2.53 (0.26), residues: 387
  sheet:  0.90 (0.30), residues: 270
  loop :  0.23 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 211 
 HIS   0.002   0.001   HIS B  91 
 PHE   0.012   0.001   PHE R 175 
 TYR   0.010   0.001   TYR A 296 
 ARG   0.005   0.001   ARG B  49 

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 135
  time to evaluate  : 1.200 
Fit side-chains
REVERT: A  208 ARG cc_start: 0.8068 (ttm-80) cc_final: 0.7775 (ttp-110)
REVERT: A  306 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7444 (mm110)
REVERT: B  130 GLU cc_start: 0.8467 (mp0) cc_final: 0.8260 (mp0)
REVERT: B  197 ARG cc_start: 0.8420 (mmt90) cc_final: 0.7774 (mmm160)
REVERT: B  215 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7295 (mp0)
REVERT: B  217 MET cc_start: 0.7440 (mmm) cc_final: 0.6874 (mmm)
REVERT: B  280 LYS cc_start: 0.8781 (tttm) cc_final: 0.8560 (tttp)
REVERT: G   15 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7514 (tt)
REVERT: R  189 MET cc_start: 0.7749 (tpp) cc_final: 0.7341 (mmt)
REVERT: R  215 LYS cc_start: 0.8376 (mttt) cc_final: 0.8172 (mttm)
REVERT: R  217 ARG cc_start: 0.7497 (ttm110) cc_final: 0.6995 (ttm-80)
REVERT: R  296 PHE cc_start: 0.6563 (t80) cc_final: 0.4832 (m-80)
  outliers start: 26
  outliers final: 7
  residues processed: 152
  average time/residue: 1.4555
  time to fit residues: 233.8220
Evaluate side-chains
  132 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 123
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue   85 SER
Chi-restraints excluded: chain G residue   15 LEU
Chi-restraints excluded: chain R residue  288 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 66 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 58 optimal weight:    0.1980
   chunk 107 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 52 optimal weight:    0.8980
   chunk 24 optimal weight:    7.9990
   overall best weight:    0.7382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.161506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.105003 restraints weight = 9585.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 2.25
r_work: 0.3123 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.1573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8840  Z= 0.164
  Angle     :  0.507   6.166  11978  Z= 0.272
  Chirality :  0.042   0.172   1369
  Planarity :  0.003   0.032   1511
  Dihedral  :  6.464  57.822   1214
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 13.76 %
    Favored  : 83.66 %
  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:  1.80 (0.26), residues: 1084
  helix:  2.65 (0.26), residues: 387
  sheet:  0.62 (0.30), residues: 271
  loop :  0.29 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.012   0.001   PHE R  63 
 TYR   0.010   0.001   TYR E 190 
 ARG   0.004   0.000   ARG E 160 

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 134
  time to evaluate  : 1.007 
Fit side-chains
REVERT: A  208 ARG cc_start: 0.8007 (ttm-80) cc_final: 0.7709 (ttp-110)
REVERT: A  306 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7535 (mm110)
REVERT: B  197 ARG cc_start: 0.8393 (mmt90) cc_final: 0.7734 (mmm160)
REVERT: B  215 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7287 (mp0)
REVERT: B  217 MET cc_start: 0.7475 (mmm) cc_final: 0.6913 (mmm)
REVERT: B  226 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7524 (mp0)
REVERT: B  256 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.6402 (mtp180)
REVERT: B  280 LYS cc_start: 0.8782 (tttm) cc_final: 0.8552 (tttm)
REVERT: E  189 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8390 (mp)
REVERT: G   42 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7091 (tp30)
REVERT: G   52 THR cc_start: 0.7777 (m) cc_final: 0.7529 (p)
REVERT: R  189 MET cc_start: 0.7790 (tpp) cc_final: 0.7412 (mmt)
REVERT: R  203 MET cc_start: 0.7941 (ttm) cc_final: 0.7650 (ttt)
REVERT: R  217 ARG cc_start: 0.7468 (ttm110) cc_final: 0.6837 (tpp-160)
REVERT: R  296 PHE cc_start: 0.6650 (t80) cc_final: 0.4846 (m-80)
REVERT: R  307 MET cc_start: 0.3439 (OUTLIER) cc_final: 0.3051 (mpt)
