Starting phenix.real_space_refine
on Thu Jul  2 08:02:16 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7epz_31251/07_2026/7epz_31251.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7epz_31251/07_2026/7epz_31251.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7epz_31251/07_2026/7epz_31251.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7epz_31251/07_2026/7epz_31251.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7epz_31251/07_2026/7epz_31251.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7epz_31251/07_2026/7epz_31251.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7epz_31251/07_2026/7epz_31251.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7epz_31251/07_2026/7epz_31251.map"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.004
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: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      27      5.16       5
     Cl      1      4.86       5
     C    4867      2.51       5
     N    1192      2.21       5
     O    1342      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7431
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3643
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 468, 3643
          Classifications: {'peptide': 468}
          Link IDs: {'PTRANS': 22, 'TRANS': 445}
    Chain: "B"
      Number of atoms: 3541
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 453, 3541
          Classifications: {'peptide': 453}
          Link IDs: {'PTRANS': 23, 'TRANS': 429}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 135
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 135
          Unusual residues: {'J9O': 1, 'PX8': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.60, per 1000 atoms: 0.22
  Number of scatterers: 7431
  At special positions: 0
  Unit cell: (83.699, 83.699, 127.179, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      1     17.00
     S      27     16.00
     P       2     15.00
     O    1342      8.00
     N    1192      7.00
     C    4867      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 211 " - pdb=" SG  CYS B 158 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG C   1 " - " ASN A 507 "
      " NAG D   1 " - " ASN A 366 "
      " NAG E   1 " - " ASN A 382 "
      " NAG F   1 " - " ASN A 425 "
  Time building additional restraints: 0.50
  Conformation dependent library (CDL) restraints added in 344.7 milliseconds
  

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1698

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 6 sheets defined
      52.7% alpha, 5.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 178 through 207
      removed outlier: 3.605A  pdb=" N   ARG A 183 " --> pdb=" O   TRP A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 236
      removed outlier: 4.183A  pdb=" N   GLN A 235 " --> pdb=" O   LEU A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 247
    Processing helix  chain 'A' and resid 248 through 256
    Processing helix  chain 'A' and resid 287 through 301
    Processing helix  chain 'A' and resid 324 through 342
      removed outlier: 3.804A  pdb=" N   VAL A 331 " --> pdb=" O   VAL A 327 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   LYS A 332 " --> pdb=" O   ALA A 328 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   GLU A 336 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   GLN A 340 " --> pdb=" O   GLU A 336 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ALA A 341 " --> pdb=" O   PHE A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 354
    Processing helix  chain 'A' and resid 356 through 372
      removed outlier: 3.567A  pdb=" N   ALA A 362 " --> pdb=" O   SER A 358 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLU A 363 " --> pdb=" O   SER A 359 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   SER A 372 " --> pdb=" O   THR A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 393
      removed outlier: 3.782A  pdb=" N   LEU A 392 " --> pdb=" O   GLN A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 428
      removed outlier: 3.615A  pdb=" N   THR A 416 " --> pdb=" O   THR A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 460
      removed outlier: 3.659A  pdb=" N   PHE A 459 " --> pdb=" O   GLN A 455 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   THR A 460 " --> pdb=" O   LEU A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 534
      removed outlier: 3.647A  pdb=" N   LEU A 523 " --> pdb=" O   SER A 519 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ASP A 529 " --> pdb=" O   ARG A 525 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   GLN A 530 " --> pdb=" O   ARG A 526 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   SER A 532 " --> pdb=" O   SER A 528 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLU A 534 " --> pdb=" O   GLN A 530 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 58
      removed outlier: 3.745A  pdb=" N   ILE B  58 " --> pdb=" O   ILE B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 72
      removed outlier: 3.735A  pdb=" N   ILE B  64 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
      Proline residue:  B  66  - end of helix
      removed outlier: 3.525A  pdb=" N   ASN B  72 " --> pdb=" O   GLY B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 105
      removed outlier: 3.657A  pdb=" N   SER B  79 " --> pdb=" O   SER B  75 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   GLY B  87 " --> pdb=" O   TRP B  83 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   VAL B  88 " --> pdb=" O   THR B  84 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   THR B 102 " --> pdb=" O   ALA B  98 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   THR B 103 " --> pdb=" O   GLU B  99 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ILE B 104 " --> pdb=" O   LEU B 100 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   LYS B 105 " --> pdb=" O   GLY B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 115
    Processing helix  chain 'B' and resid 121 through 133
      removed outlier: 3.668A  pdb=" N   ARG B 126 " --> pdb=" O   PRO B 122 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   VAL B 127 " --> pdb=" O   ALA B 123 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   LEU B 131 " --> pdb=" O   VAL B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 133 through 149
      removed outlier: 3.784A  pdb=" N   VAL B 141 " --> pdb=" O   ALA B 137 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ILE B 142 " --> pdb=" O   ALA B 138 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   LEU B 144 " --> pdb=" O   ALA B 140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 155
      removed outlier: 3.563A  pdb=" N   PHE B 154 " --> pdb=" O   LEU B 151 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   PHE B 155 " --> pdb=" O   GLU B 152 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 151 through 155'
    Processing helix  chain 'B' and resid 161 through 182
      removed outlier: 3.788A  pdb=" N   LEU B 167 " --> pdb=" O   LEU B 163 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   ILE B 168 " --> pdb=" O   ALA B 164 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   VAL B 171 " --> pdb=" O   LEU B 167 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   THR B 174 " --> pdb=" O   ALA B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 207
      removed outlier: 3.661A  pdb=" N   SER B 187 " --> pdb=" O   SER B 183 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ARG B 189 " --> pdb=" O   SER B 185 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   GLN B 191 " --> pdb=" O   SER B 187 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   PHE B 193 " --> pdb=" O   ARG B 189 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   ILE B 205 " --> pdb=" O   ALA B 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 234 through 244
      removed outlier: 4.005A  pdb=" N   ALA B 238 " --> pdb=" O   ARG B 234 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   TYR B 244 " --> pdb=" O   TYR B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 247
      No H-bonds generated for 'chain 'B' and resid 245 through 247'
    Processing helix  chain 'B' and resid 248 through 252
    Processing helix  chain 'B' and resid 264 through 290
      removed outlier: 3.549A  pdb=" N   LEU B 268 " --> pdb=" O   LYS B 264 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ALA B 275 " --> pdb=" O   CYS B 271 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   VAL B 277 " --> pdb=" O   SER B 273 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   THR B 284 " --> pdb=" O   GLY B 280 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ASN B 285 " --> pdb=" O   TYR B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 309
      removed outlier: 3.693A  pdb=" N   SER B 308 " --> pdb=" O   ALA B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 318 through 333
      removed outlier: 3.698A  pdb=" N   ALA B 324 " --> pdb=" O   PRO B 320 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   SER B 330 " --> pdb=" O   SER B 326 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLY B 333 " --> pdb=" O   GLY B 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 347
    Processing helix  chain 'B' and resid 365 through 382
      removed outlier: 4.195A  pdb=" N   VAL B 369 " --> pdb=" O   PRO B 365 " (cutoff:3.500A)
      Proline residue:  B 374  - end of helix
      removed outlier: 3.657A  pdb=" N   ILE B 378 " --> pdb=" O   PRO B 374 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 413
      removed outlier: 3.973A  pdb=" N   ASN B 390 " --> pdb=" O   ASP B 386 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   ALA B 395 " --> pdb=" O   PHE B 391 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   ILE B 408 " --> pdb=" O   VAL B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 442
      removed outlier: 3.966A  pdb=" N   ALA B 429 " --> pdb=" O   LEU B 425 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 459
      removed outlier: 3.540A  pdb=" N   THR B 450 " --> pdb=" O   ASP B 446 " (cutoff:3.500A)
      removed outlier: 5.107A  pdb=" N   ILE B 452 " --> pdb=" O   PHE B 448 " (cutoff:3.500A)
      removed outlier: 4.768A  pdb=" N   GLY B 453 " --> pdb=" O   SER B 449 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 460 through 464
    Processing helix  chain 'B' and resid 477 through 493
      removed outlier: 3.704A  pdb=" N   LYS B 483 " --> pdb=" O   ILE B 479 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 402
      removed outlier: 6.722A  pdb=" N   LEU A 377 " --> pdb=" O   LEU A 400 " (cutoff:3.500A)
      removed outlier: 7.878A  pdb=" N   THR A 402 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   ALA A 379 " --> pdb=" O   THR A 402 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   LEU A 307 " --> pdb=" O   GLN A 347 " (cutoff:3.500A)
      removed outlier: 8.723A  pdb=" N   ARG A 349 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   CYS A 432 " --> pdb=" O   THR A 464 " (cutoff:3.500A)
      removed outlier: 7.991A  pdb=" N   VAL A 466 " --> pdb=" O   CYS A 432 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   TRP A 434 " --> pdb=" O   VAL A 466 " (cutoff:3.500A)
      removed outlier: 8.799A  pdb=" N   SER A 468 " --> pdb=" O   TRP A 434 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 267
      removed outlier: 6.425A  pdb=" N   GLN A 280 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 544
      removed outlier: 3.674A  pdb=" N   HIS A 557 " --> pdb=" O   ASP A 541 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   VAL A 567 " --> pdb=" O   LEU A 623 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 575 through 576
    Processing sheet with id=AA5, first strand: chain 'A' and resid 593 through 594
    Processing sheet with id=AA6, first strand: chain 'B' and resid 358 through 359

