Starting phenix.real_space_refine
on Thu Mar 13 08:10:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wwj_37890/03_2025/8wwj_37890.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wwj_37890/03_2025/8wwj_37890.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wwj_37890/03_2025/8wwj_37890.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wwj_37890/03_2025/8wwj_37890.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wwj_37890/03_2025/8wwj_37890.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wwj_37890/03_2025/8wwj_37890.cif"
  }
  resolution = 3.03
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.054
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      64      5.16       5
     C    5618      2.51       5
     N    1491      2.21       5
     O    1648      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8821
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1749
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 2, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 67
          Unresolved non-hydrogen dihedrals: 47
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 32
    Chain: "B"
      Number of atoms: 2622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 342, 2622
          Classifications: {'peptide': 342}
          Link IDs: {'PTRANS': 5, 'TRANS': 336}
    Chain: "C"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "E"
      Number of atoms: 1779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1779
          Classifications: {'peptide': 231}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2235
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2235
          Classifications: {'peptide': 289}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 15, 'TRANS': 273}
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 69
          Unresolved non-hydrogen dihedrals: 46
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 32
  Time building chain proxies: 5.02, per 1000 atoms: 0.57
  Number of scatterers: 8821
  At special positions: 0
  Unit cell: (87.74, 117.7, 126.26, 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      64     16.00
     O    1648      8.00
     N    1491      7.00
     C    5618      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 185 " - pdb=" SG  CYS R 263 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.02
  Conformation dependent library (CDL) restraints added in 992.6 milliseconds
  

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2140

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 14 sheets defined
      38.4% alpha, 23.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.627A  pdb=" N   VAL A  50 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 4.224A  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 241 through 255
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.662A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 4.403A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 352
    Processing helix  chain 'B' and resid 3 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 7 through 24
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 55 through 59
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.577A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 108 through 138
      Proline residue:  R 113  - end of helix
    Processing helix  chain 'R' and resid 145 through 164
    Processing helix  chain 'R' and resid 165 through 170
    Processing helix  chain 'R' and resid 180 through 216
      removed outlier: 3.950A  pdb=" N   MET R 184 " --> pdb=" O   PHE R 180 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 218 through 223
      removed outlier: 3.584A  pdb=" N   THR R 221 " --> pdb=" O   ILE R 218 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LYS R 222 " --> pdb=" O   SER R 219 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 225 through 244
    Processing helix  chain 'R' and resid 244 through 250
    Processing helix  chain 'R' and resid 269 through 286
      removed outlier: 3.758A  pdb=" N   LEU R 274 " --> pdb=" O   PRO R 270 " (cutoff:3.500A)
      removed outlier: 5.789A  pdb=" N   TYR R 275 " --> pdb=" O   ASP R 271 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   TRP R 276 " --> pdb=" O   THR R 272 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 286 through 303
    Processing helix  chain 'R' and resid 313 through 337
      removed outlier: 3.617A  pdb=" N   ALA R 329 " --> pdb=" O   ARG R 325 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 338 through 351
      removed outlier: 4.037A  pdb=" N   LEU R 349 " --> pdb=" O   GLN R 345 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   SER R 350 " --> pdb=" O   LEU R 346 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 355 through 384
      removed outlier: 4.287A  pdb=" N   SER R 373 " --> pdb=" O   GLY R 369 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   CYS R 374 " --> pdb=" O   TYR R 370 " (cutoff:3.500A)
      Proline residue:  R 377  - end of helix
    Processing helix  chain 'R' and resid 384 through 395
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.281A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.715A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.674A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.099A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.783A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.895A  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: 6.076A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.146A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.215A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.608A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.855A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.396A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.094A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.507A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.926A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.088A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.878A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.723A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12
      removed outlier: 6.859A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12