  outliers start: 24
  outliers final: 9
  residues processed: 147
  average time/residue: 1.4750
  time to fit residues: 228.6613
Evaluate side-chains
  142 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue   85 SER
Chi-restraints excluded: chain E residue  189 ILE
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain R residue  288 SER
Chi-restraints excluded: chain R residue  307 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 75 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 91 optimal weight:    0.7980
   chunk 92 optimal weight:    0.7980
   chunk 63 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9980
   chunk 76 optimal weight:    0.7980
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.161342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.104866 restraints weight = 9514.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 2.24
r_work: 0.3123 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.1748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8840  Z= 0.169
  Angle     :  0.508   6.386  11978  Z= 0.271
  Chirality :  0.041   0.189   1369
  Planarity :  0.003   0.039   1511
  Dihedral  :  6.366  58.037   1214
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 14.95 %
    Favored  : 82.04 %
  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:  1.80 (0.26), residues: 1084
  helix:  2.69 (0.26), residues: 389
  sheet:  0.47 (0.30), residues: 279
  loop :  0.35 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 188 
 PHE   0.013   0.001   PHE R  63 
 TYR   0.010   0.001   TYR E 103 
 ARG   0.005   0.000   ARG E 160 

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 128
  time to evaluate  : 0.982 
Fit side-chains
REVERT: A  208 ARG cc_start: 0.7973 (ttm-80) cc_final: 0.7674 (ttp-110)
REVERT: A  306 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7496 (mm110)
REVERT: B  130 GLU cc_start: 0.8478 (mp0) cc_final: 0.8248 (mp0)
REVERT: B  197 ARG cc_start: 0.8377 (mmt90) cc_final: 0.7709 (mmm160)
REVERT: B  215 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7300 (mp0)
REVERT: B  217 MET cc_start: 0.7407 (mmm) cc_final: 0.6923 (mmm)
REVERT: B  256 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.6439 (mtt180)
REVERT: B  280 LYS cc_start: 0.8808 (tttm) cc_final: 0.8571 (tttm)
REVERT: E  189 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8382 (mp)
REVERT: G   38 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7918 (ttp)
REVERT: G   42 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7014 (mt-10)
REVERT: G   52 THR cc_start: 0.7755 (m) cc_final: 0.7521 (p)
REVERT: R  189 MET cc_start: 0.7731 (tpp) cc_final: 0.7380 (mmt)
REVERT: R  217 ARG cc_start: 0.7454 (ttm110) cc_final: 0.6875 (tpt90)
REVERT: R  296 PHE cc_start: 0.6676 (t80) cc_final: 0.4840 (m-80)
REVERT: R  307 MET cc_start: 0.3502 (OUTLIER) cc_final: 0.3068 (mpt)
  outliers start: 28
  outliers final: 11
  residues processed: 143
  average time/residue: 1.4568
  time to fit residues: 219.9872
Evaluate side-chains
  142 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue   76 LYS
Chi-restraints excluded: chain E residue   85 SER
Chi-restraints excluded: chain E residue  189 ILE
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain R residue  288 SER
Chi-restraints excluded: chain R residue  293 VAL
Chi-restraints excluded: chain R residue  307 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 65 optimal weight:    6.9990
   chunk 54 optimal weight:    5.9990
   chunk 4 optimal weight:    0.8980
   chunk 12 optimal weight:    0.2980
   chunk 101 optimal weight:    4.9990
   chunk 93 optimal weight:   10.0000
   chunk 94 optimal weight:    0.9990
   chunk 103 optimal weight:    5.9990
   chunk 76 optimal weight:    6.9990
   chunk 33 optimal weight:    0.0970
   overall best weight:    1.4582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.157964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.103512 restraints weight = 9472.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 2.15
