Starting phenix.real_space_refine
on Fri Sep 11 08:58:07 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yjo_33876/09_2026/7yjo_33876.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yjo_33876/09_2026/7yjo_33876.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yjo_33876/09_2026/7yjo_33876.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yjo_33876/09_2026/7yjo_33876.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yjo_33876/09_2026/7yjo_33876.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yjo_33876/09_2026/7yjo_33876.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 22 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      49      5.16       5
     C    5651      2.51       5
     N    1482      2.21       5
     O    1586      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 82 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8769
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 418, 3226
          Classifications: {'peptide': 418}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 400}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 3643
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 467, 3643
          Classifications: {'peptide': 467}
          Link IDs: {'PTRANS': 20, 'TRANS': 446}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1201
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1201
          Classifications: {'peptide': 146}
          Link IDs: {'PTRANS': 7, 'TRANS': 138}
    Chain: "E"
      Number of atoms: 195
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 195
          Classifications: {'peptide': 27}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 2, 'TRANS': 24}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 21
    Chain: "C"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 48, 436
          Classifications: {'peptide': 48}
          Link IDs: {'TRANS': 47}
    Chain: "B"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Classifications: {'peptide': 1}
    Chain: "D"
      Number of atoms: 46
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 46
          Unusual residues: {'Z1T': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.75, per 1000 atoms: 0.20
  Number of scatterers: 8769
  At special positions: 0
  Unit cell: (88.56, 82.08, 118.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      49     16.00
     P       1     15.00
     O    1586      8.00
     N    1482      7.00
     C    5651      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.76
  Conformation dependent library (CDL) restraints added in 279.3 milliseconds
  

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2048

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 7 sheets defined
      50.6% alpha, 8.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 76
      removed outlier: 3.673A  pdb=" N   ASP A  70 " --> pdb=" O   GLU A  66 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   GLU A  71 " --> pdb=" O   GLN A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 140
      removed outlier: 3.732A  pdb=" N   SER A 134 " --> pdb=" O   GLU A 130 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ALA A 135 " --> pdb=" O   SER A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 168
      removed outlier: 3.840A  pdb=" N   LEU A 157 " --> pdb=" O   ILE A 153 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   THR A 161 " --> pdb=" O   LEU A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 184
      removed outlier: 4.109A  pdb=" N   PHE A 183 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 190
    Processing helix  chain 'A' and resid 203 through 213
    Processing helix  chain 'A' and resid 224 through 239
    Processing helix  chain 'A' and resid 263 through 275
      removed outlier: 3.704A  pdb=" N   LYS A 269 " --> pdb=" O   ASP A 265 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LYS A 273 " --> pdb=" O   LYS A 269 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   TYR A 274 " --> pdb=" O   LEU A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 307
    Processing helix  chain 'A' and resid 328 through 336
    Processing helix  chain 'A' and resid 349 through 366
      removed outlier: 3.527A  pdb=" N   ALA A 355 " --> pdb=" O   TYR A 351 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ILE A 357 " --> pdb=" O   ALA A 353 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   THR A 358 " --> pdb=" O   SER A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 383
      removed outlier: 3.769A  pdb=" N   LYS A 374 " --> pdb=" O   LEU A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 431
      removed outlier: 3.693A  pdb=" N   LEU A 417 " --> pdb=" O   LYS A 413 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LEU A 418 " --> pdb=" O   ASP A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 473
      removed outlier: 3.801A  pdb=" N   LEU A 471 " --> pdb=" O   ALA A 467 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ARG A 473 " --> pdb=" O   GLU A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 479
    Processing helix  chain 'B' and resid 6 through 31
      removed outlier: 3.677A  pdb=" N   PHE B  29 " --> pdb=" O   LEU B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 59
    Processing helix  chain 'B' and resid 119 through 132
      removed outlier: 3.871A  pdb=" N   ARG B 123 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLU B 126 " --> pdb=" O   PRO B 122 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LYS B 130 " --> pdb=" O   GLU B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 145 through 160
