Starting phenix.real_space_refine
on Wed Sep 17 12:08:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ykv_39373/09_2025/8ykv_39373_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ykv_39373/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ykv_39373/09_2025/8ykv_39373_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ykv_39373/09_2025/8ykv_39373_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ykv_39373/09_2025/8ykv_39373.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ykv_39373/09_2025/8ykv_39373.map"
  }
  resolution = 2.48
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: {'ARG:plan': 1, 'GLU:plan': 5, 'ASP:plan': 2, 'PHE:plan': 1}
          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: {'TRP:plan': 1, 'TYR:plan': 1, 'PHE: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: 2.25, per 1000 atoms: 0.26
  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: 0.92
  Conformation dependent library (CDL) restraints added in 336.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.38
  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: 1.60

  Time building geometry restraints manager: 1.16 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:             1.070
  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:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.190
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.020
-------------------------------------------------------------------------------
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= 0.203
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  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
 ARG   0.006   0.000   ARG R 303 
 TYR   0.015   0.001   TYR R  83 
 PHE   0.012   0.001   PHE R 115 
 TRP   0.008   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 8840)
  covalent geometry    : angle       0.63019 (11978)
  hydrogen bonds       : bond        0.17358 (  470)
  hydrogen bonds       : angle       6.35762 ( 1308)

*********************** 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  : 0.313 
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: 0.7822 (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: 0.7288
  time to fit residues: 111.0799
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  : 0.240 
-------------------------------------------------------------------------------
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 108 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 106 optimal weight:    0.7980
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.3895 r_free = 0.3895 target = 0.158220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.103721 restraints weight = 9543.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 2.16
r_work: 0.3085 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.1208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8840  Z= 0.155
  Angle     :  0.564   6.734  11978  Z= 0.302
  Chirality :  0.043   0.186   1369
  Planarity :  0.004   0.035   1511
  Dihedral  :  6.772  57.793   1215
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 12.04 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.70 (0.26), residues: 1084
  helix:  2.43 (0.26), residues: 387
  sheet:  0.77 (0.30), residues: 274
  loop :  0.23 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R 303 
 TYR   0.013   0.001   TYR E 103 
 PHE   0.013   0.002   PHE R 201 
 TRP   0.019   0.002   TRP B 211 
 HIS   0.003   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8840)
  covalent geometry    : angle       0.56386 (11978)
  hydrogen bonds       : bond        0.04786 (  470)
  hydrogen bonds       : angle       4.95179 ( 1308)

*********************** 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
  165 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 134
  time to evaluate  : 0.394 
Fit side-chains
REVERT: A  205 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7361 (mmp-170)
REVERT: A  208 ARG cc_start: 0.8143 (ttm-80) cc_final: 0.7808 (ttp-110)
REVERT: A  306 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7455 (mm110)
REVERT: B  215 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7318 (mp0)
REVERT: B  217 MET cc_start: 0.7420 (mmm) cc_final: 0.6846 (mmm)
REVERT: B  280 LYS cc_start: 0.8756 (tttm) cc_final: 0.8516 (tttp)
REVERT: G   15 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7533 (tt)
REVERT: G   36 ASP cc_start: 0.7948 (m-30) cc_final: 0.7686 (m-30)
REVERT: G   42 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7106 (tp30)
REVERT: R  189 MET cc_start: 0.7766 (tpp) cc_final: 0.7391 (mmt)
REVERT: R  217 ARG cc_start: 0.7521 (ttm110) cc_final: 0.6781 (tpp-160)
REVERT: R  296 PHE cc_start: 0.6592 (t80) cc_final: 0.4851 (m-80)
  outliers start: 31
  outliers final: 9
  residues processed: 153
  average time/residue: 0.7087
  time to fit residues: 114.3540
Evaluate side-chains
  135 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 ARG
Chi-restraints excluded: chain A residue  225 VAL
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 E residue  158 SER
Chi-restraints excluded: chain G residue   15 LEU
Chi-restraints excluded: chain G residue   42 GLU
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 69 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 83 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    1.9990

