Starting phenix.real_space_refine
on Sun Jul 27 22:50:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kb5_22787/07_2025/7kb5_22787.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kb5_22787/07_2025/7kb5_22787.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kb5_22787/07_2025/7kb5_22787.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kb5_22787/07_2025/7kb5_22787.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kb5_22787/07_2025/7kb5_22787.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kb5_22787/07_2025/7kb5_22787.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.016
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      40      5.16       5
     C    6382      2.51       5
     N    1645      2.21       5
     O    1710      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 9777
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 427, 3269
          Classifications: {'peptide': 427}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 19, 'TRANS': 407}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 63
          Unresolved non-hydrogen angles: 78
          Unresolved non-hydrogen dihedrals: 54
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 48
    Chain: "B"
      Number of atoms: 229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 229
          Classifications: {'peptide': 32}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 1, 'TRANS': 30}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "C"
      Number of atoms: 435
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 435
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 2, 'TRANS': 52}
    Chain: "D"
      Number of atoms: 3244
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 410, 3244
          Classifications: {'peptide': 410}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 24, 'TRANS': 385}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 79
          Unresolved non-hydrogen angles: 99
          Unresolved non-hydrogen dihedrals: 61
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 11, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 68
    Chain: "E"
      Number of atoms: 1129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1129
          Classifications: {'peptide': 138}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 2, 'TRANS': 135}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "F"
      Number of atoms: 1471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 190, 1471
          Classifications: {'peptide': 190}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 7, 'TRANS': 182}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
  Time building chain proxies: 6.26, per 1000 atoms: 0.64
  Number of scatterers: 9777
  At special positions: 0
  Unit cell: (99, 124.2, 135.9, 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      40     16.00
     O    1710      8.00
     N    1645      7.00
     C    6382      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.54
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2364

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 7 sheets defined
      67.3% alpha, 5.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 49
      removed outlier: 3.591A  pdb=" N   GLN A  48 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ILE A  49 " --> pdb=" O   ILE A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 70
      removed outlier: 3.742A  pdb=" N   ALA A  68 " --> pdb=" O   TYR A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 98
      removed outlier: 3.557A  pdb=" N   THR A  98 " --> pdb=" O   PHE A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 137
      removed outlier: 3.619A  pdb=" N   LEU A 131 " --> pdb=" O   LEU A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 174
      removed outlier: 3.655A  pdb=" N   VAL A 164 " --> pdb=" O   ALA A 160 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   GLY A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 198
      removed outlier: 3.672A  pdb=" N   LEU A 183 " --> pdb=" O   SER A 179 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   THR A 185 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 225
      removed outlier: 3.643A  pdb=" N   ALA A 223 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 238
      removed outlier: 3.676A  pdb=" N   VAL A 233 " --> pdb=" O   LYS A 229 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   TYR A 237 " --> pdb=" O   VAL A 233 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ARG A 238 " --> pdb=" O   GLU A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 262
      removed outlier: 3.632A  pdb=" N   VAL A 247 " --> pdb=" O   ASN A 243 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   TYR A 259 " --> pdb=" O   LEU A 255 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LEU A 260 " --> pdb=" O   PHE A 256 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLN A 261 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   GLY A 262 " --> pdb=" O   LEU A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 314
    Processing helix  chain 'A' and resid 317 through 324
    Processing helix  chain 'A' and resid 341 through 347
      removed outlier: 3.661A  pdb=" N   TYR A 345 " --> pdb=" O   GLY A 341 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ILE A 346 " --> pdb=" O   LEU A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 358
      removed outlier: 3.830A  pdb=" N   ASP A 358 " --> pdb=" O   GLU A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 385
      removed outlier: 3.636A  pdb=" N   THR A 362 " --> pdb=" O   ASP A 358 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   CYS A 373 " --> pdb=" O   VAL A 369 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LYS A 378 " --> pdb=" O   ALA A 374 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   GLU A 382 " --> pdb=" O   LYS A 378 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ILE A 383 " --> pdb=" O   THR A 379 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   GLY A 385 " --> pdb=" O   ILE A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 399
    Processing helix  chain 'A' and resid 406 through 440
      removed outlier: 3.564A  pdb=" N   ILE A 410 " --> pdb=" O   ARG A 406 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   TYR A 411 " --> pdb=" O   GLU A 407 " (cutoff:3.500A)
      Proline residue:  A 419  - end of helix
    Processing helix  chain 'A' and resid 444 through 466
      removed outlier: 4.036A  pdb=" N   ILE A 448 " --> pdb=" O   SER A 444 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   LEU A 449 " --> pdb=" O   GLY A 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 82