      removed outlier: 3.592A  pdb=" N   GLU B 152 " --> pdb=" O   HIS B 148 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   GLU B 153 " --> pdb=" O   ALA B 149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 169 through 176
      removed outlier: 3.893A  pdb=" N   ASN B 174 " --> pdb=" O   GLY B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 182
      removed outlier: 3.591A  pdb=" N   LEU B 181 " --> pdb=" O   ILE B 177 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ILE B 182 " --> pdb=" O   ILE B 178 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 177 through 182'
    Processing helix  chain 'B' and resid 195 through 205
      removed outlier: 3.579A  pdb=" N   SER B 205 " --> pdb=" O   GLY B 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 231
      removed outlier: 3.567A  pdb=" N   GLU B 221 " --> pdb=" O   PRO B 217 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ARG B 222 " --> pdb=" O   SER B 218 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLU B 230 " --> pdb=" O   GLU B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 270
    Processing helix  chain 'B' and resid 290 through 296
    Processing helix  chain 'B' and resid 298 through 302
      removed outlier: 3.837A  pdb=" N   VAL B 302 " --> pdb=" O   THR B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 323 through 334
      removed outlier: 3.618A  pdb=" N   HIS B 332 " --> pdb=" O   GLN B 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 340
      removed outlier: 3.522A  pdb=" N   ALA B 340 " --> pdb=" O   ALA B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 344 through 360
      removed outlier: 3.637A  pdb=" N   GLN B 350 " --> pdb=" O   PRO B 346 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   ILE B 351 " --> pdb=" O   SER B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 387
      removed outlier: 3.689A  pdb=" N   LEU B 371 " --> pdb=" O   GLY B 367 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ARG B 375 " --> pdb=" O   LEU B 371 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   SER B 378 " --> pdb=" O   ILE B 374 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ASN B 379 " --> pdb=" O   ARG B 375 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   LYS B 387 " --> pdb=" O   ALA B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 409 through 421
      removed outlier: 3.760A  pdb=" N   ALA B 413 " --> pdb=" O   ALA B 409 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLN B 421 " --> pdb=" O   GLU B 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 449 through 468
      removed outlier: 4.101A  pdb=" N   ARG B 455 " --> pdb=" O   GLU B 451 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LYS B 462 " --> pdb=" O   LYS B 458 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 18 through 23
      removed outlier: 3.725A  pdb=" N   MET D  22 " --> pdb=" O   GLU D  19 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   TYR D  23 " --> pdb=" O   TRP D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 25 through 45
      removed outlier: 3.529A  pdb=" N   LEU D  34 " --> pdb=" O   TYR D  30 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   SER D  45 " --> pdb=" O   VAL D  41 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 48 through 70
      removed outlier: 3.587A  pdb=" N   VAL D  55 " --> pdb=" O   MET D  51 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   PHE D  61 " --> pdb=" O   ASN D  57 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   VAL D  62 " --> pdb=" O   LEU D  58 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   VAL D  63 " --> pdb=" O   ALA D  59 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   THR D  64 " --> pdb=" O   HIS D  60 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   TRP D  70 " --> pdb=" O   HIS D  66 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 92
    Processing helix  chain 'D' and resid 93 through 96
    Processing helix  chain 'D' and resid 99 through 119
      Proline residue:  D 109  - end of helix
    Processing helix  chain 'D' and resid 123 through 140
      removed outlier: 3.512A  pdb=" N   PHE D 128 " --> pdb=" O   HIS D 124 " (cutoff:3.500A)
      removed outlier: 4.802A  pdb=" N   LEU D 129 " --> pdb=" O   PRO D 125 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   VAL D 134 " --> pdb=" O   ASN D 130 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 141 through 146
      removed outlier: 6.219A  pdb=" N   ASN D 144 " --> pdb=" O   LYS D 141 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   HIS D 146 " --> pdb=" O   PRO D 143 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 38 through 52
      removed outlier: 3.907A  pdb=" N   GLY E  42 " --> pdb=" O   PHE E  38 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2 through 15
      removed outlier: 3.515A  pdb=" N   TYR C   9 " --> pdb=" O   GLN C   5 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 20
      removed outlier: 3.550A  pdb=" N   MET C  19 " --> pdb=" O   GLY C  16 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU C  20 " --> pdb=" O   LEU C  17 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 16 through 20'
    Processing helix  chain 'C' and resid 21 through 42
      removed outlier: 3.556A  pdb=" N   PHE C  28 " --> pdb=" O   GLU C  24 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   LEU C  31 " --> pdb=" O   LEU C  27 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   PHE C  38 " --> pdb=" O   VAL C  34 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 97