-------------------------------------------------------------------------------
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 = 0.3887 r_free = 0.3887 target = 0.157545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.100448 restraints weight = 9374.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 2.23
r_work: 0.3058 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2931 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.1483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8840  Z= 0.196
  Angle     :  0.576   7.028  11978  Z= 0.309
  Chirality :  0.045   0.189   1369
  Planarity :  0.004   0.036   1511
  Dihedral  :  6.854  59.631   1214
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 13.33 %
    Favored  : 82.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.57 (0.26), residues: 1084
  helix:  2.37 (0.26), residues: 387
  sheet:  0.61 (0.30), residues: 283
  loop :  0.17 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG R 303 
 TYR   0.016   0.002   TYR E 103 
 PHE   0.014   0.002   PHE R 115 
 TRP   0.017   0.002   TRP B  82 
 HIS   0.003   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 8840)
  covalent geometry    : angle       0.57553 (11978)
  hydrogen bonds       : bond        0.04789 (  470)
  hydrogen bonds       : angle       4.82860 ( 1308)

*********************** 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
  170 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 134
  time to evaluate  : 0.354 
Fit side-chains
REVERT: A  205 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7351 (mmp-170)
REVERT: A  208 ARG cc_start: 0.8061 (ttm-80) cc_final: 0.7785 (ttp-110)
REVERT: A  306 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7480 (mm110)
REVERT: B  215 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7333 (mp0)
REVERT: B  217 MET cc_start: 0.7415 (mmm) cc_final: 0.6910 (mmm)
REVERT: B  226 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7660 (mp0)
REVERT: B  256 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.6470 (mtp180)
REVERT: B  280 LYS cc_start: 0.8794 (tttm) cc_final: 0.8560 (tttp)
REVERT: E  189 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8486 (mp)
REVERT: G   36 ASP cc_start: 0.8051 (m-30) cc_final: 0.7737 (m-30)
REVERT: R   63 PHE cc_start: 0.7009 (t80) cc_final: 0.6807 (t80)
REVERT: R  189 MET cc_start: 0.7766 (tpp) cc_final: 0.7386 (mmt)
REVERT: R  203 MET cc_start: 0.8009 (ttm) cc_final: 0.7728 (ttt)
REVERT: R  217 ARG cc_start: 0.7553 (ttm110) cc_final: 0.6990 (tpt90)
REVERT: R  296 PHE cc_start: 0.6616 (t80) cc_final: 0.4813 (m-80)
REVERT: R  307 MET cc_start: 0.3391 (OUTLIER) cc_final: 0.3031 (mpt)
  outliers start: 36
  outliers final: 15
  residues processed: 154
  average time/residue: 0.7157
  time to fit residues: 116.2654
Evaluate side-chains
  144 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 ARG
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   44 GLN
Chi-restraints excluded: chain B residue  153 ASP
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   76 LYS
Chi-restraints excluded: chain E residue   85 SER
Chi-restraints excluded: chain E residue  189 ILE
Chi-restraints excluded: chain E residue  204 SER
Chi-restraints excluded: chain G residue   24 ASN
Chi-restraints excluded: chain G residue   25 ILE
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 47 optimal weight:    0.0170
   chunk 44 optimal weight:    0.8980
   chunk 102 optimal weight:    0.7980
   chunk 106 optimal weight:    0.1980
   chunk 71 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 107 optimal weight:    0.7980
   chunk 88 optimal weight:   10.0000
   overall best weight:    0.5418

