Starting phenix.real_space_refine
on Tue Mar  3 22:02:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vl8_32020/03_2026/7vl8_32020.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vl8_32020/03_2026/7vl8_32020.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vl8_32020/03_2026/7vl8_32020.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vl8_32020/03_2026/7vl8_32020.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vl8_32020/03_2026/7vl8_32020.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vl8_32020/03_2026/7vl8_32020.map"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      58      5.16       5
     C    5681      2.51       5
     N    1495      2.21       5
     O    1600      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8834
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1666
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1666
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 90
          Unresolved non-hydrogen angles: 108
          Unresolved non-hydrogen dihedrals: 72
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 7, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 57
    Chain: "B"
      Number of atoms: 2593
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2593
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 13
    Chain: "G"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 438
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "R"
      Number of atoms: 2358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2358
          Classifications: {'peptide': 284}
          Link IDs: {'PTRANS': 9, 'TRANS': 274}
    Chain: "S"
      Number of atoms: 1751
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1751
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "R"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.29, per 1000 atoms: 0.26
  Number of scatterers: 8834
  At special positions: 0
  Unit cell: (111.54, 133.848, 116.61, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      58     16.00
     O    1600      8.00
     N    1495      7.00
     C    5681      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 183 " distance=2.04

  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: 0.67
  Conformation dependent library (CDL) restraints added in 295.7 milliseconds
  

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2122

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 15 sheets defined
      38.1% alpha, 23.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
      removed outlier: 3.616A  pdb=" N   ASN A  22 " --> pdb=" O   MET A  18 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ALA A  31 " --> pdb=" O   GLY A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 3.950A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 216
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 4.078A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 241 through 255
      removed outlier: 3.522A  pdb=" N   ASN A 255 " --> pdb=" O   ASP A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 278
      removed outlier: 4.132A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 308
      removed outlier: 3.911A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 352
      removed outlier: 3.840A  pdb=" N   VAL A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 26
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.638A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 6 through 24
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.543A  pdb=" N   HIS G  44 " --> pdb=" O   TYR G  40 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 36 through 62
      removed outlier: 3.982A  pdb=" N   LEU R  40 " --> pdb=" O   LEU R  36 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 67 through 85
    Processing helix  chain 'R' and resid 86 through 97
    Processing helix  chain 'R' and resid 102 through 136
      removed outlier: 3.802A  pdb=" N   GLY R 111 " --> pdb=" O   LYS R 107 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 165
    Processing helix  chain 'R' and resid 165 through 171
    Processing helix  chain 'R' and resid 188 through 190
      No H-bonds generated for 'chain 'R' and resid 188 through 190'
    Processing helix  chain 'R' and resid 191 through 206
    Processing helix  chain 'R' and resid 208 through 227
      removed outlier: 4.069A  pdb=" N   ILE R 225 " --> pdb=" O   GLY R 221 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 231 through 264
      Proline residue:  R 254  - end of helix
    Processing helix  chain 'R' and resid 264 through 269
    Processing helix  chain 'R' and resid 275 through 302
      removed outlier: 4.342A  pdb=" N   LEU R 281 " --> pdb=" O   ARG R 277 " (cutoff:3.500A)
      Proline residue:  R 298  - end of helix
    Processing helix  chain 'R' and resid 305 through 316
    Processing helix  chain 'S' and resid 28 through 32
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 8.952A  pdb=" N   ALA A 220 " --> pdb=" O   GLU A  33 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.958A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.481A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.672A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.119A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.693A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.880A  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: 3.619A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.791A  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: 6.978A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.396A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.138A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 5.945A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.724A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.005A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.218A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.630A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.404A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.564A  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: 3.662A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 172 through 176
      removed outlier: 3.697A  pdb=" N   SER R 184 " --> pdb=" O   LYS R 173 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 5.855A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.444A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12
      removed outlier: 5.855A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148
      removed outlier: 3.734A  pdb=" N   GLU S 246 " --> pdb=" O   VAL S 147 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 155 through 160
    Processing sheet with id=AB6, first strand: chain 'S' and resid 185 through 189
      removed outlier: 6.555A  pdb=" N   TRP S 176 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)

    443 hydrogen bonds defined for protein.