      removed outlier: 3.771A  pdb=" N   THR A 105 " --> pdb=" O   GLU A  97 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   THR A 104 " --> pdb=" O   VAL A 111 " (cutoff:3.500A)
      removed outlier: 8.521A  pdb=" N   LEU A 433 " --> pdb=" O   ASP A 110 " (cutoff:3.500A)
      removed outlier: 7.074A  pdb=" N   VAL A 112 " --> pdb=" O   LEU A 433 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 175
      removed outlier: 3.692A  pdb=" N   ASP A 171 " --> pdb=" O   GLY A 327 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLY A 327 " --> pdb=" O   ASP A 171 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ASP A 281 " --> pdb=" O   ALA A 251 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   VAL A 195 " --> pdb=" O   TYR A 248 " (cutoff:3.500A)
      removed outlier: 7.756A  pdb=" N   VAL A 250 " --> pdb=" O   VAL A 195 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   VAL A 197 " --> pdb=" O   VAL A 250 " (cutoff:3.500A)
      removed outlier: 8.686A  pdb=" N   GLU A 252 " --> pdb=" O   VAL A 197 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 390 through 392
    Processing sheet with id=AA4, first strand: chain 'B' and resid 78 through 81
      removed outlier: 7.984A  pdb=" N   ALA B 424 " --> pdb=" O   ARG B 101 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   LEU B 103 " --> pdb=" O   ALA B 424 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 163 through 167
      removed outlier: 6.505A  pdb=" N   VAL B 273 " --> pdb=" O   VAL B 304 " (cutoff:3.500A)
      removed outlier: 7.963A  pdb=" N   MET B 306 " --> pdb=" O   VAL B 273 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   LEU B 275 " --> pdb=" O   MET B 306 " (cutoff:3.500A)
      removed outlier: 8.530A  pdb=" N   THR B 308 " --> pdb=" O   LEU B 275 " (cutoff:3.500A)
      removed outlier: 7.948A  pdb=" N   GLU B 247 " --> pdb=" O   ASP B 191 " (cutoff:3.500A)
      removed outlier: 5.999A  pdb=" N   ILE B 188 " --> pdb=" O   ARG B 210 " (cutoff:3.500A)
      removed outlier: 7.452A  pdb=" N   PHE B 212 " --> pdb=" O   ILE B 188 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   SER B 190 " --> pdb=" O   PHE B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 249 through 250
    Processing sheet with id=AA7, first strand: chain 'B' and resid 403 through 404
      removed outlier: 3.921A  pdb=" N   VAL B 426 " --> pdb=" O   ARG B 441 " (cutoff:3.500A)

    380 hydrogen bonds defined for protein.
    1086 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.13

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1670
        1.32 -     1.45: 2208
        1.45 -     1.57: 5017
        1.57 -     1.69: 1
        1.69 -     1.81: 76
  Bond restraints: 8972
  Sorted by residual:
  bond pdb=" C14 Z1T D 201 "
       pdb=" C15 Z1T D 201 "
    ideal  model  delta    sigma   weight residual
    1.329  1.523 -0.194 2.00e-02 2.50e+03 9.36e+01
  bond pdb=" C   HIS B 236 "
       pdb=" N   ARG B 237 "
    ideal  model  delta    sigma   weight residual
    1.330  1.201  0.129 1.47e-02 4.63e+03 7.75e+01
  bond pdb=" O4P PLS B 601 "
       pdb=" P   PLS B 601 "
    ideal  model  delta    sigma   weight residual
    1.712  1.610  0.102 2.00e-02 2.50e+03 2.58e+01
  bond pdb=" C   CYS D  47 "
       pdb=" N   SER D  48 "
    ideal  model  delta    sigma   weight residual
    1.327  1.252  0.075 1.71e-02 3.42e+03 1.93e+01
  bond pdb=" C4  PLS B 601 "
       pdb=" C5  PLS B 601 "
    ideal  model  delta    sigma   weight residual
    1.399  1.483 -0.084 2.00e-02 2.50e+03 1.76e+01
  ... (remaining 8967 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.78: 11876
        2.78 -     5.55: 236
        5.55 -     8.33: 19
        8.33 -    11.11: 9
       11.11 -    13.88: 1
  Bond angle restraints: 12141
  Sorted by residual:
  angle pdb=" N   PHE B 430 "
        pdb=" CA  PHE B 430 "
        pdb=" C   PHE B 430 "
      ideal   model   delta    sigma   weight residual
     109.81  123.69  -13.88 2.21e+00 2.05e-01 3.95e+01
  angle pdb=" N   HIS D 124 "
        pdb=" CA  HIS D 124 "
        pdb=" C   HIS D 124 "
      ideal   model   delta    sigma   weight residual
     109.81  120.75  -10.94 2.21e+00 2.05e-01 2.45e+01
  angle pdb=" C   HIS D 124 "
        pdb=" N   PRO D 125 "
        pdb=" CA  PRO D 125 "
      ideal   model   delta    sigma   weight residual
     119.32  114.33    4.99 1.14e+00 7.69e-01 1.92e+01
  angle pdb=" N   TYR B  85 "
        pdb=" CA  TYR B  85 "
        pdb=" C   TYR B  85 "
      ideal   model   delta    sigma   weight residual
     111.71  117.32   -5.61 1.34e+00 5.57e-01 1.75e+01
  angle pdb=" N   LEU B 437 "
        pdb=" CA  LEU B 437 "
        pdb=" C   LEU B 437 "
      ideal   model   delta    sigma   weight residual
     110.44  115.40   -4.96 1.20e+00 6.94e-01 1.71e+01
  ... (remaining 12136 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 4844
       17.98 -    35.96: 399
       35.96 -    53.94: 77
       53.94 -    71.92: 11
       71.92 -    89.91: 10
  Dihedral angle restraints: 5341
    sinusoidal: 2146
      harmonic: 3195
  Sorted by residual:
  dihedral pdb=" CA  ASP D  79 "
           pdb=" C   ASP D  79 "
           pdb=" N   GLN D  80 "
           pdb=" CA  GLN D  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.86  -27.14     0      5.00e+00 4.00e-02 2.95e+01
  dihedral pdb=" N   PHE B 430 "
           pdb=" C   PHE B 430 "
           pdb=" CA  PHE B 430 "
           pdb=" CB  PHE B 430 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  135.22  -12.42     0      2.50e+00 1.60e-01 2.47e+01
  dihedral pdb=" CA  VAL A 288 "
           pdb=" C   VAL A 288 "