-------------------------------------------------------------------------------
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 = 0.3930 r_free = 0.3930 target = 0.161615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.105137 restraints weight = 9588.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 2.25
r_work: 0.3126 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3001 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.1799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8840  Z= 0.108
  Angle     :  0.502   6.777  11978  Z= 0.268
  Chirality :  0.041   0.200   1369
  Planarity :  0.004   0.042   1511
  Dihedral  :  6.375  57.791   1214
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 14.52 %
    Favored  : 82.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.66 (0.26), residues: 1084
  helix:  2.53 (0.26), residues: 389
  sheet:  0.48 (0.29), residues: 279
  loop :  0.26 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 303 
 TYR   0.009   0.001   TYR E 190 
 PHE   0.010   0.001   PHE B 199 
 TRP   0.019   0.002   TRP B  82 
 HIS   0.004   0.000   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 8840)
  covalent geometry    : angle       0.50229 (11978)
  hydrogen bonds       : bond        0.03860 (  470)
  hydrogen bonds       : angle       4.49690 ( 1308)

*********************** 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
  158 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 133
  time to evaluate  : 0.356 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.8169 (ttm110) cc_final: 0.7919 (ttp-110)
REVERT: A   51 LYS cc_start: 0.8096 (ttpt) cc_final: 0.7759 (mtmt)
REVERT: A  197 LYS cc_start: 0.8567 (mmtp) cc_final: 0.8348 (mmtt)
REVERT: A  208 ARG cc_start: 0.7951 (ttm-80) cc_final: 0.7669 (ttp-110)
REVERT: A  306 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7493 (mm110)
REVERT: B  215 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7261 (mp0)
REVERT: B  217 MET cc_start: 0.7454 (mmm) cc_final: 0.6948 (mmm)
REVERT: B  256 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.6476 (mtp180)
REVERT: E  163 LYS cc_start: 0.8365 (mtpp) cc_final: 0.7963 (ttmt)
REVERT: E  189 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8289 (mp)
REVERT: G   36 ASP cc_start: 0.7950 (m-30) cc_final: 0.7647 (m-30)
REVERT: G   38 MET cc_start: 0.7898 (ttm) cc_final: 0.7664 (ttp)
REVERT: G   42 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7005 (mt-10)
REVERT: G   52 THR cc_start: 0.7734 (m) cc_final: 0.7516 (p)
REVERT: R   63 PHE cc_start: 0.6936 (t80) cc_final: 0.6718 (t80)
REVERT: R  189 MET cc_start: 0.7719 (tpp) cc_final: 0.7372 (mmt)
REVERT: R  203 MET cc_start: 0.7931 (ttm) cc_final: 0.7599 (ttt)
REVERT: R  217 ARG cc_start: 0.7462 (ttm110) cc_final: 0.6887 (tpt90)
REVERT: R  296 PHE cc_start: 0.6695 (t80) cc_final: 0.4817 (m-80)
REVERT: R  307 MET cc_start: 0.3473 (OUTLIER) cc_final: 0.3055 (mpt)
  outliers start: 25
  outliers final: 9
  residues processed: 145
  average time/residue: 0.7335
  time to fit residues: 111.8814
Evaluate side-chains
  138 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 124
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
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  189 ILE
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain R residue  216 GLN
Chi-restraints excluded: chain R residue  288 SER
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 107 optimal weight:    0.0270
   chunk 78 optimal weight:    2.9990
   chunk 108 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   chunk 47 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 81 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 69 optimal weight:    3.9990
   chunk 90 optimal weight:    2.9990
   overall best weight:    1.5844

-------------------------------------------------------------------------------
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 = 0.3897 r_free = 0.3897 target = 0.158434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.101351 restraints weight = 9392.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.3209 rms_B_bonded: 2.23
r_work: 0.3069 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2946 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.1828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8840  Z= 0.166
  Angle     :  0.541   8.513  11978  Z= 0.289
  Chirality :  0.043   0.196   1369
  Planarity :  0.004   0.042   1511
  Dihedral  :  6.507  59.834   1214
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 14.09 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.61 (0.26), residues: 1084
  helix:  2.55 (0.26), residues: 387
  sheet:  0.35 (0.29), residues: 292
  loop :  0.25 (0.32), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 160 
 TYR   0.015   0.001   TYR E 103 
 PHE   0.013   0.002   PHE R 115 
 TRP   0.015   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 8840)
  covalent geometry    : angle       0.54143 (11978)
  hydrogen bonds       : bond        0.04312 (  470)
  hydrogen bonds       : angle       4.61110 ( 1308)

