Starting phenix.real_space_refine
on Wed Mar  4 15:17:04 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8evb_28625/03_2026/8evb_28625_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8evb_28625/03_2026/8evb_28625.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8evb_28625/03_2026/8evb_28625_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8evb_28625/03_2026/8evb_28625_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8evb_28625/03_2026/8evb_28625.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8evb_28625/03_2026/8evb_28625.map"
  }
  resolution = 3.6
  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=   0.001 sd=   0.024
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: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      65      5.16       5
     C    9427      2.51       5
     N    2354      2.21       5
     O    2606      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 137 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14456
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3629
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 444, 3618
          Classifications: {'peptide': 444}
          Link IDs: {'PTRANS': 13, 'TRANS': 430}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 444, 3618
          Classifications: {'peptide': 444}
          Link IDs: {'PTRANS': 13, 'TRANS': 430}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 3686
    Chain: "B"
      Number of atoms: 3532
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 432, 3532
          Classifications: {'peptide': 432}
          Link IDs: {'PTRANS': 13, 'TRANS': 418}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 3576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 438, 3576
          Classifications: {'peptide': 438}
          Link IDs: {'PTRANS': 14, 'TRANS': 423}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 3585
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 437, 3585
          Classifications: {'peptide': 437}
          Link IDs: {'PTRANS': 13, 'TRANS': 423}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 37
          Unusual residues: {'NAG': 1, 'PCG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 37
          Unusual residues: {'NAG': 1, 'PCG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 37
          Unusual residues: {'NAG': 1, 'PCG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Unusual residues: {'PCG': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  APHE A 392 " occ=0.60
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 392 " occ=0.40
  Time building chain proxies: 3.35, per 1000 atoms: 0.23
  Number of scatterers: 14456
  At special positions: 0
  Unit cell: (103.75, 110.39, 125.33, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      65     16.00
     P       4     15.00
     O    2606      8.00
     N    2354      7.00
     C    9427      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 801 " - " ASN A 339 "
      " NAG B 801 " - " ASN B 339 "
      " NAG C 801 " - " ASN C 339 "
  Time building additional restraints: 1.01
  Conformation dependent library (CDL) restraints added in 605.9 milliseconds
  

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3322

  Finding SS restraints...
    Secondary structure from input PDB file:
      69 helices and 12 sheets defined
      64.8% alpha, 6.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 165 through 192
      Proline residue:  A 178  - end of helix
      removed outlier: 5.431A  pdb=" N   ILE A 187 " --> pdb=" O   TRP A 183 " (cutoff:3.500A)
      removed outlier: 4.624A  pdb=" N   CYS A 188 " --> pdb=" O   TYR A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 198
      removed outlier: 3.970A  pdb=" N   GLN A 196 " --> pdb=" O   PHE A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 222
    Processing helix  chain 'A' and resid 235 through 245
    Processing helix  chain 'A' and resid 246 through 256
      removed outlier: 3.916A  pdb=" N   LYS A 250 " --> pdb=" O   THR A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 279
      removed outlier: 4.164A  pdb=" N   ASN A 276 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ARG A 277 " --> pdb=" O   ARG A 274 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   LEU A 279 " --> pdb=" O   ASN A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 295
    Processing helix  chain 'A' and resid 297 through 329
    Processing helix  chain 'A' and resid 347 through 364
    Processing helix  chain 'A' and resid 374 through 406
    Processing helix  chain 'A' and resid 409 through 428
      removed outlier: 3.559A  pdb=" N   PHE A 413 " --> pdb=" O   SER A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 447
    Processing helix  chain 'A' and resid 452 through 457
    Processing helix  chain 'A' and resid 461 through 473
      removed outlier: 3.551A  pdb=" N   HIS A 473 " --> pdb=" O   ALA A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 478
    Processing helix  chain 'A' and resid 487 through 497
    Processing helix  chain 'A' and resid 548 through 553
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 592 through 609
    Processing helix  chain 'B' and resid 165 through 193
      Proline residue:  B 178  - end of helix
    Processing helix  chain 'B' and resid 194 through 199
    Processing helix  chain 'B' and resid 199 through 223
      removed outlier: 4.336A  pdb=" N   TRP B 203 " --> pdb=" O   TYR B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 245
    Processing helix  chain 'B' and resid 246 through 256
    Processing helix  chain 'B' and resid 270 through 277
    Processing helix  chain 'B' and resid 280 through 295
      removed outlier: 4.177A  pdb=" N   LEU B 284 " --> pdb=" O   LYS B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 329
    Processing helix  chain 'B' and resid 343 through 346
    Processing helix  chain 'B' and resid 347 through 364
    Processing helix  chain 'B' and resid 374 through 404
      removed outlier: 3.577A  pdb=" N   VAL B 399 " --> pdb=" O   ILE B 395 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   GLY B 400 " --> pdb=" O   VAL B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 408 through 427
    Processing helix  chain 'B' and resid 430 through 447
    Processing helix  chain 'B' and resid 452 through 457
    Processing helix  chain 'B' and resid 461 through 477
    Processing helix  chain 'B' and resid 580 through 587
    Processing helix  chain 'B' and resid 591 through 610
    Processing helix  chain 'C' and resid 165 through 193
      removed outlier: 3.896A  pdb=" N   LEU C 177 " --> pdb=" O   THR C 173 " (cutoff:3.500A)
      Proline residue:  C 178  - end of helix
      removed outlier: 3.818A  pdb=" N   CYS C 191 " --> pdb=" O   ILE C 187 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ASP C 193 " --> pdb=" O   ARG C 189 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 199 through 222
    Processing helix  chain 'C' and resid 235 through 246
    Processing helix  chain 'C' and resid 247 through 255
    Processing helix  chain 'C' and resid 271 through 278
    Processing helix  chain 'C' and resid 281 through 295
      removed outlier: 3.706A  pdb=" N   PHE C 285 " --> pdb=" O   PHE C 281 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 297 through 329
    Processing helix  chain 'C' and resid 347 through 364
    Processing helix  chain 'C' and resid 374 through 407
    Processing helix  chain 'C' and resid 407 through 428
    Processing helix  chain 'C' and resid 430 through 447
    Processing helix  chain 'C' and resid 453 through 458
    Processing helix  chain 'C' and resid 461 through 478
      removed outlier: 4.595A  pdb=" N   ASN C 471 " --> pdb=" O   GLU C 467 " (cutoff:3.500A)
      removed outlier: 5.487A  pdb=" N   VAL C 472 " --> pdb=" O   ILE C 468 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   HIS C 473 " --> pdb=" O   ALA C 469 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 487 through 496
      removed outlier: 3.818A  pdb=" N   LEU C 491 " --> pdb=" O   GLU C 487 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 581 through 588
    Processing helix  chain 'C' and resid 592 through 607
    Processing helix  chain 'D' and resid 215 through 242
      removed outlier: 4.069A  pdb=" N   ASN D 232 " --> pdb=" O   ALA D 228 " (cutoff:3.500A)
      Proline residue:  D 237  - end of helix
    Processing helix  chain 'D' and resid 249 through 270
    Processing helix  chain 'D' and resid 271 through 275
      removed outlier: 4.046A  pdb=" N   LEU D 275 " --> pdb=" O   GLN D 272 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 286 through 297
      removed outlier: 3.738A  pdb=" N   LEU D 290 " --> pdb=" O   ASP D 286 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 298 through 307
    Processing helix  chain 'D' and resid 310 through 315
    Processing helix  chain 'D' and resid 330 through 345
    Processing helix  chain 'D' and resid 347 through 379
      removed outlier: 4.372A  pdb=" N   TYR D 351 " --> pdb=" O   LYS D 347 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   VAL D 353 " --> pdb=" O   TYR D 349 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 392 through 406
    Processing helix  chain 'D' and resid 416 through 449
      removed outlier: 3.756A  pdb=" N   GLY D 439 " --> pdb=" O   SER D 435 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 449 through 469
    Processing helix  chain 'D' and resid 472 through 491
    Processing helix  chain 'D' and resid 495 through 500
    Processing helix  chain 'D' and resid 503 through 520
      removed outlier: 3.507A  pdb=" N   SER D 517 " --> pdb=" O   ASP D 513 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 529 through 539
    Processing helix  chain 'D' and resid 621 through 629
    Processing helix  chain 'D' and resid 631 through 645
      removed outlier: 3.504A  pdb=" N   GLU D 635 " --> pdb=" O   TYR D 631 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 499 through 503
      removed outlier: 3.530A  pdb=" N   ARG A 499 " --> pdb=" O   CYS A 578 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   SER A 574 " --> pdb=" O   PHE A 503 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ILE A 521 " --> pdb=" O   PHE A 577 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 508 through 510
      removed outlier: 3.777A  pdb=" N   CYS A 510 " --> pdb=" O   ILE A 568 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ASN A 567 " --> pdb=" O   VAL A 530 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   ARG A 569 " --> pdb=" O   ALA A 528 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   ALA A 528 " --> pdb=" O   ARG A 569 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   LEU A 527 " --> pdb=" O   VAL A 540 " (cutoff:3.500A)
      removed outlier: 5.510A  pdb=" N   VAL A 540 " --> pdb=" O   LEU A 527 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   VAL A 529 " --> pdb=" O   PHE A 538 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 227 through 228
    Processing sheet with id=AA4, first strand: chain 'B' and resid 499 through 503
      removed outlier: 4.153A  pdb=" N   ASP B 575 " --> pdb=" O   ASN B 523 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ASN B 523 " --> pdb=" O   ASP B 575 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 508 through 510
      removed outlier: 6.849A  pdb=" N   ILE B 568 " --> pdb=" O   ILE B 509 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ASN B 567 " --> pdb=" O   VAL B 530 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ARG B 569 " --> pdb=" O   ALA B 528 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ALA B 528 " --> pdb=" O   ARG B 569 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LEU B 527 " --> pdb=" O   LEU B 541 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 514 through 515
      removed outlier: 3.957A  pdb=" N   ASP B 514 " --> pdb=" O   ARG B 564 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ARG B 564 " --> pdb=" O   ASP B 514 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'C' and resid 227 through 228
    Processing sheet with id=AA8, first strand: chain 'C' and resid 501 through 503
    Processing sheet with id=AA9, first strand: chain 'C' and resid 508 through 510
      removed outlier: 7.166A  pdb=" N   ILE C 568 " --> pdb=" O   ILE C 509 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ASN C 567 " --> pdb=" O   VAL C 530 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   VAL C 539 " --> pdb=" O   VAL C 529 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 278 through 279
    Processing sheet with id=AB2, first strand: chain 'D' and resid 541 through 545
      removed outlier: 3.810A  pdb=" N   LYS D 541 " --> pdb=" O   THR D 618 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 550 through 552
      removed outlier: 7.380A  pdb=" N   VAL D 608 " --> pdb=" O   VAL D 551 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   VAL D 569 " --> pdb=" O   LEU D 584 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LEU D 584 " --> pdb=" O   VAL D 569 " (cutoff:3.500A)
      removed outlier: 5.060A  pdb=" N   VAL D 582 " --> pdb=" O   VAL D 571 " (cutoff:3.500A)