           pdb=" N   LEU A 289 "
           pdb=" CA  LEU A 289 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.64  -24.36     0      5.00e+00 4.00e-02 2.37e+01
  ... (remaining 5338 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.117: 1285
       0.117 -    0.233: 66
       0.233 -    0.350: 1
       0.350 -    0.466: 1
       0.466 -    0.583: 1
  Chirality restraints: 1354
  Sorted by residual:
  chirality pdb=" CA  PHE B 430 "
            pdb=" N   PHE B 430 "
            pdb=" C   PHE B 430 "
            pdb=" CB  PHE B 430 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.93    0.58 2.00e-01 2.50e+01 8.50e+00
  chirality pdb=" CA  HIS D 124 "
            pdb=" N   HIS D 124 "
            pdb=" C   HIS D 124 "
            pdb=" CB  HIS D 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.74e+00
  chirality pdb=" CA  PHE B  79 "
            pdb=" N   PHE B  79 "
            pdb=" C   PHE B  79 "
            pdb=" CB  PHE B  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.82e+00
  ... (remaining 1351 not shown)

  Planarity restraints: 1522
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 380 "   -0.017 2.00e-02 2.50e+03   3.57e-02 1.27e+01
        pdb=" C   LEU A 380 "    0.062 2.00e-02 2.50e+03
        pdb=" O   LEU A 380 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   TRP A 381 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP D  20 "   -0.012 2.00e-02 2.50e+03   2.38e-02 5.66e+00
        pdb=" C   TRP D  20 "    0.041 2.00e-02 2.50e+03
        pdb=" O   TRP D  20 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   PHE D  21 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 406 "   -0.010 2.00e-02 2.50e+03   2.10e-02 4.39e+00
        pdb=" C   TYR B 406 "    0.036 2.00e-02 2.50e+03
        pdb=" O   TYR B 406 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ASN B 407 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1519 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 336
        2.71 -     3.26: 8228
        3.26 -     3.80: 13002
        3.80 -     4.35: 17194
        4.35 -     4.90: 29964
  Nonbonded interactions: 68724
  Sorted by model distance:
  nonbonded pdb=" O   SER B 132 "
            pdb=" OG  SER B 132 "
     model   vdw
     2.161 3.040
  nonbonded pdb=" O   PHE B 430 "
            pdb=" O   THR B 433 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" OG1 THR B 287 "
            pdb=" OE2 GLU B 293 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" OE2 GLU A  66 "
            pdb=" NH2 ARG B 225 "
     model   vdw
     2.297 3.120
  nonbonded pdb=" NH1 ARG B 373 "
            pdb=" O   ALA B 446 "
     model   vdw
     2.310 3.120
  ... (remaining 68719 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.430
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8860
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      :  0.011   0.194   8972  Z= 0.465
  Angle     :  1.010  13.884  12141  Z= 0.578
  Chirality :  0.063   0.583   1354
  Planarity :  0.006   0.045   1522
  Dihedral  : 14.171  89.905   3293
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.03 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  0.84 %
    Favored  : 98.42 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.89 (0.24), residues: 1094
  helix: -1.18 (0.21), residues: 526
  sheet: -0.60 (0.46), residues: 121
  loop : -1.34 (0.28), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 277 
 TYR   0.024   0.003   TYR A 177 
 PHE   0.025   0.003   PHE A 220 
 TRP   0.019   0.003   TRP B 239 
 HIS   0.007   0.002   HIS A 299 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01084 /  0.47 ( 8972)
  covalent geometry    : angle       1.01019 /  0.58 (12141)
  hydrogen bonds       : bond        0.25165 / 17.17 (  380)
  hydrogen bonds       : angle       7.60436 /  5.19 ( 1086)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 104
  time to evaluate  : 0.331 
Fit side-chains
REVERT: B   31 ARG cc_start: 0.7749 (ttp-170) cc_final: 0.7019 (ttt90)
REVERT: B  475 GLU cc_start: 0.5859 (OUTLIER) cc_final: 0.5659 (pp20)
REVERT: C    2 ASN cc_start: 0.7983 (p0) cc_final: 0.7778 (p0)
  outliers start: 7
  outliers final: 2
  residues processed: 110
  average time/residue: 0.7017
  time to fit residues: 81.2462
Evaluate side-chains
  91 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 88
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 GLU
Chi-restraints excluded: chain B residue   79 PHE
Chi-restraints excluded: chain B residue  475 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 49 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 69.2935 > 50:)
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    4.9990
   chunk 106 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    1.2986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  90 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.109322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.086600 restraints weight = 11738.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.2937 rms_B_bonded: 1.74
r_work: 0.2828 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2708 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8809
moved from start:          0.1262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8972  Z= 0.153
  Angle     :  0.609   7.508  12141  Z= 0.319
  Chirality :  0.046   0.158   1354
  Planarity :  0.005   0.051   1522
  Dihedral  :  8.413  59.949   1261
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  7.29 %
    Favored  : 91.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.89 (0.25), residues: 1094