    314 hydrogen bonds defined for protein.
    900 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: 0.85

  Time building geometry restraints manager: 0.67 seconds

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

  Histogram of bond lengths:
        0.97 -     1.14: 2
        1.14 -     1.31: 1147
        1.31 -     1.48: 3131
        1.48 -     1.64: 3280
        1.64 -     1.81: 50
  Bond restraints: 7610
  Sorted by residual:
  bond pdb=" C11 J9O B 601 "
       pdb=" N06 J9O B 601 "
    ideal  model  delta    sigma   weight residual
    1.449  0.974  0.475 2.00e-02 2.50e+03 5.64e+02
  bond pdb=" C10 J9O B 601 "
       pdb=" N06 J9O B 601 "
    ideal  model  delta    sigma   weight residual
    1.454  1.121  0.333 2.00e-02 2.50e+03 2.77e+02
  bond pdb=" C12 J9O B 601 "
       pdb=" N06 J9O B 601 "
    ideal  model  delta    sigma   weight residual
    1.448  1.148  0.300 2.00e-02 2.50e+03 2.26e+02
  bond pdb=" C10 J9O B 601 "
       pdb=" C15 J9O B 601 "
    ideal  model  delta    sigma   weight residual
    1.518  1.724 -0.206 2.00e-02 2.50e+03 1.07e+02
  bond pdb=" C10 J9O B 601 "
       pdb=" C16 J9O B 601 "
    ideal  model  delta    sigma   weight residual
    1.526  1.722 -0.196 2.00e-02 2.50e+03 9.57e+01
  ... (remaining 7605 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.59: 10125
        3.59 -     7.17: 176
        7.17 -    10.76: 22
       10.76 -    14.35: 2
       14.35 -    17.93: 2
  Bond angle restraints: 10327
  Sorted by residual:
  angle pdb=" C11 J9O B 601 "
        pdb=" N06 J9O B 601 "
        pdb=" C12 J9O B 601 "
      ideal   model   delta    sigma   weight residual
     111.83  129.76  -17.93 3.00e+00 1.11e-01 3.57e+01
  angle pdb=" N   VAL B 171 "
        pdb=" CA  VAL B 171 "
        pdb=" C   VAL B 171 "
      ideal   model   delta    sigma   weight residual
     111.81  106.69    5.12 8.60e-01 1.35e+00 3.55e+01
  angle pdb=" N   ILE B 168 "
        pdb=" CA  ILE B 168 "
        pdb=" C   ILE B 168 "
      ideal   model   delta    sigma   weight residual
     111.90  107.09    4.81 8.10e-01 1.52e+00 3.53e+01
  angle pdb=" C   ALA A 208 "
        pdb=" N   PRO A 209 "
        pdb=" CA  PRO A 209 "
      ideal   model   delta    sigma   weight residual
     119.76  114.11    5.65 1.00e+00 1.00e+00 3.19e+01
  angle pdb=" N   VAL A 173 "
        pdb=" CA  VAL A 173 "
        pdb=" C   VAL A 173 "
      ideal   model   delta    sigma   weight residual
     111.90  107.78    4.12 8.10e-01 1.52e+00 2.58e+01
  ... (remaining 10322 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.37: 3848
       17.37 -    34.73: 466
       34.73 -    52.10: 96
       52.10 -    69.46: 11
       69.46 -    86.83: 5
  Dihedral angle restraints: 4426
    sinusoidal: 1783
      harmonic: 2643
  Sorted by residual:
  dihedral pdb=" CA  LYS B 473 "
           pdb=" C   LYS B 473 "
           pdb=" N   PRO B 474 "
           pdb=" CA  PRO B 474 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.94   26.06     0      5.00e+00 4.00e-02 2.72e+01
  dihedral pdb=" CA  PRO B 474 "
           pdb=" C   PRO B 474 "
           pdb=" N   ARG B 475 "
           pdb=" CA  ARG B 475 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.13   24.87     0      5.00e+00 4.00e-02 2.47e+01
  dihedral pdb=" CA  SER B 445 "
           pdb=" C   SER B 445 "
           pdb=" N   ASP B 446 "
           pdb=" CA  ASP B 446 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.44  -24.56     0      5.00e+00 4.00e-02 2.41e+01
  ... (remaining 4423 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.139: 1156
       0.139 -    0.278: 39
       0.278 -    0.417: 3
       0.417 -    0.556: 1
       0.556 -    0.695: 1
  Chirality restraints: 1200
  Sorted by residual:
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 366 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.71   -0.69 2.00e-01 2.50e+01 1.21e+01
  chirality pdb=" C10 J9O B 601 "
            pdb=" C15 J9O B 601 "
            pdb=" C16 J9O B 601 "
            pdb=" N06 J9O B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.30    1.81    0.50 2.00e-01 2.50e+01 6.13e+00
  chirality pdb=" C4  NAG D   1 "
            pdb=" C3  NAG D   1 "
            pdb=" C5  NAG D   1 "
            pdb=" O4  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.19   -0.34 2.00e-01 2.50e+01 2.86e+00
  ... (remaining 1197 not shown)