    890 hydrogen bonds defined for protein.
    2629 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.29

  Time building geometry restraints manager: 1.35 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 2294
        1.32 -     1.44: 4170
        1.44 -     1.57: 8234
        1.57 -     1.70: 0
        1.70 -     1.83: 104
  Bond restraints: 14802
  Sorted by residual:
  bond pdb=" O5' PCG D 901 "
       pdb=" PA  PCG D 901 "
    ideal  model  delta    sigma   weight residual
    1.606  1.489  0.117 2.00e-02 2.50e+03 3.40e+01
  bond pdb=" O5' PCG A 802 "
       pdb=" PA  PCG A 802 "
    ideal  model  delta    sigma   weight residual
    1.606  1.490  0.116 2.00e-02 2.50e+03 3.39e+01
  bond pdb=" O5' PCG B 802 "
       pdb=" PA  PCG B 802 "
    ideal  model  delta    sigma   weight residual
    1.606  1.490  0.116 2.00e-02 2.50e+03 3.38e+01
  bond pdb=" O5' PCG C 802 "
       pdb=" PA  PCG C 802 "
    ideal  model  delta    sigma   weight residual
    1.606  1.491  0.115 2.00e-02 2.50e+03 3.33e+01
  bond pdb=" O3' PCG D 901 "
       pdb=" PA  PCG D 901 "
    ideal  model  delta    sigma   weight residual
    1.617  1.513  0.104 2.00e-02 2.50e+03 2.71e+01
  ... (remaining 14797 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.66: 19669
        3.66 -     7.33: 351
        7.33 -    10.99: 52
       10.99 -    14.66: 4
       14.66 -    18.32: 12
  Bond angle restraints: 20088
  Sorted by residual:
  angle pdb=" C   GLN D 272 "
        pdb=" N   PRO D 273 "
        pdb=" CA  PRO D 273 "
      ideal   model   delta    sigma   weight residual
     121.65  114.66    6.99 1.01e+00 9.80e-01 4.79e+01
  angle pdb=" C3' PCG D 901 "
        pdb=" C4' PCG D 901 "
        pdb=" C5' PCG D 901 "
      ideal   model   delta    sigma   weight residual
     109.85  128.17  -18.32 3.00e+00 1.11e-01 3.73e+01
  angle pdb=" C3' PCG C 802 "
        pdb=" C4' PCG C 802 "
        pdb=" C5' PCG C 802 "
      ideal   model   delta    sigma   weight residual
     109.85  128.11  -18.26 3.00e+00 1.11e-01 3.70e+01
  angle pdb=" C3' PCG A 802 "
        pdb=" C4' PCG A 802 "
        pdb=" C5' PCG A 802 "
      ideal   model   delta    sigma   weight residual
     109.85  128.10  -18.25 3.00e+00 1.11e-01 3.70e+01
  angle pdb=" C3' PCG B 802 "
        pdb=" C4' PCG B 802 "
        pdb=" C5' PCG B 802 "
      ideal   model   delta    sigma   weight residual
     109.85  128.09  -18.24 3.00e+00 1.11e-01 3.70e+01
  ... (remaining 20083 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.94: 8257
       25.94 -    51.88: 548
       51.88 -    77.82: 36
       77.82 -   103.75: 2
      103.75 -   129.69: 16
  Dihedral angle restraints: 8859
    sinusoidal: 3693
      harmonic: 5166
  Sorted by residual:
  dihedral pdb=" CA  VAL C 480 "
           pdb=" C   VAL C 480 "
           pdb=" N   ARG C 481 "
           pdb=" CA  ARG C 481 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.41  -27.59     0      5.00e+00 4.00e-02 3.05e+01
  dihedral pdb=" CA  GLY B 544 "
           pdb=" C   GLY B 544 "
           pdb=" N   SER B 545 "
           pdb=" CA  SER B 545 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.57  -24.43     0      5.00e+00 4.00e-02 2.39e+01
  dihedral pdb=" CA  ALA A 469 "
           pdb=" C   ALA A 469 "
           pdb=" N   ILE A 470 "
           pdb=" CA  ILE A 470 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.66   23.34     0      5.00e+00 4.00e-02 2.18e+01
  ... (remaining 8856 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.356: 2279
       0.356 -    0.713: 0
       0.713 -    1.069: 0
       1.069 -    1.425: 0
       1.425 -    1.782: 4
  Chirality restraints: 2283
  Sorted by residual:
  chirality pdb=" C4' PCG A 802 "
            pdb=" C3' PCG A 802 "
            pdb=" C5' PCG A 802 "
            pdb=" O4' PCG A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -0.72   -1.78 2.00e-01 2.50e+01 7.94e+01
  chirality pdb=" C4' PCG C 802 "
            pdb=" C3' PCG C 802 "
            pdb=" C5' PCG C 802 "
            pdb=" O4' PCG C 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -0.72   -1.78 2.00e-01 2.50e+01 7.93e+01
  chirality pdb=" C4' PCG D 901 "
            pdb=" C3' PCG D 901 "
            pdb=" C5' PCG D 901 "
            pdb=" O4' PCG D 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -0.72   -1.78 2.00e-01 2.50e+01 7.92e+01
  ... (remaining 2280 not shown)