*********************** 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
  169 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 131
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A   22 ASN cc_start: 0.8419 (m110) cc_final: 0.8052 (m110)
REVERT: A  205 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7438 (mmp-170)
REVERT: A  208 ARG cc_start: 0.8018 (ttm-80) cc_final: 0.7790 (ttp-110)
REVERT: A  306 GLN cc_start: 0.7816 (mm-40) cc_final: 0.7428 (mm110)
REVERT: B  215 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7251 (mp0)
REVERT: B  217 MET cc_start: 0.7414 (mmm) cc_final: 0.6892 (mmm)
REVERT: B  256 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.6475 (mtp180)
REVERT: E    3 GLN cc_start: 0.8553 (tt0) cc_final: 0.8321 (tt0)
REVERT: E  163 LYS cc_start: 0.8268 (mtpp) cc_final: 0.7895 (ttmt)
REVERT: G   36 ASP cc_start: 0.8020 (m-30) cc_final: 0.7692 (m-30)
REVERT: G   38 MET cc_start: 0.8027 (ttm) cc_final: 0.7788 (ttp)
REVERT: G   42 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7060 (mt-10)
REVERT: R   63 PHE cc_start: 0.7013 (t80) cc_final: 0.6769 (t80)
REVERT: R  189 MET cc_start: 0.7745 (tpp) cc_final: 0.7388 (mmt)
REVERT: R  217 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.6966 (tpt90)
REVERT: R  296 PHE cc_start: 0.6724 (t80) cc_final: 0.4821 (m-80)
REVERT: R  307 MET cc_start: 0.3550 (OUTLIER) cc_final: 0.3028 (mpt)
  outliers start: 38
  outliers final: 15
  residues processed: 153
  average time/residue: 0.7180
  time to fit residues: 115.6978
Evaluate side-chains
  146 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  205 ARG
Chi-restraints excluded: chain A residue  225 VAL
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  256 ARG
Chi-restraints excluded: chain B residue  263 THR
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 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  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 83 optimal weight:    0.9990
   chunk 92 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 85 optimal weight:    9.9990
   chunk 101 optimal weight:    1.9990
   chunk 54 optimal weight:    7.9990
   chunk 71 optimal weight:    4.9990
   chunk 68 optimal weight:    8.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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 = 0.3872 r_free = 0.3872 target = 0.156064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.098948 restraints weight = 9399.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3174 rms_B_bonded: 2.22
r_work: 0.3034 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2909 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.1928

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= 0.239
  Angle     :  0.603   7.854  11978  Z= 0.321
  Chirality :  0.046   0.201   1369
  Planarity :  0.004   0.048   1511
  Dihedral  :  6.780  59.643   1214
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 14.95 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.38 (0.26), residues: 1084
  helix:  2.25 (0.26), residues: 389
  sheet:  0.39 (0.30), residues: 285
  loop :  0.10 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 160 
 TYR   0.019   0.002   TYR E 103 
 PHE   0.015   0.002   PHE R 115 
 TRP   0.014   0.002   TRP B  82 
 HIS   0.007   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00557 ( 8840)
  covalent geometry    : angle       0.60307 (11978)
  hydrogen bonds       : bond        0.04781 (  470)
  hydrogen bonds       : angle       4.80406 ( 1308)

