Starting phenix.real_space_refine
on Fri Jun 13 04:12:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8eu3_28603/06_2025/8eu3_28603_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8eu3_28603/06_2025/8eu3_28603.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.62
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8eu3_28603/06_2025/8eu3_28603.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8eu3_28603/06_2025/8eu3_28603.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8eu3_28603/06_2025/8eu3_28603_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8eu3_28603/06_2025/8eu3_28603_neut.cif"
  }
  resolution = 3.62
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.072
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      66      5.16       5
     C    9511      2.51       5
     N    2378      2.21       5
     O    2637      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 155 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 14596
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3631
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 444, 3623
          Classifications: {'peptide': 444}
          Link IDs: {'PTRANS': 14, 'TRANS': 429}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 444, 3623
          Classifications: {'peptide': 444}
          Link IDs: {'PTRANS': 14, 'TRANS': 429}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 3695
    Chain: "B"
      Number of atoms: 3616
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 443, 3616
          Classifications: {'peptide': 443}
          Link IDs: {'PTRANS': 14, 'TRANS': 428}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 3624
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 445, 3624
          Classifications: {'peptide': 445}
          Link IDs: {'PTRANS': 14, 'TRANS': 430}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 3591
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 438, 3583
          Classifications: {'peptide': 438}
          Link IDs: {'PTRANS': 12, 'TRANS': 425}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 438, 3583
          Classifications: {'peptide': 438}
          Link IDs: {'PTRANS': 12, 'TRANS': 425}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 3663
    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}
  Time building chain proxies: 11.89, per 1000 atoms: 0.81
  Number of scatterers: 14596
  At special positions: 0
  Unit cell: (132.25, 108.974, 106.858, 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      66     16.00
     P       4     15.00
     O    2637      8.00
     N    2378      7.00
     C    9511      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: 3.38
  Conformation dependent library (CDL) restraints added in 2.6 seconds
  