      removed outlier: 4.192A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148
      removed outlier: 3.629A  pdb=" N   GLY E 225 " --> pdb=" O   LEU E 245 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   LEU E 178 " --> pdb=" O   LEU E 187 " (cutoff:3.500A)
      removed outlier: 5.619A  pdb=" N   LEU E 187 " --> pdb=" O   LEU E 178 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'R' and resid 251 through 254
      removed outlier: 3.546A  pdb=" N   ARG R 252 " --> pdb=" O   GLY R 264 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   GLY R 264 " --> pdb=" O   ARG R 252 " (cutoff:3.500A)

    466 hydrogen bonds defined for protein.
    1311 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.48

  Time building geometry restraints manager: 2.42 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2842
        1.34 -     1.46: 1806
        1.46 -     1.58: 4269
        1.58 -     1.69: 0
        1.69 -     1.81: 93
  Bond restraints: 9010
  Sorted by residual:
  bond pdb=" CG1 ILE B  81 "
       pdb=" CD1 ILE B  81 "
    ideal  model  delta    sigma   weight residual
    1.513  1.472  0.041 3.90e-02 6.57e+02 1.13e+00
  bond pdb=" CB  TRP B  99 "
       pdb=" CG  TRP B  99 "
    ideal  model  delta    sigma   weight residual
    1.498  1.475  0.023 3.10e-02 1.04e+03 5.70e-01
  bond pdb=" CG1 ILE B  58 "
       pdb=" CD1 ILE B  58 "
    ideal  model  delta    sigma   weight residual
    1.513  1.486  0.027 3.90e-02 6.57e+02 4.68e-01
  bond pdb=" CB  ASP A  20 "
       pdb=" CG  ASP A  20 "
    ideal  model  delta    sigma   weight residual
    1.516  1.499  0.017 2.50e-02 1.60e+03 4.62e-01
  bond pdb=" C   LEU B 336 "
       pdb=" N   LYS B 337 "
    ideal  model  delta    sigma   weight residual
    1.331  1.321  0.010 1.55e-02 4.16e+03 4.28e-01
  ... (remaining 9005 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.09: 11919
        1.09 -     2.18: 252
        2.18 -     3.26: 42
        3.26 -     4.35: 9
        4.35 -     5.44: 11
  Bond angle restraints: 12233
  Sorted by residual:
  angle pdb=" C   ARG E 191 "
        pdb=" N   MET E 192 "
        pdb=" CA  MET E 192 "
      ideal   model   delta    sigma   weight residual
     121.54  125.78   -4.24 1.91e+00 2.74e-01 4.94e+00
  angle pdb=" N   TYR E 102 "
        pdb=" CA  TYR E 102 "
        pdb=" C   TYR E 102 "
      ideal   model   delta    sigma   weight residual
     108.96  106.16    2.80 1.49e+00 4.50e-01 3.52e+00
  angle pdb=" C   ASP B 163 "
        pdb=" N   THR B 164 "
        pdb=" CA  THR B 164 "
      ideal   model   delta    sigma   weight residual
     124.31  127.18   -2.87 1.67e+00 3.59e-01 2.95e+00
  angle pdb=" CA  TYR E 103 "
        pdb=" CB  TYR E 103 "
        pdb=" CG  TYR E 103 "
      ideal   model   delta    sigma   weight residual
     113.90  110.85    3.05 1.80e+00 3.09e-01 2.88e+00
  angle pdb=" C   ASP B 333 "
        pdb=" N   SER B 334 "
        pdb=" CA  SER B 334 "
      ideal   model   delta    sigma   weight residual
     123.93  126.49   -2.56 1.54e+00 4.22e-01 2.76e+00
  ... (remaining 12228 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.41: 5148
       16.41 -    32.83: 145
       32.83 -    49.24: 33
       49.24 -    65.66: 4
       65.66 -    82.07: 1
  Dihedral angle restraints: 5331
    sinusoidal: 2014
      harmonic: 3317
  Sorted by residual:
  dihedral pdb=" CA  GLN B  75 "
           pdb=" C   GLN B  75 "
           pdb=" N   ASP B  76 "
           pdb=" CA  ASP B  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.34   20.66     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" CA  ARG E 191 "
           pdb=" C   ARG E 191 "
           pdb=" N   MET E 192 "
           pdb=" CA  MET E 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.36   18.64     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" CA  PHE E  32 "
           pdb=" C   PHE E  32 "
           pdb=" N   GLY E  33 "
           pdb=" CA  GLY E  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.82   18.18     0      5.00e+00 4.00e-02 1.32e+01
  ... (remaining 5328 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 814
       0.028 -    0.055: 372
       0.055 -    0.083: 126
       0.083 -    0.110: 73
       0.110 -    0.138: 21
  Chirality restraints: 1406
  Sorted by residual:
  chirality pdb=" CA  ILE A 221 "
            pdb=" N   ILE A 221 "
            pdb=" C   ILE A 221 "
            pdb=" CB  ILE A 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.75e-01
  chirality pdb=" CA  ILE B 120 "
            pdb=" N   ILE B 120 "
            pdb=" C   ILE B 120 "
            pdb=" CB  ILE B 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.69e-01
  chirality pdb=" CA  THR B 164 "
            pdb=" N   THR B 164 "
            pdb=" C   THR B 164 "
            pdb=" CB  THR B 164 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.39    0.14 2.00e-01 2.50e+01 4.66e-01
  ... (remaining 1403 not shown)

  Planarity restraints: 1547
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.030 5.00e-02 4.00e+02   4.50e-02 3.24e+00
        pdb=" N   PRO B 236 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 193 "   -0.022 5.00e-02 4.00e+02   3.37e-02 1.82e+00
        pdb=" N   PRO B 194 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO B 194 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 194 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 151 "   -0.010 2.00e-02 2.50e+03   7.30e-03 9.32e-01
        pdb=" CG  PHE B 151 "    0.016 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 151 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 151 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 151 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 151 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 151 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 1544 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 138
        2.67 -     3.23: 8324
        3.23 -     3.79: 13871
        3.79 -     4.34: 19515
        4.34 -     4.90: 32609
  Nonbonded interactions: 74457
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR E 175 "
     model   vdw
     2.118 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.119 3.040
  nonbonded pdb=" O   SER R 243 "
            pdb=" OH  TYR R 280 "