    Processing helix  chain 'C' and resid 27 through 39
    Processing helix  chain 'C' and resid 43 through 80
      removed outlier: 3.732A  pdb=" N   TYR C  47 " --> pdb=" O   ASP C  43 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LYS C  49 " --> pdb=" O   LYS C  45 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ILE C  73 " --> pdb=" O   LYS C  69 " (cutoff:3.500A)
      Proline residue:  C  74  - end of helix
    Processing helix  chain 'D' and resid 68 through 78
    Processing helix  chain 'D' and resid 221 through 233
    Processing helix  chain 'D' and resid 234 through 249
    Processing helix  chain 'D' and resid 255 through 268
      removed outlier: 3.784A  pdb=" N   ALA D 259 " --> pdb=" O   HIS D 255 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   ASN D 268 " --> pdb=" O   SER D 264 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 276 through 285
      removed outlier: 3.633A  pdb=" N   ILE D 280 " --> pdb=" O   THR D 276 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 298 through 311
    Processing helix  chain 'D' and resid 318 through 343
      removed outlier: 4.125A  pdb=" N   ARG D 324 " --> pdb=" O   ASN D 320 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   HIS D 330 " --> pdb=" O   VAL D 326 " (cutoff:3.500A)
      removed outlier: 5.592A  pdb=" N   SER D 331 " --> pdb=" O   ALA D 327 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   LEU D 332 " --> pdb=" O   LYS D 328 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 346 through 362
    Processing helix  chain 'D' and resid 378 through 386
      removed outlier: 4.416A  pdb=" N   THR D 384 " --> pdb=" O   GLU D 380 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 391 through 397
    Processing helix  chain 'D' and resid 399 through 408
      removed outlier: 3.578A  pdb=" N   ILE D 403 " --> pdb=" O   GLU D 399 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   GLY D 404 " --> pdb=" O   ASP D 400 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 411 through 423
      removed outlier: 4.365A  pdb=" N   GLU D 417 " --> pdb=" O   ALA D 413 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 466 through 470
    Processing helix  chain 'D' and resid 480 through 486
      removed outlier: 3.650A  pdb=" N   ASP D 486 " --> pdb=" O   GLU D 482 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 487 through 492
      removed outlier: 4.409A  pdb=" N   MET D 491 " --> pdb=" O   PRO D 487 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 537 through 541
      removed outlier: 3.691A  pdb=" N   ASN D 541 " --> pdb=" O   LYS D 538 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 554 through 558
    Processing helix  chain 'E' and resid 72 through 86
      removed outlier: 3.773A  pdb=" N   PHE E  76 " --> pdb=" O   HIS E  72 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   ASN E  84 " --> pdb=" O   GLU E  80 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   LYS E  86 " --> pdb=" O   SER E  82 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 88 through 124
      removed outlier: 4.197A  pdb=" N   LEU E  92 " --> pdb=" O   HIS E  88 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   LYS E  93 " --> pdb=" O   GLU E  89 " (cutoff:3.500A)
      Proline residue:  E 115  - end of helix
    Processing helix  chain 'E' and resid 128 through 156
      removed outlier: 3.855A  pdb=" N   LYS E 132 " --> pdb=" O   GLU E 128 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   LYS E 139 " --> pdb=" O   GLU E 135 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLU E 142 " --> pdb=" O   VAL E 138 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 162 through 182
      removed outlier: 4.008A  pdb=" N   PHE E 172 " --> pdb=" O   LYS E 168 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 182 through 195
      removed outlier: 5.080A  pdb=" N   GLU E 188 " --> pdb=" O   LEU E 184 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   VAL E 189 " --> pdb=" O   LYS E 185 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   CYS E 190 " --> pdb=" O   ARG E 186 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ILE E 191 " --> pdb=" O   LYS E 187 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 199 through 203
      removed outlier: 3.549A  pdb=" N   GLY E 202 " --> pdb=" O   ASN E 199 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ARG E 203 " --> pdb=" O   ASN E 200 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 199 through 203'
    Processing helix  chain 'F' and resid 21 through 41
    Processing helix  chain 'F' and resid 52 through 67
    Processing helix  chain 'F' and resid 68 through 70
      No H-bonds generated for 'chain 'F' and resid 68 through 70'
    Processing helix  chain 'F' and resid 75 through 91
      removed outlier: 3.727A  pdb=" N   LYS F  79 " --> pdb=" O   ASN F  75 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 101 through 120
      removed outlier: 3.637A  pdb=" N   LEU F 105 " --> pdb=" O   GLN F 101 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   SER F 111 " --> pdb=" O   PHE F 107 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 122 through 135
    Processing helix  chain 'F' and resid 139 through 153
      removed outlier: 3.940A  pdb=" N   VAL F 144 " --> pdb=" O   PRO F 140 " (cutoff:3.500A)
      removed outlier: 5.268A  pdb=" N   ARG F 145 " --> pdb=" O   ASP F 141 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 156 through 168
    Processing helix  chain 'F' and resid 175 through 192
    Processing sheet with id=AA1, first strand: chain 'A' and resid 278 through 284
    Processing sheet with id=AA2, first strand: chain 'A' and resid 325 through 327
    Processing sheet with id=AA3, first strand: chain 'D' and resid 426 through 427
    Processing sheet with id=AA4, first strand: chain 'D' and resid 430 through 434
      removed outlier: 4.005A  pdb=" N   LYS D 432 " --> pdb=" O   LYS D 454 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ASP D 434 " --> pdb=" O   SER D 452 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   SER D 452 " --> pdb=" O   ASP D 434 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 532
      removed outlier: 3.511A  pdb=" N   ILE D 604 " --> pdb=" O   VAL D 590 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   LEU D 602 " --> pdb=" O   VAL D 592 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 530 through 532
    Processing sheet with id=AA7, first strand: chain 'F' and resid 5 through 6

    609 hydrogen bonds defined for protein.