  Planarity restraints: 2468
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE D 406 "    0.017 2.00e-02 2.50e+03   3.45e-02 1.19e+01
        pdb=" C   ILE D 406 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   ILE D 406 "    0.023 2.00e-02 2.50e+03
        pdb=" N   THR D 407 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 609 "    0.016 2.00e-02 2.50e+03   3.29e-02 1.09e+01
        pdb=" CG  ASP A 609 "   -0.057 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 609 "    0.020 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 609 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN C 182 "   -0.016 2.00e-02 2.50e+03   3.24e-02 1.05e+01
        pdb=" C   ASN C 182 "    0.056 2.00e-02 2.50e+03
        pdb=" O   ASN C 182 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   TRP C 183 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 2465 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 287
        2.67 -     3.23: 12867
        3.23 -     3.79: 23742
        3.79 -     4.34: 29107
        4.34 -     4.90: 47892
  Nonbonded interactions: 113895
  Sorted by model distance:
  nonbonded pdb=" O   LEU C 278 "
            pdb=" CD1 LEU C 278 "
     model   vdw
     2.116 3.460
  nonbonded pdb=" OD1 ASN B 299 "
            pdb=" CE  MET B 402 "
     model   vdw
     2.199 3.460
  nonbonded pdb=" O   ASN C 182 "
            pdb=" CB  LEU C 186 "
     model   vdw
     2.261 2.752
  nonbonded pdb=" O   GLY D 591 "
            pdb=" O2A PCG D 901 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" OG  SER C 558 "
            pdb=" O   ILE C 605 "
     model   vdw
     2.308 3.040
  ... (remaining 113890 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 'A' and (resid 159 through 257 or resid 270 through 391 or resid 393 thro \ 
ugh 483 or resid 489 through 552 or resid 557 through 607 or resid 801 through 8 \ 
02))
  selection = (chain 'B' and (resid 159 through 257 or resid 270 through 391 or resid 393 thro \ 
ugh 607 or resid 801 through 802))
  selection = (chain 'C' and (resid 159 through 257 or resid 270 through 391 or resid 393 thro \ 
ugh 483 or resid 489 through 552 or resid 557 through 802))
}

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=0.40 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.050
  Set scattering table:                    0.030
  Process input model:                     13.450
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
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      :  0.009   0.117  14805  Z= 0.407
  Angle     :  1.280  18.320  20097  Z= 0.659
  Chirality :  0.101   1.782   2283
  Planarity :  0.010   0.076   2465
  Dihedral  : 17.036 129.692   5537
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 12.25 %
    Favored  : 87.12 %
  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: -5.11 (0.13), residues: 1734
  helix: -3.41 (0.08), residues: 1111
  sheet: -2.06 (0.55), residues: 53
  loop : -3.02 (0.21), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG D 324 
 TYR   0.037   0.003   TYR B 199 
 PHE   0.028   0.003   PHE A 301 
 TRP   0.037   0.003   TRP D 221 
 HIS   0.005   0.002   HIS C 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00876 (14802)
  covalent geometry    : angle       1.27763 (20088)
  hydrogen bonds       : bond        0.11860 (  890)
  hydrogen bonds       : angle       7.05023 ( 2629)
  link_NAG-ASN         : bond        0.00336 (    3)
  link_NAG-ASN         : angle       3.88540 (    9)

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

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

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 279
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  414 GLN cc_start: 0.7890 (tp-100) cc_final: 0.7613 (tp-100)
REVERT: A  467 GLU cc_start: 0.7997 (tp30) cc_final: 0.7754 (tp30)
REVERT: B  229 GLN cc_start: 0.7969 (tt0) cc_final: 0.7162 (tt0)
REVERT: B  417 ILE cc_start: 0.9083 (mt) cc_final: 0.8076 (mt)
REVERT: B  422 GLN cc_start: 0.8959 (tm-30) cc_final: 0.8709 (tm-30)
REVERT: B  607 MET cc_start: 0.6931 (mmp) cc_final: 0.6605 (ttm)
REVERT: C  188 CYS cc_start: 0.8204 (t) cc_final: 0.7686 (t)
REVERT: C  228 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7269 (tp30)
REVERT: C  229 GLN cc_start: 0.7560 (mt0) cc_final: 0.7235 (pt0)
REVERT: C  276 ASN cc_start: 0.6253 (m-40) cc_final: 0.6035 (m-40)
REVERT: C  299 ASN cc_start: 0.7670 (m110) cc_final: 0.7030 (p0)
REVERT: C  422 GLN cc_start: 0.9167 (tm-30) cc_final: 0.8796 (tm-30)
REVERT: C  573 TYR cc_start: 0.8805 (m-80) cc_final: 0.8361 (m-80)
REVERT: C  585 MET cc_start: 0.8930 (mmp) cc_final: 0.8540 (mmp)
  outliers start: 9
  outliers final: 5
  residues processed: 284
  average time/residue: 0.1044
  time to fit residues: 44.7442
Evaluate side-chains
  191 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 186
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  300 MET
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain D residue  272 GLN
Chi-restraints excluded: chain D residue  438 ILE
Chi-restraints excluded: chain D residue  537 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:    0.0970
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    5.9990
   chunk 149 optimal weight:    0.7980
   overall best weight:    0.7378

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

Flipped N/Q/H residues before XYZ refinement:
A 242 HIS
A 407 ASN
** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 523 ASN
** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 276 ASN
B 317 ASN
B 398 ASN
C 241 GLN
C 276 ASN
C 317 ASN
C 345 HIS
D 367 ASN
D 426 ASN
D 611 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.135426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.105697 restraints weight = 36477.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.109129 restraints weight = 17041.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.111347 restraints weight = 10472.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.112727 restraints weight = 7654.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.113668 restraints weight = 6275.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3618
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3618 r_free = 0.3618    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3618 r_free = 0.3618    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3618
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.1684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  14805  Z= 0.130
  Angle     :  0.647  12.887  20097  Z= 0.329
  Chirality :  0.041   0.244   2283
  Planarity :  0.005   0.054   2465
  Dihedral  : 13.645 163.868   2135
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.39 %
    Favored  : 80.46 %
  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 (0.17), residues: 1734
  helix: -0.85 (0.13), residues: 1115
  sheet: -1.48 (0.60), residues: 56
  loop : -2.49 (0.23), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 302 
 TYR   0.017   0.001   TYR C 546 
 PHE   0.044   0.001   PHE B 413 
 TRP   0.020   0.001   TRP D 221 
 HIS   0.010   0.001   HIS C 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (14802)
  covalent geometry    : angle       0.64462 (20088)
  hydrogen bonds       : bond        0.04521 (  890)
  hydrogen bonds       : angle       5.05348 ( 2629)
  link_NAG-ASN         : bond        0.00147 (    3)
  link_NAG-ASN         : angle       2.81347 (    9)