     model   vdw
     2.131 3.040
  nonbonded pdb=" OH  TYR A 320 "
            pdb=" OD2 ASP A 341 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP C  48 "
     model   vdw
     2.271 3.040
  ... (remaining 74452 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     21.630
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
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      :  0.003   0.041   9010  Z= 0.217
  Angle     :  0.435   5.439  12233  Z= 0.230
  Chirality :  0.041   0.138   1406
  Planarity :  0.003   0.045   1547
  Dihedral  :  8.315  82.072   3182
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  2.63 %
    Favored  : 96.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.25), residues: 1129
  helix:  1.24 (0.26), residues: 394
  sheet:  0.77 (0.29), residues: 291
  loop :  0.44 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  99 
 HIS   0.002   0.001   HIS E  35 
 PHE   0.016   0.001   PHE B 151 
 TYR   0.013   0.001   TYR E 190 
 ARG   0.002   0.000   ARG A  21 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 256
  time to evaluate  : 1.063 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.8562 (mmm) cc_final: 0.8336 (mmm)
REVERT: A  290 TYR cc_start: 0.8615 (t80) cc_final: 0.8302 (t80)
REVERT: A  314 LYS cc_start: 0.7632 (mttt) cc_final: 0.7338 (mtpt)
REVERT: B   19 ARG cc_start: 0.8038 (ttp80) cc_final: 0.7614 (ttp80)
REVERT: B   57 LYS cc_start: 0.8581 (mppt) cc_final: 0.8211 (mtmt)
REVERT: B  186 ASP cc_start: 0.8597 (m-30) cc_final: 0.8327 (m-30)
REVERT: B  214 ARG cc_start: 0.7856 (mmt180) cc_final: 0.7598 (mmt180)
REVERT: B  333 ASP cc_start: 0.8531 (p0) cc_final: 0.8281 (p0)
REVERT: C   17 GLU cc_start: 0.8599 (tp30) cc_final: 0.8389 (tp30)
REVERT: C   38 MET cc_start: 0.7048 (ttp) cc_final: 0.6564 (tpt)
REVERT: E   46 GLU cc_start: 0.7824 (tt0) cc_final: 0.7310 (tt0)
REVERT: E   83 MET cc_start: 0.8259 (mtm) cc_final: 0.8003 (mtm)
REVERT: E   85 SER cc_start: 0.9066 (m) cc_final: 0.8804 (p)
REVERT: E  160 ARG cc_start: 0.7391 (mtp-110) cc_final: 0.6832 (ttm-80)
REVERT: E  186 GLN cc_start: 0.8114 (tt0) cc_final: 0.7718 (tt0)
REVERT: E  213 THR cc_start: 0.8269 (m) cc_final: 0.8035 (p)
REVERT: E  215 THR cc_start: 0.7716 (m) cc_final: 0.7326 (t)
REVERT: E  217 SER cc_start: 0.8255 (m) cc_final: 0.7821 (t)
  outliers start: 6
  outliers final: 2
  residues processed: 260
  average time/residue: 0.2676
  time to fit residues: 90.1540
Evaluate side-chains
  188 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 186
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  192 ASP
Chi-restraints excluded: chain R residue  280 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   chunk 47 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 87 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 65 optimal weight:    0.2980
   chunk 101 optimal weight:    2.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 322 HIS
B  91 HIS
B 259 GLN
E 171 ASN
E 179 GLN
R 194 ASN
R 216 HIS
R 281 GLN
R 345 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.186094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.134129 restraints weight = 10775.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3588 rms_B_bonded: 2.40
r_work: 0.3439 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3289 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9010  Z= 0.234
  Angle     :  0.555   6.365  12233  Z= 0.300
  Chirality :  0.043   0.151   1406
  Planarity :  0.004   0.043   1547
  Dihedral  :  4.558  52.940   1236
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 11.03 %
    Favored  : 86.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.25), residues: 1129
  helix:  2.10 (0.26), residues: 395
  sheet:  0.73 (0.29), residues: 299
  loop :  0.21 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP R 248 
 HIS   0.003   0.001   HIS R 216 
 PHE   0.016   0.001   PHE B 151 
 TYR   0.018   0.002   TYR E 190 
 ARG   0.004   0.001   ARG B 134 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 203
  time to evaluate  : 1.034 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  290 TYR cc_start: 0.8565 (t80) cc_final: 0.8299 (t80)
REVERT: A  314 LYS cc_start: 0.7818 (mttt) cc_final: 0.7394 (mtpt)
REVERT: B   19 ARG cc_start: 0.8012 (ttp80) cc_final: 0.7664 (ttp80)
REVERT: B   57 LYS cc_start: 0.8605 (mppt) cc_final: 0.8396 (mtpt)
REVERT: B  170 ASP cc_start: 0.8574 (t70) cc_final: 0.8254 (t0)
REVERT: B  186 ASP cc_start: 0.8751 (m-30) cc_final: 0.8373 (m-30)
REVERT: B  188 MET cc_start: 0.8701 (mmm) cc_final: 0.8007 (mmp)
REVERT: B  214 ARG cc_start: 0.8291 (mmt180) cc_final: 0.7940 (mmt180)
REVERT: B  277 SER cc_start: 0.8139 (t) cc_final: 0.7849 (m)
REVERT: B  303 ASP cc_start: 0.7557 (m-30) cc_final: 0.7258 (m-30)
REVERT: C   15 LEU cc_start: 0.9150 (mm) cc_final: 0.8845 (tt)
REVERT: C   17 GLU cc_start: 0.8987 (tp30) cc_final: 0.8585 (tp30)
REVERT: C   32 LYS cc_start: 0.8188 (tppt) cc_final: 0.7844 (tttt)
REVERT: C   38 MET cc_start: 0.7116 (ttp) cc_final: 0.6421 (tpt)
REVERT: E   46 GLU cc_start: 0.8259 (tt0) cc_final: 0.7674 (tt0)
REVERT: E   83 MET cc_start: 0.8225 (mtm) cc_final: 0.8010 (mtm)
REVERT: E  160 ARG cc_start: 0.7701 (mtp-110) cc_final: 0.6908 (ttm-80)
REVERT: E  186 GLN cc_start: 0.8450 (tt0) cc_final: 0.8055 (tt0)
REVERT: E  224 VAL cc_start: 0.7450 (t) cc_final: 0.7244 (p)
REVERT: R  169 ILE cc_start: 0.7625 (pt) cc_final: 0.7106 (pp)
REVERT: R  303 ARG cc_start: 0.7410 (mtp85) cc_final: 0.7199 (mtp85)
REVERT: R  342 TYR cc_start: 0.7927 (m-80) cc_final: 0.7537 (m-80)
REVERT: R  380 TYR cc_start: 0.7937 (t80) cc_final: 0.7703 (t80)
REVERT: R  388 ARG cc_start: 0.7753 (ttp-170) cc_final: 0.7237 (ttp-110)
  outliers start: 21
  outliers final: 10
  residues processed: 214
  average time/residue: 0.2550
  time to fit residues: 71.2085
Evaluate side-chains
  189 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 179
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain R residue  138 SER
Chi-restraints excluded: chain R residue  156 VAL
Chi-restraints excluded: chain R residue  188 ILE
Chi-restraints excluded: chain R residue  239 LEU
Chi-restraints excluded: chain R residue  343 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 10 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   chunk 79 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 52 optimal weight:    0.2980