r_work: 0.3085 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2961 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.1809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8840  Z= 0.231
  Angle     :  0.533   7.366  11978  Z= 0.284
  Chirality :  0.042   0.188   1369
  Planarity :  0.004   0.038   1511
  Dihedral  :  6.444  59.569   1214
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 14.95 %
    Favored  : 81.40 %
  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:  1.75 (0.26), residues: 1084
  helix:  2.61 (0.26), residues: 389
  sheet:  0.52 (0.30), residues: 286
  loop :  0.32 (0.32), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 188 
 PHE   0.013   0.001   PHE R  63 
 TYR   0.013   0.001   TYR E 103 
 ARG   0.005   0.000   ARG E 160 

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 126
  time to evaluate  : 1.038 
Fit side-chains
REVERT: A  208 ARG cc_start: 0.7968 (ttm-80) cc_final: 0.7653 (ttp-110)
REVERT: A  306 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7409 (mm110)
REVERT: B  197 ARG cc_start: 0.8416 (mmt90) cc_final: 0.7736 (mmm160)
REVERT: B  215 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7231 (mp0)
REVERT: B  217 MET cc_start: 0.7404 (mmm) cc_final: 0.6892 (mmm)
REVERT: B  256 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.6496 (mtt180)
REVERT: E  163 LYS cc_start: 0.8281 (mtpp) cc_final: 0.7836 (tttt)
REVERT: G   38 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7921 (ttp)
REVERT: G   42 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7031 (mt-10)
REVERT: G   52 THR cc_start: 0.7854 (m) cc_final: 0.7568 (p)
REVERT: R  189 MET cc_start: 0.7756 (tpp) cc_final: 0.7376 (mmt)
REVERT: R  203 MET cc_start: 0.7964 (ttm) cc_final: 0.7760 (ttt)
REVERT: R  217 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.6950 (tpt90)
REVERT: R  296 PHE cc_start: 0.6739 (t80) cc_final: 0.4848 (m-80)
REVERT: R  307 MET cc_start: 0.3525 (OUTLIER) cc_final: 0.3091 (mpt)
  outliers start: 34
  outliers final: 15
  residues processed: 148
  average time/residue: 1.4691
  time to fit residues: 229.7117
Evaluate side-chains
  143 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 122
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue   76 LYS
Chi-restraints excluded: chain E residue   85 SER
Chi-restraints excluded: chain E residue  117 LEU
Chi-restraints excluded: chain E residue  145 SER
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain R residue  217 ARG
Chi-restraints excluded: chain R residue  279 VAL
Chi-restraints excluded: chain R residue  288 SER
Chi-restraints excluded: chain R residue  293 VAL
Chi-restraints excluded: chain R residue  307 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 106 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 89 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 108 optimal weight:    0.9990
   chunk 107 optimal weight:    0.0370
   chunk 75 optimal weight:    2.9990
   chunk 85 optimal weight:    9.9990
   chunk 52 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 24 optimal weight:    5.9990
   overall best weight:    1.0862

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.159830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.103427 restraints weight = 9343.534|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 2.21
r_work: 0.3100 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2977 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8840  Z= 0.191
  Angle     :  0.512   6.201  11978  Z= 0.273
  Chirality :  0.041   0.175   1369
  Planarity :  0.004   0.040   1511
  Dihedral  :  6.271  58.866   1214
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 15.27 %
    Favored  : 81.29 %
  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:  1.74 (0.26), residues: 1084
  helix:  2.68 (0.26), residues: 387
  sheet:  0.41 (0.30), residues: 292
  loop :  0.32 (0.33), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 188 
 PHE   0.033   0.001   PHE R  63 
 TYR   0.011   0.001   TYR E 103 
 ARG   0.006   0.000   ARG E 160 

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 127
  time to evaluate  : 0.948 
Fit side-chains