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

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

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 218
  time to evaluate  : 0.552 
Fit side-chains
   revert: symmetry clash
REVERT: A  424 MET cc_start: 0.7833 (mmp) cc_final: 0.7589 (mmp)
REVERT: A  467 GLU cc_start: 0.8184 (tp30) cc_final: 0.7975 (tp30)
REVERT: A  496 LEU cc_start: 0.8875 (tt) cc_final: 0.8641 (pp)
REVERT: B  276 ASN cc_start: 0.7954 (OUTLIER) cc_final: 0.7595 (t0)
REVERT: B  279 LEU cc_start: 0.9023 (mp) cc_final: 0.8806 (mp)
REVERT: B  305 ASN cc_start: 0.7785 (OUTLIER) cc_final: 0.7437 (t0)
REVERT: B  422 GLN cc_start: 0.8929 (tm-30) cc_final: 0.8669 (tm-30)
REVERT: C  175 ILE cc_start: 0.8757 (tp) cc_final: 0.8470 (tp)
REVERT: C  188 CYS cc_start: 0.8207 (t) cc_final: 0.7747 (t)
REVERT: C  299 ASN cc_start: 0.7698 (m110) cc_final: 0.7022 (p0)
REVERT: C  422 GLN cc_start: 0.9249 (tm-30) cc_final: 0.9043 (tm-30)
REVERT: C  467 GLU cc_start: 0.7906 (tp30) cc_final: 0.7676 (tp30)
REVERT: C  573 TYR cc_start: 0.8843 (m-80) cc_final: 0.8399 (m-80)
REVERT: C  585 MET cc_start: 0.9063 (mmp) cc_final: 0.8737 (mmm)
REVERT: D  268 MET cc_start: 0.8017 (tmm) cc_final: 0.7722 (tmm)
REVERT: D  405 LEU cc_start: 0.9208 (tp) cc_final: 0.8819 (mp)
REVERT: D  426 ASN cc_start: 0.8931 (OUTLIER) cc_final: 0.8414 (t0)
  outliers start: 33
  outliers final: 15
  residues processed: 243
  average time/residue: 0.1007
  time to fit residues: 38.3356
Evaluate side-chains
  188 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 170
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  359 SER
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain B residue  242 HIS
Chi-restraints excluded: chain B residue  276 ASN
Chi-restraints excluded: chain B residue  305 ASN
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain C residue  356 LEU
Chi-restraints excluded: chain D residue  260 CYS
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  426 ASN
Chi-restraints excluded: chain D residue  438 ILE
Chi-restraints excluded: chain D residue  582 VAL
Chi-restraints excluded: chain D residue  626 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 6 optimal weight:    6.9990
   chunk 26 optimal weight:    5.9990
   chunk 128 optimal weight:   10.0000
   chunk 136 optimal weight:    0.6980
   chunk 93 optimal weight:    0.8980
   chunk 129 optimal weight:    6.9990
   chunk 90 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 138 optimal weight:    3.9990
   chunk 108 optimal weight:    0.5980
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 345 HIS
D 367 ASN
D 426 ASN
** D 531 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 = 0.3909 r_free = 0.3909 target = 0.135123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.104278 restraints weight = 50023.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.108194 restraints weight = 20615.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.110738 restraints weight = 11758.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.112369 restraints weight = 8203.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.113331 restraints weight = 6517.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3617
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3617 r_free = 0.3617    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3617 r_free = 0.3617    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3617
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.2107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14805  Z= 0.122
  Angle     :  0.604  13.644  20097  Z= 0.303
  Chirality :  0.040   0.201   2283
  Planarity :  0.004   0.047   2465
  Dihedral  : 13.255 164.219   2125
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 19.10 %
    Favored  : 79.12 %
  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: -1.01 (0.19), residues: 1734
  helix:  0.15 (0.15), residues: 1126
  sheet: -1.37 (0.61), residues: 56
  loop : -2.22 (0.24), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 302 
 TYR   0.021   0.001   TYR B 184 
 PHE   0.030   0.001   PHE B 413 
 TRP   0.025   0.001   TRP D 221 
 HIS   0.005   0.001   HIS C 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (14802)
  covalent geometry    : angle       0.60185 (20088)
  hydrogen bonds       : bond        0.04169 (  890)
  hydrogen bonds       : angle       4.64820 ( 2629)
  link_NAG-ASN         : bond        0.00201 (    3)
  link_NAG-ASN         : angle       2.54693 (    9)

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

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

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 204
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  279 LEU cc_start: 0.9059 (mp) cc_final: 0.8799 (mp)
REVERT: B  422 GLN cc_start: 0.8869 (tm-30) cc_final: 0.8658 (tm-30)
REVERT: B  434 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8537 (mm-30)
REVERT: C  175 ILE cc_start: 0.8720 (tp) cc_final: 0.8427 (tp)
REVERT: C  188 CYS cc_start: 0.8310 (t) cc_final: 0.7795 (t)
REVERT: C  299 ASN cc_start: 0.7506 (m110) cc_final: 0.6989 (p0)
REVERT: C  410 ARG cc_start: 0.8627 (mtt90) cc_final: 0.8196 (mtp85)
REVERT: C  573 TYR cc_start: 0.8826 (m-80) cc_final: 0.8399 (m-80)
REVERT: C  585 MET cc_start: 0.9068 (mmp) cc_final: 0.8635 (mmp)
REVERT: D  330 LYS cc_start: 0.8640 (mmmm) cc_final: 0.7832 (mmmt)
REVERT: D  405 LEU cc_start: 0.9171 (tp) cc_final: 0.8765 (mp)
REVERT: D  419 GLU cc_start: 0.7692 (pt0) cc_final: 0.7470 (pt0)
REVERT: D  426 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8319 (t0)
REVERT: D  539 ARG cc_start: 0.7955 (mmp-170) cc_final: 0.7505 (mmp-170)
  outliers start: 27
  outliers final: 17
  residues processed: 222
  average time/residue: 0.0948
  time to fit residues: 33.1154
Evaluate side-chains
  203 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 185
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  359 SER
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain B residue  242 HIS
Chi-restraints excluded: chain B residue  403 ILE
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain C residue  356 LEU
Chi-restraints excluded: chain C residue  451 VAL
Chi-restraints excluded: chain D residue  260 CYS
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  346 ASP
Chi-restraints excluded: chain D residue  367 ASN
Chi-restraints excluded: chain D residue  369 CYS
Chi-restraints excluded: chain D residue  426 ASN
Chi-restraints excluded: chain D residue  537 LEU
Chi-restraints excluded: chain D residue  582 VAL
Chi-restraints excluded: chain D residue  626 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 95 optimal weight:    6.9990
   chunk 36 optimal weight:    3.9990
   chunk 167 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 150 optimal weight:    0.3980
   chunk 102 optimal weight:    4.9990
   chunk 83 optimal weight:    3.9990
   chunk 113 optimal weight:    5.9990
   chunk 116 optimal weight:    0.9980
   chunk 110 optimal weight:    0.9980
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 473 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.133246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.103892 restraints weight = 34319.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.107154 restraints weight = 16534.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.109271 restraints weight = 10361.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.110629 restraints weight = 7685.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.111340 restraints weight = 6351.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3588
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3588 r_free = 0.3588    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3588 r_free = 0.3588    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3588
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.2293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  14805  Z= 0.149
  Angle     :  0.607  14.696  20097  Z= 0.304
  Chirality :  0.041   0.256   2283
  Planarity :  0.004   0.049   2465
  Dihedral  : 13.239 175.480   2123
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 19.29 %
    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: -0.39 (0.20), residues: 1734
  helix:  0.65 (0.15), residues: 1120
  sheet: -1.13 (0.62), residues: 56
  loop : -2.01 (0.25), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 569 
 TYR   0.014   0.001   TYR A 423 
 PHE   0.020   0.001   PHE B 413 
 TRP   0.025   0.001   TRP D 221 
 HIS   0.004   0.001   HIS C 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (14802)
  covalent geometry    : angle       0.60521 (20088)
  hydrogen bonds       : bond        0.04140 (  890)
  hydrogen bonds       : angle       4.50433 ( 2629)
  link_NAG-ASN         : bond        0.00122 (    3)
  link_NAG-ASN         : angle       2.47639 (    9)