  Planarity restraints: 1270
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 473 "   -0.058 5.00e-02 4.00e+02   8.69e-02 1.21e+01
        pdb=" N   PRO B 474 "    0.150 5.00e-02 4.00e+02
        pdb=" CA  PRO B 474 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO B 474 "   -0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 461 "   -0.048 5.00e-02 4.00e+02   7.24e-02 8.39e+00
        pdb=" N   PRO B 462 "    0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO B 462 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 462 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 366 "   -0.025 2.00e-02 2.50e+03   2.49e-02 7.74e+00
        pdb=" CG  ASN A 366 "    0.042 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 366 "   -0.013 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 366 "    0.014 2.00e-02 2.50e+03
        pdb=" C1  NAG D   1 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1267 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2179
        2.81 -     3.33: 6548
        3.33 -     3.86: 11838
        3.86 -     4.38: 13453
        4.38 -     4.90: 23290
  Nonbonded interactions: 57308
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 493 "
            pdb=" OG  SER A 496 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" O   TYR A 251 "
            pdb=" OG  SER A 254 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" OH  TYR B 241 "
            pdb=" OD1 ASP B 386 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" OG  SER A 505 "
            pdb=" OD1 ASN A 507 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" OG  SER B  75 "
            pdb=" O   ALA B 224 "
     model   vdw
     2.294 3.040
  ... (remaining 57303 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
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.120
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:0.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
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      :  0.013   0.475   7619  Z= 0.610
  Angle     :  1.203  17.934  10353  Z= 0.634
  Chirality :  0.066   0.695   1200
  Planarity :  0.008   0.087   1266
  Dihedral  : 15.395  86.825   2725
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  9.81 %
    Favored  : 89.75 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 11.55 %
    Favored  : 87.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.43 (0.21), residues: 917
  helix: -2.79 (0.17), residues: 456
  sheet: -1.61 (0.62), residues: 63
  loop : -3.27 (0.24), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 183 
 TYR   0.014   0.002   TYR A 226 
 PHE   0.021   0.002   PHE A 627 
 TRP   0.016   0.002   TRP B 397 
 HIS   0.005   0.002   HIS A 539 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01255 /  0.61 ( 7610)
  covalent geometry    : angle       1.18322 /  0.63 (10327)
  SS BOND              : bond        0.00096 /  0.06 (    1)
  SS BOND              : angle       2.89042 /  1.00 (    2)
  hydrogen bonds       : bond        0.17402 / 10.81 (  314)
  hydrogen bonds       : angle       6.86983 /  4.84 (  900)
  link_BETA1-4         : bond        0.01093 /  0.63 (    4)
  link_BETA1-4         : angle       4.52177 /  1.64 (   12)
  link_NAG-ASN         : bond        0.00456 /  0.25 (    4)
  link_NAG-ASN         : angle       4.68139 /  2.74 (   12)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 170
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 TRP cc_start: 0.8073 (OUTLIER) cc_final: 0.7206 (t60)
REVERT: B  221 PHE cc_start: 0.6759 (OUTLIER) cc_final: 0.6214 (m-80)
REVERT: B  296 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8066 (mt-10)
REVERT: B  338 VAL cc_start: 0.8972 (t) cc_final: 0.8237 (t)
REVERT: B  438 MET cc_start: 0.7882 (mmt) cc_final: 0.7534 (mmt)
REVERT: B  470 TRP cc_start: 0.7151 (t-100) cc_final: 0.6576 (t-100)
REVERT: B  472 LYS cc_start: 0.8881 (mmpt) cc_final: 0.8124 (tptm)
REVERT: B  473 LYS cc_start: 0.4679 (tttm) cc_final: 0.4391 (mttt)
REVERT: B  478 ARG cc_start: 0.7455 (ttm170) cc_final: 0.7214 (ttp80)
  outliers start: 8
  outliers final: 2
  residues processed: 174
  average time/residue: 0.0761
  time to fit residues: 17.7140
Evaluate side-chains
  131 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 127
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  128 TRP
Chi-restraints excluded: chain B residue  221 PHE
Chi-restraints excluded: chain B residue  223 ASP
Chi-restraints excluded: chain B residue  319 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0070
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.2980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.7800