  3512 Ramachandran restraints generated.
    1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3358

  Finding SS restraints...
    Secondary structure from input PDB file:
      73 helices and 12 sheets defined
      67.9% alpha, 4.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 166 through 193
      Proline residue:  A 178  - end of helix
      removed outlier: 3.708A  pdb=" N   ASP A 193 " --> pdb=" O   ARG A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 199
      removed outlier: 3.671A  pdb=" N   SER A 197 " --> pdb=" O   ASP A 193 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   TYR A 199 " --> pdb=" O   LEU A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 222
    Processing helix  chain 'A' and resid 235 through 245
    Processing helix  chain 'A' and resid 246 through 255
      removed outlier: 3.860A  pdb=" N   LYS A 250 " --> pdb=" O   THR A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 3.696A  pdb=" N   VAL A 273 " --> pdb=" O   TYR A 270 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ARG A 274 " --> pdb=" O   PRO A 271 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   ASN A 276 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 295
      removed outlier: 4.342A  pdb=" N   LEU A 284 " --> pdb=" O   LYS A 280 " (cutoff:3.500A)
    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 427
      removed outlier: 4.806A  pdb=" N   SER A 409 " --> pdb=" O   ASN A 405 " (cutoff:3.500A)
      removed outlier: 5.346A  pdb=" N   ARG A 410 " --> pdb=" O   MET A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 447
    Processing helix  chain 'A' and resid 452 through 458
    Processing helix  chain 'A' and resid 461 through 473
    Processing helix  chain 'A' and resid 473 through 478
    Processing helix  chain 'A' and resid 487 through 498
    Processing helix  chain 'A' and resid 548 through 554
    Processing helix  chain 'A' and resid 581 through 589
      removed outlier: 3.825A  pdb=" N   ALA A 587 " --> pdb=" O   ASP A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 609
      removed outlier: 4.026A  pdb=" N   LYS A 595 " --> pdb=" O   TYR A 591 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 193
      removed outlier: 3.876A  pdb=" N   TYR B 169 " --> pdb=" O   SER B 165 " (cutoff:3.500A)
      Proline residue:  B 178  - end of helix
      removed outlier: 4.022A  pdb=" N   ASP B 193 " --> pdb=" O   ARG B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 199
    Processing helix  chain 'B' and resid 199 through 223
    Processing helix  chain 'B' and resid 235 through 245
    Processing helix  chain 'B' and resid 246 through 256
      removed outlier: 4.040A  pdb=" N   LYS B 250 " --> pdb=" O   THR B 246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 279
      removed outlier: 4.107A  pdb=" N   VAL B 273 " --> pdb=" O   TYR B 270 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ARG B 274 " --> pdb=" O   PRO B 271 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   PHE B 275 " --> pdb=" O   GLU B 272 " (cutoff:3.500A)
      removed outlier: 4.733A  pdb=" N   ASN B 276 " --> pdb=" O   VAL B 273 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LEU B 278 " --> pdb=" O   PHE B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 295
      removed outlier: 4.049A  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 347 through 364
    Processing helix  chain 'B' and resid 374 through 406
    Processing helix  chain 'B' and resid 407 through 427
    Processing helix  chain 'B' and resid 430 through 448
    Processing helix  chain 'B' and resid 452 through 457
    Processing helix  chain 'B' and resid 461 through 478
      removed outlier: 5.044A  pdb=" N   ASP B 475 " --> pdb=" O   ASN B 471 " (cutoff:3.500A)
      removed outlier: 5.073A  pdb=" N   THR B 476 " --> pdb=" O   VAL B 472 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 487 through 498
    Processing helix  chain 'B' and resid 580 through 588
    Processing helix  chain 'B' and resid 591 through 610
    Processing helix  chain 'C' and resid 166 through 193
      Proline residue:  C 178  - end of helix
      removed outlier: 3.939A  pdb=" N   ASP C 193 " --> pdb=" O   ARG C 189 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 194 through 199
    Processing helix  chain 'C' and resid 199 through 222
    Processing helix  chain 'C' and resid 235 through 245
    Processing helix  chain 'C' and resid 247 through 256
    Processing helix  chain 'C' and resid 270 through 279
      removed outlier: 4.184A  pdb=" N   VAL C 273 " --> pdb=" O   TYR C 270 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   PHE C 275 " --> pdb=" O   GLU C 272 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   ASN C 276 " --> pdb=" O   VAL C 273 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 280 through 295
      removed outlier: 3.965A  pdb=" N   LEU C 284 " --> pdb=" O   LYS C 280 " (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
      removed outlier: 3.818A  pdb=" N   ASN C 407 " --> pdb=" O   ILE C 403 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 407 through 428
    Processing helix  chain 'C' and resid 430 through 447
    Processing helix  chain 'C' and resid 452 through 458
    Processing helix  chain 'C' and resid 461 through 478
      removed outlier: 5.422A  pdb=" N   ASP C 475 " --> pdb=" O   ASN C 471 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   THR C 476 " --> pdb=" O   VAL C 472 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 487 through 498
    Processing helix  chain 'C' and resid 581 through 589
    Processing helix  chain 'C' and resid 591 through 609
    Processing helix  chain 'D' and resid 215 through 242
      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: 3.910A  pdb=" N   LEU D 275 " --> pdb=" O   GLN D 272 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 286 through 296
    Processing helix  chain 'D' and resid 297 through 307
      removed outlier: 3.940A  pdb=" N   GLN D 301 " --> pdb=" O   SER D 297 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU D 302 " --> pdb=" O   THR D 298 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 309 through 312
      removed outlier: 3.707A  pdb=" N   ILE D 312 " --> pdb=" O   PRO D 309 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 309 through 312'
    Processing helix  chain 'D' and resid 313 through 318
    Processing helix  chain 'D' and resid 320 through 329
      removed outlier: 4.284A  pdb=" N   ASN D 326 " --> pdb=" O   PHE D 323 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LEU D 329 " --> pdb=" O   ASN D 326 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 330 through 345
      removed outlier: 3.606A  pdb=" N   PHE D 337 " --> pdb=" O   SER D 333 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 347 through 379
      removed outlier: 4.018A  pdb=" N   TYR D 351 " --> pdb=" O   LYS D 347 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 392 through 406
    Processing helix  chain 'D' and resid 416 through 449
    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 521
      removed outlier: 3.596A  pdb=" N   VAL D 514 " --> pdb=" O   LEU D 510 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   SER D 517 " --> pdb=" O   ASP D 513 " (cutoff:3.500A)
      removed outlier: 5.691A  pdb=" N   ILE D 518 " --> pdb=" O   VAL D 514 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 523 through 527
      removed outlier: 3.955A  pdb=" N   LYS D 526 " --> pdb=" O   ASP D 523 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   GLY D 527 " --> pdb=" O   LEU D 524 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 523 through 527'
    Processing helix  chain 'D' and resid 529 through 539
    Processing helix  chain 'D' and resid 592 through 597
      removed outlier: 3.724A  pdb=" N   LEU D 596 " --> pdb=" O   GLU D 592 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ALA D 597 " --> pdb=" O   ILE D 593 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 592 through 597'
    Processing helix  chain 'D' and resid 621 through 629
    Processing helix  chain 'D' and resid 631 through 646
    Processing sheet with id=AA1, first strand: chain 'A' and resid 226 through 228
      removed outlier: 4.143A  pdb=" N   PHE A 226 " --> pdb=" O   VAL A 233 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LEU A 231 " --> pdb=" O   GLU A 228 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 499 through 500
    Processing sheet with id=AA3, first strand: chain 'A' and resid 540 through 541
      removed outlier: 3.902A  pdb=" N   ASN A 567 " --> pdb=" O   VAL A 530 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 227 through 228
    Processing sheet with id=AA5, first strand: chain 'B' and resid 499 through 503
    Processing sheet with id=AA6, first strand: chain 'B' and resid 520 through 521
    Processing sheet with id=AA7, first strand: chain 'B' and resid 529 through 530
    Processing sheet with id=AA8, first strand: chain 'C' and resid 227 through 228
    Processing sheet with id=AA9, first strand: chain 'C' and resid 499 through 502
    Processing sheet with id=AB1, first strand: chain 'C' and resid 508 through 510
      removed outlier: 6.735A  pdb=" N   ILE C 568 " --> pdb=" O   ILE C 509 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   VAL C 539 " --> pdb=" O   VAL C 529 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 541 through 542
    Processing sheet with id=AB3, first strand: chain 'D' and resid 550 through 552
      removed outlier: 6.741A  pdb=" N   PHE D 550 " --> pdb=" O   ALA D 610 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   ALA D 610 " --> pdb=" O   PHE D 550 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   CYS D 552 " --> pdb=" O   VAL D 608 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   VAL D 569 " --> pdb=" O   THR D 583 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   THR D 583 " --> pdb=" O   VAL D 569 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   VAL D 571 " --> pdb=" O   LEU D 581 " (cutoff:3.500A)