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

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

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 193
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
REVERT: B  422 GLN cc_start: 0.8853 (tm-30) cc_final: 0.8342 (tm-30)
REVERT: B  434 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8291 (mm-30)
REVERT: B  607 MET cc_start: 0.7494 (ptp) cc_final: 0.7182 (ptm)
REVERT: C  175 ILE cc_start: 0.8792 (tp) cc_final: 0.8459 (tp)
REVERT: C  188 CYS cc_start: 0.8374 (t) cc_final: 0.7883 (t)
REVERT: C  299 ASN cc_start: 0.7482 (m110) cc_final: 0.6922 (p0)
REVERT: C  410 ARG cc_start: 0.8651 (mtt90) cc_final: 0.8215 (mtp85)
REVERT: C  573 TYR cc_start: 0.8835 (m-80) cc_final: 0.8390 (m-80)
REVERT: C  585 MET cc_start: 0.9030 (mmp) cc_final: 0.8642 (mmp)
REVERT: C  593 GLU cc_start: 0.8022 (mp0) cc_final: 0.7810 (mp0)
REVERT: C  595 LYS cc_start: 0.8882 (mptt) cc_final: 0.8215 (pptt)
REVERT: D  405 LEU cc_start: 0.9163 (tp) cc_final: 0.8808 (mp)
REVERT: D  419 GLU cc_start: 0.7835 (pt0) cc_final: 0.7586 (pt0)
REVERT: D  539 ARG cc_start: 0.7971 (mmp-170) cc_final: 0.7549 (mmp-170)
REVERT: D  628 LEU cc_start: 0.7956 (mm) cc_final: 0.7730 (pp)
  outliers start: 43
  outliers final: 30
  residues processed: 225
  average time/residue: 0.0975
  time to fit residues: 35.2837
Evaluate side-chains
  211 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 181
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  359 SER
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  242 HIS
Chi-restraints excluded: chain B residue  246 THR
Chi-restraints excluded: chain B residue  305 ASN
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  403 ILE
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  450 THR
Chi-restraints excluded: chain B residue  456 VAL
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain C residue  187 ILE
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  359 SER
Chi-restraints excluded: chain C residue  451 VAL
Chi-restraints excluded: chain D residue  260 CYS
Chi-restraints excluded: chain D residue  264 TYR
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  346 ASP
Chi-restraints excluded: chain D residue  369 CYS
Chi-restraints excluded: chain D residue  417 LEU
Chi-restraints excluded: chain D residue  537 LEU
Chi-restraints excluded: chain D residue  582 VAL
Chi-restraints excluded: chain D residue  626 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 126 optimal weight:    2.9990
   chunk 60 optimal weight:    0.5980
   chunk 43 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9990
   chunk 149 optimal weight:    0.9980
   chunk 83 optimal weight:    8.9990
   chunk 54 optimal weight:    0.3980
   chunk 66 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 111 optimal weight:    4.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 473 HIS
D 367 ASN
D 426 ASN
D 476 GLN
D 531 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.134938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.104046 restraints weight = 52110.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.108005 restraints weight = 21226.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.110603 restraints weight = 12022.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.112249 restraints weight = 8325.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.113129 restraints weight = 6598.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3615
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3615 r_free = 0.3615    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3615 r_free = 0.3615    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3615
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.2552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  14805  Z= 0.116
  Angle     :  0.592  14.039  20097  Z= 0.290
  Chirality :  0.040   0.287   2283
  Planarity :  0.004   0.045   2465
  Dihedral  : 13.114 178.565   2123
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 20.24 %
    Favored  : 77.54 %
  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:  0.05 (0.20), residues: 1734
  helix:  1.03 (0.15), residues: 1119
  sheet: -0.92 (0.65), residues: 56
  loop : -1.92 (0.26), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 569 
 TYR   0.013   0.001   TYR C 184 
 PHE   0.021   0.001   PHE B 413 
 TRP   0.022   0.001   TRP D 221 
 HIS   0.004   0.001   HIS C 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (14802)
  covalent geometry    : angle       0.58958 (20088)
  hydrogen bonds       : bond        0.03870 (  890)
  hydrogen bonds       : angle       4.35690 ( 2629)
  link_NAG-ASN         : bond        0.00175 (    3)
  link_NAG-ASN         : angle       2.48806 (    9)

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

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

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 210
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  406 MET cc_start: 0.7496 (ptm) cc_final: 0.7233 (ptm)
REVERT: A  519 MET cc_start: 0.7649 (ttp) cc_final: 0.7404 (ttp)
REVERT: B  422 GLN cc_start: 0.8864 (tm-30) cc_final: 0.8352 (tm-30)
REVERT: B  434 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8275 (mm-30)
REVERT: B  519 MET cc_start: 0.7263 (mmm) cc_final: 0.6995 (mmt)
REVERT: B  607 MET cc_start: 0.7491 (ptp) cc_final: 0.7207 (ptm)
REVERT: C  175 ILE cc_start: 0.8662 (tp) cc_final: 0.8377 (tp)
REVERT: C  188 CYS cc_start: 0.8348 (t) cc_final: 0.7819 (t)
REVERT: C  410 ARG cc_start: 0.8644 (mtt90) cc_final: 0.8228 (mtp85)
REVERT: C  573 TYR cc_start: 0.8783 (m-80) cc_final: 0.8360 (m-80)
REVERT: C  585 MET cc_start: 0.9045 (mmp) cc_final: 0.8631 (mmp)
REVERT: C  595 LYS cc_start: 0.8903 (mptt) cc_final: 0.8252 (pptt)
REVERT: D  330 LYS cc_start: 0.8656 (mmmm) cc_final: 0.7804 (mmmt)
REVERT: D  405 LEU cc_start: 0.9081 (tp) cc_final: 0.8690 (mp)
REVERT: D  419 GLU cc_start: 0.7784 (pt0) cc_final: 0.7515 (pt0)
REVERT: D  426 ASN cc_start: 0.8858 (OUTLIER) cc_final: 0.8376 (t0)
REVERT: D  628 LEU cc_start: 0.7947 (mm) cc_final: 0.7728 (pp)
  outliers start: 34
  outliers final: 21
  residues processed: 231
  average time/residue: 0.0965
  time to fit residues: 35.7895
Evaluate side-chains
  216 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 194
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  359 SER
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  242 HIS
Chi-restraints excluded: chain B residue  403 ILE
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain C residue  187 ILE
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain C residue  356 LEU
Chi-restraints excluded: chain C residue  451 VAL
Chi-restraints excluded: chain C residue  536 THR
Chi-restraints excluded: chain D residue  260 CYS
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  346 ASP
Chi-restraints excluded: chain D residue  369 CYS
Chi-restraints excluded: chain D residue  426 ASN
Chi-restraints excluded: chain D residue  537 LEU
Chi-restraints excluded: chain D residue  626 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   chunk 126 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   chunk 61 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 75 optimal weight:    9.9990
   chunk 49 optimal weight:    0.6980
   chunk 90 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 473 HIS
D 272 GLN
D 339 HIS
D 367 ASN
D 426 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.141136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.112011 restraints weight = 34781.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.115450 restraints weight = 16744.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.117657 restraints weight = 10455.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.119085 restraints weight = 7740.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.119962 restraints weight = 6389.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3722
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3722 r_free = 0.3722    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3722 r_free = 0.3722    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3722
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.2689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14805  Z= 0.119
  Angle     :  0.596  13.826  20097  Z= 0.293
  Chirality :  0.041   0.282   2283
  Planarity :  0.004   0.064   2465
  Dihedral  : 13.037 178.866   2123
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 21.19 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.20), residues: 1734
  helix:  1.17 (0.15), residues: 1116
  sheet: -0.82 (0.64), residues: 56
  loop : -1.84 (0.26), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 189 
 TYR   0.016   0.001   TYR C 546 
 PHE   0.018   0.001   PHE B 413 
 TRP   0.026   0.001   TRP A 171 
 HIS   0.003   0.001   HIS C 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (14802)
  covalent geometry    : angle       0.59409 (20088)
  hydrogen bonds       : bond        0.03850 (  890)
  hydrogen bonds       : angle       4.29952 ( 2629)
  link_NAG-ASN         : bond        0.00130 (    3)
  link_NAG-ASN         : angle       2.33900 (    9)