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 217 GLN
A 221 HIS
A 266 HIS
A 353 ASN
B 110 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.129777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.103369 restraints weight = 13548.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3268 rms_B_bonded: 3.21
r_work: 0.3128 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7619  Z= 0.138
  Angle     :  0.738  10.256  10353  Z= 0.360
  Chirality :  0.046   0.383   1200
  Planarity :  0.005   0.067   1266
  Dihedral  :  8.249  57.327   1084
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  8.72 %
    Favored  : 91.17 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 15.15 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.84 (0.25), residues: 917
  helix: -1.19 (0.22), residues: 455
  sheet: -0.89 (0.64), residues: 59
  loop : -2.85 (0.27), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 475 
 TYR   0.011   0.001   TYR A 629 
 PHE   0.014   0.001   PHE B 426 
 TRP   0.014   0.001   TRP B 397 
 HIS   0.004   0.001   HIS A 266 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00297 /  0.14 ( 7610)
  covalent geometry    : angle       0.72548 /  0.36 (10327)
  SS BOND              : bond        0.00527 /  0.33 (    1)
  SS BOND              : angle       1.38393 /  0.66 (    2)
  hydrogen bonds       : bond        0.04998 /  3.24 (  314)
  hydrogen bonds       : angle       4.88566 /  3.48 (  900)
  link_BETA1-4         : bond        0.00524 /  0.33 (    4)
  link_BETA1-4         : angle       2.53417 /  0.99 (   12)
  link_NAG-ASN         : bond        0.00578 /  0.36 (    4)
  link_NAG-ASN         : angle       3.18496 /  1.94 (   12)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 149
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: A  296 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7751 (mm-40)
REVERT: A  313 TYR cc_start: 0.8551 (p90) cc_final: 0.7638 (p90)
REVERT: A  374 ASP cc_start: 0.7685 (p0) cc_final: 0.7322 (m-30)
REVERT: A  508 MET cc_start: 0.8489 (ttm) cc_final: 0.8214 (ttt)
REVERT: A  534 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7828 (tm-30)
REVERT: B  296 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7966 (tt0)
REVERT: B  410 LEU cc_start: 0.9269 (tp) cc_final: 0.8917 (tt)
REVERT: B  438 MET cc_start: 0.8311 (mmt) cc_final: 0.7975 (mmt)
REVERT: B  472 LYS cc_start: 0.8760 (mmpt) cc_final: 0.7956 (tptt)
  outliers start: 20
  outliers final: 12
  residues processed: 157
  average time/residue: 0.0782
  time to fit residues: 16.5904
Evaluate side-chains
  132 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 120
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  266 HIS
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  315 PHE
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  412 TYR
Chi-restraints excluded: chain B residue  455 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 57 optimal weight:    0.8980
   chunk 87 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 75 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   chunk 76 optimal weight:    5.9990
   chunk 83 optimal weight:    0.4980
   chunk 77 optimal weight:    4.9990
   chunk 78 optimal weight:    0.7980
   chunk 52 optimal weight:    3.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.130575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.104079 restraints weight = 13400.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 3.22
r_work: 0.3139 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7619  Z= 0.127
  Angle     :  0.687   9.583  10353  Z= 0.334
  Chirality :  0.045   0.351   1200
  Planarity :  0.005   0.060   1266
  Dihedral  :  7.594  59.902   1077
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  8.62 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 17.46 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.19 (0.26), residues: 917
  helix: -0.57 (0.24), residues: 456
  sheet: -0.85 (0.65), residues: 59
  loop : -2.62 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 126 
 TYR   0.012   0.001   TYR B 464 
 PHE   0.029   0.001   PHE B 239 
 TRP   0.012   0.001   TRP B 397 
 HIS   0.005   0.001   HIS A 266 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.13 ( 7610)
  covalent geometry    : angle       0.67559 /  0.33 (10327)
  SS BOND              : bond        0.00006 /  0.00 (    1)
  SS BOND              : angle       1.38808 /  0.49 (    2)
  hydrogen bonds       : bond        0.04413 /  2.86 (  314)
  hydrogen bonds       : angle       4.57388 /  3.26 (  900)
  link_BETA1-4         : bond        0.00568 /  0.34 (    4)
  link_BETA1-4         : angle       2.40452 /  0.93 (   12)
  link_NAG-ASN         : bond        0.00477 /  0.28 (    4)
  link_NAG-ASN         : angle       2.97443 /  1.79 (   12)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 140
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
REVERT: A  296 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7792 (mm-40)
REVERT: A  313 TYR cc_start: 0.8731 (p90) cc_final: 0.7607 (p90)
REVERT: A  374 ASP cc_start: 0.7668 (p0) cc_final: 0.7322 (m-30)
REVERT: B  128 TRP cc_start: 0.8165 (OUTLIER) cc_final: 0.7397 (t60)
REVERT: B  297 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8177 (tt)
REVERT: B  348 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7654 (pt0)
REVERT: B  357 MET cc_start: 0.7739 (mmt) cc_final: 0.7251 (mmt)
REVERT: B  410 LEU cc_start: 0.9241 (tp) cc_final: 0.8916 (tt)
REVERT: B  435 CYS cc_start: 0.9263 (t) cc_final: 0.8877 (t)
REVERT: B  472 LYS cc_start: 0.8709 (mmpt) cc_final: 0.7919 (tptt)
REVERT: B  473 LYS cc_start: 0.4990 (ttpt) cc_final: 0.4533 (mttt)
REVERT: B  478 ARG cc_start: 0.7526 (ttm170) cc_final: 0.7055 (ttp80)
  outliers start: 19
  outliers final: 12
  residues processed: 149
  average time/residue: 0.0619
  time to fit residues: 12.8618
Evaluate side-chains
  131 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  128 TRP
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  315 PHE
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  408 ILE
Chi-restraints excluded: chain B residue  412 TYR
Chi-restraints excluded: chain B residue  455 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 47 optimal weight:    0.5980
   chunk 40 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0170
   chunk 80 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 42 optimal weight:    8.9990
   chunk 85 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.6418