    1260 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: 1.57

  Time building geometry restraints manager: 0.92 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1563
        1.32 -     1.45: 2420
        1.45 -     1.57: 4962
        1.57 -     1.69: 3
        1.69 -     1.81: 83
  Bond restraints: 9031
  Sorted by residual:
  bond pdb=" NE  ARG R 143 "
       pdb=" CZ  ARG R 143 "
    ideal  model  delta    sigma   weight residual
    1.326  1.365 -0.039 1.10e-02 8.26e+03 1.29e+01
  bond pdb=" CB  LEU R  65 "
       pdb=" CG  LEU R  65 "
    ideal  model  delta    sigma   weight residual
    1.530  1.598 -0.068 2.00e-02 2.50e+03 1.14e+01
  bond pdb=" N   LEU R  37 "
       pdb=" CA  LEU R  37 "
    ideal  model  delta    sigma   weight residual
    1.461  1.492 -0.031 9.20e-03 1.18e+04 1.13e+01
  bond pdb=" N   MET R 166 "
       pdb=" CA  MET R 166 "
    ideal  model  delta    sigma   weight residual
    1.461  1.492 -0.031 9.20e-03 1.18e+04 1.12e+01
  bond pdb=" N   ASN R 297 "
       pdb=" CA  ASN R 297 "
    ideal  model  delta    sigma   weight residual
    1.461  1.491 -0.030 9.20e-03 1.18e+04 1.08e+01
  ... (remaining 9026 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.50: 11881
        2.50 -     5.01: 351
        5.01 -     7.51: 20
        7.51 -    10.02: 1
       10.02 -    12.52: 1
  Bond angle restraints: 12254
  Sorted by residual:
  angle pdb=" N   ASP B  76 "
        pdb=" CA  ASP B  76 "
        pdb=" C   ASP B  76 "
      ideal   model   delta    sigma   weight residual
     113.16  100.64   12.52 1.24e+00 6.50e-01 1.02e+02
  angle pdb=" N   PRO R  38 "
        pdb=" CA  PRO R  38 "
        pdb=" C   PRO R  38 "
      ideal   model   delta    sigma   weight residual
     110.70  119.62   -8.92 1.22e+00 6.72e-01 5.34e+01
  angle pdb=" CA  PRO R  38 "
        pdb=" C   PRO R  38 "
        pdb=" N   PRO R  39 "
      ideal   model   delta    sigma   weight residual
     117.93  123.08   -5.15 1.20e+00 6.94e-01 1.84e+01
  angle pdb=" N   GLN A 204 "
        pdb=" CA  GLN A 204 "
        pdb=" C   GLN A 204 "
      ideal   model   delta    sigma   weight residual
     108.24  101.02    7.22 1.81e+00 3.05e-01 1.59e+01
  angle pdb=" C   ILE R 247 "
        pdb=" CA  ILE R 247 "
        pdb=" CB  ILE R 247 "
      ideal   model   delta    sigma   weight residual
     111.97  106.87    5.10 1.28e+00 6.10e-01 1.59e+01
  ... (remaining 12249 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.06: 4827
       16.06 -    32.12: 437
       32.12 -    48.18: 78
       48.18 -    64.24: 9
       64.24 -    80.31: 7
  Dihedral angle restraints: 5358
    sinusoidal: 2069
      harmonic: 3289
  Sorted by residual:
  dihedral pdb=" CB  CYS R 106 "
           pdb=" SG  CYS R 106 "
           pdb=" SG  CYS R 183 "
           pdb=" CB  CYS R 183 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -164.42   78.42     1      1.00e+01 1.00e-02 7.67e+01
  dihedral pdb=" CA  TYR S 190 "
           pdb=" C   TYR S 190 "
           pdb=" N   ARG S 191 "
           pdb=" CA  ARG S 191 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.38   22.62     0      5.00e+00 4.00e-02 2.05e+01
  dihedral pdb=" CA  LYS S  76 "
           pdb=" C   LYS S  76 "
           pdb=" N   ASN S  77 "
           pdb=" CA  ASN S  77 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.11  -19.89     0      5.00e+00 4.00e-02 1.58e+01
  ... (remaining 5355 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 1142
       0.082 -    0.164: 216
       0.164 -    0.246: 42
       0.246 -    0.328: 7
       0.328 -    0.410: 1
  Chirality restraints: 1408
  Sorted by residual:
  chirality pdb=" CA  PRO R  38 "
            pdb=" N   PRO R  38 "
            pdb=" C   PRO R  38 "
            pdb=" CB  PRO R  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.31    0.41 2.00e-01 2.50e+01 4.20e+00
  chirality pdb=" CA  TYR R 219 "
            pdb=" N   TYR R 219 "
            pdb=" C   TYR R 219 "
            pdb=" CB  TYR R 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.29e+00
  chirality pdb=" CA  LYS R 107 "
            pdb=" N   LYS R 107 "
            pdb=" C   LYS R 107 "
            pdb=" CB  LYS R 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.22e+00
  ... (remaining 1405 not shown)

  Planarity restraints: 1529
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B  75 "    0.017 2.00e-02 2.50e+03   3.47e-02 1.20e+01
        pdb=" C   GLN B  75 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   GLN B  75 "    0.023 2.00e-02 2.50e+03
        pdb=" N   ASP B  76 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R 158 "   -0.039 2.00e-02 2.50e+03   1.98e-02 9.84e+00
        pdb=" CG  TRP R 158 "    0.008 2.00e-02 2.50e+03
        pdb=" CD1 TRP R 158 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 TRP R 158 "    0.024 2.00e-02 2.50e+03
        pdb=" NE1 TRP R 158 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP R 158 "    0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP R 158 "    0.027 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R 158 "   -0.017 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R 158 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP R 158 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU R 306 "   -0.014 2.00e-02 2.50e+03   2.96e-02 8.74e+00
        pdb=" C   GLU R 306 "    0.051 2.00e-02 2.50e+03
        pdb=" O   GLU R 306 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ARG R 307 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1526 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2515
        2.81 -     3.33: 7922
        3.33 -     3.86: 14126
        3.86 -     4.38: 17321
        4.38 -     4.90: 29848
  Nonbonded interactions: 71732
  Sorted by model distance:
  nonbonded pdb=" O   MET B 325 "
            pdb=" OD1 ASN B 340 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" OG  SER S 161 "
            pdb=" O   LYS S 163 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" NH1 ARG S  67 "
            pdb=" OD2 ASP S  90 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" O   SER A 281 "
            pdb=" OG  SER A 281 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.308 3.040
  ... (remaining 71727 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:             1.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     9.270
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6759
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      :  0.008   0.068   9032  Z= 0.475
  Angle     :  0.929  12.521  12256  Z= 0.654
  Chirality :  0.068   0.410   1408
  Planarity :  0.005   0.037   1529
  Dihedral  : 12.527  80.306   3233
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 are not related in a simple way.