REVERT: A  208 ARG cc_start: 0.7964 (ttm-80) cc_final: 0.7685 (ttp-110)
REVERT: A  306 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7482 (mm110)
REVERT: B  197 ARG cc_start: 0.8404 (mmt90) cc_final: 0.7722 (mmm160)
REVERT: B  215 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7256 (mp0)
REVERT: B  217 MET cc_start: 0.7416 (mmm) cc_final: 0.6938 (mmm)
REVERT: B  256 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.6517 (mtt180)
REVERT: E    3 GLN cc_start: 0.8548 (tt0) cc_final: 0.8307 (tt0)
REVERT: E   43 LYS cc_start: 0.8090 (mtpm) cc_final: 0.7494 (mttp)
REVERT: E  163 LYS cc_start: 0.8251 (mtpp) cc_final: 0.7835 (tttt)
REVERT: E  189 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8253 (mp)
REVERT: G   38 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7841 (ttp)
REVERT: G   42 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7059 (mt-10)
REVERT: G   52 THR cc_start: 0.7821 (m) cc_final: 0.7572 (p)
REVERT: R  189 MET cc_start: 0.7720 (tpp) cc_final: 0.7354 (mmt)
REVERT: R  203 MET cc_start: 0.7957 (ttm) cc_final: 0.7684 (ttt)
REVERT: R  217 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.6885 (tpt90)
REVERT: R  296 PHE cc_start: 0.6727 (t80) cc_final: 0.4858 (m-80)
REVERT: R  307 MET cc_start: 0.3564 (OUTLIER) cc_final: 0.2988 (mpt)
  outliers start: 32
  outliers final: 16
  residues processed: 146
  average time/residue: 1.4770
  time to fit residues: 227.4229
Evaluate side-chains
  146 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 123
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue   85 SER
Chi-restraints excluded: chain E residue  117 LEU
Chi-restraints excluded: chain E residue  159 CYS
Chi-restraints excluded: chain E residue  189 ILE
Chi-restraints excluded: chain G residue    9 ILE
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain R residue  217 ARG
Chi-restraints excluded: chain R residue  279 VAL
Chi-restraints excluded: chain R residue  293 VAL
Chi-restraints excluded: chain R residue  307 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 63 optimal weight:    6.9990
   chunk 62 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 93 optimal weight:    0.6980
   chunk 91 optimal weight:    0.0980
   chunk 78 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 72 optimal weight:    6.9990
   chunk 86 optimal weight:    2.9990
   overall best weight:    1.0984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.159722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.103281 restraints weight = 9450.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 2.22
r_work: 0.3098 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8840  Z= 0.193
  Angle     :  0.513   7.291  11978  Z= 0.273
  Chirality :  0.042   0.148   1369
  Planarity :  0.004   0.037   1511
  Dihedral  :  6.137  56.029   1214
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 15.91 %
    Favored  : 80.75 %
  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:  1.70 (0.26), residues: 1084
  helix:  2.68 (0.26), residues: 389
  sheet:  0.34 (0.30), residues: 282
  loop :  0.29 (0.32), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 188 
 PHE   0.011   0.001   PHE R 115 
 TYR   0.011   0.001   TYR E 103 
 ARG   0.006   0.000   ARG E 160 

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 128
  time to evaluate  : 1.056 
Fit side-chains
REVERT: A  208 ARG cc_start: 0.7968 (ttm-80) cc_final: 0.7643 (ttp-110)
REVERT: B  197 ARG cc_start: 0.8404 (mmt90) cc_final: 0.7712 (mmm160)
REVERT: B  215 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7232 (mp0)
REVERT: B  217 MET cc_start: 0.7505 (mmm) cc_final: 0.7017 (mmm)
REVERT: B  256 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.6552 (mtt180)
REVERT: E    3 GLN cc_start: 0.8552 (tt0) cc_final: 0.8307 (tt0)
REVERT: E   43 LYS cc_start: 0.8105 (mtpm) cc_final: 0.7519 (mttp)
REVERT: E  163 LYS cc_start: 0.8248 (mtpp) cc_final: 0.7841 (tttt)
REVERT: E  189 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8262 (mp)
REVERT: G   38 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7746 (ttp)