  helix: -0.22 (0.23), residues: 543
  sheet: -0.08 (0.51), residues: 113
  loop : -1.04 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E  62 
 TYR   0.013   0.001   TYR B 269 
 PHE   0.027   0.002   PHE A 183 
 TRP   0.012   0.001   TRP A 204 
 HIS   0.003   0.001   HIS A 299 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00358 /  0.15 ( 8972)
  covalent geometry    : angle       0.60866 /  0.32 (12141)
  hydrogen bonds       : bond        0.05759 /  3.87 (  380)
  hydrogen bonds       : angle       4.75699 /  3.24 ( 1086)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.320 
Fit side-chains
REVERT: B   30 ARG cc_start: 0.7501 (tpt170) cc_final: 0.5587 (tpp-160)
REVERT: B   31 ARG cc_start: 0.7679 (ttp-170) cc_final: 0.6701 (ttt90)
REVERT: B  420 ARG cc_start: 0.8833 (ttp80) cc_final: 0.8565 (ttp80)
  outliers start: 11
  outliers final: 3
  residues processed: 110
  average time/residue: 0.6522
  time to fit residues: 75.6968
Evaluate side-chains
  98 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 95
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   79 PHE
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain D residue   22 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 92 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 55 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 49 optimal weight:   10.0000
   chunk 77 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0970
   chunk 74 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  90 ASN
D  57 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.110531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.087134 restraints weight = 11637.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.2907 rms_B_bonded: 1.86
r_work: 0.2790 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2666 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8814
moved from start:          0.1417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8972  Z= 0.149
  Angle     :  0.578   7.713  12141  Z= 0.303
  Chirality :  0.045   0.161   1354
  Planarity :  0.005   0.048   1522
  Dihedral  :  7.612  58.073   1255
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  :  9.61 %
    Favored  : 89.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.50 (0.26), residues: 1094
  helix:  0.22 (0.23), residues: 541
  sheet:  0.16 (0.52), residues: 111
  loop : -1.05 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  62 
 TYR   0.012   0.001   TYR B  55 
 PHE   0.027   0.002   PHE A 183 
 TRP   0.014   0.001   TRP A 204 
 HIS   0.003   0.001   HIS A 299 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00357 /  0.15 ( 8972)
  covalent geometry    : angle       0.57768 /  0.30 (12141)
  hydrogen bonds       : bond        0.05407 /  3.66 (  380)
  hydrogen bonds       : angle       4.43158 /  3.01 ( 1086)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.261 
Fit side-chains
REVERT: A  107 ASN cc_start: 0.9052 (t0) cc_final: 0.8847 (t0)
REVERT: A  366 ASN cc_start: 0.8444 (m110) cc_final: 0.7962 (m-40)
REVERT: B   31 ARG cc_start: 0.7793 (ttp-170) cc_final: 0.6847 (ttt90)
REVERT: B  420 ARG cc_start: 0.8844 (ttp80) cc_final: 0.8584 (ttp80)
  outliers start: 13
  outliers final: 8
  residues processed: 114
  average time/residue: 0.6096
  time to fit residues: 73.6017
Evaluate side-chains
  102 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  365 GLN
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain B residue   79 PHE
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  397 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 72 optimal weight:    0.6980
   chunk 74 optimal weight:    0.0980
   chunk 32 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 395 ASN
B  90 ASN
D  57 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.112618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.089300 restraints weight = 11658.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.2902 rms_B_bonded: 1.84
r_work: 0.2786 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2665 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8808
moved from start:          0.1690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8972  Z= 0.118
  Angle     :  0.523   7.440  12141  Z= 0.277
  Chirality :  0.044   0.150   1354
  Planarity :  0.004   0.048   1522
  Dihedral  :  7.208  59.616   1255
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 10.98 %
    Favored  : 87.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.26 (0.26), residues: 1094
  helix:  0.45 (0.24), residues: 543
  sheet:  0.22 (0.53), residues: 111
  loop : -0.99 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  62 
 TYR   0.011   0.001   TYR B 269 
 PHE   0.025   0.001   PHE A 183 
 TRP   0.012   0.001   TRP A 204 
 HIS   0.002   0.001   HIS A 299 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.12 ( 8972)
  covalent geometry    : angle       0.52337 /  0.28 (12141)
  hydrogen bonds       : bond        0.04542 /  3.08 (  380)
  hydrogen bonds       : angle       4.18557 /  2.84 ( 1086)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.280 
Fit side-chains
REVERT: A  107 ASN cc_start: 0.9024 (t0) cc_final: 0.8813 (t0)
REVERT: A  256 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8176 (tp-100)
REVERT: A  366 ASN cc_start: 0.8400 (m110) cc_final: 0.7884 (m-40)
REVERT: B   31 ARG cc_start: 0.7784 (ttp-170) cc_final: 0.6920 (ttp80)
REVERT: B  420 ARG cc_start: 0.8815 (ttp80) cc_final: 0.8568 (ttp80)
  outliers start: 17
  outliers final: 9
  residues processed: 119
  average time/residue: 0.6331
  time to fit residues: 79.7050