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 191 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.131652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.105106 restraints weight = 13709.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 3.25
r_work: 0.3151 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.2387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7619  Z= 0.115
  Angle     :  0.649   9.396  10353  Z= 0.315
  Chirality :  0.044   0.324   1200
  Planarity :  0.005   0.061   1266
  Dihedral  :  7.275  59.227   1077
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  8.72 %
    Favored  : 91.17 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 19.38 %
    Favored  : 77.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.75 (0.27), residues: 917
  helix: -0.14 (0.24), residues: 455
  sheet: -0.74 (0.64), residues: 59
  loop : -2.46 (0.29), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 212 
 TYR   0.009   0.001   TYR A 629 
 PHE   0.017   0.001   PHE B 239 
 TRP   0.010   0.001   TRP B 397 
 HIS   0.004   0.001   HIS B 110 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.11 ( 7610)
  covalent geometry    : angle       0.63732 /  0.31 (10327)
  SS BOND              : bond        0.01128 /  0.70 (    1)
  SS BOND              : angle       3.16305 /  1.41 (    2)
  hydrogen bonds       : bond        0.03964 /  2.58 (  314)
  hydrogen bonds       : angle       4.33275 /  3.09 (  900)
  link_BETA1-4         : bond        0.00509 /  0.30 (    4)
  link_BETA1-4         : angle       2.29074 /  0.89 (   12)
  link_NAG-ASN         : bond        0.00428 /  0.25 (    4)
  link_NAG-ASN         : angle       2.67283 /  1.60 (   12)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 148
  time to evaluate  : 0.334 
Fit side-chains
REVERT: A  296 GLN cc_start: 0.8400 (mm-40) cc_final: 0.7977 (mm-40)
REVERT: A  313 TYR cc_start: 0.8654 (p90) cc_final: 0.7802 (p90)
REVERT: A  534 GLU cc_start: 0.8276 (tm-30) cc_final: 0.8003 (tm-30)
REVERT: B  128 TRP cc_start: 0.8138 (OUTLIER) cc_final: 0.7334 (t60)
REVERT: B  212 GLN cc_start: 0.7477 (tt0) cc_final: 0.7014 (tt0)
REVERT: B  297 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8138 (tt)
REVERT: B  357 MET cc_start: 0.7838 (mmt) cc_final: 0.7349 (mmt)
REVERT: B  410 LEU cc_start: 0.9221 (tp) cc_final: 0.8940 (tt)
REVERT: B  435 CYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8924 (t)
REVERT: B  472 LYS cc_start: 0.8723 (mmpt) cc_final: 0.7906 (tptt)
REVERT: B  473 LYS cc_start: 0.4927 (ttpt) cc_final: 0.4346 (mttt)
REVERT: B  478 ARG cc_start: 0.7525 (ttm170) cc_final: 0.7052 (ttp80)
  outliers start: 21
  outliers final: 13
  residues processed: 158
  average time/residue: 0.0747
  time to fit residues: 16.2855
Evaluate side-chains
  136 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  128 TRP
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  315 PHE
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  408 ILE
Chi-restraints excluded: chain B residue  412 TYR
Chi-restraints excluded: chain B residue  435 CYS
Chi-restraints excluded: chain B residue  455 VAL
Chi-restraints excluded: chain B residue  491 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 76 optimal weight:    7.9990
   chunk 15 optimal weight:    0.0770
   chunk 23 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0870
   chunk 77 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   overall best weight:    0.9718

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 191 GLN
** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.131098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.104552 restraints weight = 13595.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 3.24
r_work: 0.3143 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7619  Z= 0.130
  Angle     :  0.677  12.877  10353  Z= 0.323
  Chirality :  0.045   0.311   1200
  Planarity :  0.005   0.060   1266
  Dihedral  :  7.191  58.909   1077
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  8.40 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 19.90 %
    Favored  : 77.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.41 (0.27), residues: 917
  helix:  0.16 (0.25), residues: 453
  sheet: -0.71 (0.64), residues: 59
  loop : -2.29 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 183 
 TYR   0.015   0.001   TYR B 464 
 PHE   0.014   0.001   PHE B 239 
 TRP   0.011   0.001   TRP B 397 
 HIS   0.004   0.001   HIS B 110 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00300 /  0.13 ( 7610)
  covalent geometry    : angle       0.66813 /  0.32 (10327)
  SS BOND              : bond        0.00070 /  0.04 (    1)
  SS BOND              : angle       0.95321 /  0.37 (    2)
  hydrogen bonds       : bond        0.04001 /  2.62 (  314)
  hydrogen bonds       : angle       4.30096 /  3.07 (  900)
  link_BETA1-4         : bond        0.00548 /  0.32 (    4)
  link_BETA1-4         : angle       2.25239 /  0.88 (   12)
  link_NAG-ASN         : bond        0.00360 /  0.21 (    4)
  link_NAG-ASN         : angle       2.55798 /  1.53 (   12)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 129
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
REVERT: A  313 TYR cc_start: 0.8689 (p90) cc_final: 0.7744 (p90)
REVERT: A  469 TYR cc_start: 0.9094 (p90) cc_final: 0.8791 (p90)
REVERT: B  128 TRP cc_start: 0.8134 (OUTLIER) cc_final: 0.7370 (t60)
REVERT: B  212 GLN cc_start: 0.7520 (tt0) cc_final: 0.7103 (tt0)
REVERT: B  297 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8153 (tt)
REVERT: B  357 MET cc_start: 0.7996 (mmt) cc_final: 0.7396 (mmt)
REVERT: B  410 LEU cc_start: 0.9226 (tp) cc_final: 0.8956 (tt)
REVERT: B  435 CYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8914 (t)
REVERT: B  472 LYS cc_start: 0.8684 (mmpt) cc_final: 0.7904 (tptm)
  outliers start: 24
  outliers final: 17
  residues processed: 141
  average time/residue: 0.0714
  time to fit residues: 14.0652
Evaluate side-chains
  136 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  128 TRP
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  315 PHE
Chi-restraints excluded: chain B residue  363 HIS
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  412 TYR
Chi-restraints excluded: chain B residue  435 CYS
Chi-restraints excluded: chain B residue  455 VAL
Chi-restraints excluded: chain B residue  491 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 90 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0060
   chunk 73 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.7796