  whole: -1.45 (0.24), residues: 1116
  helix:  0.84 (0.26), residues: 391
  sheet: -1.55 (0.27), residues: 299
  loop : -2.18 (0.26), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG R 277 
 TYR   0.019   0.002   TYR S 175 
 PHE   0.017   0.002   PHE R 308 
 TRP   0.039   0.003   TRP R 158 
 HIS   0.006   0.001   HIS R 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00756 ( 9031)
  covalent geometry    : angle       0.92777 (12254)
  SS BOND              : bond        0.01217 (    1)
  SS BOND              : angle       3.87963 (    2)
  hydrogen bonds       : bond        0.15712 (  439)
  hydrogen bonds       : angle       6.00809 ( 1260)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASN cc_start: 0.8294 (m-40) cc_final: 0.7886 (m110)
REVERT: A  208 ARG cc_start: 0.6833 (ttm110) cc_final: 0.6212 (ttp80)
REVERT: A  247 MET cc_start: 0.8267 (mtp) cc_final: 0.8028 (mtm)
REVERT: B  153 ASP cc_start: 0.7386 (p0) cc_final: 0.7123 (p0)
REVERT: B  217 MET cc_start: 0.6130 (ptt) cc_final: 0.5916 (ptt)
REVERT: B  219 ARG cc_start: 0.7629 (ttm-80) cc_final: 0.7428 (mtp180)
REVERT: B  280 LYS cc_start: 0.8052 (tttp) cc_final: 0.7566 (ttmt)
REVERT: G   38 MET cc_start: 0.7038 (ttp) cc_final: 0.6717 (tpt)
REVERT: S  110 PHE cc_start: 0.5871 (t80) cc_final: 0.5240 (t80)
REVERT: S  228 TYR cc_start: 0.7489 (m-80) cc_final: 0.6711 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 0.5185
  time to fit residues: 98.6685
Evaluate side-chains
  104 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0010
   chunk 100 optimal weight:   40.0000
   chunk 106 optimal weight:   20.0000
   overall best weight:    1.1992

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
A 331 ASN
B  91 HIS
R 181 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.220634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.131645 restraints weight = 9249.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 3.33
r_work: 0.3340 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5672
moved from start:          0.2142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9032  Z= 0.161
  Angle     :  0.588   7.565  12256  Z= 0.309
  Chirality :  0.043   0.164   1408
  Planarity :  0.004   0.036   1529
  Dihedral  :  4.632  44.491   1287
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 14.06 %
    Favored  : 82.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 are not related in a simple way.
  whole: -0.47 (0.25), residues: 1116
  helix:  1.66 (0.26), residues: 405
  sheet: -0.97 (0.29), residues: 278
  loop : -1.76 (0.26), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG S 160 
 TYR   0.018   0.002   TYR S 227 
 PHE   0.014   0.001   PHE A 196 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.008   0.001   HIS R 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 9031)
  covalent geometry    : angle       0.58803 (12254)
  SS BOND              : bond        0.00148 (    1)
  SS BOND              : angle       0.48503 (    2)
  hydrogen bonds       : bond        0.04653 (  439)
  hydrogen bonds       : angle       4.57749 ( 1260)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 116
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
REVERT: A  247 MET cc_start: 0.6727 (mtp) cc_final: 0.6502 (mtm)
REVERT: A  308 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7227 (mt-10)
REVERT: A  341 ASP cc_start: 0.6558 (t0) cc_final: 0.6313 (t0)
REVERT: B  105 TYR cc_start: 0.7953 (OUTLIER) cc_final: 0.7499 (t80)
REVERT: B  111 TYR cc_start: 0.6982 (m-80) cc_final: 0.6648 (m-80)
REVERT: B  217 MET cc_start: 0.5166 (ptt) cc_final: 0.4668 (ttt)
REVERT: B  219 ARG cc_start: 0.7550 (ttm-80) cc_final: 0.7190 (mtp180)
REVERT: B  262 MET cc_start: 0.6316 (OUTLIER) cc_final: 0.5159 (mmt)
REVERT: B  280 LYS cc_start: 0.7220 (tttp) cc_final: 0.6613 (ttmt)
REVERT: B  323 ASP cc_start: 0.6771 (m-30) cc_final: 0.6548 (m-30)
REVERT: R   59 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6439 (mm)
REVERT: S   39 GLN cc_start: 0.5968 (tt0) cc_final: 0.5753 (tt0)
REVERT: S   87 ARG cc_start: 0.6207 (ptp-170) cc_final: 0.5782 (mmt90)
REVERT: S  150 THR cc_start: 0.7059 (p) cc_final: 0.6826 (t)
REVERT: S  160 ARG cc_start: 0.8244 (ttp80) cc_final: 0.7754 (ttt90)
REVERT: S  228 TYR cc_start: 0.6387 (m-80) cc_final: 0.5584 (m-80)
REVERT: S  230 MET cc_start: 0.6155 (OUTLIER) cc_final: 0.5670 (ttp)
  outliers start: 32
  outliers final: 13
  residues processed: 133
  average time/residue: 0.4913
  time to fit residues: 70.3241
Evaluate side-chains
  112 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain R residue   59 LEU
Chi-restraints excluded: chain R residue  130 ASP
Chi-restraints excluded: chain R residue  177 GLU
Chi-restraints excluded: chain R residue  289 ILE
Chi-restraints excluded: chain R residue  299 VAL
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue  230 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 63 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 67 optimal weight:    0.7980
   chunk 109 optimal weight:    0.2980
   chunk 36 optimal weight:    7.9990
   chunk 101 optimal weight:    9.9990
   chunk 25 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   chunk 96 optimal weight:    9.9990
   chunk 77 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A 331 ASN
R 314 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.221935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.134493 restraints weight = 9090.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 3.21
r_work: 0.3369 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5667
moved from start:          0.2706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9032  Z= 0.110
  Angle     :  0.510   8.088  12256  Z= 0.268
  Chirality :  0.041   0.179   1408
  Planarity :  0.003   0.034   1529
  Dihedral  :  4.371  45.974   1287
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 16.51 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 are not related in a simple way.