REVERT: G   42 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6959 (mm-30)
REVERT: G   52 THR cc_start: 0.7802 (m) cc_final: 0.7547 (p)
REVERT: R  189 MET cc_start: 0.7743 (tpp) cc_final: 0.7382 (mmt)
REVERT: R  203 MET cc_start: 0.7972 (ttm) cc_final: 0.7687 (ttt)
REVERT: R  217 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.6898 (tpt90)
REVERT: R  296 PHE cc_start: 0.6780 (t80) cc_final: 0.4914 (m-80)
REVERT: R  307 MET cc_start: 0.3482 (OUTLIER) cc_final: 0.2949 (mpt)
  outliers start: 31
  outliers final: 15
  residues processed: 149
  average time/residue: 1.4490
  time to fit residues: 228.0728
Evaluate side-chains
  146 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue   85 SER
Chi-restraints excluded: chain E residue  117 LEU
Chi-restraints excluded: chain E residue  145 SER
Chi-restraints excluded: chain E residue  189 ILE
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain R residue  217 ARG
Chi-restraints excluded: chain R residue  279 VAL
Chi-restraints excluded: chain R residue  293 VAL
Chi-restraints excluded: chain R residue  307 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 67 optimal weight:   10.0000
   chunk 79 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 104 optimal weight:   10.0000
   chunk 94 optimal weight:    3.9990
   chunk 37 optimal weight:    6.9990
   chunk 53 optimal weight:    3.9990
   chunk 80 optimal weight:    0.8980
   chunk 45 optimal weight:    5.9990
   overall best weight:    2.5788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.156375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.099570 restraints weight = 9498.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 2.21
r_work: 0.3041 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2916 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.2050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   8840  Z= 0.363
  Angle     :  0.606   8.094  11978  Z= 0.321
  Chirality :  0.045   0.215   1369
  Planarity :  0.004   0.039   1511
  Dihedral  :  6.506  54.975   1214
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 16.99 %
    Favored  : 79.68 %
  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:  1.49 (0.26), residues: 1084
  helix:  2.42 (0.26), residues: 389
  sheet:  0.36 (0.30), residues: 275
  loop :  0.15 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 188 
 PHE   0.036   0.002   PHE R  63 
 TYR   0.018   0.002   TYR E 103 
 ARG   0.007   0.001   ARG E 160 

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 125
  time to evaluate  : 1.033 
Fit side-chains
REVERT: A   22 ASN cc_start: 0.8438 (m110) cc_final: 0.8044 (m110)
REVERT: A  208 ARG cc_start: 0.8010 (ttm-80) cc_final: 0.7678 (ttp-110)
REVERT: B  197 ARG cc_start: 0.8441 (mmt90) cc_final: 0.7727 (mmm160)
REVERT: B  215 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7188 (mp0)
REVERT: B  217 MET cc_start: 0.7444 (mmm) cc_final: 0.6929 (mmm)
REVERT: B  256 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.6557 (mtt180)
REVERT: E    3 GLN cc_start: 0.8561 (tt0) cc_final: 0.8324 (tt0)
REVERT: E  163 LYS cc_start: 0.8244 (mtpp) cc_final: 0.7842 (tttt)
REVERT: E  189 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8406 (mp)
REVERT: G   38 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7906 (ttp)
REVERT: G   42 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7075 (mt-10)
REVERT: R  203 MET cc_start: 0.8023 (ttm) cc_final: 0.7731 (ttt)
REVERT: R  217 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6972 (tpt90)
REVERT: R  296 PHE cc_start: 0.6818 (t80) cc_final: 0.4894 (m-80)
REVERT: R  307 MET cc_start: 0.3454 (OUTLIER) cc_final: 0.2887 (mpt)
  outliers start: 31
  outliers final: 18
  residues processed: 147
  average time/residue: 1.4904
  time to fit residues: 230.9598
Evaluate side-chains
  148 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue   85 SER
Chi-restraints excluded: chain E residue  117 LEU
Chi-restraints excluded: chain E residue  145 SER
Chi-restraints excluded: chain E residue  189 ILE
Chi-restraints excluded: chain G residue    9 ILE