Evaluate side-chains
  109 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 GLN
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  381 TRP
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain B residue   79 PHE
Chi-restraints excluded: chain B residue  249 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 76 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 88 optimal weight:    4.9990
   chunk 91 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 95 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0980
   overall best weight:    1.6186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  90 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.108403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.085541 restraints weight = 11623.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.2878 rms_B_bonded: 1.73
r_work: 0.2765 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2645 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8813
moved from start:          0.1602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8972  Z= 0.164
  Angle     :  0.575   8.137  12141  Z= 0.302
  Chirality :  0.046   0.165   1354
  Planarity :  0.005   0.049   1522
  Dihedral  :  7.272  59.206   1255
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 12.14 %
    Favored  : 85.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.23 (0.26), residues: 1094
  helix:  0.51 (0.24), residues: 541
  sheet:  0.29 (0.53), residues: 111
  loop : -1.03 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E  62 
 TYR   0.014   0.001   TYR B  55 
 PHE   0.027   0.002   PHE A 183 
 TRP   0.014   0.001   TRP A 204 
 HIS   0.004   0.001   HIS A 299 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00403 /  0.16 ( 8972)
  covalent geometry    : angle       0.57539 /  0.30 (12141)
  hydrogen bonds       : bond        0.05331 /  3.61 (  380)
  hydrogen bonds       : angle       4.26661 /  2.90 ( 1086)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.336 
Fit side-chains
REVERT: A  107 ASN cc_start: 0.9006 (t0) cc_final: 0.8784 (t0)
REVERT: A  256 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8189 (tp-100)
REVERT: A  366 ASN cc_start: 0.8417 (m110) cc_final: 0.7949 (m-40)
REVERT: A  417 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8498 (tt)
REVERT: B   31 ARG cc_start: 0.7752 (ttp-170) cc_final: 0.6894 (ttp80)
REVERT: B  375 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.8607 (ttt-90)
REVERT: B  420 ARG cc_start: 0.8801 (ttp80) cc_final: 0.8556 (ttp80)
  outliers start: 19
  outliers final: 10
  residues processed: 114
  average time/residue: 0.6395
  time to fit residues: 77.1731
Evaluate side-chains
  107 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 GLN
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  365 GLN
Chi-restraints excluded: chain A residue  381 TRP
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain B residue   79 PHE
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  249 ILE
Chi-restraints excluded: chain B residue  375 ARG
Chi-restraints excluded: chain B residue  397 ASP
Chi-restraints excluded: chain D residue   22 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   chunk 92 optimal weight:    0.7980
   chunk 97 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   chunk 80 optimal weight:    0.5980
   chunk 102 optimal weight:    6.9990
   chunk 73 optimal weight:    0.9980
   overall best weight:    1.0582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  90 ASN
D  57 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.110030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.087076 restraints weight = 11731.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.2905 rms_B_bonded: 1.75
r_work: 0.2793 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2672 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8788
moved from start:          0.1785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8972  Z= 0.124
  Angle     :  0.525   7.992  12141  Z= 0.277
  Chirality :  0.044   0.153   1354
  Planarity :  0.004   0.048   1522
  Dihedral  :  7.062  59.009   1255
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 13.09 %
    Favored  : 85.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.26), residues: 1094
  helix:  0.66 (0.24), residues: 543
  sheet:  0.32 (0.53), residues: 111
  loop : -0.98 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  62 
 TYR   0.011   0.001   TYR B 269 
 PHE   0.025   0.001   PHE A 183 
 TRP   0.014   0.001   TRP A 204 
 HIS   0.003   0.001   HIS A 299 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.12 ( 8972)
  covalent geometry    : angle       0.52505 /  0.28 (12141)
  hydrogen bonds       : bond        0.04530 /  3.07 (  380)
  hydrogen bonds       : angle       4.10429 /  2.78 ( 1086)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.343 
Fit side-chains
REVERT: A  107 ASN cc_start: 0.9000 (t0) cc_final: 0.8778 (t0)
REVERT: A  366 ASN cc_start: 0.8375 (m110) cc_final: 0.7911 (m-40)
REVERT: B   31 ARG cc_start: 0.7853 (ttp-170) cc_final: 0.6986 (ttp80)
REVERT: B  375 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8617 (ttt-90)
REVERT: B  420 ARG cc_start: 0.8765 (ttp80) cc_final: 0.8536 (ttp80)
  outliers start: 16
  outliers final: 11
  residues processed: 110
  average time/residue: 0.6214
  time to fit residues: 72.2839
Evaluate side-chains
  102 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  365 GLN
Chi-restraints excluded: chain A residue  381 TRP
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain B residue   79 PHE