    1779 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: 2.94

  Time building geometry restraints manager: 3.01 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: 3069
        1.34 -     1.46: 1891
        1.46 -     1.58: 4948
        1.58 -     1.69: 0
        1.69 -     1.81: 63
  Bond restraints: 9971
  Sorted by residual:
  bond pdb=" CB  CYS E 167 "
       pdb=" SG  CYS E 167 "
    ideal  model  delta    sigma   weight residual
    1.808  1.762  0.046 3.30e-02 9.18e+02 1.96e+00
  bond pdb=" C   ILE A 418 "
       pdb=" N   PRO A 419 "
    ideal  model  delta    sigma   weight residual
    1.335  1.352 -0.016 1.36e-02 5.41e+03 1.44e+00
  bond pdb=" CB  GLN F 155 "
       pdb=" CG  GLN F 155 "
    ideal  model  delta    sigma   weight residual
    1.520  1.488  0.032 3.00e-02 1.11e+03 1.14e+00
  bond pdb=" C   THR D 595 "
       pdb=" N   ASP D 596 "
    ideal  model  delta    sigma   weight residual
    1.333  1.319  0.014 1.41e-02 5.03e+03 9.83e-01
  bond pdb=" C   ILE D 531 "
       pdb=" N   ILE D 532 "
    ideal  model  delta    sigma   weight residual
    1.335  1.321  0.014 1.41e-02 5.03e+03 9.69e-01
  ... (remaining 9966 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 13237
        1.88 -     3.75: 227
        3.75 -     5.63: 36
        5.63 -     7.51: 4
        7.51 -     9.38: 1
  Bond angle restraints: 13505
  Sorted by residual:
  angle pdb=" N   VAL E 205 "
        pdb=" CA  VAL E 205 "
        pdb=" C   VAL E 205 "
      ideal   model   delta    sigma   weight residual
     112.17  108.28    3.89 9.50e-01 1.11e+00 1.68e+01
  angle pdb=" N   ILE E 126 "
        pdb=" CA  ILE E 126 "
        pdb=" C   ILE E 126 "
      ideal   model   delta    sigma   weight residual
     113.71  110.11    3.60 9.50e-01 1.11e+00 1.44e+01
  angle pdb=" C   ILE A 417 "
        pdb=" N   ILE A 418 "
        pdb=" CA  ILE A 418 "
      ideal   model   delta    sigma   weight residual
     120.33  122.80   -2.47 8.00e-01 1.56e+00 9.52e+00
  angle pdb=" C   PRO F  94 "
        pdb=" N   TRP F  95 "
        pdb=" CA  TRP F  95 "
      ideal   model   delta    sigma   weight residual
     122.56  117.83    4.73 1.72e+00 3.38e-01 7.57e+00
  angle pdb=" CA  TYR F 190 "
        pdb=" CB  TYR F 190 "
        pdb=" CG  TYR F 190 "
      ideal   model   delta    sigma   weight residual
     113.90  118.77   -4.87 1.80e+00 3.09e-01 7.33e+00
  ... (remaining 13500 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.72: 5362
       16.72 -    33.43: 526
       33.43 -    50.15: 111
       50.15 -    66.87: 9
       66.87 -    83.58: 8
  Dihedral angle restraints: 6016
    sinusoidal: 2376
      harmonic: 3640
  Sorted by residual:
  dihedral pdb=" CA  VAL D 437 "
           pdb=" C   VAL D 437 "
           pdb=" N   PRO D 438 "
           pdb=" CA  PRO D 438 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.46   21.54     0      5.00e+00 4.00e-02 1.86e+01
  dihedral pdb=" CA  ASP D 545 "
           pdb=" CB  ASP D 545 "
           pdb=" CG  ASP D 545 "
           pdb=" OD1 ASP D 545 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.94   58.94     1      2.00e+01 2.50e-03 1.16e+01
  dihedral pdb=" CA  ASN E  84 "
           pdb=" C   ASN E  84 "
           pdb=" N   GLU E  85 "
           pdb=" CA  GLU E  85 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.25  -16.75     0      5.00e+00 4.00e-02 1.12e+01
  ... (remaining 6013 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 860
       0.027 -    0.054: 499
       0.054 -    0.081: 136
       0.081 -    0.108: 82
       0.108 -    0.135: 20
  Chirality restraints: 1597
  Sorted by residual:
  chirality pdb=" CA  ILE D 470 "
            pdb=" N   ILE D 470 "
            pdb=" C   ILE D 470 "
            pdb=" CB  ILE D 470 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.55e-01
  chirality pdb=" CA  ILE D 389 "
            pdb=" N   ILE D 389 "
            pdb=" C   ILE D 389 "
            pdb=" CB  ILE D 389 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.44e-01
  chirality pdb=" CA  PRO F  94 "
            pdb=" N   PRO F  94 "
            pdb=" C   PRO F  94 "
            pdb=" CB  PRO F  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.20e-01
  ... (remaining 1594 not shown)

  Planarity restraints: 1677
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR F  47 "    0.029 5.00e-02 4.00e+02   4.39e-02 3.09e+00
        pdb=" N   PRO F  48 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO F  48 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO F  48 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL D 437 "   -0.028 5.00e-02 4.00e+02   4.22e-02 2.85e+00
        pdb=" N   PRO D 438 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO D 438 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO D 438 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA F  93 "   -0.028 5.00e-02 4.00e+02   4.22e-02 2.85e+00
        pdb=" N   PRO F  94 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO F  94 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO F  94 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 1674 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 285
        2.71 -     3.26: 10117
        3.26 -     3.81: 14954
        3.81 -     4.35: 17322
        4.35 -     4.90: 29626
  Nonbonded interactions: 72304
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN D 370 "
            pdb=" OG1 THR D 391 "
     model   vdw
     2.163 3.040
  nonbonded pdb=" OG  SER A 271 "
            pdb=" O   VAL A 274 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" O   PRO F 171 "
            pdb=" NH2 ARG F 177 "
     model   vdw
     2.252 3.120
  nonbonded pdb=" O   PRO A  18 "
            pdb=" NZ  LYS A 119 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" O   SER D 423 "
            pdb=" OG  SER D 423 "
     model   vdw
     2.271 3.040
  ... (remaining 72299 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 group one per residue
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:             2.110
  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:             0.010
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     25.450
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.050
  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:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9971  Z= 0.190
  Angle     :  0.635   9.382  13505  Z= 0.354
  Chirality :  0.040   0.135   1597