    918 hydrogen bonds defined for protein.
    2668 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: 4.74

  Time building geometry restraints manager: 4.01 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4341
        1.34 -     1.46: 2764
        1.46 -     1.57: 7736
        1.57 -     1.69: 0
        1.69 -     1.81: 105
  Bond restraints: 14946
  Sorted by residual:
  bond pdb=" O5' PCG B 802 "
       pdb=" PA  PCG B 802 "
    ideal  model  delta    sigma   weight residual
    1.606  1.488  0.118 2.00e-02 2.50e+03 3.47e+01
  bond pdb=" O5' PCG C 802 "
       pdb=" PA  PCG C 802 "
    ideal  model  delta    sigma   weight residual
    1.606  1.488  0.118 2.00e-02 2.50e+03 3.47e+01
  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 3.43e+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 3.38e+01
  bond pdb=" O3' PCG C 802 "
       pdb=" PA  PCG C 802 "
    ideal  model  delta    sigma   weight residual
    1.617  1.513  0.104 2.00e-02 2.50e+03 2.72e+01
  ... (remaining 14941 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.68: 20066
        3.68 -     7.36: 165
        7.36 -    11.04: 42
       11.04 -    14.72: 5
       14.72 -    18.40: 10
  Bond angle restraints: 20288
  Sorted by residual:
  angle pdb=" C3' PCG C 802 "
        pdb=" C4' PCG C 802 "
        pdb=" C5' PCG C 802 "
      ideal   model   delta    sigma   weight residual
     109.85  128.25  -18.40 3.00e+00 1.11e-01 3.76e+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  127.96  -18.11 3.00e+00 1.11e-01 3.64e+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  127.89  -18.04 3.00e+00 1.11e-01 3.62e+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  127.88  -18.03 3.00e+00 1.11e-01 3.61e+01
  angle pdb=" O1A PCG D 901 "
        pdb=" PA  PCG D 901 "
        pdb=" O5' PCG D 901 "
      ideal   model   delta    sigma   weight residual
     102.28  118.01  -15.73 3.00e+00 1.11e-01 2.75e+01
  ... (remaining 20283 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.12: 8710
       35.12 -    70.25: 214
       70.25 -   105.37: 27
      105.37 -   140.50: 0
      140.50 -   175.62: 4
  Dihedral angle restraints: 8955
    sinusoidal: 3730
      harmonic: 5225
  Sorted by residual:
  dihedral pdb=" CA  LEU B 588 "
           pdb=" C   LEU B 588 "
           pdb=" N   THR B 589 "
           pdb=" CA  THR B 589 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.32   26.68     0      5.00e+00 4.00e-02 2.85e+01
  dihedral pdb=" CA  VAL A 480 "
           pdb=" C   VAL A 480 "
           pdb=" N   ARG A 481 "
           pdb=" CA  ARG A 481 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.87  -24.13     0      5.00e+00 4.00e-02 2.33e+01
  dihedral pdb=" CA  ASP C 193 "
           pdb=" C   ASP C 193 "
           pdb=" N   GLU C 194 "
           pdb=" CA  GLU C 194 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.70   23.30     0      5.00e+00 4.00e-02 2.17e+01
  ... (remaining 8952 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.347: 2303
       0.347 -    0.693: 0
       0.693 -    1.040: 0
       1.040 -    1.386: 0
       1.386 -    1.733: 4
  Chirality restraints: 2307
  Sorted by residual:
  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   -0.77   -1.73 2.00e-01 2.50e+01 7.50e+01
  chirality pdb=" C4' PCG B 802 "
            pdb=" C3' PCG B 802 "
            pdb=" C5' PCG B 802 "
            pdb=" O4' PCG B 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -0.79   -1.71 2.00e-01 2.50e+01 7.33e+01
  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   -0.83   -1.67 2.00e-01 2.50e+01 6.94e+01
  ... (remaining 2304 not shown)