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 269 GLN
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 560 GLN
B 191 GLN
** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.131766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.105227 restraints weight = 13515.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 3.24
r_work: 0.3155 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.2614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7619  Z= 0.119
  Angle     :  0.651   9.134  10353  Z= 0.313
  Chirality :  0.044   0.301   1200
  Planarity :  0.005   0.068   1266
  Dihedral  :  7.087  58.961   1077
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  8.29 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 20.15 %
    Favored  : 77.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.20 (0.28), residues: 917
  helix:  0.36 (0.25), residues: 453
  sheet: -0.59 (0.64), residues: 59
  loop : -2.23 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 212 
 TYR   0.015   0.001   TYR B 464 
 PHE   0.016   0.001   PHE B 426 
 TRP   0.010   0.001   TRP B 397 
 HIS   0.004   0.001   HIS B 110 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.12 ( 7610)
  covalent geometry    : angle       0.64054 /  0.31 (10327)
  SS BOND              : bond        0.00340 /  0.21 (    1)
  SS BOND              : angle       2.61410 /  1.12 (    2)
  hydrogen bonds       : bond        0.03870 /  2.53 (  314)
  hydrogen bonds       : angle       4.19340 /  2.99 (  900)
  link_BETA1-4         : bond        0.00531 /  0.31 (    4)
  link_BETA1-4         : angle       2.25759 /  0.88 (   12)
  link_NAG-ASN         : bond        0.00359 /  0.21 (    4)
  link_NAG-ASN         : angle       2.43610 /  1.45 (   12)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A  313 TYR cc_start: 0.8689 (p90) cc_final: 0.7765 (p90)
REVERT: B  128 TRP cc_start: 0.8085 (OUTLIER) cc_final: 0.7302 (t60)
REVERT: B  212 GLN cc_start: 0.7550 (tt0) cc_final: 0.7210 (tt0)
REVERT: B  297 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8175 (tt)
REVERT: B  357 MET cc_start: 0.7880 (mmt) cc_final: 0.7240 (mmt)
REVERT: B  410 LEU cc_start: 0.9216 (tp) cc_final: 0.8954 (tt)
REVERT: B  435 CYS cc_start: 0.9244 (t) cc_final: 0.8933 (t)
REVERT: B  472 LYS cc_start: 0.8612 (mmpt) cc_final: 0.7997 (mtmt)
  outliers start: 20
  outliers final: 15
  residues processed: 140
  average time/residue: 0.0647
  time to fit residues: 13.1544
Evaluate side-chains
  137 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  128 TRP
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  315 PHE
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  412 TYR
Chi-restraints excluded: chain B residue  455 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 58 optimal weight:    0.7980
   chunk 75 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 10 optimal weight:    0.3980
   chunk 27 optimal weight:    6.9990
   chunk 71 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9980
   chunk 86 optimal weight:    4.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 191 GLN
** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.132316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.105708 restraints weight = 13536.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 3.23
r_work: 0.3160 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.2746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7619  Z= 0.119
  Angle     :  0.662  14.450  10353  Z= 0.316
  Chirality :  0.044   0.293   1200
  Planarity :  0.005   0.073   1266
  Dihedral  :  7.038  59.015   1077
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  8.40 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 19.90 %
    Favored  : 77.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.07 (0.28), residues: 917
  helix:  0.48 (0.25), residues: 452
  sheet: -0.47 (0.66), residues: 59
  loop : -2.19 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 210 
 TYR   0.015   0.001   TYR B 464 
 PHE   0.033   0.001   PHE A 346 
 TRP   0.010   0.001   TRP B 397 
 HIS   0.004   0.001   HIS B 110 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.12 ( 7610)
  covalent geometry    : angle       0.65292 /  0.31 (10327)
  SS BOND              : bond        0.00185 /  0.12 (    1)
  SS BOND              : angle       0.72756 /  0.29 (    2)
  hydrogen bonds       : bond        0.03782 /  2.47 (  314)
  hydrogen bonds       : angle       4.16060 /  2.96 (  900)
  link_BETA1-4         : bond        0.00532 /  0.32 (    4)
  link_BETA1-4         : angle       2.23955 /  0.87 (   12)
  link_NAG-ASN         : bond        0.00362 /  0.21 (    4)
  link_NAG-ASN         : angle       2.38775 /  1.42 (   12)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 129
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  313 TYR cc_start: 0.8683 (p90) cc_final: 0.7808 (p90)
REVERT: A  534 GLU cc_start: 0.8289 (tm-30) cc_final: 0.8086 (tm-30)
REVERT: B  128 TRP cc_start: 0.8107 (OUTLIER) cc_final: 0.7344 (t60)
REVERT: B  212 GLN cc_start: 0.7571 (tt0) cc_final: 0.7224 (tt0)
REVERT: B  221 PHE cc_start: 0.7389 (m-80) cc_final: 0.7132 (m-80)
REVERT: B  297 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8182 (tt)
REVERT: B  357 MET cc_start: 0.7769 (mmt) cc_final: 0.7139 (mmt)
REVERT: B  410 LEU cc_start: 0.9212 (tp) cc_final: 0.8962 (tt)
REVERT: B  435 CYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8921 (t)
REVERT: B  473 LYS cc_start: 0.6103 (OUTLIER) cc_final: 0.5833 (ptmt)
  outliers start: 24
  outliers final: 18
  residues processed: 138
  average time/residue: 0.0669
  time to fit residues: 13.6081
Evaluate side-chains
  145 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 123
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  128 TRP
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  315 PHE
Chi-restraints excluded: chain B residue  363 HIS
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  412 TYR
Chi-restraints excluded: chain B residue  435 CYS
Chi-restraints excluded: chain B residue  455 VAL
Chi-restraints excluded: chain B residue  473 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0570
   chunk 69 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 65 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0070
   chunk 18 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   overall best weight:    0.4516