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  249 ILE
Chi-restraints excluded: chain B residue  375 ARG
Chi-restraints excluded: chain B residue  397 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 95 optimal weight:    0.5980
   chunk 7 optimal weight:    4.9990
   chunk 103 optimal weight:    0.8980
   chunk 77 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  90 ASN
D  57 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.112008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.089497 restraints weight = 11716.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.2924 rms_B_bonded: 1.68
r_work: 0.2818 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2699 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8763
moved from start:          0.1931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8972  Z= 0.107
  Angle     :  0.504   8.533  12141  Z= 0.265
  Chirality :  0.043   0.146   1354
  Planarity :  0.004   0.047   1522
  Dihedral  :  6.877  63.337   1255
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 13.41 %
    Favored  : 85.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.12 (0.26), residues: 1094
  helix:  0.83 (0.24), residues: 544
  sheet:  0.33 (0.52), residues: 112
  loop : -0.88 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  62 
 TYR   0.011   0.001   TYR B 269 
 PHE   0.023   0.001   PHE A 183 
 TRP   0.013   0.001   TRP A 204 
 HIS   0.002   0.001   HIS A 203 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00247 /  0.11 ( 8972)
  covalent geometry    : angle       0.50378 /  0.27 (12141)
  hydrogen bonds       : bond        0.04084 /  2.78 (  380)
  hydrogen bonds       : angle       3.99397 /  2.70 ( 1086)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A  107 ASN cc_start: 0.8985 (t0) cc_final: 0.8764 (t0)
REVERT: A  366 ASN cc_start: 0.8352 (m110) cc_final: 0.7878 (m-40)
REVERT: B   31 ARG cc_start: 0.7700 (ttp-170) cc_final: 0.6924 (ttp80)
REVERT: B  375 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8593 (ttt-90)
REVERT: B  420 ARG cc_start: 0.8769 (ttp80) cc_final: 0.8524 (ttp80)
  outliers start: 15
  outliers final: 9
  residues processed: 111
  average time/residue: 0.6339
  time to fit residues: 74.4484
Evaluate side-chains
  106 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  381 TRP
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain B residue   79 PHE
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  249 ILE
Chi-restraints excluded: chain B residue  375 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 80 optimal weight:    1.9990
   chunk 68 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 88 optimal weight:    0.8980
   overall best weight:    1.2984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  90 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.109473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.086522 restraints weight = 11639.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.2894 rms_B_bonded: 1.73
r_work: 0.2783 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2662 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8797
moved from start:          0.1841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8972  Z= 0.141
  Angle     :  0.549   9.056  12141  Z= 0.289
  Chirality :  0.045   0.161   1354
  Planarity :  0.004   0.047   1522
  Dihedral  :  6.999  67.259   1255
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 13.73 %
    Favored  : 84.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.10 (0.26), residues: 1094
  helix:  0.83 (0.24), residues: 541
  sheet:  0.38 (0.52), residues: 111
  loop : -0.91 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  62 
 TYR   0.013   0.001   TYR B  55 
 PHE   0.026   0.002   PHE A 183 
 TRP   0.013   0.001   TRP A 204 
 HIS   0.003   0.001   HIS A 203 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00345 /  0.14 ( 8972)
  covalent geometry    : angle       0.54881 /  0.29 (12141)
  hydrogen bonds       : bond        0.04780 /  3.23 (  380)
  hydrogen bonds       : angle       4.09439 /  2.77 ( 1086)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.238 
Fit side-chains
REVERT: B   31 ARG cc_start: 0.7749 (ttp-170) cc_final: 0.6948 (ttp80)
REVERT: B  375 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.8604 (ttt-90)
REVERT: B  420 ARG cc_start: 0.8799 (ttp80) cc_final: 0.8541 (ttp80)
  outliers start: 15
  outliers final: 10
  residues processed: 107
  average time/residue: 0.6324
  time to fit residues: 71.6622
Evaluate side-chains
  104 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  381 TRP
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain B residue   79 PHE
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  249 ILE
Chi-restraints excluded: chain B residue  375 ARG
Chi-restraints excluded: chain B residue  400 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 102 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9990
   chunk 22 optimal weight:    7.9990
   chunk 47 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 90 optimal weight:    0.0980
   overall best weight:    0.7384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  90 ASN
D  57 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.112592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.089291 restraints weight = 11670.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.2911 rms_B_bonded: 1.85
r_work: 0.2796 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2674 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8787
moved from start:          0.2020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8972  Z= 0.106