  whole:  0.04 (0.25), residues: 1116
  helix:  2.08 (0.26), residues: 401
  sheet: -0.67 (0.30), residues: 278
  loop : -1.46 (0.27), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  42 
 TYR   0.015   0.001   TYR S 190 
 PHE   0.011   0.001   PHE A 274 
 TRP   0.018   0.001   TRP B  82 
 HIS   0.007   0.001   HIS R 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 9031)
  covalent geometry    : angle       0.51023 (12254)
  SS BOND              : bond        0.00047 (    1)
  SS BOND              : angle       0.34807 (    2)
  hydrogen bonds       : bond        0.03818 (  439)
  hydrogen bonds       : angle       4.23938 ( 1260)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 112
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 ASN cc_start: 0.8886 (m110) cc_final: 0.8563 (m110)
REVERT: A  341 ASP cc_start: 0.6516 (t0) cc_final: 0.6210 (t0)
REVERT: B  111 TYR cc_start: 0.7072 (m-80) cc_final: 0.6659 (m-80)
REVERT: B  135 VAL cc_start: 0.6676 (OUTLIER) cc_final: 0.6373 (p)
REVERT: B  138 GLU cc_start: 0.7654 (mt-10) cc_final: 0.6641 (mp0)
REVERT: B  217 MET cc_start: 0.5197 (ptt) cc_final: 0.4936 (ptm)
REVERT: B  219 ARG cc_start: 0.7615 (ttm-80) cc_final: 0.7314 (mtp180)
REVERT: B  280 LYS cc_start: 0.7201 (tttp) cc_final: 0.6450 (ttmt)
REVERT: B  323 ASP cc_start: 0.6837 (m-30) cc_final: 0.6632 (m-30)
REVERT: R   59 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6367 (mm)
REVERT: R  117 LEU cc_start: 0.5520 (OUTLIER) cc_final: 0.5143 (mp)
REVERT: S   39 GLN cc_start: 0.6101 (tt0) cc_final: 0.5828 (tt0)
REVERT: S   87 ARG cc_start: 0.6111 (ptp-170) cc_final: 0.5794 (mmt90)
REVERT: S  160 ARG cc_start: 0.8148 (ttp80) cc_final: 0.7738 (ttt180)
REVERT: S  228 TYR cc_start: 0.6319 (m-80) cc_final: 0.5475 (m-80)
REVERT: S  230 MET cc_start: 0.6133 (OUTLIER) cc_final: 0.5865 (ttp)
  outliers start: 33
  outliers final: 14
  residues processed: 132
  average time/residue: 0.5068
  time to fit residues: 71.6874
Evaluate side-chains
  118 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain R residue   59 LEU
Chi-restraints excluded: chain R residue  117 LEU
Chi-restraints excluded: chain R residue  177 GLU
Chi-restraints excluded: chain R residue  289 ILE
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue  230 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 42 optimal weight:   10.0000
   chunk 51 optimal weight:    5.9990
   chunk 25 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   chunk 45 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   chunk 77 optimal weight:    0.5980
   chunk 86 optimal weight:    0.9990
   chunk 84 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 125 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4450 r_free = 0.4450 target = 0.222463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.134424 restraints weight = 9300.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 3.29
r_work: 0.3365 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5757
moved from start:          0.3090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   9032  Z= 0.113
  Angle     :  0.506   8.517  12256  Z= 0.263
  Chirality :  0.041   0.151   1408
  Planarity :  0.003   0.036   1529
  Dihedral  :  4.278  43.092   1287
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 17.47 %
    Favored  : 79.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 are not related in a simple way.