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.133501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.106954 restraints weight = 13602.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 3.25
r_work: 0.3176 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.2888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7619  Z= 0.111
  Angle     :  0.648   9.565  10353  Z= 0.312
  Chirality :  0.044   0.288   1200
  Planarity :  0.005   0.076   1266
  Dihedral  :  6.902  59.275   1077
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  8.29 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 20.92 %
    Favored  : 76.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.28), residues: 917
  helix:  0.55 (0.25), residues: 458
  sheet: -0.44 (0.65), residues: 59
  loop : -2.27 (0.29), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 126 
 TYR   0.018   0.001   TYR A 629 
 PHE   0.030   0.001   PHE A 346 
 TRP   0.009   0.001   TRP B 397 
 HIS   0.004   0.001   HIS B 110 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00252 /  0.11 ( 7610)
  covalent geometry    : angle       0.63839 /  0.31 (10327)
  SS BOND              : bond        0.01181 /  0.74 (    1)
  SS BOND              : angle       3.29202 /  1.45 (    2)
  hydrogen bonds       : bond        0.03605 /  2.34 (  314)
  hydrogen bonds       : angle       4.07056 /  2.90 (  900)
  link_BETA1-4         : bond        0.00530 /  0.31 (    4)
  link_BETA1-4         : angle       2.21648 /  0.85 (   12)
  link_NAG-ASN         : bond        0.00391 /  0.23 (    4)
  link_NAG-ASN         : angle       2.29119 /  1.36 (   12)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 131
  time to evaluate  : 0.213 
Fit side-chains
REVERT: A  313 TYR cc_start: 0.8658 (p90) cc_final: 0.7790 (p90)
REVERT: A  476 ASP cc_start: 0.8682 (t0) cc_final: 0.8391 (t0)
REVERT: A  534 GLU cc_start: 0.8273 (tm-30) cc_final: 0.8048 (tm-30)
REVERT: A  595 ASP cc_start: 0.6575 (m-30) cc_final: 0.6277 (p0)
REVERT: B  128 TRP cc_start: 0.8077 (OUTLIER) cc_final: 0.7292 (t60)
REVERT: B  212 GLN cc_start: 0.7494 (tt0) cc_final: 0.7099 (tt0)
REVERT: B  221 PHE cc_start: 0.7318 (m-80) cc_final: 0.7075 (m-80)
REVERT: B  297 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8161 (tt)
REVERT: B  357 MET cc_start: 0.7706 (mmt) cc_final: 0.7065 (mmt)
REVERT: B  410 LEU cc_start: 0.9171 (tp) cc_final: 0.8956 (tt)
REVERT: B  435 CYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8968 (t)
  outliers start: 21
  outliers final: 15
  residues processed: 139
  average time/residue: 0.0704
  time to fit residues: 14.1914
Evaluate side-chains
  145 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  128 TRP
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  315 PHE
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  408 ILE
Chi-restraints excluded: chain B residue  412 TYR
Chi-restraints excluded: chain B residue  435 CYS
Chi-restraints excluded: chain B residue  455 VAL
Chi-restraints excluded: chain B residue  494 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0370
   chunk 10 optimal weight:    0.0170
   chunk 58 optimal weight:    0.8980
   chunk 27 optimal weight:    6.9990
   chunk 86 optimal weight:    4.9990
   chunk 18 optimal weight:    0.6980
   chunk 22 optimal weight:    3.9990
   chunk 87 optimal weight:    0.1980
   chunk 19 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   overall best weight:    0.3696

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.134422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.107910 restraints weight = 13477.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 3.25
r_work: 0.3194 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.3040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7619  Z= 0.111
  Angle     :  0.671  13.649  10353  Z= 0.317
  Chirality :  0.045   0.285   1200
  Planarity :  0.004   0.084   1266
  Dihedral  :  6.814  59.559   1077
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  8.29 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 20.92 %
    Favored  : 76.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.85 (0.28), residues: 917
  helix:  0.68 (0.25), residues: 460
  sheet: -0.38 (0.66), residues: 59
  loop : -2.15 (0.29), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 126 
 TYR   0.016   0.001   TYR A 629 
 PHE   0.028   0.001   PHE A 346 
 TRP   0.009   0.001   TRP B 470 
 HIS   0.002   0.001   HIS B 110 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.11 ( 7610)
  covalent geometry    : angle       0.66235 /  0.31 (10327)
  SS BOND              : bond        0.00112 /  0.07 (    1)
  SS BOND              : angle       1.99058 /  0.93 (    2)
  hydrogen bonds       : bond        0.03501 /  2.27 (  314)
  hydrogen bonds       : angle       4.05612 /  2.89 (  900)
  link_BETA1-4         : bond        0.00513 /  0.29 (    4)
  link_BETA1-4         : angle       2.17182 /  0.84 (   12)
  link_NAG-ASN         : bond        0.00389 /  0.23 (    4)
  link_NAG-ASN         : angle       2.24763 /  1.34 (   12)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 133
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A  313 TYR cc_start: 0.8614 (p90) cc_final: 0.7839 (p90)
REVERT: A  476 ASP cc_start: 0.8663 (t0) cc_final: 0.8379 (t0)
REVERT: A  534 GLU cc_start: 0.8261 (tm-30) cc_final: 0.8023 (tm-30)
REVERT: A  595 ASP cc_start: 0.6680 (m-30) cc_final: 0.6320 (p0)
REVERT: B  128 TRP cc_start: 0.8008 (OUTLIER) cc_final: 0.7264 (t60)
REVERT: B  212 GLN cc_start: 0.7609 (tt0) cc_final: 0.7183 (tt0)
REVERT: B  221 PHE cc_start: 0.7392 (m-80) cc_final: 0.7141 (m-80)
REVERT: B  297 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8130 (tt)
REVERT: B  357 MET cc_start: 0.7712 (mmt) cc_final: 0.7066 (mmt)
REVERT: B  410 LEU cc_start: 0.9163 (tp) cc_final: 0.8956 (tt)
REVERT: B  435 CYS cc_start: 0.9233 (OUTLIER) cc_final: 0.9016 (t)
  outliers start: 19
  outliers final: 14
  residues processed: 141
  average time/residue: 0.0667
  time to fit residues: 13.6907
Evaluate side-chains
  145 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 128
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  128 TRP
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  315 PHE
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  408 ILE
Chi-restraints excluded: chain B residue  412 TYR
Chi-restraints excluded: chain B residue  435 CYS
Chi-restraints excluded: chain B residue  455 VAL
Chi-restraints excluded: chain B residue  494 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 86 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0980
   chunk 55 optimal weight:    0.3980
   chunk 56 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0470
   chunk 27 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0970
   chunk 57 optimal weight:    0.1980
   overall best weight:    0.1676