*********************** 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
  169 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 129
  time to evaluate  : 0.383 
Fit side-chains
REVERT: A   22 ASN cc_start: 0.8451 (m110) cc_final: 0.8080 (m110)
REVERT: A  205 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7401 (mmp-170)
REVERT: A  208 ARG cc_start: 0.8061 (ttm-80) cc_final: 0.7829 (ttp-110)
REVERT: A  306 GLN cc_start: 0.7858 (mm-40) cc_final: 0.7460 (mm110)
REVERT: B  215 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7278 (mp0)
REVERT: B  217 MET cc_start: 0.7458 (mmm) cc_final: 0.6963 (mmm)
REVERT: B  256 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.6560 (mtp180)
REVERT: E    3 GLN cc_start: 0.8565 (tt0) cc_final: 0.8318 (tt0)
REVERT: G   36 ASP cc_start: 0.8069 (m-30) cc_final: 0.7756 (m-30)
REVERT: G   38 MET cc_start: 0.8085 (ttm) cc_final: 0.7841 (ttp)
REVERT: G   42 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7098 (mt-10)
REVERT: R   63 PHE cc_start: 0.7008 (t80) cc_final: 0.6757 (t80)
REVERT: R  189 MET cc_start: 0.7758 (tpp) cc_final: 0.7387 (mmt)
REVERT: R  217 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.6991 (tpt90)
REVERT: R  296 PHE cc_start: 0.6763 (t80) cc_final: 0.4815 (m-80)
REVERT: R  297 LEU cc_start: 0.7398 (mp) cc_final: 0.6955 (mp)
  outliers start: 40
  outliers final: 17
  residues processed: 153
  average time/residue: 0.7409
  time to fit residues: 119.0732
Evaluate side-chains
  148 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 126
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  205 ARG
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  153 ASP
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  204 SER
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  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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 81 optimal weight:    0.0060
   chunk 107 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 23 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 76 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 96 optimal weight:    8.9990
   chunk 11 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0770
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.4160

-------------------------------------------------------------------------------
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 = 0.157954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.101115 restraints weight = 9432.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 2.23
r_work: 0.3065 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
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      :  0.003   0.033   8840  Z= 0.154
  Angle     :  0.537   6.502  11978  Z= 0.287
  Chirality :  0.042   0.153   1369
  Planarity :  0.004   0.044   1511
  Dihedral  :  6.587  59.831   1214
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 17.20 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.41 (0.26), residues: 1084
  helix:  2.39 (0.26), residues: 387
  sheet:  0.25 (0.30), residues: 282
  loop :  0.13 (0.31), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 160 
 TYR   0.013   0.001   TYR E 103 
 PHE   0.011   0.001   PHE R 115 
 TRP   0.017   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 8840)
  covalent geometry    : angle       0.53737 (11978)
  hydrogen bonds       : bond        0.04202 (  470)
  hydrogen bonds       : angle       4.62692 ( 1308)

*********************** 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: 26
    poor density    : 133
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.8419 (m110) cc_final: 0.8050 (m110)
REVERT: A  208 ARG cc_start: 0.8012 (ttm-80) cc_final: 0.7792 (ttp-110)
REVERT: A  306 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7484 (mm110)
REVERT: B   22 ARG cc_start: 0.6886 (mtt180) cc_final: 0.6684 (mtt-85)
REVERT: B  215 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7225 (mp0)
REVERT: B  217 MET cc_start: 0.7456 (mmm) cc_final: 0.6935 (mmm)
REVERT: B  256 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.6489 (mtt180)
REVERT: E    3 GLN cc_start: 0.8555 (tt0) cc_final: 0.8304 (tt0)
REVERT: E  163 LYS cc_start: 0.8255 (mtpp) cc_final: 0.7935 (ttmt)
REVERT: E  204 SER cc_start: 0.8473 (OUTLIER) cc_final: 0.8230 (t)
REVERT: G   36 ASP cc_start: 0.8006 (m-30) cc_final: 0.7699 (m-30)
REVERT: G   38 MET cc_start: 0.7968 (ttm) cc_final: 0.7743 (ttp)
REVERT: G   42 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7054 (mt-10)
REVERT: R   63 PHE cc_start: 0.7014 (t80) cc_final: 0.6767 (t80)
REVERT: R  189 MET cc_start: 0.7757 (tpp) cc_final: 0.7392 (mmt)
REVERT: R  203 MET cc_start: 0.8241 (ttt) cc_final: 0.7999 (mtp)
REVERT: R  217 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6954 (tpt90)
REVERT: R  296 PHE cc_start: 0.6885 (t80) cc_final: 0.4987 (m-80)
  outliers start: 26
  outliers final: 13
  residues processed: 149
  average time/residue: 0.7524
  time to fit residues: 117.7462
Evaluate side-chains
  143 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
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  277 LYS
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  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  204 SER
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  217 ARG
Chi-restraints excluded: chain R residue  279 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 93 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 108 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   chunk 65 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0170
   chunk 72 optimal weight:    4.9990
   overall best weight:    1.2024