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain G residue   24 ASN
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain R residue  217 ARG
Chi-restraints excluded: chain R residue  279 VAL
Chi-restraints excluded: chain R residue  288 SER
Chi-restraints excluded: chain R residue  293 VAL
Chi-restraints excluded: chain R residue  307 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 99 optimal weight:    0.9990
   chunk 93 optimal weight:    6.9990
   chunk 22 optimal weight:    6.9990
   chunk 59 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 51 optimal weight:    5.9990
   chunk 58 optimal weight:    0.8980
   chunk 61 optimal weight:    7.9990
   overall best weight:    2.7788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.155681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.098969 restraints weight = 9433.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 2.21
r_work: 0.3034 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2910 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.2102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   8840  Z= 0.384
  Angle     :  0.618   8.828  11978  Z= 0.327
  Chirality :  0.046   0.210   1369
  Planarity :  0.004   0.040   1511
  Dihedral  :  6.720  59.968   1214
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 17.10 %
    Favored  : 79.35 %
  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:  1.33 (0.26), residues: 1084
  helix:  2.24 (0.26), residues: 390
  sheet:  0.34 (0.30), residues: 275
  loop :  0.05 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  99 
 HIS   0.006   0.001   HIS A 188 
 PHE   0.016   0.002   PHE R 115 
 TYR   0.019   0.002   TYR E 103 
 ARG   0.006   0.001   ARG E 160 

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 128
  time to evaluate  : 0.998 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.8430 (m110) cc_final: 0.8030 (m110)
REVERT: A  208 ARG cc_start: 0.8028 (ttm-80) cc_final: 0.7815 (ttp-110)
REVERT: B  197 ARG cc_start: 0.8463 (mmt90) cc_final: 0.7729 (mmm160)
REVERT: B  215 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7165 (mp0)
REVERT: B  217 MET cc_start: 0.7442 (mmm) cc_final: 0.6958 (mmm)
REVERT: B  256 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.6549 (mtt180)
REVERT: E    3 GLN cc_start: 0.8565 (tt0) cc_final: 0.8323 (tt0)
REVERT: E  189 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8407 (mp)
REVERT: G   42 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7155 (pt0)
REVERT: R  189 MET cc_start: 0.7799 (tpp) cc_final: 0.7473 (mmt)
REVERT: R  203 MET cc_start: 0.8031 (ttm) cc_final: 0.7735 (ttt)
REVERT: R  217 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.6988 (tpt90)
REVERT: R  296 PHE cc_start: 0.6909 (t80) cc_final: 0.4978 (m-80)
REVERT: R  297 LEU cc_start: 0.7421 (mp) cc_final: 0.6998 (mp)
REVERT: R  307 MET cc_start: 0.3429 (OUTLIER) cc_final: 0.2892 (mpt)
  outliers start: 33
  outliers final: 19
  residues processed: 151
  average time/residue: 1.6656
  time to fit residues: 264.6052
Evaluate side-chains
  148 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue   85 SER
Chi-restraints excluded: chain E residue  117 LEU
Chi-restraints excluded: chain E residue  145 SER
Chi-restraints excluded: chain E residue  189 ILE
Chi-restraints excluded: chain G residue    9 ILE
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain G residue   24 ASN
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain R residue  217 ARG
Chi-restraints excluded: chain R residue  279 VAL
Chi-restraints excluded: chain R residue  288 SER
Chi-restraints excluded: chain R residue  293 VAL
Chi-restraints excluded: chain R residue  307 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 4 optimal weight:    4.9990
   chunk 69 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   chunk 96 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    1.1584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.158329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.102069 restraints weight = 9444.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 2.21