   chunk 16 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 82 optimal weight:    3.9990
   overall best weight:    2.0588

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

Flipped N/Q/H residues before XYZ refinement:
B 125 ASN
E 179 GLN
R 179 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.182959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.130424 restraints weight = 10898.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 2.41
r_work: 0.3394 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3244 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.2589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075   9010  Z= 0.344
  Angle     :  0.582   7.131  12233  Z= 0.309
  Chirality :  0.044   0.154   1406
  Planarity :  0.004   0.043   1547
  Dihedral  :  4.327  29.379   1232
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 12.39 %
    Favored  : 84.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.25), residues: 1129
  helix:  2.04 (0.26), residues: 395
  sheet:  0.29 (0.28), residues: 305
  loop :  0.15 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  99 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.034   0.002   PHE R 387 
 TYR   0.036   0.002   TYR R 360 
 ARG   0.006   0.001   ARG R 322 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 182
  time to evaluate  : 1.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.8172 (ttm) cc_final: 0.7832 (ttm)
REVERT: A  244 HIS cc_start: 0.8176 (m90) cc_final: 0.7872 (m-70)
REVERT: A  290 TYR cc_start: 0.8624 (t80) cc_final: 0.8189 (t80)
REVERT: A  314 LYS cc_start: 0.7898 (mttt) cc_final: 0.7568 (mtpt)
REVERT: B   13 GLN cc_start: 0.8437 (tm-30) cc_final: 0.8206 (pp30)
REVERT: B   19 ARG cc_start: 0.8026 (ttp80) cc_final: 0.7752 (ttp80)
REVERT: B   57 LYS cc_start: 0.8676 (mppt) cc_final: 0.8382 (mtpt)
REVERT: B  170 ASP cc_start: 0.8584 (t70) cc_final: 0.8279 (t0)
REVERT: B  186 ASP cc_start: 0.8902 (m-30) cc_final: 0.8589 (m-30)
REVERT: B  217 MET cc_start: 0.8117 (ptm) cc_final: 0.7567 (ptm)
REVERT: B  277 SER cc_start: 0.8231 (t) cc_final: 0.7928 (m)
REVERT: B  303 ASP cc_start: 0.7825 (m-30) cc_final: 0.7502 (m-30)
REVERT: C   17 GLU cc_start: 0.8977 (tp30) cc_final: 0.8701 (tp30)
REVERT: C   38 MET cc_start: 0.7280 (ttp) cc_final: 0.6980 (ttp)
REVERT: E   46 GLU cc_start: 0.8224 (tt0) cc_final: 0.7658 (tt0)
REVERT: E  142 GLN cc_start: 0.6919 (mt0) cc_final: 0.6156 (mt0)
REVERT: E  160 ARG cc_start: 0.7946 (mtp-110) cc_final: 0.7275 (ttm-80)
REVERT: E  186 GLN cc_start: 0.8536 (tt0) cc_final: 0.8128 (tt0)
REVERT: E  215 THR cc_start: 0.7803 (m) cc_final: 0.7435 (t)
REVERT: E  224 VAL cc_start: 0.7559 (t) cc_final: 0.7350 (p)
REVERT: E  234 GLU cc_start: 0.8469 (tp30) cc_final: 0.8094 (tp30)
REVERT: R  278 THR cc_start: 0.8672 (m) cc_final: 0.8443 (t)
REVERT: R  325 ARG cc_start: 0.8467 (ptp90) cc_final: 0.7988 (ttp80)
REVERT: R  342 TYR cc_start: 0.8440 (m-80) cc_final: 0.7937 (m-80)
REVERT: R  380 TYR cc_start: 0.8028 (t80) cc_final: 0.7821 (t80)
  outliers start: 31
  outliers final: 21
  residues processed: 196
  average time/residue: 0.2765
  time to fit residues: 69.9851
Evaluate side-chains
  198 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 177
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue   85 SER
Chi-restraints excluded: chain E residue  113 GLN
Chi-restraints excluded: chain E residue  238 THR
Chi-restraints excluded: chain R residue  138 SER
Chi-restraints excluded: chain R residue  156 VAL
Chi-restraints excluded: chain R residue  188 ILE
Chi-restraints excluded: chain R residue  221 THR
Chi-restraints excluded: chain R residue  232 VAL
Chi-restraints excluded: chain R residue  247 VAL
Chi-restraints excluded: chain R residue  343 VAL
Chi-restraints excluded: chain R residue  372 ASN
Chi-restraints excluded: chain R residue  379 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 103 optimal weight:    0.6980
   chunk 87 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0470
   chunk 23 optimal weight:    4.9990
   chunk 98 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9990
   chunk 16 optimal weight:    7.9990
   chunk 92 optimal weight:    5.9990
   chunk 99 optimal weight:   10.0000
   chunk 107 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.6280

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
B  32 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.186901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.135147 restraints weight = 10848.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.3602 rms_B_bonded: 2.41
r_work: 0.3452 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3304 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.2860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9010  Z= 0.164
  Angle     :  0.496   6.296  12233  Z= 0.264
  Chirality :  0.041   0.141   1406
  Planarity :  0.003   0.041   1547
  Dihedral  :  4.017  29.343   1232
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 14.50 %
    Favored  : 83.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.25), residues: 1129
  helix:  2.28 (0.26), residues: 396
  sheet:  0.43 (0.29), residues: 294
  loop :  0.08 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.020   0.001   PHE R 387 
 TYR   0.033   0.001   TYR R 360 
 ARG   0.005   0.000   ARG R 322 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 183
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7752 (ttm)
REVERT: A  186 GLU cc_start: 0.8256 (tt0) cc_final: 0.8051 (tt0)
REVERT: A  197 LYS cc_start: 0.8384 (mtmt) cc_final: 0.7937 (mttp)
REVERT: A  290 TYR cc_start: 0.8614 (t80) cc_final: 0.8223 (t80)
REVERT: A  314 LYS cc_start: 0.7847 (mttt) cc_final: 0.7549 (mtpt)
REVERT: B   19 ARG cc_start: 0.8083 (ttp80) cc_final: 0.7788 (ttp80)
REVERT: B   36 ASN cc_start: 0.8652 (m-40) cc_final: 0.8316 (p0)
REVERT: B   57 LYS cc_start: 0.8530 (mppt) cc_final: 0.8247 (mtpt)
REVERT: B  170 ASP cc_start: 0.8581 (t70) cc_final: 0.8348 (t0)
REVERT: B  186 ASP cc_start: 0.8770 (m-30) cc_final: 0.8485 (m-30)
REVERT: B  264 TYR cc_start: 0.7958 (m-80) cc_final: 0.7071 (m-80)
REVERT: B  277 SER cc_start: 0.8065 (t) cc_final: 0.7806 (m)