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

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

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 205
  time to evaluate  : 0.586 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  406 MET cc_start: 0.7269 (ptm) cc_final: 0.7045 (ptm)
REVERT: A  519 MET cc_start: 0.7629 (ttp) cc_final: 0.7356 (ttp)
REVERT: B  252 ASP cc_start: 0.7388 (OUTLIER) cc_final: 0.6873 (m-30)
REVERT: B  417 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.7918 (mp)
REVERT: B  422 GLN cc_start: 0.8899 (tm-30) cc_final: 0.8402 (tm-30)
REVERT: B  434 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8417 (mm-30)
REVERT: B  607 MET cc_start: 0.7370 (ptp) cc_final: 0.7061 (ptm)
REVERT: C  175 ILE cc_start: 0.8738 (tp) cc_final: 0.8474 (tp)
REVERT: C  188 CYS cc_start: 0.8343 (t) cc_final: 0.7801 (t)
REVERT: C  410 ARG cc_start: 0.8600 (mtt90) cc_final: 0.8214 (mtp85)
REVERT: C  573 TYR cc_start: 0.8752 (m-80) cc_final: 0.8357 (m-80)
REVERT: C  585 MET cc_start: 0.8941 (mmp) cc_final: 0.8627 (mmp)
REVERT: C  595 LYS cc_start: 0.8870 (mptt) cc_final: 0.8216 (pptt)
REVERT: D  419 GLU cc_start: 0.7554 (pt0) cc_final: 0.7292 (pt0)
REVERT: D  426 ASN cc_start: 0.8691 (OUTLIER) cc_final: 0.8175 (t0)
REVERT: D  539 ARG cc_start: 0.8036 (mmp-170) cc_final: 0.7568 (mmp-170)
  outliers start: 44
  outliers final: 26
  residues processed: 240
  average time/residue: 0.1031
  time to fit residues: 38.8547
Evaluate side-chains
  214 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 185
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  359 SER
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  507 ASP
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  242 HIS
Chi-restraints excluded: chain B residue  252 ASP
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  403 ILE
Chi-restraints excluded: chain B residue  417 ILE
Chi-restraints excluded: chain B residue  424 MET
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  456 VAL
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain C residue  359 SER
Chi-restraints excluded: chain C residue  451 VAL
Chi-restraints excluded: chain D residue  260 CYS
Chi-restraints excluded: chain D residue  262 ILE
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  339 HIS
Chi-restraints excluded: chain D residue  346 ASP
Chi-restraints excluded: chain D residue  369 CYS
Chi-restraints excluded: chain D residue  417 LEU
Chi-restraints excluded: chain D residue  426 ASN
Chi-restraints excluded: chain D residue  537 LEU
Chi-restraints excluded: chain D residue  582 VAL
Chi-restraints excluded: chain D residue  626 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 158 optimal weight:    2.9990
   chunk 138 optimal weight:    8.9990
   chunk 171 optimal weight:    0.9990
   chunk 40 optimal weight:   20.0000
   chunk 96 optimal weight:    4.9990
   chunk 163 optimal weight:    1.9990
   chunk 75 optimal weight:    6.9990
   chunk 155 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 153 optimal weight:    1.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 473 HIS
D 339 HIS
D 367 ASN
D 426 ASN
** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.140224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.112048 restraints weight = 41333.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.115084 restraints weight = 16916.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.116281 restraints weight = 10327.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.116811 restraints weight = 9311.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.117156 restraints weight = 8340.541|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3676
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3676 r_free = 0.3676    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3676 r_free = 0.3676    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3676
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.2834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  14805  Z= 0.140
  Angle     :  0.619  13.776  20097  Z= 0.305
  Chirality :  0.042   0.287   2283
  Planarity :  0.004   0.060   2465
  Dihedral  : 13.014 177.433   2123
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 21.13 %
    Favored  : 75.63 %
  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:  0.30 (0.20), residues: 1734
  helix:  1.22 (0.15), residues: 1116
  sheet: -0.93 (0.60), residues: 56
  loop : -1.78 (0.26), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 274 
 TYR   0.014   0.001   TYR D 454 
 PHE   0.019   0.001   PHE B 301 
 TRP   0.037   0.001   TRP A 171 
 HIS   0.003   0.001   HIS C 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (14802)
  covalent geometry    : angle       0.61700 (20088)
  hydrogen bonds       : bond        0.03946 (  890)
  hydrogen bonds       : angle       4.28372 ( 2629)
  link_NAG-ASN         : bond        0.00110 (    3)
  link_NAG-ASN         : angle       2.32032 (    9)

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

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

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 194
  time to evaluate  : 0.577 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.6720 (ppp) cc_final: 0.6090 (ppp)
REVERT: A  207 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7539 (t0)
REVERT: A  406 MET cc_start: 0.7400 (ptm) cc_final: 0.7164 (ptm)
REVERT: A  426 PHE cc_start: 0.7571 (t80) cc_final: 0.7190 (t80)
REVERT: A  518 GLU cc_start: 0.6581 (mm-30) cc_final: 0.5962 (mt-10)
REVERT: B  422 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8634 (tm-30)
REVERT: B  434 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8299 (mm-30)
REVERT: B  519 MET cc_start: 0.6856 (mmm) cc_final: 0.6547 (mmt)
REVERT: B  607 MET cc_start: 0.7351 (ptp) cc_final: 0.7106 (ptm)
REVERT: C  175 ILE cc_start: 0.8803 (tp) cc_final: 0.8524 (tp)
REVERT: C  188 CYS cc_start: 0.8396 (t) cc_final: 0.7895 (t)
REVERT: C  410 ARG cc_start: 0.8650 (mtt90) cc_final: 0.8218 (mtp85)
REVERT: C  573 TYR cc_start: 0.8759 (m-80) cc_final: 0.8373 (m-80)
REVERT: C  585 MET cc_start: 0.9029 (mmp) cc_final: 0.8714 (mmp)
REVERT: C  595 LYS cc_start: 0.8862 (mptt) cc_final: 0.8234 (pptt)
REVERT: D  330 LYS cc_start: 0.8654 (mmmm) cc_final: 0.7773 (mmmt)
REVERT: D  405 LEU cc_start: 0.8994 (tp) cc_final: 0.8633 (mp)
REVERT: D  419 GLU cc_start: 0.7632 (pt0) cc_final: 0.7368 (pt0)
REVERT: D  426 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.8021 (t0)
REVERT: D  483 TYR cc_start: 0.8707 (m-80) cc_final: 0.8496 (m-80)
  outliers start: 50
  outliers final: 37
  residues processed: 233
  average time/residue: 0.0984
  time to fit residues: 36.5283
Evaluate side-chains
  222 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 183
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  207 ASP
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  359 SER
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  507 ASP
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  242 HIS
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain B residue  403 ILE
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  450 THR
Chi-restraints excluded: chain B residue  456 VAL
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain C residue  293 THR
Chi-restraints excluded: chain C residue  295 THR
Chi-restraints excluded: chain C residue  356 LEU
Chi-restraints excluded: chain C residue  359 SER
Chi-restraints excluded: chain C residue  451 VAL
Chi-restraints excluded: chain C residue  568 ILE
Chi-restraints excluded: chain D residue  260 CYS
Chi-restraints excluded: chain D residue  262 ILE
Chi-restraints excluded: chain D residue  264 TYR
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  345 MET
Chi-restraints excluded: chain D residue  346 ASP
Chi-restraints excluded: chain D residue  369 CYS
Chi-restraints excluded: chain D residue  417 LEU
Chi-restraints excluded: chain D residue  426 ASN
Chi-restraints excluded: chain D residue  537 LEU
Chi-restraints excluded: chain D residue  551 VAL
Chi-restraints excluded: chain D residue  582 VAL
Chi-restraints excluded: chain D residue  626 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 127 optimal weight:    8.9990
   chunk 22 optimal weight:    0.9990
   chunk 171 optimal weight:    6.9990
   chunk 94 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 141 optimal weight:    5.9990
   chunk 149 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 345 HIS
** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 473 HIS
D 367 ASN
D 426 ASN
** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.139954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.108730 restraints weight = 63086.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.113619 restraints weight = 24201.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.115842 restraints weight = 12039.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.116406 restraints weight = 8998.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.116621 restraints weight = 8177.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3671
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3671 r_free = 0.3671    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3671 r_free = 0.3671    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3671
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.2907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14805  Z= 0.140
  Angle     :  0.611  13.906  20097  Z= 0.303
  Chirality :  0.041   0.291   2283
  Planarity :  0.004   0.041   2465
  Dihedral  : 12.977 176.335   2123
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 20.94 %
    Favored  : 76.08 %
  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:  0.40 (0.20), residues: 1734
  helix:  1.29 (0.16), residues: 1116
  sheet: -0.44 (0.66), residues: 46
  loop : -1.75 (0.26), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 274 
 TYR   0.017   0.001   TYR A 423 
 PHE   0.026   0.001   PHE B 413 
 TRP   0.030   0.001   TRP A 171 
 HIS   0.003   0.001   HIS C 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (14802)
  covalent geometry    : angle       0.60957 (20088)
  hydrogen bonds       : bond        0.03970 (  890)
  hydrogen bonds       : angle       4.27521 ( 2629)
  link_NAG-ASN         : bond        0.00112 (    3)
  link_NAG-ASN         : angle       2.28233 (    9)