  whole:  0.22 (0.25), residues: 1116
  helix:  2.19 (0.26), residues: 402
  sheet: -0.62 (0.30), residues: 279
  loop : -1.29 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 277 
 TYR   0.013   0.001   TYR S 190 
 PHE   0.011   0.001   PHE A 189 
 TRP   0.013   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 9031)
  covalent geometry    : angle       0.50640 (12254)
  SS BOND              : bond        0.00045 (    1)
  SS BOND              : angle       0.31828 (    2)
  hydrogen bonds       : bond        0.03676 (  439)
  hydrogen bonds       : angle       4.16010 ( 1260)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 104
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 GLU cc_start: 0.7480 (mt-10) cc_final: 0.6774 (mp0)
REVERT: A  341 ASP cc_start: 0.6582 (t0) cc_final: 0.6271 (t0)
REVERT: B  105 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.7677 (t80)
REVERT: B  111 TYR cc_start: 0.7163 (m-80) cc_final: 0.6814 (m-80)
REVERT: B  138 GLU cc_start: 0.7760 (mt-10) cc_final: 0.6679 (mp0)
REVERT: B  161 SER cc_start: 0.8101 (OUTLIER) cc_final: 0.7637 (p)
REVERT: B  217 MET cc_start: 0.5311 (ptt) cc_final: 0.5005 (ptm)
REVERT: B  219 ARG cc_start: 0.7648 (ttm-80) cc_final: 0.7284 (mtp180)
REVERT: B  280 LYS cc_start: 0.7146 (tttp) cc_final: 0.6424 (ttmt)
REVERT: R   59 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6266 (mm)
REVERT: R  117 LEU cc_start: 0.5514 (OUTLIER) cc_final: 0.5168 (mp)
REVERT: S   39 GLN cc_start: 0.6110 (tt0) cc_final: 0.5904 (tt0)
REVERT: S   87 ARG cc_start: 0.6111 (ptp-170) cc_final: 0.5762 (mmt90)
REVERT: S  160 ARG cc_start: 0.8266 (ttp80) cc_final: 0.7959 (ttt90)
REVERT: S  206 SER cc_start: 0.5018 (t) cc_final: 0.4657 (p)
REVERT: S  228 TYR cc_start: 0.6402 (m-80) cc_final: 0.5695 (m-80)
REVERT: S  230 MET cc_start: 0.6141 (OUTLIER) cc_final: 0.5896 (ttp)
  outliers start: 29
  outliers final: 15
  residues processed: 123
  average time/residue: 0.5026
  time to fit residues: 66.5007
Evaluate side-chains
  114 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain R residue   59 LEU
Chi-restraints excluded: chain R residue  117 LEU
Chi-restraints excluded: chain R residue  130 ASP
Chi-restraints excluded: chain R residue  177 GLU
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue  230 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 35 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 98 optimal weight:   20.0000
   chunk 17 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 46 optimal weight:    6.9990
   chunk 69 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   overall best weight:    1.7984

-------------------------------------------------------------------------------
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 = 0.4393 r_free = 0.4393 target = 0.216036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.126366 restraints weight = 9220.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 3.27
r_work: 0.3244 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5865
moved from start:          0.3403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   9032  Z= 0.194
  Angle     :  0.572   8.779  12256  Z= 0.299
  Chirality :  0.044   0.160   1408
  Planarity :  0.004   0.039   1529
  Dihedral  :  4.573  41.423   1287
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 17.68 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 are not related in a simple way.
  whole:  0.13 (0.25), residues: 1116
  helix:  1.91 (0.26), residues: 406
  sheet: -0.64 (0.30), residues: 279
  loop : -1.14 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 277 
 TYR   0.016   0.002   TYR B 105 
 PHE   0.016   0.002   PHE S 212 
 TRP   0.009   0.001   TRP B 169 
 HIS   0.007   0.001   HIS R 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 ( 9031)
  covalent geometry    : angle       0.57207 (12254)
  SS BOND              : bond        0.00190 (    1)
  SS BOND              : angle       0.53055 (    2)
  hydrogen bonds       : bond        0.04486 (  439)
  hydrogen bonds       : angle       4.34805 ( 1260)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 101
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
REVERT: A  341 ASP cc_start: 0.6728 (t0) cc_final: 0.6408 (t0)
REVERT: B  105 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.7815 (t80)
REVERT: B  111 TYR cc_start: 0.7038 (m-80) cc_final: 0.6672 (m-80)
REVERT: B  217 MET cc_start: 0.5530 (ptt) cc_final: 0.5179 (ptm)
REVERT: B  219 ARG cc_start: 0.7552 (ttm-80) cc_final: 0.7194 (mtp180)
REVERT: B  280 LYS cc_start: 0.7125 (tttp) cc_final: 0.6372 (ttmt)
REVERT: B  323 ASP cc_start: 0.6792 (m-30) cc_final: 0.6580 (m-30)
REVERT: R   59 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6303 (mm)
REVERT: R  117 LEU cc_start: 0.5720 (OUTLIER) cc_final: 0.5408 (mp)
REVERT: S   87 ARG cc_start: 0.6047 (ptp-170) cc_final: 0.5728 (mmt90)
REVERT: S  150 THR cc_start: 0.7041 (p) cc_final: 0.6776 (t)
REVERT: S  160 ARG cc_start: 0.8136 (ttp80) cc_final: 0.7854 (ttt180)
REVERT: S  206 SER cc_start: 0.5055 (t) cc_final: 0.4683 (p)
REVERT: S  228 TYR cc_start: 0.6409 (m-80) cc_final: 0.6132 (m-80)
REVERT: S  230 MET cc_start: 0.6108 (OUTLIER) cc_final: 0.5858 (ttp)
  outliers start: 35
  outliers final: 18
  residues processed: 124
  average time/residue: 0.4707
  time to fit residues: 63.2559
Evaluate side-chains
  112 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 90
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain R residue   59 LEU
Chi-restraints excluded: chain R residue  117 LEU
Chi-restraints excluded: chain R residue  130 ASP
Chi-restraints excluded: chain R residue  177 GLU
Chi-restraints excluded: chain R residue  289 ILE
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue  230 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 13 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 24 optimal weight:    0.3980
   chunk 104 optimal weight:   10.0000
   chunk 75 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
B 125 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.220828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.131026 restraints weight = 9137.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.3530 rms_B_bonded: 3.29
r_work: 0.3321 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5759
moved from start:          0.3583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9032  Z= 0.120
  Angle     :  0.520   9.936  12256  Z= 0.268
  Chirality :  0.041   0.145   1408
  Planarity :  0.003   0.038   1529
  Dihedral  :  4.273  40.310   1287
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 19.28 %
    Favored  : 77.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 are not related in a simple way.