REVERT: B  298 ASP cc_start: 0.8409 (t0) cc_final: 0.8155 (t0)
REVERT: B  303 ASP cc_start: 0.7632 (m-30) cc_final: 0.7310 (m-30)
REVERT: C   42 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7472 (mm-30)
REVERT: E   46 GLU cc_start: 0.8148 (tt0) cc_final: 0.7569 (tt0)
REVERT: E  160 ARG cc_start: 0.8001 (mtp-110) cc_final: 0.7247 (ttm-80)
REVERT: E  179 GLN cc_start: 0.8653 (tt0) cc_final: 0.8247 (tt0)
REVERT: E  224 VAL cc_start: 0.7525 (t) cc_final: 0.7320 (p)
REVERT: E  234 GLU cc_start: 0.8453 (tp30) cc_final: 0.8065 (tp30)
REVERT: R  112 MET cc_start: 0.9040 (tmm) cc_final: 0.8827 (tmm)
REVERT: R  342 TYR cc_start: 0.8505 (m-80) cc_final: 0.7948 (m-80)
REVERT: R  388 ARG cc_start: 0.7748 (ttp-170) cc_final: 0.7285 (ttp-110)
  outliers start: 18
  outliers final: 13
  residues processed: 188
  average time/residue: 0.3012
  time to fit residues: 72.5518
Evaluate side-chains
  187 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 173
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain E residue  113 GLN
Chi-restraints excluded: chain E residue  238 THR
Chi-restraints excluded: chain R residue  184 MET
Chi-restraints excluded: chain R residue  188 ILE
Chi-restraints excluded: chain R residue  343 VAL
Chi-restraints excluded: chain R residue  379 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 48 optimal weight:    5.9990
   chunk 78 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 89 optimal weight:    7.9990
   chunk 57 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 125 ASN
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 142 GLN
R 194 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.186299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.137189 restraints weight = 10896.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 2.69
r_work: 0.3424 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.3029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9010  Z= 0.190
  Angle     :  0.503   5.466  12233  Z= 0.267
  Chirality :  0.042   0.138   1406
  Planarity :  0.003   0.040   1547
  Dihedral  :  3.964  28.948   1232
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 13.97 %
    Favored  : 83.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.25), residues: 1129
  helix:  2.30 (0.26), residues: 396
  sheet:  0.31 (0.29), residues: 303
  loop :  0.15 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.016   0.001   PHE R 387 
 TYR   0.038   0.001   TYR R 360 
 ARG   0.007   0.001   ARG B 134 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 181
  time to evaluate  : 1.062 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7502 (ttm)
REVERT: A   29 LYS cc_start: 0.8338 (ttpp) cc_final: 0.8125 (tttm)
REVERT: A  186 GLU cc_start: 0.8148 (tt0) cc_final: 0.7878 (tt0)
REVERT: A  197 LYS cc_start: 0.8269 (mtmt) cc_final: 0.7840 (mttp)
REVERT: A  290 TYR cc_start: 0.8632 (t80) cc_final: 0.8258 (t80)
REVERT: A  314 LYS cc_start: 0.7792 (mttt) cc_final: 0.7501 (mtpt)
REVERT: B   19 ARG cc_start: 0.7990 (ttp80) cc_final: 0.7704 (ttp80)
REVERT: B  170 ASP cc_start: 0.8380 (t70) cc_final: 0.8164 (t0)
REVERT: B  186 ASP cc_start: 0.8702 (m-30) cc_final: 0.8391 (m-30)
REVERT: B  217 MET cc_start: 0.8003 (ptm) cc_final: 0.7354 (ptm)
REVERT: B  264 TYR cc_start: 0.7969 (m-80) cc_final: 0.7204 (m-80)
REVERT: B  277 SER cc_start: 0.7968 (t) cc_final: 0.7738 (m)
REVERT: B  298 ASP cc_start: 0.8397 (t0) cc_final: 0.8131 (t0)
REVERT: B  303 ASP cc_start: 0.7623 (m-30) cc_final: 0.7240 (m-30)
REVERT: C   42 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7304 (mm-30)
REVERT: E   46 GLU cc_start: 0.7945 (tt0) cc_final: 0.7394 (tt0)
REVERT: E   83 MET cc_start: 0.7977 (mtm) cc_final: 0.7771 (mtm)
REVERT: E  160 ARG cc_start: 0.7886 (mtp-110) cc_final: 0.7239 (ttm-80)
REVERT: E  175 TYR cc_start: 0.8477 (m-80) cc_final: 0.8257 (m-80)
REVERT: E  215 THR cc_start: 0.7741 (m) cc_final: 0.7415 (t)
REVERT: E  224 VAL cc_start: 0.7505 (t) cc_final: 0.7293 (p)
REVERT: E  234 GLU cc_start: 0.8294 (tp30) cc_final: 0.7880 (tp30)
REVERT: R  116 PHE cc_start: 0.8668 (m-80) cc_final: 0.8310 (m-80)
REVERT: R  325 ARG cc_start: 0.8319 (ptp90) cc_final: 0.7824 (ttp80)
REVERT: R  342 TYR cc_start: 0.8440 (m-80) cc_final: 0.7893 (m-80)
REVERT: R  380 TYR cc_start: 0.8331 (t80) cc_final: 0.7854 (t80)
REVERT: R  388 ARG cc_start: 0.7641 (ttp-170) cc_final: 0.7232 (ttp-110)
  outliers start: 26
  outliers final: 21
  residues processed: 191
  average time/residue: 0.3131
  time to fit residues: 76.8553
Evaluate side-chains
  194 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 172
  time to evaluate  : 1.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue   85 SER
Chi-restraints excluded: chain E residue  238 THR
Chi-restraints excluded: chain R residue  138 SER
Chi-restraints excluded: chain R residue  188 ILE
Chi-restraints excluded: chain R residue  239 LEU
Chi-restraints excluded: chain R residue  343 VAL
Chi-restraints excluded: chain R residue  344 LEU
Chi-restraints excluded: chain R residue  372 ASN
Chi-restraints excluded: chain R residue  379 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 104 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 4 optimal weight:    7.9990
   chunk 86 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B 125 ASN
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.190103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.141009 restraints weight = 10761.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3661 rms_B_bonded: 2.71
r_work: 0.3481 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.3111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9010  Z= 0.235
  Angle     :  0.515   6.085  12233  Z= 0.275
  Chirality :  0.043   0.182   1406
  Planarity :  0.004   0.040   1547
  Dihedral  :  4.021  29.594   1232
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 14.18 %
    Favored  : 83.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.25), residues: 1129
  helix:  2.24 (0.26), residues: 398
  sheet:  0.30 (0.30), residues: 296
  loop :  0.17 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 339 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.017   0.001   PHE B 151 
 TYR   0.037   0.002   TYR R 360 