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

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

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 195
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.6715 (ppp) cc_final: 0.6083 (ppp)
REVERT: A  207 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7639 (t0)
REVERT: A  406 MET cc_start: 0.7379 (ptm) cc_final: 0.7142 (ptm)
REVERT: A  426 PHE cc_start: 0.7619 (t80) cc_final: 0.7286 (t80)
REVERT: B  198 GLU cc_start: 0.5540 (tt0) cc_final: 0.5255 (tt0)
REVERT: B  252 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.6988 (m-30)
REVERT: B  607 MET cc_start: 0.7566 (ptp) cc_final: 0.7294 (ptm)
REVERT: C  175 ILE cc_start: 0.8796 (tp) cc_final: 0.8536 (tp)
REVERT: C  188 CYS cc_start: 0.8373 (t) cc_final: 0.7810 (t)
REVERT: C  410 ARG cc_start: 0.8644 (mtt90) cc_final: 0.8227 (mtp85)
REVERT: C  573 TYR cc_start: 0.8744 (m-80) cc_final: 0.8356 (m-80)
REVERT: C  585 MET cc_start: 0.9076 (mmp) cc_final: 0.8674 (mmm)
REVERT: C  595 LYS cc_start: 0.8872 (mptt) cc_final: 0.8246 (pptt)
REVERT: D  405 LEU cc_start: 0.8991 (tp) cc_final: 0.8639 (mp)
REVERT: D  419 GLU cc_start: 0.7623 (pt0) cc_final: 0.7352 (pt0)
REVERT: D  426 ASN cc_start: 0.8691 (OUTLIER) cc_final: 0.8046 (t0)
  outliers start: 46
  outliers final: 40
  residues processed: 231
  average time/residue: 0.0914
  time to fit residues: 33.8348
Evaluate side-chains
  226 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 183
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  207 ASP
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  359 SER
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  507 ASP
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  242 HIS
Chi-restraints excluded: chain B residue  252 ASP
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain B residue  403 ILE
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  450 THR
Chi-restraints excluded: chain B residue  456 VAL
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  501 THR
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain C residue  187 ILE
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain C residue  293 THR
Chi-restraints excluded: chain C residue  295 THR
Chi-restraints excluded: chain C residue  359 SER
Chi-restraints excluded: chain C residue  451 VAL
Chi-restraints excluded: chain C residue  536 THR
Chi-restraints excluded: chain D residue  233 CYS
Chi-restraints excluded: chain D residue  260 CYS
Chi-restraints excluded: chain D residue  262 ILE
Chi-restraints excluded: chain D residue  264 TYR
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  345 MET
Chi-restraints excluded: chain D residue  346 ASP
Chi-restraints excluded: chain D residue  369 CYS
Chi-restraints excluded: chain D residue  417 LEU
Chi-restraints excluded: chain D residue  426 ASN
Chi-restraints excluded: chain D residue  537 LEU
Chi-restraints excluded: chain D residue  551 VAL
Chi-restraints excluded: chain D residue  582 VAL
Chi-restraints excluded: chain D residue  626 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 50 optimal weight:    6.9990
   chunk 8 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 134 optimal weight:    0.0050
   chunk 65 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 70 optimal weight:    0.1980
   chunk 34 optimal weight:    9.9990
   chunk 7 optimal weight:    7.9990
   chunk 37 optimal weight:    8.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    2.0400

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

Flipped N/Q/H residues before XYZ refinement:
** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 473 HIS
D 367 ASN
D 426 ASN
** D 531 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 = 0.3965 r_free = 0.3965 target = 0.138694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.107272 restraints weight = 55423.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.112658 restraints weight = 23296.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.113749 restraints weight = 11916.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.114538 restraints weight = 9583.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.114804 restraints weight = 8907.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3642
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3642 r_free = 0.3642    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3642 r_free = 0.3642    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3642
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.2948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  14805  Z= 0.170
  Angle     :  0.651  14.463  20097  Z= 0.320
  Chirality :  0.042   0.283   2283
  Planarity :  0.004   0.053   2465
  Dihedral  : 12.990 174.980   2123
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 20.94 %
    Favored  : 75.70 %
  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:  0.39 (0.20), residues: 1734
  helix:  1.25 (0.15), residues: 1115
  sheet: -0.37 (0.62), residues: 52
  loop : -1.69 (0.26), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 274 
 TYR   0.015   0.001   TYR D 483 
 PHE   0.024   0.001   PHE B 413 
 TRP   0.028   0.002   TRP D 221 
 HIS   0.003   0.001   HIS A 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 (14802)
  covalent geometry    : angle       0.64883 (20088)
  hydrogen bonds       : bond        0.04133 (  890)
  hydrogen bonds       : angle       4.31156 ( 2629)
  link_NAG-ASN         : bond        0.00109 (    3)
  link_NAG-ASN         : angle       2.32205 (    9)

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

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

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 181
  time to evaluate  : 0.572 
Fit side-chains
   revert: symmetry clash
REVERT: A  207 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7738 (t0)
REVERT: A  406 MET cc_start: 0.7420 (ptm) cc_final: 0.7161 (ptm)
REVERT: A  426 PHE cc_start: 0.7699 (t80) cc_final: 0.7289 (t80)
REVERT: B  198 GLU cc_start: 0.5475 (tt0) cc_final: 0.5089 (tt0)
REVERT: B  607 MET cc_start: 0.7559 (ptp) cc_final: 0.7300 (ptm)
REVERT: C  175 ILE cc_start: 0.8895 (tp) cc_final: 0.8622 (tp)
REVERT: C  188 CYS cc_start: 0.8382 (t) cc_final: 0.7786 (t)
REVERT: C  410 ARG cc_start: 0.8645 (mtt90) cc_final: 0.8216 (mtp85)
REVERT: C  573 TYR cc_start: 0.8765 (m-80) cc_final: 0.8393 (m-80)
REVERT: C  585 MET cc_start: 0.9130 (mmp) cc_final: 0.8704 (mmm)
REVERT: C  595 LYS cc_start: 0.8876 (mptt) cc_final: 0.8253 (pptt)
REVERT: D  405 LEU cc_start: 0.9087 (tp) cc_final: 0.8720 (mp)
REVERT: D  419 GLU cc_start: 0.7714 (pt0) cc_final: 0.7470 (pt0)
REVERT: D  426 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8050 (t0)
  outliers start: 52
  outliers final: 42
  residues processed: 221
  average time/residue: 0.0956
  time to fit residues: 34.0469
Evaluate side-chains
  218 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 174
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  207 ASP
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  359 SER
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  507 ASP
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  242 HIS
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain B residue  403 ILE
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  450 THR
Chi-restraints excluded: chain B residue  456 VAL
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  501 THR
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain C residue  187 ILE
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain C residue  293 THR
Chi-restraints excluded: chain C residue  295 THR
Chi-restraints excluded: chain C residue  359 SER
Chi-restraints excluded: chain C residue  451 VAL
Chi-restraints excluded: chain C residue  536 THR
Chi-restraints excluded: chain C residue  568 ILE
Chi-restraints excluded: chain D residue  233 CYS
Chi-restraints excluded: chain D residue  260 CYS
Chi-restraints excluded: chain D residue  262 ILE
Chi-restraints excluded: chain D residue  264 TYR
Chi-restraints excluded: chain D residue  345 MET
Chi-restraints excluded: chain D residue  346 ASP
Chi-restraints excluded: chain D residue  369 CYS
Chi-restraints excluded: chain D residue  417 LEU
Chi-restraints excluded: chain D residue  426 ASN
Chi-restraints excluded: chain D residue  474 LEU
Chi-restraints excluded: chain D residue  536 MET
Chi-restraints excluded: chain D residue  537 LEU
Chi-restraints excluded: chain D residue  551 VAL
Chi-restraints excluded: chain D residue  582 VAL
Chi-restraints excluded: chain D residue  626 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 130 optimal weight:    6.9990
   chunk 168 optimal weight:    0.3980
   chunk 86 optimal weight:    0.3980
   chunk 90 optimal weight:    0.9990
   chunk 142 optimal weight:    0.0370
   chunk 54 optimal weight:    0.7980
   chunk 31 optimal weight:    0.4980
   chunk 38 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.3858