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.135487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.108999 restraints weight = 13559.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 3.25
r_work: 0.3206 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.3224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   7619  Z= 0.112
  Angle     :  0.668  12.060  10353  Z= 0.318
  Chirality :  0.044   0.282   1200
  Planarity :  0.005   0.086   1266
  Dihedral  :  6.774  59.904   1077
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.96 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 21.57 %
    Favored  : 76.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.79 (0.28), residues: 917
  helix:  0.72 (0.25), residues: 460
  sheet: -0.26 (0.67), residues: 59
  loop : -2.12 (0.29), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 126 
 TYR   0.018   0.001   TYR B 444 
 PHE   0.028   0.001   PHE A 346 
 TRP   0.013   0.001   TRP B 470 
 HIS   0.003   0.001   HIS B 110 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00249 /  0.11 ( 7610)
  covalent geometry    : angle       0.66085 /  0.32 (10327)
  SS BOND              : bond        0.01130 /  0.71 (    1)
  SS BOND              : angle       1.04862 /  0.40 (    2)
  hydrogen bonds       : bond        0.03380 /  2.18 (  314)
  hydrogen bonds       : angle       4.03931 /  2.88 (  900)
  link_BETA1-4         : bond        0.00515 /  0.30 (    4)
  link_BETA1-4         : angle       2.13323 /  0.82 (   12)
  link_NAG-ASN         : bond        0.00409 /  0.24 (    4)
  link_NAG-ASN         : angle       2.19927 /  1.31 (   12)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 142
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A  313 TYR cc_start: 0.8590 (p90) cc_final: 0.7798 (p90)
REVERT: A  344 ASP cc_start: 0.8074 (m-30) cc_final: 0.7753 (t70)
REVERT: A  374 ASP cc_start: 0.7678 (p0) cc_final: 0.7387 (p0)
REVERT: A  476 ASP cc_start: 0.8627 (t0) cc_final: 0.8365 (t0)
REVERT: A  534 GLU cc_start: 0.8270 (tm-30) cc_final: 0.8029 (tm-30)
REVERT: B  128 TRP cc_start: 0.7930 (OUTLIER) cc_final: 0.7259 (t60)
REVERT: B  212 GLN cc_start: 0.7651 (tt0) cc_final: 0.7306 (tt0)
REVERT: B  221 PHE cc_start: 0.7424 (m-80) cc_final: 0.7172 (m-80)
REVERT: B  297 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8125 (tt)
REVERT: B  357 MET cc_start: 0.7717 (mmt) cc_final: 0.7103 (mmt)
REVERT: B  435 CYS cc_start: 0.9221 (OUTLIER) cc_final: 0.9006 (t)
REVERT: B  473 LYS cc_start: 0.5261 (ptmt) cc_final: 0.5010 (ptmm)
  outliers start: 17
  outliers final: 13
  residues processed: 150
  average time/residue: 0.0711
  time to fit residues: 15.6613
Evaluate side-chains
  147 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  128 TRP
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  315 PHE
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  408 ILE
Chi-restraints excluded: chain B residue  412 TYR
Chi-restraints excluded: chain B residue  435 CYS
Chi-restraints excluded: chain B residue  455 VAL
Chi-restraints excluded: chain B residue  494 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 24 optimal weight:    6.9990
   chunk 33 optimal weight:   10.0000
   chunk 18 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 5 optimal weight:    0.4980
   chunk 25 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0470
   overall best weight:    0.7078

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 180 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.130618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.104738 restraints weight = 13399.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 3.10
r_work: 0.3155 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.3243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7619  Z= 0.120
  Angle     :  0.680  12.162  10353  Z= 0.321
  Chirality :  0.045   0.279   1200
  Planarity :  0.005   0.085   1266
  Dihedral  :  6.716  59.651   1077
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.42 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 22.46 %
    Favored  : 75.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.78 (0.28), residues: 917
  helix:  0.75 (0.25), residues: 460
  sheet: -0.32 (0.67), residues: 59
  loop : -2.13 (0.29), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 126 
 TYR   0.015   0.001   TYR B 444 
 PHE   0.026   0.001   PHE A 346 
 TRP   0.013   0.001   TRP B 470 
 HIS   0.003   0.001   HIS B 110 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.12 ( 7610)
  covalent geometry    : angle       0.67200 /  0.32 (10327)
  SS BOND              : bond        0.00196 /  0.12 (    1)
  SS BOND              : angle       2.29408 /  1.01 (    2)
  hydrogen bonds       : bond        0.03470 /  2.24 (  314)
  hydrogen bonds       : angle       4.06365 /  2.90 (  900)
  link_BETA1-4         : bond        0.00502 /  0.30 (    4)
  link_BETA1-4         : angle       2.13504 /  0.83 (   12)
  link_NAG-ASN         : bond        0.00324 /  0.19 (    4)
  link_NAG-ASN         : angle       2.17999 /  1.30 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1542.12 seconds
wall clock time: 27 minutes 15.36 seconds (1635.36 seconds total)