  Planarity :  0.004   0.044   1677
  Dihedral  : 13.760  83.585   3652
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.22), residues: 1228
  helix: -0.09 (0.17), residues: 753
  sheet: -2.43 (0.54), residues: 85
  loop : -2.26 (0.28), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F 156 
 HIS   0.004   0.001   HIS D 334 
 PHE   0.019   0.001   PHE D 356 
 TYR   0.022   0.002   TYR F 190 
 ARG   0.003   0.000   ARG E  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14114 (  599)
  hydrogen bonds       : angle       5.02546 ( 1779)
  covalent geometry    : bond        0.00438 ( 9971)
  covalent geometry    : angle       0.63539 (13505)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 1.177 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  400 MET cc_start: 0.9334 (mmm) cc_final: 0.8861 (mmm)
REVERT: B   71 LEU cc_start: 0.9403 (mt) cc_final: 0.9151 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.2339
  time to fit residues: 26.0514
Evaluate side-chains
  48 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 1.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 103 optimal weight:    6.9990
   chunk 93 optimal weight:    4.9990
   chunk 51 optimal weight:    8.9990
   chunk 31 optimal weight:    9.9990
   chunk 62 optimal weight:    1.9990
   chunk 49 optimal weight:    9.9990
   chunk 96 optimal weight:    7.9990
   chunk 37 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 111 optimal weight:    0.4980
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
A  73 ASN
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 188 ASN
A 317 ASN
A 336 GLN
D 330 HIS
D 390 HIS
D 484 GLN
D 520 GLN
E  88 HIS
E 181 GLN
F  68 ASN
F  89 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.052256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.037508 restraints weight = 67897.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.038591 restraints weight = 35393.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.039340 restraints weight = 23845.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.1330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9971  Z= 0.125
  Angle     :  0.555   6.808  13505  Z= 0.279
  Chirality :  0.038   0.132   1597
  Planarity :  0.004   0.047   1677
  Dihedral  :  3.720  20.452   1328
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 12.52 %
    Favored  : 86.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.25), residues: 1228
  helix:  1.49 (0.19), residues: 760
  sheet: -1.87 (0.58), residues: 82
  loop : -1.72 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F  95 
 HIS   0.006   0.001   HIS D 309 
 PHE   0.007   0.001   PHE D  74 
 TYR   0.019   0.001   TYR D 227 
 ARG   0.009   0.000   ARG D 485 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04111 (  599)
  hydrogen bonds       : angle       3.71397 ( 1779)
  covalent geometry    : bond        0.00277 ( 9971)
  covalent geometry    : angle       0.55502 (13505)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 1.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 MET cc_start: 0.8231 (mmm) cc_final: 0.7698 (mtp)
REVERT: A  165 MET cc_start: 0.8975 (tmm) cc_final: 0.8771 (tmm)
REVERT: A  400 MET cc_start: 0.9443 (mmm) cc_final: 0.8804 (mmm)
REVERT: B   71 LEU cc_start: 0.9330 (mt) cc_final: 0.9112 (tp)
REVERT: C   47 TYR cc_start: 0.8544 (t80) cc_final: 0.8308 (t80)
REVERT: F   87 MET cc_start: 0.9304 (ttt) cc_final: 0.8960 (tmm)
  outliers start: 12
  outliers final: 5
  residues processed: 63
  average time/residue: 0.1835
  time to fit residues: 18.3399
Evaluate side-chains
  53 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 48
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  231 LEU
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  606 MET
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain E residue  170 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 72 optimal weight:    0.8980
   chunk 23 optimal weight:    8.9990
   chunk 47 optimal weight:    6.9990
   chunk 15 optimal weight:    9.9990
   chunk 4 optimal weight:   10.0000
   chunk 94 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 83 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
D 381 HIS
F  71 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.051531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.036560 restraints weight = 69518.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.037620 restraints weight = 36587.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.038329 restraints weight = 24804.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.1679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9971  Z= 0.153
  Angle     :  0.557   8.092  13505  Z= 0.276
  Chirality :  0.038   0.133   1597
  Planarity :  0.003   0.046   1677
  Dihedral  :  3.650  20.874   1328
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 14.05 %
    Favored  : 83.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.25), residues: 1228
  helix:  2.12 (0.19), residues: 759
  sheet: -1.58 (0.58), residues: 81
  loop : -1.44 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F 156 
 HIS   0.005   0.001   HIS C  72 
 PHE   0.024   0.001   PHE B  64 
 TYR   0.018   0.001   TYR D 227 
 ARG   0.003   0.000   ARG E  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03915 (  599)
  hydrogen bonds       : angle       3.58139 ( 1779)
  covalent geometry    : bond        0.00349 ( 9971)
  covalent geometry    : angle       0.55707 (13505)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 47
  time to evaluate  : 1.086 
Fit side-chains
   revert: symmetry clash
REVERT: A  165 MET cc_start: 0.9032 (tmm) cc_final: 0.8670 (tmm)
REVERT: A  249 MET cc_start: 0.9407 (mmm) cc_final: 0.9121 (ptp)
REVERT: A  400 MET cc_start: 0.9416 (mmm) cc_final: 0.8812 (mmm)
REVERT: C   47 TYR cc_start: 0.8562 (t80) cc_final: 0.8238 (t80)
REVERT: D  330 HIS cc_start: 0.8471 (OUTLIER) cc_final: 0.7538 (t70)
REVERT: E  126 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.9171 (pt)
REVERT: F   87 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.9057 (tmm)
  outliers start: 22
  outliers final: 11
  residues processed: 65
  average time/residue: 0.1589
  time to fit residues: 17.0888
Evaluate side-chains
  59 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 45
  time to evaluate  : 1.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain D residue  231 LEU
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  330 HIS