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

Flipped N/Q/H residues before XYZ refinement:
** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 339 HIS
D 367 ASN
D 426 ASN
** D 531 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 = 0.4010 r_free = 0.4010 target = 0.142033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.110992 restraints weight = 61176.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.115673 restraints weight = 23870.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.117517 restraints weight = 12287.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.118511 restraints weight = 9249.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.118694 restraints weight = 8177.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3701
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3701 r_free = 0.3701    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3701 r_free = 0.3701    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3701
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.3095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071  14805  Z= 0.120
  Angle     :  0.634  14.315  20097  Z= 0.311
  Chirality :  0.042   0.284   2283
  Planarity :  0.004   0.051   2465
  Dihedral  : 12.911 176.174   2123
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 22.08 %
    Favored  : 75.89 %
  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:  0.56 (0.21), residues: 1734
  helix:  1.39 (0.16), residues: 1114
  sheet:  0.08 (0.64), residues: 47
  loop : -1.68 (0.26), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 274 
 TYR   0.016   0.001   TYR A 423 
 PHE   0.025   0.001   PHE B 413 
 TRP   0.028   0.001   TRP D 221 
 HIS   0.003   0.001   HIS C 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (14802)
  covalent geometry    : angle       0.63252 (20088)
  hydrogen bonds       : bond        0.03877 (  890)
  hydrogen bonds       : angle       4.21854 ( 2629)
  link_NAG-ASN         : bond        0.00148 (    3)
  link_NAG-ASN         : angle       2.12125 (    9)

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

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

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3468 Ramachandran restraints generated.
    1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 198
  time to evaluate  : 0.580 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  207 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7710 (t0)
REVERT: A  406 MET cc_start: 0.7379 (ptm) cc_final: 0.7148 (ptm)
REVERT: A  426 PHE cc_start: 0.7688 (t80) cc_final: 0.7359 (t80)
REVERT: A  518 GLU cc_start: 0.6480 (mm-30) cc_final: 0.5970 (mt-10)
REVERT: B  252 ASP cc_start: 0.7369 (OUTLIER) cc_final: 0.6829 (m-30)
REVERT: B  607 MET cc_start: 0.7557 (ptp) cc_final: 0.7267 (ptm)
REVERT: C  186 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8276 (mt)
REVERT: C  188 CYS cc_start: 0.8316 (t) cc_final: 0.7759 (t)
REVERT: C  410 ARG cc_start: 0.8630 (mtt90) cc_final: 0.8237 (mtp85)
REVERT: C  424 MET cc_start: 0.8498 (ttp) cc_final: 0.7666 (ttm)
REVERT: C  573 TYR cc_start: 0.8691 (m-80) cc_final: 0.8304 (m-80)
REVERT: C  585 MET cc_start: 0.9053 (mmp) cc_final: 0.8652 (mmm)
REVERT: C  591 TYR cc_start: 0.7518 (m-80) cc_final: 0.7308 (m-80)
REVERT: C  595 LYS cc_start: 0.8876 (mptt) cc_final: 0.8244 (pptt)
REVERT: D  405 LEU cc_start: 0.8919 (tp) cc_final: 0.8596 (mp)
REVERT: D  419 GLU cc_start: 0.7500 (pt0) cc_final: 0.7242 (pt0)
REVERT: D  426 ASN cc_start: 0.8581 (OUTLIER) cc_final: 0.8054 (t0)
  outliers start: 31
  outliers final: 25
  residues processed: 220
  average time/residue: 0.0941
  time to fit residues: 33.6630
Evaluate side-chains
  215 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 186
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ASP
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  507 ASP
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  242 HIS
Chi-restraints excluded: chain B residue  252 ASP
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  450 THR
Chi-restraints excluded: chain B residue  456 VAL
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  501 THR
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain C residue  359 SER
Chi-restraints excluded: chain C residue  536 THR
Chi-restraints excluded: chain D residue  233 CYS
Chi-restraints excluded: chain D residue  262 ILE
Chi-restraints excluded: chain D residue  339 HIS
Chi-restraints excluded: chain D residue  346 ASP
Chi-restraints excluded: chain D residue  369 CYS
Chi-restraints excluded: chain D residue  417 LEU
Chi-restraints excluded: chain D residue  426 ASN
Chi-restraints excluded: chain D residue  536 MET
Chi-restraints excluded: chain D residue  537 LEU
Chi-restraints excluded: chain D residue  551 VAL
Chi-restraints excluded: chain D residue  582 VAL
Chi-restraints excluded: chain D residue  626 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 105 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0270
   chunk 22 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 136 optimal weight:    0.9980
   chunk 30 optimal weight:    5.9990
   chunk 72 optimal weight:    6.9990
   chunk 32 optimal weight:    0.6980
   chunk 155 optimal weight:    0.7980
   overall best weight:    0.7038

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

Flipped N/Q/H residues before XYZ refinement:
** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 473 HIS
** C 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 562 ASN
D 367 ASN
D 426 ASN
** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.142023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.112326 restraints weight = 37757.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.115900 restraints weight = 17610.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.118215 restraints weight = 10835.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.119627 restraints weight = 7954.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.120538 restraints weight = 6542.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3731
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3731 r_free = 0.3731    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3731 r_free = 0.3731    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3731
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.3180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  14805  Z= 0.120
  Angle     :  0.634  14.200  20097  Z= 0.309
  Chirality :  0.041   0.300   2283
  Planarity :  0.004   0.052   2465
  Dihedral  : 12.916 175.771   2123
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 22.59 %
    Favored  : 75.38 %
  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:  0.64 (0.21), residues: 1734
  helix:  1.44 (0.16), residues: 1113
  sheet:  0.14 (0.63), residues: 47
  loop : -1.63 (0.27), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 274 
 TYR   0.015   0.001   TYR C 546 
 PHE   0.026   0.001   PHE B 413 
 TRP   0.025   0.001   TRP A 171 
 HIS   0.013   0.001   HIS D 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (14802)
  covalent geometry    : angle       0.63273 (20088)
  hydrogen bonds       : bond        0.03834 (  890)
  hydrogen bonds       : angle       4.17700 ( 2629)
  link_NAG-ASN         : bond        0.00147 (    3)
  link_NAG-ASN         : angle       2.12659 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2760.10 seconds
wall clock time: 48 minutes 24.50 seconds (2904.50 seconds total)