  Angle     :  0.505   8.930  12141  Z= 0.266
  Chirality :  0.043   0.142   1354
  Planarity :  0.004   0.045   1522
  Dihedral  :  6.881  74.104   1255
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 14.15 %
    Favored  : 84.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.28 (0.26), residues: 1094
  helix:  0.98 (0.24), residues: 544
  sheet:  0.40 (0.52), residues: 111
  loop : -0.83 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E  62 
 TYR   0.011   0.001   TYR B 269 
 PHE   0.023   0.001   PHE A 183 
 TRP   0.013   0.001   TRP A 204 
 HIS   0.002   0.000   HIS A 299 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00244 /  0.11 ( 8972)
  covalent geometry    : angle       0.50510 /  0.27 (12141)
  hydrogen bonds       : bond        0.03984 /  2.70 (  380)
  hydrogen bonds       : angle       3.96156 /  2.68 ( 1086)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.284 
Fit side-chains
REVERT: A  107 ASN cc_start: 0.8871 (t0) cc_final: 0.8630 (t0)
REVERT: A  366 ASN cc_start: 0.8296 (m110) cc_final: 0.8016 (m-40)
REVERT: B   31 ARG cc_start: 0.7701 (ttp-170) cc_final: 0.6925 (ttp80)
REVERT: B  420 ARG cc_start: 0.8814 (ttp80) cc_final: 0.8574 (ttp80)
  outliers start: 14
  outliers final: 10
  residues processed: 111
  average time/residue: 0.6113
  time to fit residues: 71.9116
Evaluate side-chains
  106 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  381 TRP
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain B residue   79 PHE
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  249 ILE
Chi-restraints excluded: chain B residue  400 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 66 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   chunk 75 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 65 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   overall best weight:    1.1182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  90 ASN
D  57 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.111619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.088241 restraints weight = 11692.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.2908 rms_B_bonded: 1.85
r_work: 0.2792 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2670 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8805
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8972  Z= 0.129
  Angle     :  0.533   9.396  12141  Z= 0.281
  Chirality :  0.044   0.146   1354
  Planarity :  0.004   0.045   1522
  Dihedral  :  6.991  77.189   1255
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 14.26 %
    Favored  : 84.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.26), residues: 1094
  helix:  0.98 (0.24), residues: 543
  sheet:  0.19 (0.51), residues: 119
  loop : -0.81 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E  62 
 TYR   0.012   0.001   TYR B  55 
 PHE   0.025   0.001   PHE A 183 
 TRP   0.013   0.001   TRP A 204 
 HIS   0.003   0.001   HIS A 203 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.13 ( 8972)
  covalent geometry    : angle       0.53306 /  0.28 (12141)
  hydrogen bonds       : bond        0.04501 /  3.05 (  380)
  hydrogen bonds       : angle       4.03113 /  2.73 ( 1086)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.366 
Fit side-chains
REVERT: B   31 ARG cc_start: 0.7687 (ttp-170) cc_final: 0.6891 (ttp80)
REVERT: B  420 ARG cc_start: 0.8813 (ttp80) cc_final: 0.8565 (ttp80)
  outliers start: 12
  outliers final: 10
  residues processed: 107
  average time/residue: 0.6358
  time to fit residues: 72.0933
Evaluate side-chains
  104 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  381 TRP
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain B residue   79 PHE
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  249 ILE
Chi-restraints excluded: chain B residue  400 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 31 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   chunk 3 optimal weight:    3.9990
   chunk 52 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 102 optimal weight:    4.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  90 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.108794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.085837 restraints weight = 11663.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.2935 rms_B_bonded: 1.74
r_work: 0.2827 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2709 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8820
moved from start:          0.1821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8972  Z= 0.158
  Angle     :  0.567   9.363  12141  Z= 0.298
  Chirality :  0.046   0.155   1354
  Planarity :  0.005   0.046   1522
  Dihedral  :  7.229  82.422   1255
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 14.26 %
    Favored  : 84.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.26), residues: 1094
  helix:  0.89 (0.24), residues: 543
  sheet: -0.00 (0.49), residues: 126
  loop : -0.76 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E  62 
 TYR   0.013   0.001   TYR B  55 
 PHE   0.027   0.002   PHE A 183 
 TRP   0.014   0.001   TRP A 204 
 HIS   0.004   0.001   HIS A 299 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00387 /  0.16 ( 8972)
  covalent geometry    : angle       0.56654 /  0.30 (12141)
  hydrogen bonds       : bond        0.05109 /  3.45 (  380)
  hydrogen bonds       : angle       4.14662 /  2.81 ( 1086)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2771.31 seconds
wall clock time: 47 minutes 58.27 seconds (2878.27 seconds total)