-------------------------------------------------------------------------------
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 = 0.3900 r_free = 0.3900 target = 0.158653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.101974 restraints weight = 9379.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 2.21
r_work: 0.3080 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.2148

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= 0.141
  Angle     :  0.528   7.547  11978  Z= 0.281
  Chirality :  0.042   0.146   1369
  Planarity :  0.004   0.043   1511
  Dihedral  :  6.458  59.846   1214
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 16.88 %
    Favored  : 80.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.26), residues: 1084
  helix:  2.46 (0.26), residues: 387
  sheet:  0.23 (0.30), residues: 282
  loop :  0.12 (0.32), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 160 
 TYR   0.012   0.001   TYR E 103 
 PHE   0.011   0.001   PHE R 115 
 TRP   0.017   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 8840)
  covalent geometry    : angle       0.52845 (11978)
  hydrogen bonds       : bond        0.04064 (  470)
  hydrogen bonds       : angle       4.55409 ( 1308)

*********************** 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
  155 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 128
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.8408 (m110) cc_final: 0.8037 (m110)
REVERT: A  197 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8293 (mmtt)
REVERT: A  208 ARG cc_start: 0.7973 (ttm-80) cc_final: 0.7687 (ttp-110)
REVERT: A  306 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7487 (mm110)
REVERT: B   22 ARG cc_start: 0.6846 (mtt180) cc_final: 0.6624 (mtt-85)
REVERT: B  215 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7225 (mp0)
REVERT: B  217 MET cc_start: 0.7438 (mmm) cc_final: 0.6957 (mmm)
REVERT: B  256 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.6482 (mtt180)
REVERT: E    3 GLN cc_start: 0.8544 (tt0) cc_final: 0.8303 (tt0)
REVERT: E  163 LYS cc_start: 0.8171 (mtpp) cc_final: 0.7736 (ttpt)
REVERT: E  204 SER cc_start: 0.8418 (OUTLIER) cc_final: 0.8156 (t)
REVERT: G   36 ASP cc_start: 0.7967 (m-30) cc_final: 0.7648 (m-30)
REVERT: G   38 MET cc_start: 0.7944 (ttm) cc_final: 0.7737 (ttp)
REVERT: G   42 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7048 (mt-10)
REVERT: G   52 THR cc_start: 0.7901 (m) cc_final: 0.7605 (p)
REVERT: R   63 PHE cc_start: 0.7016 (t80) cc_final: 0.6780 (t80)
REVERT: R  189 MET cc_start: 0.7724 (tpp) cc_final: 0.7362 (mmt)
REVERT: R  203 MET cc_start: 0.8202 (ttt) cc_final: 0.7960 (mtp)
REVERT: R  217 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.6969 (tpt90)
REVERT: R  296 PHE cc_start: 0.6880 (t80) cc_final: 0.4972 (m-80)
  outliers start: 27
  outliers final: 13
  residues processed: 148
  average time/residue: 0.7471
  time to fit residues: 116.2141
Evaluate side-chains
  145 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 126
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  225 VAL
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  256 ARG
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  158 SER
Chi-restraints excluded: chain E residue  204 SER
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  217 ARG
Chi-restraints excluded: chain R residue  279 VAL
Chi-restraints excluded: chain R residue  293 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 69 optimal weight:    5.9990
   chunk 76 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9990
   chunk 84 optimal weight:    5.9990
   chunk 70 optimal weight:    0.7980
   chunk 66 optimal weight:    4.9990
   chunk 44 optimal weight:    0.8980
   chunk 54 optimal weight:    6.9990
   chunk 63 optimal weight:    3.9990
   chunk 81 optimal weight:    0.0770
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.7340