 ARG   0.006   0.001   ARG R 322 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 181
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7744 (ttm)
REVERT: A  186 GLU cc_start: 0.8284 (tt0) cc_final: 0.7993 (tt0)
REVERT: A  197 LYS cc_start: 0.8461 (mtmt) cc_final: 0.7943 (mttp)
REVERT: A  290 TYR cc_start: 0.8636 (t80) cc_final: 0.8237 (t80)
REVERT: A  314 LYS cc_start: 0.7971 (mttt) cc_final: 0.7636 (mtpt)
REVERT: B   19 ARG cc_start: 0.8092 (ttp80) cc_final: 0.7801 (ttp80)
REVERT: B  186 ASP cc_start: 0.8841 (m-30) cc_final: 0.8532 (m-30)
REVERT: B  264 TYR cc_start: 0.8052 (m-80) cc_final: 0.7394 (m-80)
REVERT: B  277 SER cc_start: 0.8128 (t) cc_final: 0.7881 (m)
REVERT: B  298 ASP cc_start: 0.8538 (t0) cc_final: 0.8263 (t0)
REVERT: C   28 ILE cc_start: 0.8935 (pt) cc_final: 0.8675 (tp)
REVERT: E   46 GLU cc_start: 0.8133 (tt0) cc_final: 0.7611 (tt0)
REVERT: E  103 TYR cc_start: 0.8602 (t80) cc_final: 0.8289 (t80)
REVERT: E  160 ARG cc_start: 0.7932 (mtp-110) cc_final: 0.7231 (ttm-80)
REVERT: E  186 GLN cc_start: 0.8331 (tt0) cc_final: 0.8098 (pt0)
REVERT: E  215 THR cc_start: 0.7770 (m) cc_final: 0.7450 (t)
REVERT: E  224 VAL cc_start: 0.7515 (t) cc_final: 0.7293 (p)
REVERT: E  234 GLU cc_start: 0.8484 (tp30) cc_final: 0.8003 (tp30)
REVERT: R  278 THR cc_start: 0.8707 (m) cc_final: 0.8377 (t)
REVERT: R  342 TYR cc_start: 0.8527 (m-80) cc_final: 0.8074 (m-80)
REVERT: R  380 TYR cc_start: 0.8493 (t80) cc_final: 0.8064 (t80)
REVERT: R  388 ARG cc_start: 0.7685 (ttp-170) cc_final: 0.7265 (ttp-110)
  outliers start: 26
  outliers final: 22
  residues processed: 192
  average time/residue: 0.2788
  time to fit residues: 69.6492
Evaluate side-chains
  197 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 174
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue  113 GLN
Chi-restraints excluded: chain E residue  217 SER
Chi-restraints excluded: chain E residue  238 THR
Chi-restraints excluded: chain R residue  138 SER
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  188 ILE
Chi-restraints excluded: chain R residue  232 VAL
Chi-restraints excluded: chain R residue  247 VAL
Chi-restraints excluded: chain R residue  344 LEU
Chi-restraints excluded: chain R residue  372 ASN
Chi-restraints excluded: chain R residue  379 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 106 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0000
   chunk 9 optimal weight:    0.9990
   chunk 102 optimal weight:    0.9990
   chunk 109 optimal weight:    6.9990
   chunk 87 optimal weight:    0.0010
   chunk 103 optimal weight:    0.9990
   chunk 100 optimal weight:   20.0000
   chunk 57 optimal weight:    2.9990
   chunk 104 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.5994

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

Flipped N/Q/H residues before XYZ refinement:
E 194 ASN
R 194 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.190993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.142345 restraints weight = 10758.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3690 rms_B_bonded: 2.25
r_work: 0.3538 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3397 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.3304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9010  Z= 0.154
  Angle     :  0.491   6.196  12233  Z= 0.261
  Chirality :  0.041   0.183   1406
  Planarity :  0.003   0.040   1547
  Dihedral  :  3.863  29.167   1232
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.60 %
    Favored  : 82.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.25), residues: 1129
  helix:  2.37 (0.26), residues: 398
  sheet:  0.36 (0.30), residues: 294
  loop :  0.14 (0.30), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.012   0.001   PHE R 387 
 TYR   0.037   0.001   TYR R 360 
 ARG   0.006   0.000   ARG R 303 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 182
  time to evaluate  : 1.034 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7777 (ttm)
REVERT: A  186 GLU cc_start: 0.8183 (tt0) cc_final: 0.7885 (tt0)
REVERT: A  197 LYS cc_start: 0.8617 (mtmt) cc_final: 0.8238 (mtmt)
REVERT: A  290 TYR cc_start: 0.8674 (t80) cc_final: 0.8272 (t80)
REVERT: A  314 LYS cc_start: 0.7900 (mttt) cc_final: 0.7614 (mtpt)
REVERT: B   19 ARG cc_start: 0.8130 (ttp80) cc_final: 0.7829 (ttp80)
REVERT: B  175 GLN cc_start: 0.8383 (mm-40) cc_final: 0.8019 (pt0)
REVERT: B  186 ASP cc_start: 0.8666 (m-30) cc_final: 0.8377 (m-30)
REVERT: B  217 MET cc_start: 0.8025 (ptm) cc_final: 0.7314 (ptm)
REVERT: B  264 TYR cc_start: 0.8026 (m-80) cc_final: 0.7390 (m-80)
REVERT: B  303 ASP cc_start: 0.7732 (m-30) cc_final: 0.7314 (m-30)
REVERT: C   28 ILE cc_start: 0.8900 (pt) cc_final: 0.8663 (tp)
REVERT: C   42 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7336 (mm-30)
REVERT: E   46 GLU cc_start: 0.8008 (tt0) cc_final: 0.7521 (tt0)
REVERT: E  103 TYR cc_start: 0.8418 (t80) cc_final: 0.8169 (t80)
REVERT: E  160 ARG cc_start: 0.7898 (mtp-110) cc_final: 0.7206 (ttm-80)
REVERT: E  186 GLN cc_start: 0.8332 (tt0) cc_final: 0.8109 (pt0)
REVERT: E  234 GLU cc_start: 0.8401 (tp30) cc_final: 0.7933 (tp30)
REVERT: R  342 TYR cc_start: 0.8468 (m-80) cc_final: 0.8065 (m-80)
REVERT: R  380 TYR cc_start: 0.8512 (t80) cc_final: 0.8102 (t80)
REVERT: R  388 ARG cc_start: 0.7577 (ttp-170) cc_final: 0.7203 (ttp-110)
  outliers start: 23
  outliers final: 16
  residues processed: 194
  average time/residue: 0.2609
  time to fit residues: 66.4241
Evaluate side-chains
  190 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 173
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain E residue   85 SER
Chi-restraints excluded: chain E residue  217 SER
Chi-restraints excluded: chain E residue  238 THR
Chi-restraints excluded: chain R residue  138 SER
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  188 ILE
Chi-restraints excluded: chain R residue  344 LEU
Chi-restraints excluded: chain R residue  379 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 11 optimal weight:    8.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.0980
   chunk 44 optimal weight:    3.9990
   chunk 7 optimal weight:    8.9990
   chunk 61 optimal weight:    0.6980
   chunk 4 optimal weight:    0.3980
   chunk 40 optimal weight:    0.7980
   chunk 96 optimal weight:    3.9990