  Planarity restraints: 2496
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 392 "    0.056 2.00e-02 2.50e+03   3.24e-02 1.05e+01
        pdb=" O   PHE A 392 "   -0.020 2.00e-02 2.50e+03
        pdb=" CA APHE A 392 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ALA A 393 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN D 272 "    0.052 5.00e-02 4.00e+02   7.86e-02 9.87e+00
        pdb=" N   PRO D 273 "   -0.136 5.00e-02 4.00e+02
        pdb=" CA  PRO D 273 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO D 273 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D 236 "   -0.048 5.00e-02 4.00e+02   7.27e-02 8.46e+00
        pdb=" N   PRO D 237 "    0.126 5.00e-02 4.00e+02
        pdb=" CA  PRO D 237 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO D 237 "   -0.041 5.00e-02 4.00e+02
  ... (remaining 2493 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1946
        2.75 -     3.29: 14265
        3.29 -     3.82: 24992
        3.82 -     4.36: 27235
        4.36 -     4.90: 47520
  Nonbonded interactions: 115958
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 580 "
            pdb=" OD1 ASP A 582 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" O   ASP A 162 "
            pdb=" OG  SER A 165 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" O   THR A 360 "
            pdb=" OG1 THR A 364 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O   TYR D 294 "
            pdb=" OG  SER D 297 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" OG  SER D 594 "
            pdb=" O   ASN D 602 "
     model   vdw
     2.308 3.040
  ... (remaining 115953 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 259 or resid 270 through 391 or resid 393 thro \ 
ugh 609 or resid 801 through 802))
  selection = (chain 'B' and (resid 159 through 259 or resid 270 through 391 or resid 393 thro \ 
ugh 609 or resid 801 through 802))
  selection = (chain 'C' and (resid 159 through 259 or resid 270 through 391 or resid 393 thro \ 
ugh 609 or resid 801 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:             2.150
  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:             0.020
  Extract box with map and model:          0.500
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     38.140
  Find NCS groups from input model:        0.930
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
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      :  0.007   0.118  14949  Z= 0.324
  Angle     :  1.020  18.401  20297  Z= 0.500
  Chirality :  0.088   1.733   2307
  Planarity :  0.007   0.079   2493
  Dihedral  : 16.537 175.619   5597
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  4.90 %
    Favored  : 94.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.46 (0.15), residues: 1756
  helix: -1.94 (0.11), residues: 1151
  sheet: -2.82 (0.62), residues: 59
  loop : -2.64 (0.22), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP D 400 
 HIS   0.006   0.001   HIS D 293 
 PHE   0.043   0.002   PHE A 385 
 TYR   0.023   0.002   TYR A 184 
 ARG   0.008   0.001   ARG D 539 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00317 (    3)
  link_NAG-ASN         : angle       2.53023 (    9)
  hydrogen bonds       : bond        0.11448 (  918)
  hydrogen bonds       : angle       4.90246 ( 2668)
  covalent geometry    : bond        0.00709 (14946)
  covalent geometry    : angle       1.01839 (20288)