-------------------------------------------------------------------------------
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 = 0.3916 r_free = 0.3916 target = 0.160094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.103896 restraints weight = 9373.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 2.21
r_work: 0.3109 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2985 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.2272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8840  Z= 0.113
  Angle     :  0.511   8.559  11978  Z= 0.270
  Chirality :  0.041   0.137   1369
  Planarity :  0.004   0.042   1511
  Dihedral  :  6.224  59.694   1214
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 17.31 %
    Favored  : 80.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.54 (0.26), residues: 1084
  helix:  2.59 (0.26), residues: 387
  sheet:  0.32 (0.30), residues: 275
  loop :  0.11 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 160 
 TYR   0.009   0.001   TYR E 103 
 PHE   0.010   0.001   PHE R 115 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 8840)
  covalent geometry    : angle       0.51149 (11978)
  hydrogen bonds       : bond        0.03740 (  470)
  hydrogen bonds       : angle       4.42023 ( 1308)

*********************** 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
  157 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 134
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.8373 (m110) cc_final: 0.8024 (m110)
REVERT: A  197 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8263 (mmtt)
REVERT: A  208 ARG cc_start: 0.7911 (ttm-80) cc_final: 0.7658 (ttp-110)
REVERT: B   22 ARG cc_start: 0.6809 (mtt180) cc_final: 0.6560 (mtt-85)
REVERT: B  215 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7183 (mp0)
REVERT: B  217 MET cc_start: 0.7425 (mmm) cc_final: 0.6964 (mmm)
REVERT: B  256 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.6440 (mtt180)
REVERT: E    3 GLN cc_start: 0.8536 (tt0) cc_final: 0.8298 (tt0)
REVERT: E   43 LYS cc_start: 0.7843 (mtpp) cc_final: 0.7345 (mttp)
REVERT: E  163 LYS cc_start: 0.8132 (mtpp) cc_final: 0.7769 (ttpt)
REVERT: E  204 SER cc_start: 0.8326 (OUTLIER) cc_final: 0.8104 (t)
REVERT: G   21 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.6734 (mmt)
REVERT: G   36 ASP cc_start: 0.7908 (m-30) cc_final: 0.7599 (m-30)
REVERT: G   38 MET cc_start: 0.7893 (ttm) cc_final: 0.7666 (ttp)
REVERT: G   42 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7092 (mt-10)
REVERT: G   52 THR cc_start: 0.7755 (m) cc_final: 0.7540 (p)
REVERT: R   63 PHE cc_start: 0.7073 (t80) cc_final: 0.6827 (t80)
REVERT: R  189 MET cc_start: 0.7702 (tpp) cc_final: 0.7341 (mmt)
REVERT: R  217 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.6774 (tpp-160)
REVERT: R  296 PHE cc_start: 0.6689 (t80) cc_final: 0.4827 (m-80)
  outliers start: 23
  outliers final: 9
  residues processed: 150
  average time/residue: 0.7637
  time to fit residues: 120.1982
Evaluate side-chains
  144 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  204 SER
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  217 ARG
Chi-restraints excluded: chain R residue  279 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 50 optimal weight:    0.8980
   chunk 100 optimal weight:    0.6980
   chunk 60 optimal weight:    0.8980
   chunk 65 optimal weight:    0.8980
   chunk 46 optimal weight:    0.2980
   chunk 7 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9980
   chunk 75 optimal weight:    8.9990
   chunk 12 optimal weight:    0.9990
   chunk 10 optimal weight:    9.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3916 r_free = 0.3916 target = 0.160136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.103982 restraints weight = 9359.119|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 2.20
r_work: 0.3111 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.2391