Chi-restraints excluded: chain D residue  555 LEU
Chi-restraints excluded: chain D residue  606 MET
Chi-restraints excluded: chain E residue  126 ILE
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain E residue  170 ILE
Chi-restraints excluded: chain F residue   87 MET
Chi-restraints excluded: chain F residue  162 THR
Chi-restraints excluded: chain F residue  183 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 81 optimal weight:    5.9990
   chunk 13 optimal weight:    7.9990
   chunk 63 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 21 optimal weight:   20.0000
   chunk 109 optimal weight:    7.9990
   chunk 112 optimal weight:    3.9990
   chunk 72 optimal weight:    6.9990
   chunk 50 optimal weight:    8.9990
   chunk 55 optimal weight:    7.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
D 307 GLN
E 181 GLN
F 155 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.050698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.035765 restraints weight = 68868.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.036807 restraints weight = 36858.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.037454 restraints weight = 25101.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.1928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   9971  Z= 0.201
  Angle     :  0.586   7.976  13505  Z= 0.291
  Chirality :  0.039   0.132   1597
  Planarity :  0.003   0.047   1677
  Dihedral  :  3.717  20.493   1328
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 15.87 %
    Favored  : 81.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: 1228
  helix:  2.28 (0.19), residues: 762
  sheet: -1.54 (0.59), residues: 81
  loop : -1.30 (0.32), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F 156 
 HIS   0.006   0.001   HIS C  72 
 PHE   0.021   0.001   PHE B  64 
 TYR   0.020   0.001   TYR F 190 
 ARG   0.003   0.000   ARG E  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04077 (  599)
  hydrogen bonds       : angle       3.66957 ( 1779)
  covalent geometry    : bond        0.00456 ( 9971)
  covalent geometry    : angle       0.58560 (13505)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 48
  time to evaluate  : 1.229 
Fit side-chains
   revert: symmetry clash
REVERT: A  165 MET cc_start: 0.9100 (tmm) cc_final: 0.8653 (tmm)
REVERT: A  350 MET cc_start: 0.8686 (mmp) cc_final: 0.8467 (mmp)
REVERT: A  400 MET cc_start: 0.9386 (mmm) cc_final: 0.8830 (mmm)
REVERT: C   47 TYR cc_start: 0.8604 (t80) cc_final: 0.8308 (t80)
REVERT: D  330 HIS cc_start: 0.8521 (OUTLIER) cc_final: 0.7616 (t70)
REVERT: D  414 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8970 (mtpp)
REVERT: E  126 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9178 (pt)
REVERT: F   87 MET cc_start: 0.9318 (OUTLIER) cc_final: 0.9055 (tmm)
REVERT: F  155 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7904 (mm-40)
  outliers start: 27
  outliers final: 17
  residues processed: 71
  average time/residue: 0.1839
  time to fit residues: 20.8455
Evaluate side-chains
  66 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 44
  time to evaluate  : 1.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain D residue  231 LEU
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  330 HIS
Chi-restraints excluded: chain D residue  341 CYS
Chi-restraints excluded: chain D residue  414 LYS
Chi-restraints excluded: chain D residue  516 LEU
Chi-restraints excluded: chain D residue  606 MET
Chi-restraints excluded: chain E residue  126 ILE
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain E residue  170 ILE
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue   87 MET
Chi-restraints excluded: chain F residue  155 GLN
Chi-restraints excluded: chain F residue  162 THR
Chi-restraints excluded: chain F residue  163 CYS
Chi-restraints excluded: chain F residue  183 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 30 optimal weight:   20.0000
   chunk 66 optimal weight:    1.9990
   chunk 14 optimal weight:    8.9990
   chunk 74 optimal weight:    0.0670
   chunk 89 optimal weight:    2.9990
   chunk 78 optimal weight:   20.0000
   chunk 101 optimal weight:    2.9990
   chunk 106 optimal weight:    3.9990
   chunk 69 optimal weight:    0.5980
   chunk 88 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9980
   overall best weight:    0.9320

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

Flipped N/Q/H residues before XYZ refinement:
E 181 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.051744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.037004 restraints weight = 68292.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.038085 restraints weight = 35315.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.038796 restraints weight = 23662.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.2177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9971  Z= 0.103
  Angle     :  0.530   8.151  13505  Z= 0.257
  Chirality :  0.037   0.134   1597
  Planarity :  0.003   0.048   1677
  Dihedral  :  3.487  20.052   1328
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 17.21 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.26), residues: 1228
  helix:  2.47 (0.19), residues: 765
  sheet: -1.36 (0.59), residues: 82
  loop : -1.04 (0.33), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 159 
 HIS   0.006   0.001   HIS D 309 
 PHE   0.012   0.001   PHE F  62 
 TYR   0.013   0.001   TYR F 190 
 ARG   0.003   0.000   ARG F 154 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03453 (  599)
  hydrogen bonds       : angle       3.28861 ( 1779)
  covalent geometry    : bond        0.00228 ( 9971)
  covalent geometry    : angle       0.52985 (13505)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 52
  time to evaluate  : 1.167 
Fit side-chains
   revert: symmetry clash
REVERT: A  158 MET cc_start: 0.9553 (mmm) cc_final: 0.9340 (mmm)
REVERT: A  165 MET cc_start: 0.9075 (tmm) cc_final: 0.8607 (tmm)
REVERT: A  350 MET cc_start: 0.8610 (mmp) cc_final: 0.8405 (mmp)
REVERT: A  400 MET cc_start: 0.9402 (mmm) cc_final: 0.8848 (mmm)
REVERT: C   47 TYR cc_start: 0.8642 (t80) cc_final: 0.8287 (t80)
REVERT: C   70 LEU cc_start: 0.9664 (tt) cc_final: 0.9418 (mt)
REVERT: D  330 HIS cc_start: 0.8443 (OUTLIER) cc_final: 0.7589 (t70)
REVERT: D  533 GLU cc_start: 0.7900 (tp30) cc_final: 0.7636 (tp30)
REVERT: F   87 MET cc_start: 0.9257 (OUTLIER) cc_final: 0.8943 (tmm)
  outliers start: 17