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

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

  3512 Ramachandran restraints generated.
    1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3512 Ramachandran restraints generated.
    1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  314 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 311
  time to evaluate  : 1.582 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  219 LEU cc_start: 0.8562 (tt) cc_final: 0.8358 (tt)
REVERT: A  232 MET cc_start: 0.8156 (tpp) cc_final: 0.7844 (tpp)
REVERT: A  241 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8040 (mp10)
REVERT: A  300 MET cc_start: 0.7112 (mmm) cc_final: 0.6861 (tpt)
REVERT: A  439 ARG cc_start: 0.8556 (ttt90) cc_final: 0.8245 (mtp85)
REVERT: A  467 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7494 (mm-30)
REVERT: A  478 LYS cc_start: 0.7527 (ptmt) cc_final: 0.7249 (tptp)
REVERT: B  240 TRP cc_start: 0.8482 (t-100) cc_final: 0.8199 (t60)
REVERT: B  254 LEU cc_start: 0.8782 (tp) cc_final: 0.8545 (tp)
REVERT: B  289 ASP cc_start: 0.7464 (t0) cc_final: 0.7217 (t70)
REVERT: B  314 ILE cc_start: 0.8738 (mm) cc_final: 0.8535 (mt)
REVERT: B  410 ARG cc_start: 0.8068 (tpm170) cc_final: 0.7732 (tpm170)
REVERT: B  414 GLN cc_start: 0.8704 (tp-100) cc_final: 0.8353 (tp40)
REVERT: B  546 TYR cc_start: 0.7618 (p90) cc_final: 0.7377 (p90)
REVERT: C  200 LEU cc_start: 0.9116 (tp) cc_final: 0.8811 (tp)
REVERT: C  241 GLN cc_start: 0.8618 (mm110) cc_final: 0.8368 (mm-40)
REVERT: C  406 MET cc_start: 0.7798 (ttp) cc_final: 0.7548 (mtp)
REVERT: C  604 GLN cc_start: 0.9081 (mt0) cc_final: 0.8800 (pp30)
REVERT: D  248 ASP cc_start: 0.5907 (t0) cc_final: 0.5346 (t0)
REVERT: D  250 ILE cc_start: 0.8790 (mt) cc_final: 0.8560 (mt)
REVERT: D  291 ARG cc_start: 0.8182 (ttm-80) cc_final: 0.7955 (ttp-170)
REVERT: D  327 ARG cc_start: 0.7620 (mpt180) cc_final: 0.7336 (mpt-90)
REVERT: D  635 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7704 (tm-30)
  outliers start: 3
  outliers final: 0
  residues processed: 312
  average time/residue: 0.2903
  time to fit residues: 128.3563
Evaluate side-chains
  221 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 1.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 147 optimal weight:    0.7980
   chunk 132 optimal weight:    0.7980
   chunk 73 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   chunk 89 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 137 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 83 optimal weight:    6.9990
   chunk 102 optimal weight:    0.7980
   chunk 158 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 345 HIS
** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 425 GLN
A 471 ASN
** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 196 GLN
B 229 GLN
B 305 ASN
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 537 GLN
B 554 ASN
B 604 GLN
C 242 HIS
** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 554 ASN
D 245 GLN
** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 288 ASN
D 340 HIS
D 365 HIS
D 423 GLN
D 570 GLN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.180128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.148973 restraints weight = 19597.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.148431 restraints weight = 35977.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.149417 restraints weight = 32268.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3755
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3755 r_free = 0.3755    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3754 r_free = 0.3754    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3754
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.1414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  14949  Z= 0.149
  Angle     :  0.633   8.784  20297  Z= 0.328
  Chirality :  0.042   0.170   2307
  Planarity :  0.005   0.064   2493
  Dihedral  : 11.274 179.064   2147
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 10.93 %
    Favored  : 87.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.18), residues: 1756
  helix: -0.16 (0.14), residues: 1155
  sheet: -2.73 (0.65), residues: 49
  loop : -2.06 (0.24), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 373 
 HIS   0.010   0.001   HIS C 242 
 PHE   0.029   0.002   PHE A 577 
 TYR   0.025   0.002   TYR C 184 
 ARG   0.006   0.001   ARG C 563 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00072 (    3)
  link_NAG-ASN         : angle       2.17998 (    9)
  hydrogen bonds       : bond        0.04637 (  918)
  hydrogen bonds       : angle       4.33125 ( 2668)
  covalent geometry    : bond        0.00329 (14946)
  covalent geometry    : angle       0.63136 (20288)