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= 0.115
  Angle     :  0.516   9.064  11978  Z= 0.272
  Chirality :  0.041   0.131   1369
  Planarity :  0.004   0.041   1511
  Dihedral  :  6.089  58.261   1214
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 18.60 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.56 (0.26), residues: 1084
  helix:  2.61 (0.26), residues: 387
  sheet:  0.34 (0.30), residues: 275
  loop :  0.10 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG E 160 
 TYR   0.009   0.001   TYR E 103 
 PHE   0.010   0.001   PHE B 199 
 TRP   0.018   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 8840)
  covalent geometry    : angle       0.51618 (11978)
  hydrogen bonds       : bond        0.03710 (  470)
  hydrogen bonds       : angle       4.41605 ( 1308)

********************** 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
  146 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.8354 (m110) cc_final: 0.8012 (m110)
REVERT: A  197 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8220 (mmtt)
REVERT: A  208 ARG cc_start: 0.7866 (ttm-80) cc_final: 0.7623 (ttp-110)
REVERT: B   22 ARG cc_start: 0.6854 (mtt180) cc_final: 0.6617 (mtt-85)
REVERT: B  217 MET cc_start: 0.7405 (mmm) cc_final: 0.6931 (mmm)
REVERT: B  256 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.6448 (mtt180)
REVERT: E    3 GLN cc_start: 0.8540 (tt0) cc_final: 0.8301 (tt0)
REVERT: E   43 LYS cc_start: 0.7893 (mtpp) cc_final: 0.7392 (mttp)
REVERT: E  163 LYS cc_start: 0.8093 (mtpp) cc_final: 0.7743 (ttpt)
REVERT: E  204 SER cc_start: 0.8318 (OUTLIER) cc_final: 0.8092 (t)
REVERT: G   36 ASP cc_start: 0.7876 (m-30) cc_final: 0.7595 (m-30)
REVERT: G   38 MET cc_start: 0.7867 (ttm) cc_final: 0.7651 (ttp)
REVERT: G   42 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7117 (mt-10)
REVERT: R   63 PHE cc_start: 0.7068 (t80) cc_final: 0.6815 (t80)
REVERT: R  189 MET cc_start: 0.7735 (tpp) cc_final: 0.7384 (mmt)
REVERT: R  217 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.6767 (tpp-160)
REVERT: R  296 PHE cc_start: 0.6665 (t80) cc_final: 0.4806 (m-80)
  outliers start: 15
  outliers final: 9
  residues processed: 145
  average time/residue: 0.7737
  time to fit residues: 117.8620
Evaluate side-chains
  141 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 127
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  277 LYS
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  256 ARG
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  204 SER
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  217 ARG
Chi-restraints excluded: chain R residue  279 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 51 optimal weight:    7.9990
   chunk 74 optimal weight:    0.4980
   chunk 77 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 24 optimal weight:    7.9990
   chunk 99 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9990
   chunk 103 optimal weight:    3.9990
   chunk 82 optimal weight:   20.0000
   overall best weight:    1.4988

-------------------------------------------------------------------------------
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 = 0.3894 r_free = 0.3894 target = 0.158046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.101378 restraints weight = 9360.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 2.20
r_work: 0.3072 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2948 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8840  Z= 0.159
  Angle     :  0.552   8.998  11978  Z= 0.291
  Chirality :  0.042   0.146   1369
  Planarity :  0.004   0.043   1511
  Dihedral  :  6.229  54.383   1214
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 18.49 %
    Favored  : 79.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.49 (0.26), residues: 1084
  helix:  2.55 (0.26), residues: 387
  sheet:  0.26 (0.30), residues: 276
  loop :  0.10 (0.32), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 160 
 TYR   0.014   0.001   TYR E 103 
 PHE   0.011   0.001   PHE R 115 
 TRP   0.015   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 8840)
  covalent geometry    : angle       0.55158 (11978)
  hydrogen bonds       : bond        0.04097 (  470)
  hydrogen bonds       : angle       4.54438 ( 1308)
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.

===============================================================================
Job complete
usr+sys time: 4619.99 seconds
wall clock time: 78 minutes 50.95 seconds (4730.95 seconds total)