  outliers final: 11
  residues processed: 65
  average time/residue: 0.1900
  time to fit residues: 19.2915
Evaluate side-chains
  58 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 45
  time to evaluate  : 1.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain C residue   72 HIS
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  231 LEU
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  330 HIS
Chi-restraints excluded: chain D residue  414 LYS
Chi-restraints excluded: chain D residue  606 MET
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain E residue  170 ILE
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue   87 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 14 optimal weight:    9.9990
   chunk 57 optimal weight:    6.9990
   chunk 20 optimal weight:    6.9990
   chunk 50 optimal weight:   10.0000
   chunk 72 optimal weight:    6.9990
   chunk 100 optimal weight:    7.9990
   chunk 15 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 86 optimal weight:    7.9990
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
E 181 GLN
F 155 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.050665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.035712 restraints weight = 68907.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.036758 restraints weight = 37200.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.037454 restraints weight = 25050.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9971  Z= 0.183
  Angle     :  0.575   8.687  13505  Z= 0.283
  Chirality :  0.039   0.133   1597
  Planarity :  0.003   0.047   1677
  Dihedral  :  3.570  19.965   1328
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 18.93 %
    Favored  : 79.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.25), residues: 1228
  helix:  2.51 (0.19), residues: 765
  sheet: -1.36 (0.58), residues: 81
  loop : -1.00 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F 156 
 HIS   0.005   0.001   HIS C  72 
 PHE   0.023   0.001   PHE C  58 
 TYR   0.020   0.001   TYR F 190 
 ARG   0.003   0.000   ARG E  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03849 (  599)
  hydrogen bonds       : angle       3.50458 ( 1779)
  covalent geometry    : bond        0.00420 ( 9971)
  covalent geometry    : angle       0.57502 (13505)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 45
  time to evaluate  : 1.079 
Fit side-chains
   revert: symmetry clash
REVERT: A  165 MET cc_start: 0.9121 (tmm) cc_final: 0.8607 (tmm)
REVERT: A  350 MET cc_start: 0.8638 (mmp) cc_final: 0.8418 (mmp)
REVERT: A  400 MET cc_start: 0.9415 (mmm) cc_final: 0.8939 (mmm)
REVERT: C   47 TYR cc_start: 0.8677 (t80) cc_final: 0.8332 (t80)
REVERT: C   70 LEU cc_start: 0.9689 (tt) cc_final: 0.9367 (mt)
REVERT: D  330 HIS cc_start: 0.8528 (OUTLIER) cc_final: 0.7632 (t70)
REVERT: F   57 MET cc_start: 0.9010 (ptp) cc_final: 0.8796 (ptp)
REVERT: F   87 MET cc_start: 0.9294 (OUTLIER) cc_final: 0.8972 (tmm)
  outliers start: 20
  outliers final: 16
  residues processed: 61
  average time/residue: 0.1712
  time to fit residues: 16.9039
Evaluate side-chains
  61 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 43
  time to evaluate  : 1.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain C residue   72 HIS
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  231 LEU
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  330 HIS
Chi-restraints excluded: chain D residue  414 LYS
Chi-restraints excluded: chain D residue  516 LEU
Chi-restraints excluded: chain D residue  606 MET
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain E residue  170 ILE
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue   87 MET
Chi-restraints excluded: chain F residue  163 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 59 optimal weight:    8.9990
   chunk 82 optimal weight:    2.9990
   chunk 92 optimal weight:    9.9990
   chunk 19 optimal weight:   40.0000
   chunk 91 optimal weight:    6.9990
   chunk 78 optimal weight:    8.9990
   chunk 61 optimal weight:    4.9990
   chunk 87 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 71 optimal weight:    9.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    3.3186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.050762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.036099 restraints weight = 69588.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.037090 restraints weight = 37340.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.037767 restraints weight = 25697.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.2399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9971  Z= 0.172
  Angle     :  0.573   9.304  13505  Z= 0.281
  Chirality :  0.038   0.132   1597
  Planarity :  0.003   0.048   1677
  Dihedral  :  3.606  19.962   1328
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 18.74 %
    Favored  : 79.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.25), residues: 1228
  helix:  2.53 (0.19), residues: 765
  sheet: -1.34 (0.58), residues: 81
  loop : -0.97 (0.34), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 156 
 HIS   0.005   0.001   HIS C  72 
 PHE   0.010   0.001   PHE D 356 
 TYR   0.019   0.001   TYR F 190 
 ARG   0.003   0.000   ARG E  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03810 (  599)
  hydrogen bonds       : angle       3.49800 ( 1779)
  covalent geometry    : bond        0.00392 ( 9971)
  covalent geometry    : angle       0.57286 (13505)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 46
  time to evaluate  : 1.250 
Fit side-chains
REVERT: A  165 MET cc_start: 0.9115 (tmm) cc_final: 0.8606 (tmm)
REVERT: A  194 PHE cc_start: 0.9192 (OUTLIER) cc_final: 0.8951 (t80)
REVERT: A  350 MET cc_start: 0.8642 (mmp) cc_final: 0.8426 (mmp)
REVERT: A  400 MET cc_start: 0.9431 (mmm) cc_final: 0.8963 (mmm)
REVERT: C   47 TYR cc_start: 0.8705 (t80) cc_final: 0.8354 (t80)
REVERT: C   70 LEU cc_start: 0.9695 (tt) cc_final: 0.9377 (mt)
REVERT: D  330 HIS cc_start: 0.8579 (OUTLIER) cc_final: 0.7749 (t70)
REVERT: D  414 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.9010 (mtpp)
REVERT: F   87 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8970 (tmm)
  outliers start: 22
  outliers final: 16
  residues processed: 64
  average time/residue: 0.1712
  time to fit residues: 18.2460
Evaluate side-chains
  64 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 44
  time to evaluate  : 1.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  194 PHE