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

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

  3512 Ramachandran restraints generated.
    1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3512 Ramachandran restraints generated.
    1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 256
  time to evaluate  : 1.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  300 MET cc_start: 0.6914 (mmm) cc_final: 0.6658 (tpt)
REVERT: A  410 ARG cc_start: 0.7253 (tpm170) cc_final: 0.6767 (tpp-160)
REVERT: A  473 HIS cc_start: 0.6599 (OUTLIER) cc_final: 0.5318 (t-90)
REVERT: A  478 LYS cc_start: 0.6725 (ptmt) cc_final: 0.6355 (tppt)
REVERT: B  254 LEU cc_start: 0.8610 (tp) cc_final: 0.8313 (tp)
REVERT: C  422 GLN cc_start: 0.8506 (tp40) cc_final: 0.8226 (tp40)
REVERT: D  248 ASP cc_start: 0.5421 (t0) cc_final: 0.5093 (t0)
  outliers start: 30
  outliers final: 14
  residues processed: 268
  average time/residue: 0.2833
  time to fit residues: 111.7228
Evaluate side-chains
  243 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 228
  time to evaluate  : 1.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  473 HIS
Chi-restraints excluded: chain A residue  546 TYR
Chi-restraints excluded: chain A residue  581 LYS
Chi-restraints excluded: chain A residue  589 THR
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  353 ILE
Chi-restraints excluded: chain B residue  459 SER
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain C residue  420 ILE
Chi-restraints excluded: chain C residue  462 ASP
Chi-restraints excluded: chain C residue  486 CYS
Chi-restraints excluded: chain C residue  496 LEU
Chi-restraints excluded: chain C residue  540 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 169 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 75 optimal weight:   10.0000
   chunk 164 optimal weight:    8.9990
   chunk 174 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 139 optimal weight:    0.0020
   chunk 57 optimal weight:    0.9980
   chunk 47 optimal weight:    0.7980
   chunk 171 optimal weight:   10.0000
   overall best weight:    0.9390

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

Flipped N/Q/H residues before XYZ refinement:
A 405 ASN
** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 229 GLN
B 425 GLN
B 473 HIS
B 604 GLN
** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 288 ASN
D 340 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.179325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.149321 restraints weight = 22691.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.149102 restraints weight = 39946.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.150600 restraints weight = 32527.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3749
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3749 r_free = 0.3749    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3749 r_free = 0.3749    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3749
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14949  Z= 0.150
  Angle     :  0.605   9.672  20297  Z= 0.312
  Chirality :  0.041   0.173   2307
  Planarity :  0.004   0.057   2493
  Dihedral  : 10.788 171.405   2147
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 13.25 %
    Favored  : 84.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.20), residues: 1756
  helix:  0.66 (0.15), residues: 1157
  sheet: -2.03 (0.60), residues: 69
  loop : -1.76 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 373 
 HIS   0.009   0.001   HIS C 242 
 PHE   0.030   0.001   PHE D 310 
 TYR   0.027   0.002   TYR C 591 
 ARG   0.006   0.000   ARG D 384 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00034 (    3)
  link_NAG-ASN         : angle       2.02240 (    9)
  hydrogen bonds       : bond        0.04328 (  918)
  hydrogen bonds       : angle       4.16360 ( 2668)
  covalent geometry    : bond        0.00339 (14946)
  covalent geometry    : angle       0.60408 (20288)