  whole:  0.30 (0.25), residues: 1116
  helix:  2.06 (0.26), residues: 405
  sheet: -0.53 (0.30), residues: 277
  loop : -1.08 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 277 
 TYR   0.013   0.001   TYR S 190 
 PHE   0.014   0.001   PHE R  45 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 9031)
  covalent geometry    : angle       0.51996 (12254)
  SS BOND              : bond        0.00000 (    1)
  SS BOND              : angle       0.18666 (    2)
  hydrogen bonds       : bond        0.03782 (  439)
  hydrogen bonds       : angle       4.19930 ( 1260)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 100
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
REVERT: A  308 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6813 (mp0)
REVERT: A  341 ASP cc_start: 0.6570 (t0) cc_final: 0.6232 (t0)
REVERT: B  105 TYR cc_start: 0.7938 (OUTLIER) cc_final: 0.7683 (t80)
REVERT: B  111 TYR cc_start: 0.7152 (m-80) cc_final: 0.6788 (m-80)
REVERT: B  217 MET cc_start: 0.5759 (ptt) cc_final: 0.5428 (ptm)
REVERT: B  219 ARG cc_start: 0.7531 (ttm-80) cc_final: 0.7190 (mtp180)
REVERT: B  280 LYS cc_start: 0.7103 (tttp) cc_final: 0.6274 (ttmt)
REVERT: B  323 ASP cc_start: 0.6858 (m-30) cc_final: 0.6639 (m-30)
REVERT: G   21 MET cc_start: 0.7784 (mtt) cc_final: 0.7404 (mtm)
REVERT: R   59 LEU cc_start: 0.6776 (OUTLIER) cc_final: 0.6182 (mm)
REVERT: R  193 ARG cc_start: 0.5101 (ttp-170) cc_final: 0.4871 (tpp80)
REVERT: S   87 ARG cc_start: 0.6028 (ptp-170) cc_final: 0.5728 (mmt90)
REVERT: S  150 THR cc_start: 0.7112 (p) cc_final: 0.6846 (t)
REVERT: S  160 ARG cc_start: 0.8099 (ttp80) cc_final: 0.7836 (ttt180)
REVERT: S  206 SER cc_start: 0.5264 (t) cc_final: 0.4947 (p)
REVERT: S  228 TYR cc_start: 0.6205 (m-80) cc_final: 0.5870 (m-80)
  outliers start: 26
  outliers final: 17
  residues processed: 117
  average time/residue: 0.4906
  time to fit residues: 61.8323
Evaluate side-chains
  112 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain R residue   59 LEU
Chi-restraints excluded: chain R residue  117 LEU
Chi-restraints excluded: chain R residue  130 ASP
Chi-restraints excluded: chain R residue  259 ILE
Chi-restraints excluded: chain R residue  289 ILE
Chi-restraints excluded: chain R residue  295 CYS
Chi-restraints excluded: chain R residue  299 VAL
Chi-restraints excluded: chain S residue    2 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 77 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0980
   chunk 11 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 57 optimal weight:    6.9990
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    0.0970
   chunk 76 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
B  88 ASN
B 125 ASN
S  39 GLN
S 179 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4442 r_free = 0.4442 target = 0.221589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.133175 restraints weight = 9218.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 3.27
r_work: 0.3322 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5790
moved from start:          0.3774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9032  Z= 0.105
  Angle     :  0.504   9.166  12256  Z= 0.259
  Chirality :  0.041   0.184   1408
  Planarity :  0.003   0.039   1529
  Dihedral  :  4.098  36.194   1287
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 20.02 %
    Favored  : 77.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 are not related in a simple way.
  whole:  0.45 (0.26), residues: 1116
  helix:  2.19 (0.26), residues: 408
  sheet: -0.45 (0.30), residues: 277
  loop : -1.03 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 277 
 TYR   0.013   0.001   TYR S 190 
 PHE   0.015   0.001   PHE R  45 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 9031)
  covalent geometry    : angle       0.50385 (12254)
  SS BOND              : bond        0.00001 (    1)
  SS BOND              : angle       0.09898 (    2)
  hydrogen bonds       : bond        0.03535 (  439)
  hydrogen bonds       : angle       4.12394 ( 1260)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 96
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
REVERT: A  308 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6793 (mp0)
REVERT: A  331 ASN cc_start: 0.8795 (m-40) cc_final: 0.8496 (m110)
REVERT: A  341 ASP cc_start: 0.6610 (t0) cc_final: 0.6272 (t0)
REVERT: B  105 TYR cc_start: 0.7820 (OUTLIER) cc_final: 0.7617 (t80)
REVERT: B  111 TYR cc_start: 0.7201 (m-80) cc_final: 0.6844 (m-80)
REVERT: B  217 MET cc_start: 0.5906 (ptt) cc_final: 0.5579 (ptm)
REVERT: B  219 ARG cc_start: 0.7516 (ttm-80) cc_final: 0.7123 (mtp180)
REVERT: B  280 LYS cc_start: 0.7137 (tttp) cc_final: 0.6407 (ttmt)
REVERT: G   21 MET cc_start: 0.7796 (mtt) cc_final: 0.7445 (mtm)
REVERT: R   59 LEU cc_start: 0.6693 (OUTLIER) cc_final: 0.6094 (mm)
REVERT: R  193 ARG cc_start: 0.5171 (ttp-170) cc_final: 0.4935 (tpp80)
REVERT: S   87 ARG cc_start: 0.5735 (ptp-170) cc_final: 0.5464 (mmt90)
REVERT: S  150 THR cc_start: 0.7153 (p) cc_final: 0.6883 (t)
REVERT: S  160 ARG cc_start: 0.8052 (ttp80) cc_final: 0.7834 (ttt180)
REVERT: S  206 SER cc_start: 0.5025 (t) cc_final: 0.4614 (p)
REVERT: S  228 TYR cc_start: 0.6106 (m-80) cc_final: 0.5775 (m-80)
  outliers start: 25
  outliers final: 15
  residues processed: 115
  average time/residue: 0.4976
  time to fit residues: 61.5453
Evaluate side-chains
  107 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue   59 LEU
Chi-restraints excluded: chain R residue  130 ASP
Chi-restraints excluded: chain R residue  259 ILE
Chi-restraints excluded: chain R residue  295 CYS
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue  194 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 63 optimal weight:    0.7980
   chunk 79 optimal weight:    3.9990
   chunk 82 optimal weight:   20.0000
   chunk 3 optimal weight:    2.9990
   chunk 109 optimal weight:    0.5980
   chunk 32 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 105 optimal weight:    4.9990
   chunk 93 optimal weight:    0.3980
   chunk 107 optimal weight:    0.8980
   chunk 78 optimal weight:    5.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
S  39 GLN
S 179 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.220174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.130483 restraints weight = 9101.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 3.27
r_work: 0.3301 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5842
moved from start:          0.3840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9032  Z= 0.138
  Angle     :  0.536   9.302  12256  Z= 0.273
  Chirality :  0.042   0.202   1408
  Planarity :  0.003   0.042   1529
  Dihedral  :  4.182  34.344   1287
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 19.70 %
    Favored  : 77.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 are not related in a simple way.