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain C residue   72 HIS
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  231 LEU
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  330 HIS
Chi-restraints excluded: chain D residue  341 CYS
Chi-restraints excluded: chain D residue  414 LYS
Chi-restraints excluded: chain D residue  516 LEU
Chi-restraints excluded: chain D residue  606 MET
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain E residue  170 ILE
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue   87 MET
Chi-restraints excluded: chain F residue  163 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 99 optimal weight:    3.9990
   chunk 33 optimal weight:    9.9990
   chunk 112 optimal weight:    7.9990
   chunk 3 optimal weight:    0.8980
   chunk 98 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 115 optimal weight:    9.9990
   chunk 68 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 86 optimal weight:    7.9990
   chunk 46 optimal weight:    8.9990
   overall best weight:    2.7788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.050947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.036255 restraints weight = 69718.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.037265 restraints weight = 36812.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.037782 restraints weight = 25116.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9971  Z= 0.151
  Angle     :  0.578   9.772  13505  Z= 0.278
  Chirality :  0.038   0.144   1597
  Planarity :  0.003   0.049   1677
  Dihedral  :  3.562  19.838   1328
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 18.45 %
    Favored  : 78.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.25), residues: 1228
  helix:  2.59 (0.19), residues: 765
  sheet: -1.32 (0.57), residues: 86
  loop : -0.91 (0.34), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F 156 
 HIS   0.004   0.001   HIS C  72 
 PHE   0.022   0.001   PHE C  58 
 TYR   0.018   0.001   TYR F 190 
 ARG   0.003   0.000   ARG E  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03707 (  599)
  hydrogen bonds       : angle       3.40822 ( 1779)
  covalent geometry    : bond        0.00346 ( 9971)
  covalent geometry    : angle       0.57839 (13505)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 46
  time to evaluate  : 1.315 
Fit side-chains
REVERT: A   90 MET cc_start: 0.9564 (tmm) cc_final: 0.9257 (ppp)
REVERT: A  135 MET cc_start: 0.8114 (mmm) cc_final: 0.7740 (mtp)
REVERT: A  165 MET cc_start: 0.9129 (tmm) cc_final: 0.8610 (tmm)
REVERT: A  350 MET cc_start: 0.8647 (mmp) cc_final: 0.8436 (mmp)
REVERT: A  400 MET cc_start: 0.9439 (mmm) cc_final: 0.8988 (mmm)
REVERT: B   66 PHE cc_start: 0.9003 (t80) cc_final: 0.8506 (t80)
REVERT: C   47 TYR cc_start: 0.8709 (t80) cc_final: 0.8360 (t80)
REVERT: C   70 LEU cc_start: 0.9694 (tt) cc_final: 0.9374 (mt)
REVERT: D  330 HIS cc_start: 0.8545 (OUTLIER) cc_final: 0.7733 (t70)
REVERT: D  414 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.9034 (mtpp)
REVERT: D  533 GLU cc_start: 0.7968 (tp30) cc_final: 0.7729 (tp30)
REVERT: D  547 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8055 (t80)
REVERT: F   87 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8965 (tmm)
  outliers start: 28
  outliers final: 18
  residues processed: 70
  average time/residue: 0.2052
  time to fit residues: 23.8409
Evaluate side-chains
  67 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 45
  time to evaluate  : 1.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain C residue   72 HIS
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  231 LEU
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  330 HIS
Chi-restraints excluded: chain D residue  341 CYS
Chi-restraints excluded: chain D residue  414 LYS
Chi-restraints excluded: chain D residue  516 LEU
Chi-restraints excluded: chain D residue  547 PHE
Chi-restraints excluded: chain D residue  606 MET
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain E residue  170 ILE
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue   87 MET
Chi-restraints excluded: chain F residue  183 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 104 optimal weight:   10.0000
   chunk 87 optimal weight:    5.9990
   chunk 37 optimal weight:    4.9990
   chunk 57 optimal weight:    0.0570
   chunk 118 optimal weight:    0.9980
   chunk 77 optimal weight:   10.0000
   chunk 85 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 44 optimal weight:    9.9990
   chunk 25 optimal weight:   20.0000
   chunk 76 optimal weight:    8.9990
   overall best weight:    3.0104

-------------------------------------------------------------------------------
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 = 0.3325 r_free = 0.3325 target = 0.050841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.036572 restraints weight = 69454.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.037618 restraints weight = 35897.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.038174 restraints weight = 23092.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.2609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9971  Z= 0.160
  Angle     :  0.601  13.011  13505  Z= 0.288
  Chirality :  0.039   0.147   1597
  Planarity :  0.003   0.043   1677
  Dihedral  :  3.565  19.743   1328
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 18.83 %
    Favored  : 78.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.25), residues: 1228
  helix:  2.59 (0.19), residues: 765
  sheet: -1.37 (0.56), residues: 86
  loop : -0.91 (0.34), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F 156 
 HIS   0.004   0.001   HIS C  72 
 PHE   0.010   0.001   PHE A 254 
 TYR   0.019   0.001   TYR F 190 
 ARG   0.003   0.000   ARG E  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03737 (  599)
  hydrogen bonds       : angle       3.44258 ( 1779)
  covalent geometry    : bond        0.00366 ( 9971)
  covalent geometry    : angle       0.60092 (13505)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 44
  time to evaluate  : 1.423 
Fit side-chains
   revert: symmetry clash
REVERT: A  165 MET cc_start: 0.9117 (tmm) cc_final: 0.8600 (tmm)
REVERT: A  350 MET cc_start: 0.8546 (mmp) cc_final: 0.8339 (mmp)
REVERT: A  400 MET cc_start: 0.9437 (mmm) cc_final: 0.8989 (mmm)
REVERT: B   66 PHE cc_start: 0.9023 (t80) cc_final: 0.8532 (t80)
REVERT: C   47 TYR cc_start: 0.8701 (t80) cc_final: 0.8350 (t80)