r_work: 0.3078 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.2216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8840  Z= 0.210
  Angle     :  0.543   9.242  11978  Z= 0.288
  Chirality :  0.042   0.190   1369
  Planarity :  0.004   0.038   1511
  Dihedral  :  6.435  57.968   1214
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 18.06 %
    Favored  : 79.35 %
  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:  1.45 (0.26), residues: 1084
  helix:  2.45 (0.26), residues: 388
  sheet:  0.27 (0.30), residues: 281
  loop :  0.12 (0.32), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 188 
 PHE   0.034   0.002   PHE R  63 
 TYR   0.012   0.001   TYR E 103 
 ARG   0.008   0.000   ARG E 160 

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 130
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.8386 (m110) cc_final: 0.8002 (m110)
REVERT: A  208 ARG cc_start: 0.7984 (ttm-80) cc_final: 0.7670 (ttp-110)
REVERT: B   33 ILE cc_start: 0.7702 (mm) cc_final: 0.7493 (mt)
REVERT: B  197 ARG cc_start: 0.8426 (mmt90) cc_final: 0.7712 (mmm160)
REVERT: B  215 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7103 (mp0)
REVERT: B  217 MET cc_start: 0.7430 (mmm) cc_final: 0.6949 (mmm)
REVERT: B  256 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.6508 (mtt180)
REVERT: E    3 GLN cc_start: 0.8544 (tt0) cc_final: 0.8297 (tt0)
REVERT: E  189 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8251 (mp)
REVERT: G   42 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7180 (pt0)
REVERT: G   52 THR cc_start: 0.7883 (m) cc_final: 0.7582 (p)
REVERT: R  189 MET cc_start: 0.7823 (tpp) cc_final: 0.7499 (mmt)
REVERT: R  203 MET cc_start: 0.7995 (ttm) cc_final: 0.7708 (ttt)
REVERT: R  217 ARG cc_start: 0.7511 (ttm110) cc_final: 0.6902 (tpt90)
REVERT: R  296 PHE cc_start: 0.6830 (t80) cc_final: 0.4920 (m-80)
REVERT: R  307 MET cc_start: 0.3429 (OUTLIER) cc_final: 0.2837 (mpt)
  outliers start: 24
  outliers final: 17
  residues processed: 149
  average time/residue: 1.5270
  time to fit residues: 239.9151
Evaluate side-chains
  150 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 128
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue   85 SER
Chi-restraints excluded: chain E residue  117 LEU
Chi-restraints excluded: chain E residue  145 SER
Chi-restraints excluded: chain E residue  189 ILE
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain R residue  279 VAL
Chi-restraints excluded: chain R residue  288 SER
Chi-restraints excluded: chain R residue  293 VAL
Chi-restraints excluded: chain R residue  307 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 103 optimal weight:    0.9990
   chunk 12 optimal weight:    0.4980
   chunk 33 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 76 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.8384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.159653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.103598 restraints weight = 9495.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 2.22
r_work: 0.3103 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2979 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.2357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8840  Z= 0.175
  Angle     :  0.527   9.064  11978  Z= 0.276
  Chirality :  0.041   0.192   1369
  Planarity :  0.004   0.036   1511
  Dihedral  :  6.174  57.117   1214
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 17.85 %
    Favored  : 80.00 %
  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:  1.56 (0.26), residues: 1084
  helix:  2.59 (0.26), residues: 388
  sheet:  0.27 (0.30), residues: 282
  loop :  0.17 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 188 
 PHE   0.010   0.001   PHE B 199 
 TYR   0.011   0.001   TYR R 100 
 ARG   0.008   0.000   ARG E 160 
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.

===============================================================================
Job complete
usr+sys time: 9108.51 seconds
wall clock time: 160 minutes 27.81 seconds (9627.81 seconds total)