  whole:  0.44 (0.25), residues: 1116
  helix:  2.18 (0.26), residues: 407
  sheet: -0.45 (0.30), residues: 278
  loop : -1.03 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 277 
 TYR   0.013   0.001   TYR S 190 
 PHE   0.013   0.001   PHE R  45 
 TRP   0.009   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 9031)
  covalent geometry    : angle       0.53649 (12254)
  SS BOND              : bond        0.00124 (    1)
  SS BOND              : angle       0.30022 (    2)
  hydrogen bonds       : bond        0.03910 (  439)
  hydrogen bonds       : angle       4.19862 ( 1260)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 99
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6790 (mp0)
REVERT: A  341 ASP cc_start: 0.6674 (t0) cc_final: 0.6298 (t0)
REVERT: B  111 TYR cc_start: 0.7200 (m-80) cc_final: 0.6873 (m-80)
REVERT: B  137 ARG cc_start: 0.4635 (mmm160) cc_final: 0.3834 (tpp-160)
REVERT: B  217 MET cc_start: 0.6202 (ptt) cc_final: 0.5808 (ptm)
REVERT: B  219 ARG cc_start: 0.7499 (ttm-80) cc_final: 0.7102 (mtp180)
REVERT: B  280 LYS cc_start: 0.7122 (tttp) cc_final: 0.6393 (ttmt)
REVERT: G   21 MET cc_start: 0.7784 (mtt) cc_final: 0.7441 (mtm)
REVERT: R   59 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.6121 (mm)
REVERT: R  193 ARG cc_start: 0.5113 (ttp-170) cc_final: 0.4871 (tpp80)
REVERT: S   87 ARG cc_start: 0.5983 (ptp-170) cc_final: 0.5676 (mmt90)
REVERT: S  150 THR cc_start: 0.7117 (p) cc_final: 0.6843 (t)
REVERT: S  206 SER cc_start: 0.5184 (t) cc_final: 0.4826 (p)
REVERT: S  228 TYR cc_start: 0.6263 (m-80) cc_final: 0.5598 (m-80)
  outliers start: 27
  outliers final: 20
  residues processed: 119
  average time/residue: 0.4890
  time to fit residues: 62.6096
Evaluate side-chains
  115 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain R residue   59 LEU
Chi-restraints excluded: chain R residue  130 ASP
Chi-restraints excluded: chain R residue  259 ILE
Chi-restraints excluded: chain R residue  295 CYS
Chi-restraints excluded: chain R residue  299 VAL
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue  194 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 76 optimal weight:    0.7980
   chunk 38 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0980
   chunk 70 optimal weight:    3.9990
   chunk 88 optimal weight:   30.0000
   chunk 104 optimal weight:    6.9990
   chunk 97 optimal weight:    0.9980
   chunk 39 optimal weight:    9.9990
   chunk 15 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 125 ASN
B 156 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.221344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.131784 restraints weight = 9164.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3552 rms_B_bonded: 3.30
r_work: 0.3350 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5779
moved from start:          0.4032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9032  Z= 0.106
  Angle     :  0.510   9.468  12256  Z= 0.258
  Chirality :  0.041   0.220   1408
  Planarity :  0.003   0.042   1529
  Dihedral  :  4.010  32.298   1287
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 20.45 %
    Favored  : 77.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 are not related in a simple way.