   chunk 85 optimal weight:    5.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
E 142 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.190154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.139019 restraints weight = 10828.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.3670 rms_B_bonded: 2.37
r_work: 0.3524 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3377 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.3405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9010  Z= 0.178
  Angle     :  0.515   7.376  12233  Z= 0.273
  Chirality :  0.042   0.179   1406
  Planarity :  0.004   0.040   1547
  Dihedral  :  3.899  28.656   1232
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 14.92 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.25), residues: 1129
  helix:  2.23 (0.26), residues: 398
  sheet:  0.36 (0.30), residues: 294
  loop :  0.14 (0.30), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.014   0.001   PHE B 151 
 TYR   0.042   0.001   TYR R 360 
 ARG   0.008   0.001   ARG B  46 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 172
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7819 (ttm)
REVERT: A   29 LYS cc_start: 0.8390 (tttm) cc_final: 0.7830 (tptp)
REVERT: A  186 GLU cc_start: 0.8218 (tt0) cc_final: 0.7921 (tt0)
REVERT: A  197 LYS cc_start: 0.8713 (mtmt) cc_final: 0.8334 (mtmt)
REVERT: A  290 TYR cc_start: 0.8663 (t80) cc_final: 0.8263 (t80)
REVERT: A  314 LYS cc_start: 0.7907 (mttt) cc_final: 0.7613 (mtpt)
REVERT: B   19 ARG cc_start: 0.8151 (ttp80) cc_final: 0.7868 (ttp80)
REVERT: B  175 GLN cc_start: 0.8339 (mm-40) cc_final: 0.8006 (pt0)
REVERT: B  186 ASP cc_start: 0.8688 (m-30) cc_final: 0.8371 (m-30)
REVERT: B  217 MET cc_start: 0.8012 (ptm) cc_final: 0.7276 (ptm)
REVERT: B  264 TYR cc_start: 0.8037 (m-80) cc_final: 0.7474 (m-80)
REVERT: B  303 ASP cc_start: 0.7763 (m-30) cc_final: 0.7332 (m-30)
REVERT: C   28 ILE cc_start: 0.8926 (pt) cc_final: 0.8702 (tp)
REVERT: C   42 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7087 (mm-30)
REVERT: E   46 GLU cc_start: 0.7990 (tt0) cc_final: 0.7514 (tt0)
REVERT: E  103 TYR cc_start: 0.8473 (t80) cc_final: 0.8213 (t80)
REVERT: E  142 GLN cc_start: 0.7290 (mt0) cc_final: 0.6964 (mt0)
REVERT: E  160 ARG cc_start: 0.7903 (mtp-110) cc_final: 0.7184 (ttm-80)
REVERT: E  175 TYR cc_start: 0.8526 (m-80) cc_final: 0.8308 (m-80)
REVERT: E  186 GLN cc_start: 0.8334 (tt0) cc_final: 0.8121 (pt0)
REVERT: E  218 ARG cc_start: 0.6795 (ttp-170) cc_final: 0.6555 (ttp-170)
REVERT: E  234 GLU cc_start: 0.8456 (tp30) cc_final: 0.7957 (tp30)
REVERT: R  185 CYS cc_start: 0.5485 (OUTLIER) cc_final: 0.4575 (t)
REVERT: R  280 TYR cc_start: 0.7183 (OUTLIER) cc_final: 0.6597 (t80)
REVERT: R  342 TYR cc_start: 0.8475 (m-80) cc_final: 0.8058 (m-80)
REVERT: R  380 TYR cc_start: 0.8495 (t80) cc_final: 0.8109 (t80)
REVERT: R  388 ARG cc_start: 0.7589 (ttp-170) cc_final: 0.7208 (ttp-110)
  outliers start: 26
  outliers final: 18
  residues processed: 186
  average time/residue: 0.2438
  time to fit residues: 60.0998
Evaluate side-chains
  190 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 169
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain E residue   85 SER
Chi-restraints excluded: chain E residue  163 LYS
Chi-restraints excluded: chain E residue  217 SER
Chi-restraints excluded: chain E residue  238 THR
Chi-restraints excluded: chain R residue  138 SER
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  188 ILE
Chi-restraints excluded: chain R residue  247 VAL
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  344 LEU
Chi-restraints excluded: chain R residue  379 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 110 optimal weight:   10.0000
   chunk 77 optimal weight:    1.9990
   chunk 83 optimal weight:    0.8980
   chunk 11 optimal weight:    8.9990
   chunk 95 optimal weight:   20.0000
   chunk 75 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.186969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.137546 restraints weight = 10819.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 2.25
r_work: 0.3477 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3335 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.3368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   9010  Z= 0.324
  Angle     :  0.576   6.924  12233  Z= 0.306
  Chirality :  0.044   0.175   1406
  Planarity :  0.004   0.041   1547
  Dihedral  :  4.175  30.567   1232
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 15.23 %
    Favored  : 81.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.25), residues: 1129
  helix:  2.13 (0.27), residues: 396
  sheet:  0.20 (0.30), residues: 304
  loop :  0.03 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 339 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.020   0.002   PHE B 151 
 TYR   0.042   0.002   TYR R 360 
 ARG   0.007   0.001   ARG R 322 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 176
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7779 (ttm)
REVERT: A  186 GLU cc_start: 0.8330 (tt0) cc_final: 0.8007 (tt0)
REVERT: A  197 LYS cc_start: 0.8607 (mtmt) cc_final: 0.7973 (mttp)
REVERT: A  290 TYR cc_start: 0.8697 (t80) cc_final: 0.8331 (t80)
REVERT: A  314 LYS cc_start: 0.8006 (mttt) cc_final: 0.7682 (mtpt)
REVERT: B   19 ARG cc_start: 0.8118 (ttp80) cc_final: 0.7827 (ttp80)
REVERT: B  186 ASP cc_start: 0.8809 (m-30) cc_final: 0.8497 (m-30)
REVERT: B  217 MET cc_start: 0.8135 (ptm) cc_final: 0.7344 (ptm)
REVERT: B  264 TYR cc_start: 0.8125 (m-80) cc_final: 0.7424 (m-80)
REVERT: C   28 ILE cc_start: 0.8911 (pt) cc_final: 0.8656 (tp)
REVERT: C   42 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7045 (mm-30)
REVERT: E   46 GLU cc_start: 0.8146 (tt0) cc_final: 0.7667 (tt0)
REVERT: E  160 ARG cc_start: 0.7919 (mtp-110) cc_final: 0.7208 (ttm-80)
REVERT: E  175 TYR cc_start: 0.8481 (m-80) cc_final: 0.8186 (m-80)
REVERT: R  249 LEU cc_start: 0.8265 (mp) cc_final: 0.7921 (tt)
REVERT: R  325 ARG cc_start: 0.8466 (ptp90) cc_final: 0.7958 (ttp80)
REVERT: R  342 TYR cc_start: 0.8478 (m-80) cc_final: 0.8060 (m-80)
REVERT: R  380 TYR cc_start: 0.8531 (t80) cc_final: 0.8233 (t80)
REVERT: R  388 ARG cc_start: 0.7614 (ttp-170) cc_final: 0.7233 (ttp-110)
  outliers start: 27
  outliers final: 23