REVERT: D  330 HIS cc_start: 0.8570 (OUTLIER) cc_final: 0.7758 (t70)
REVERT: D  533 GLU cc_start: 0.7953 (tp30) cc_final: 0.7747 (tp30)
REVERT: D  547 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8043 (t80)
REVERT: F   87 MET cc_start: 0.9292 (ttt) cc_final: 0.9022 (tmm)
  outliers start: 23
  outliers final: 20
  residues processed: 65
  average time/residue: 0.1785
  time to fit residues: 19.0851
Evaluate side-chains
  66 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 44
  time to evaluate  : 1.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain C residue   72 HIS
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  231 LEU
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  330 HIS
Chi-restraints excluded: chain D residue  341 CYS
Chi-restraints excluded: chain D residue  359 ILE
Chi-restraints excluded: chain D residue  516 LEU
Chi-restraints excluded: chain D residue  547 PHE
Chi-restraints excluded: chain D residue  606 MET
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain E residue  170 ILE
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue  179 LEU
Chi-restraints excluded: chain F residue  183 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 44 optimal weight:    9.9990
   chunk 69 optimal weight:    5.9990
   chunk 105 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 113 optimal weight:    2.9990
   chunk 52 optimal weight:    8.9990
   chunk 65 optimal weight:    6.9990
   chunk 29 optimal weight:   10.0000
   chunk 18 optimal weight:   20.0000
   chunk 95 optimal weight:    0.4980
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
** D 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 181 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.051731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.037171 restraints weight = 69200.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.038241 restraints weight = 35812.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.038946 restraints weight = 24137.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9971  Z= 0.105
  Angle     :  0.580  13.004  13505  Z= 0.272
  Chirality :  0.037   0.143   1597
  Planarity :  0.003   0.045   1677
  Dihedral  :  3.396  19.416   1328
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 19.22 %
    Favored  : 78.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.09 (0.26), residues: 1228
  helix:  2.70 (0.19), residues: 764
  sheet: -1.20 (0.57), residues: 86
  loop : -0.82 (0.34), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 159 
 HIS   0.006   0.001   HIS D 309 
 PHE   0.009   0.001   PHE E 134 
 TYR   0.024   0.001   TYR D 227 
 ARG   0.003   0.000   ARG E  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03265 (  599)
  hydrogen bonds       : angle       3.19032 ( 1779)
  covalent geometry    : bond        0.00236 ( 9971)
  covalent geometry    : angle       0.57951 (13505)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 49
  time to evaluate  : 1.307 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.9513 (tmm) cc_final: 0.9213 (ppp)
REVERT: A  135 MET cc_start: 0.7945 (mmm) cc_final: 0.7575 (mtp)
REVERT: A  165 MET cc_start: 0.9118 (tmm) cc_final: 0.8640 (tmm)
REVERT: A  168 ASP cc_start: 0.8912 (t70) cc_final: 0.8474 (t70)
REVERT: A  294 MET cc_start: 0.9272 (tpp) cc_final: 0.8983 (mmp)
REVERT: A  400 MET cc_start: 0.9472 (mmm) cc_final: 0.8969 (mmm)
REVERT: B   66 PHE cc_start: 0.8981 (t80) cc_final: 0.8478 (t80)
REVERT: C   47 TYR cc_start: 0.8666 (t80) cc_final: 0.8275 (t80)
REVERT: C   72 HIS cc_start: 0.9176 (OUTLIER) cc_final: 0.8695 (t70)
REVERT: D  330 HIS cc_start: 0.8487 (OUTLIER) cc_final: 0.7728 (t70)
REVERT: D  491 MET cc_start: 0.9027 (ttm) cc_final: 0.8548 (tpp)
REVERT: D  533 GLU cc_start: 0.7811 (tp30) cc_final: 0.7591 (tp30)
REVERT: D  547 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.8054 (t80)
  outliers start: 19
  outliers final: 14
  residues processed: 67
  average time/residue: 0.1802
  time to fit residues: 20.3205
Evaluate side-chains
  63 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 46
  time to evaluate  : 1.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain C residue   72 HIS
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  231 LEU
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  330 HIS
Chi-restraints excluded: chain D residue  341 CYS
Chi-restraints excluded: chain D residue  516 LEU
Chi-restraints excluded: chain D residue  547 PHE
Chi-restraints excluded: chain E residue  170 ILE
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue  179 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 113 optimal weight:    5.9990
   chunk 47 optimal weight:    8.9990
   chunk 66 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 96 optimal weight:    8.9990
   chunk 94 optimal weight:    7.9990
   chunk 107 optimal weight:    0.9990
   chunk 81 optimal weight:    5.9990
   chunk 93 optimal weight:    0.9980
   chunk 44 optimal weight:   20.0000
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 181 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.050598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.036464 restraints weight = 69777.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.037404 restraints weight = 36313.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.037783 restraints weight = 23823.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.2766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   9971  Z= 0.184
  Angle     :  0.643  12.132  13505  Z= 0.306
  Chirality :  0.039   0.200   1597
  Planarity :  0.003   0.041   1677
  Dihedral  :  3.567  19.476   1328
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 19.50 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.25), residues: 1228
  helix:  2.60 (0.19), residues: 766
  sheet: -1.25 (0.57), residues: 86
  loop : -0.86 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F 156 
 HIS   0.004   0.001   HIS C  72 
 PHE   0.027   0.001   PHE C  58 
 TYR   0.023   0.001   TYR D 227 
 ARG   0.003   0.000   ARG E  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03837 (  599)
  hydrogen bonds       : angle       3.51623 ( 1779)
  covalent geometry    : bond        0.00420 ( 9971)
  covalent geometry    : angle       0.64348 (13505)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3276.47 seconds
wall clock time: 59 minutes 37.33 seconds (3577.33 seconds total)