  whole:  0.59 (0.26), residues: 1116
  helix:  2.29 (0.26), residues: 408
  sheet: -0.31 (0.30), residues: 276
  loop : -0.97 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 277 
 TYR   0.013   0.001   TYR S 190 
 PHE   0.016   0.001   PHE R  89 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 9031)
  covalent geometry    : angle       0.50956 (12254)
  SS BOND              : bond        0.00003 (    1)
  SS BOND              : angle       0.11050 (    2)
  hydrogen bonds       : bond        0.03516 (  439)
  hydrogen bonds       : angle       4.11619 ( 1260)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 94
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6774 (mp0)
REVERT: A  341 ASP cc_start: 0.6603 (t0) cc_final: 0.6228 (t0)
REVERT: B  111 TYR cc_start: 0.7211 (m-80) cc_final: 0.6893 (m-80)
REVERT: B  217 MET cc_start: 0.6294 (ptt) cc_final: 0.5840 (ptm)
REVERT: B  219 ARG cc_start: 0.7490 (ttm-80) cc_final: 0.7087 (mtp180)
REVERT: B  280 LYS cc_start: 0.7031 (tttp) cc_final: 0.6341 (ttmt)
REVERT: G   21 MET cc_start: 0.7781 (mtt) cc_final: 0.7415 (mtm)
REVERT: R   59 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6325 (mm)
REVERT: R  193 ARG cc_start: 0.5063 (ttp-170) cc_final: 0.4693 (tpp80)
REVERT: S   87 ARG cc_start: 0.5663 (ptp-170) cc_final: 0.5462 (mmt90)
REVERT: S  150 THR cc_start: 0.7182 (p) cc_final: 0.6921 (t)
REVERT: S  206 SER cc_start: 0.5177 (t) cc_final: 0.4813 (p)
REVERT: S  228 TYR cc_start: 0.6082 (m-80) cc_final: 0.5507 (m-80)
  outliers start: 23
  outliers final: 17
  residues processed: 112
  average time/residue: 0.4681
  time to fit residues: 56.5971
Evaluate side-chains
  111 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain R residue   59 LEU
Chi-restraints excluded: chain R residue  130 ASP
Chi-restraints excluded: chain R residue  259 ILE
Chi-restraints excluded: chain R residue  295 CYS
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue  194 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 64 optimal weight:    4.9990
   chunk 69 optimal weight:    3.9990
   chunk 90 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0060
   chunk 53 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0030
   overall best weight:    0.5610

-------------------------------------------------------------------------------
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 = 0.4443 r_free = 0.4443 target = 0.221660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.132716 restraints weight = 9174.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 3.30
r_work: 0.3365 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5799
moved from start:          0.4114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9032  Z= 0.102
  Angle     :  0.509   9.589  12256  Z= 0.257
  Chirality :  0.041   0.198   1408
  Planarity :  0.003   0.042   1529
  Dihedral  :  3.932  29.046   1287
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 20.66 %
    Favored  : 77.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 are not related in a simple way.
  whole:  0.69 (0.26), residues: 1116
  helix:  2.38 (0.27), residues: 408
  sheet: -0.27 (0.30), residues: 276
  loop : -0.92 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 277 
 TYR   0.013   0.001   TYR S 190 
 PHE   0.016   0.001   PHE R  89 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 9031)
  covalent geometry    : angle       0.50924 (12254)
  SS BOND              : bond        0.00024 (    1)
  SS BOND              : angle       0.13365 (    2)
  hydrogen bonds       : bond        0.03446 (  439)
  hydrogen bonds       : angle       4.09507 ( 1260)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6773 (mp0)
REVERT: A  331 ASN cc_start: 0.8539 (m-40) cc_final: 0.8315 (m110)
REVERT: A  341 ASP cc_start: 0.6677 (t0) cc_final: 0.6294 (t0)
REVERT: B  111 TYR cc_start: 0.7214 (m-80) cc_final: 0.6894 (m-80)
REVERT: B  217 MET cc_start: 0.6301 (ptt) cc_final: 0.5873 (ptm)
REVERT: B  219 ARG cc_start: 0.7496 (ttm-80) cc_final: 0.7108 (mtp180)
REVERT: B  280 LYS cc_start: 0.7054 (tttp) cc_final: 0.6372 (ttmt)
REVERT: G   21 MET cc_start: 0.7779 (mtt) cc_final: 0.7418 (mtm)
REVERT: R   59 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6339 (mm)
REVERT: R  193 ARG cc_start: 0.5125 (ttp-170) cc_final: 0.4763 (tpp80)
REVERT: S   83 MET cc_start: 0.3007 (mtp) cc_final: 0.2530 (mmt)
REVERT: S  206 SER cc_start: 0.5099 (t) cc_final: 0.4713 (p)
REVERT: S  228 TYR cc_start: 0.6115 (m-80) cc_final: 0.5568 (m-80)
  outliers start: 21
  outliers final: 16
  residues processed: 119
  average time/residue: 0.4687
  time to fit residues: 60.2818
Evaluate side-chains
  114 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain R residue   59 LEU
Chi-restraints excluded: chain R residue  259 ILE
Chi-restraints excluded: chain R residue  295 CYS
Chi-restraints excluded: chain S residue    2 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 78 optimal weight:    0.9990
   chunk 88 optimal weight:    7.9990
   chunk 30 optimal weight:    0.8980
   chunk 99 optimal weight:    0.0370
   chunk 69 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 103 optimal weight:    9.9990
   chunk 56 optimal weight:    6.9990
   chunk 104 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.7860

-------------------------------------------------------------------------------
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 = 0.4543 r_free = 0.4543 target = 0.226410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.137349 restraints weight = 9118.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 3.25
r_work: 0.3427 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6133
moved from start:          0.4175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9032  Z= 0.114
  Angle     :  0.522   9.589  12256  Z= 0.264
  Chirality :  0.041   0.202   1408
  Planarity :  0.003   0.041   1529
  Dihedral  :  3.963  28.246   1287
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 20.98 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 are not related in a simple way.
  whole:  0.68 (0.26), residues: 1116
  helix:  2.35 (0.26), residues: 408
  sheet: -0.28 (0.30), residues: 276
  loop : -0.90 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG S  87 
 TYR   0.013   0.001   TYR S 190 
 PHE   0.013   0.001   PHE S 203 
 TRP   0.012   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 9031)
  covalent geometry    : angle       0.52229 (12254)
  SS BOND              : bond        0.00071 (    1)
  SS BOND              : angle       0.22025 (    2)
  hydrogen bonds       : bond        0.03569 (  439)
  hydrogen bonds       : angle       4.11972 ( 1260)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3676.12 seconds
wall clock time: 63 minutes 9.63 seconds (3789.63 seconds total)