  residues processed: 187
  average time/residue: 0.2794
  time to fit residues: 68.4372
Evaluate side-chains
  190 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 166
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain E residue   85 SER
Chi-restraints excluded: chain E residue  113 GLN
Chi-restraints excluded: chain E residue  163 LYS
Chi-restraints excluded: chain E residue  208 SER
Chi-restraints excluded: chain E residue  217 SER
Chi-restraints excluded: chain E residue  238 THR
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  188 ILE
Chi-restraints excluded: chain R residue  221 THR
Chi-restraints excluded: chain R residue  232 VAL
Chi-restraints excluded: chain R residue  247 VAL
Chi-restraints excluded: chain R residue  344 LEU
Chi-restraints excluded: chain R residue  372 ASN
Chi-restraints excluded: chain R residue  379 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 25 optimal weight:    0.4980
   chunk 94 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 79 optimal weight:    0.0570
   chunk 26 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 111 optimal weight:    0.7980
   chunk 74 optimal weight:    7.9990
   overall best weight:    0.8300

-------------------------------------------------------------------------------
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 = 0.4248 r_free = 0.4248 target = 0.191308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.139386 restraints weight = 10755.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3658 rms_B_bonded: 2.37
r_work: 0.3512 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3368 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.3486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9010  Z= 0.190
  Angle     :  0.539   7.476  12233  Z= 0.284
  Chirality :  0.042   0.183   1406
  Planarity :  0.004   0.039   1547
  Dihedral  :  4.020  30.539   1232
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 16.60 %
    Favored  : 81.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.26), residues: 1129
  helix:  2.15 (0.27), residues: 396
  sheet:  0.19 (0.30), residues: 308
  loop :  0.09 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.015   0.001   PHE B 151 
 TYR   0.043   0.001   TYR R 360 
 ARG   0.007   0.001   ARG R 303 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 171
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7744 (ttm)
REVERT: A   29 LYS cc_start: 0.8409 (tttm) cc_final: 0.8068 (tmtt)
REVERT: A  186 GLU cc_start: 0.8200 (tt0) cc_final: 0.7897 (tt0)
REVERT: A  197 LYS cc_start: 0.8637 (mtmt) cc_final: 0.8224 (mtmt)
REVERT: A  290 TYR cc_start: 0.8636 (t80) cc_final: 0.8234 (t80)
REVERT: A  314 LYS cc_start: 0.8010 (mttt) cc_final: 0.7684 (mtpt)
REVERT: B   19 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7763 (ttp80)
REVERT: B  175 GLN cc_start: 0.8347 (mm-40) cc_final: 0.8027 (pt0)
REVERT: B  186 ASP cc_start: 0.8764 (m-30) cc_final: 0.8473 (m-30)
REVERT: B  217 MET cc_start: 0.8072 (ptm) cc_final: 0.7355 (ptm)
REVERT: B  264 TYR cc_start: 0.8062 (m-80) cc_final: 0.7386 (m-80)
REVERT: B  303 ASP cc_start: 0.7884 (m-30) cc_final: 0.7458 (m-30)
REVERT: C   28 ILE cc_start: 0.8914 (pt) cc_final: 0.8663 (tp)
REVERT: C   42 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7061 (mm-30)
REVERT: E   46 GLU cc_start: 0.8030 (tt0) cc_final: 0.7530 (tt0)
REVERT: E  160 ARG cc_start: 0.7899 (mtp-110) cc_final: 0.7199 (ttm-80)
REVERT: E  175 TYR cc_start: 0.8525 (m-80) cc_final: 0.8205 (m-80)
REVERT: E  186 GLN cc_start: 0.8339 (tt0) cc_final: 0.8120 (pt0)
REVERT: E  218 ARG cc_start: 0.6826 (ttp-170) cc_final: 0.6620 (ttp-170)
REVERT: R  280 TYR cc_start: 0.7286 (OUTLIER) cc_final: 0.6695 (t80)
REVERT: R  325 ARG cc_start: 0.8443 (ptp90) cc_final: 0.7937 (ttp80)
REVERT: R  342 TYR cc_start: 0.8451 (m-80) cc_final: 0.8034 (m-80)
REVERT: R  362 TYR cc_start: 0.8681 (t80) cc_final: 0.8337 (t80)
REVERT: R  380 TYR cc_start: 0.8469 (t80) cc_final: 0.8112 (t80)
REVERT: R  388 ARG cc_start: 0.7586 (ttp-170) cc_final: 0.7261 (ttp-110)
  outliers start: 21
  outliers final: 19
  residues processed: 180
  average time/residue: 0.2548
  time to fit residues: 59.9919
Evaluate side-chains
  190 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 169
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain E residue   85 SER
Chi-restraints excluded: chain E residue  113 GLN
Chi-restraints excluded: chain E residue  208 SER
Chi-restraints excluded: chain E residue  217 SER
Chi-restraints excluded: chain E residue  238 THR
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  188 ILE
Chi-restraints excluded: chain R residue  221 THR
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  344 LEU
Chi-restraints excluded: chain R residue  379 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0980
   chunk 22 optimal weight:    6.9990
   chunk 103 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 90 optimal weight:    0.0170
   chunk 104 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 7 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9980
   chunk 100 optimal weight:    6.9990
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
E 142 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.190590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.150054 restraints weight = 10555.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3778 rms_B_bonded: 2.30
r_work: 0.3539 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3400 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.3622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9010  Z= 0.160
  Angle     :  0.518   7.515  12233  Z= 0.274
  Chirality :  0.042   0.188   1406
  Planarity :  0.004   0.040   1547
  Dihedral  :  3.864  29.158   1232
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 16.49 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.25), residues: 1129
  helix:  2.18 (0.26), residues: 396
  sheet:  0.28 (0.30), residues: 293
  loop :  0.04 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.011   0.001   PHE B 151 
 TYR   0.045   0.001   TYR R 360 
 ARG   0.009   0.001   ARG B  46 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6212.92 seconds
wall clock time: 109 minutes 38.59 seconds (6578.59 seconds total)