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

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

  3512 Ramachandran restraints generated.
    1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3512 Ramachandran restraints generated.
    1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 242
  time to evaluate  : 1.783 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 LEU cc_start: 0.8738 (tp) cc_final: 0.8420 (tp)
REVERT: A  410 ARG cc_start: 0.7151 (tpm170) cc_final: 0.6713 (tpp-160)
REVERT: A  439 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.7745 (ttm-80)
REVERT: A  478 LYS cc_start: 0.6891 (ptmt) cc_final: 0.6433 (tppt)
REVERT: B  175 ILE cc_start: 0.9046 (tp) cc_final: 0.8707 (tp)
REVERT: B  254 LEU cc_start: 0.8535 (tp) cc_final: 0.8230 (tp)
REVERT: B  425 GLN cc_start: 0.8169 (tp40) cc_final: 0.7801 (tp-100)
REVERT: C  200 LEU cc_start: 0.9051 (tp) cc_final: 0.8775 (tp)
REVERT: C  422 GLN cc_start: 0.8495 (tp40) cc_final: 0.8225 (tp40)
REVERT: C  462 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7637 (t0)
REVERT: D  210 ILE cc_start: 0.8277 (mm) cc_final: 0.8015 (mm)
REVERT: D  248 ASP cc_start: 0.5298 (t0) cc_final: 0.5044 (t0)
  outliers start: 34
  outliers final: 19
  residues processed: 259
  average time/residue: 0.2890
  time to fit residues: 111.7529
Evaluate side-chains
  246 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 226
  time to evaluate  : 1.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  473 HIS
Chi-restraints excluded: chain A residue  581 LYS
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  359 SER
Chi-restraints excluded: chain B residue  459 SER
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  539 VAL
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain C residue  311 LEU
Chi-restraints excluded: chain C residue  420 ILE
Chi-restraints excluded: chain C residue  462 ASP
Chi-restraints excluded: chain C residue  486 CYS
Chi-restraints excluded: chain C residue  496 LEU
Chi-restraints excluded: chain C residue  540 VAL
Chi-restraints excluded: chain D residue  350 ILE
Chi-restraints excluded: chain D residue  506 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 111 optimal weight:    0.5980
   chunk 9 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 79 optimal weight:    6.9990
   chunk 95 optimal weight:    2.9990
   chunk 92 optimal weight:    0.7980
   chunk 37 optimal weight:    9.9990
   chunk 39 optimal weight:   20.0000
   chunk 121 optimal weight:    4.9990
   chunk 143 optimal weight:    0.0870
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.0962

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
A 523 ASN
** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 229 GLN
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 604 GLN
** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 272 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 = 0.4031 r_free = 0.4031 target = 0.174381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.138914 restraints weight = 25224.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.133836 restraints weight = 31887.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.131349 restraints weight = 29956.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3552
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3552 r_free = 0.3552    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3552 r_free = 0.3552    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3552
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.2015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  14949  Z= 0.160
  Angle     :  0.592  11.160  20297  Z= 0.306
  Chirality :  0.041   0.172   2307
  Planarity :  0.004   0.054   2493
  Dihedral  : 10.615 174.001   2147
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.51 %
    Favored  : 83.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.20), residues: 1756
  helix:  0.95 (0.15), residues: 1158
  sheet: -1.93 (0.62), residues: 69
  loop : -1.68 (0.26), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 373 
 HIS   0.013   0.001   HIS C 242 
 PHE   0.022   0.001   PHE D 310 
 TYR   0.022   0.001   TYR A 423 
 ARG   0.003   0.000   ARG D 539 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00072 (    3)
  link_NAG-ASN         : angle       1.97162 (    9)
  hydrogen bonds       : bond        0.04258 (  918)
  hydrogen bonds       : angle       4.13617 ( 2668)
  covalent geometry    : bond        0.00365 (14946)
  covalent geometry    : angle       0.59056 (20288)

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

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

  3512 Ramachandran restraints generated.
    1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3512 Ramachandran restraints generated.
    1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 240
  time to evaluate  : 1.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 LEU cc_start: 0.8900 (tp) cc_final: 0.8688 (tp)
REVERT: A  410 ARG cc_start: 0.7070 (tpm170) cc_final: 0.6716 (tpp-160)
REVERT: A  478 LYS cc_start: 0.6958 (ptmt) cc_final: 0.6572 (tppt)
REVERT: A  604 GLN cc_start: 0.7610 (pp30) cc_final: 0.7176 (mm-40)
REVERT: B  175 ILE cc_start: 0.9059 (tp) cc_final: 0.8713 (tp)
REVERT: B  254 LEU cc_start: 0.8630 (tp) cc_final: 0.8294 (tp)
REVERT: B  425 GLN cc_start: 0.8595 (tp40) cc_final: 0.8171 (tp-100)
REVERT: C  232 MET cc_start: 0.8190 (tpp) cc_final: 0.7934 (tpp)
REVERT: C  353 ILE cc_start: 0.8866 (mm) cc_final: 0.8567 (mt)
REVERT: C  422 GLN cc_start: 0.8642 (tp40) cc_final: 0.8340 (tp40)
REVERT: C  462 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7833 (t0)
REVERT: C  546 TYR cc_start: 0.7727 (p90) cc_final: 0.7367 (p90)
REVERT: C  580 SER cc_start: 0.8284 (OUTLIER) cc_final: 0.7981 (p)
REVERT: D  210 ILE cc_start: 0.8447 (mm) cc_final: 0.8244 (mm)
REVERT: D  248 ASP cc_start: 0.5399 (t0) cc_final: 0.5052 (t0)
  outliers start: 29
  outliers final: 16
  residues processed: 257
  average time/residue: 0.2633
  time to fit residues: 100.1844
Evaluate side-chains
  249 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 231
  time to evaluate  : 1.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  581 LYS
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  359 SER
Chi-restraints excluded: chain B residue  459 SER
Chi-restraints excluded: chain B residue  539 VAL
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain C residue  311 LEU
Chi-restraints excluded: chain C residue  420 ILE
Chi-restraints excluded: chain C residue  462 ASP
Chi-restraints excluded: chain C residue  486 CYS
Chi-restraints excluded: chain C residue  496 LEU
Chi-restraints excluded: chain C residue  540 VAL
Chi-restraints excluded: chain C residue  580 SER
Chi-restraints excluded: chain D residue  350 ILE
Chi-restraints excluded: chain D residue  506 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 89 optimal weight:    0.6980
   chunk 163 optimal weight:    0.9990
   chunk 146 optimal weight:    0.0050
   chunk 145 optimal weight:    0.9990
   chunk 46 optimal weight:    0.5980
   chunk 108 optimal weight:    0.9980
   chunk 140 optimal weight:    6.9990
   chunk 19 optimal weight:    0.5980
   chunk 164 optimal weight:    1.9990
   chunk 64 optimal weight:    0.3980
   chunk 162 optimal weight:    2.9990
   overall best weight:    0.4594

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

Flipped N/Q/H residues before XYZ refinement:
** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 229 GLN
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 523 ASN
B 604 GLN
C 317 ASN
C 471 ASN
D 272 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.177404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.146689 restraints weight = 25069.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.150126 restraints weight = 48979.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.151109 restraints weight = 21055.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3758
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3758 r_free = 0.3758    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3758 r_free = 0.3758    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3758
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.2251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14949  Z= 0.119
  Angle     :  0.558  10.418  20297  Z= 0.289
  Chirality :  0.040   0.165   2307
  Planarity :  0.004   0.054   2493
  Dihedral  : 10.431 173.962   2147
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 16.02 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.20), residues: 1756
  helix:  1.29 (0.15), residues: 1154
  sheet: -1.95 (0.60), residues: 69
  loop : -1.52 (0.27), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 373 
 HIS   0.012   0.001   HIS C 242 
 PHE   0.020   0.001   PHE D 310 
 TYR   0.024   0.001   TYR C 591 
 ARG   0.003   0.000   ARG A 274 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00065 (    3)
  link_NAG-ASN         : angle       1.89162 (    9)
  hydrogen bonds       : bond        0.03985 (  918)
  hydrogen bonds       : angle       4.02930 ( 2668)
  covalent geometry    : bond        0.00255 (14946)
  covalent geometry    : angle       0.55696 (20288)

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

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

  3512 Ramachandran restraints generated.
    1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3512 Ramachandran restraints generated.
    1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 242
  time to evaluate  : 1.680 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  410 ARG cc_start: 0.7015 (tpm170) cc_final: 0.6654 (tpp-160)
REVERT: A  473 HIS cc_start: 0.6018 (OUTLIER) cc_final: 0.5633 (t-90)
REVERT: A  478 LYS cc_start: 0.6726 (ptmt) cc_final: 0.6404 (tppt)
REVERT: B  254 LEU cc_start: 0.8424 (tp) cc_final: 0.8076 (tp)
REVERT: B  425 GLN cc_start: 0.8325 (tp40) cc_final: 0.7929 (tp-100)
REVERT: C  200 LEU cc_start: 0.9010 (tp) cc_final: 0.8714 (tp)
REVERT: C  422 GLN cc_start: 0.8471 (tp40) cc_final: 0.8257 (tp40)
REVERT: C  509 ILE cc_start: 0.8224 (mm) cc_final: 0.7811 (mt)
REVERT: D  210 ILE cc_start: 0.8238 (mm) cc_final: 0.7929 (mm)
REVERT: D  248 ASP cc_start: 0.5272 (t0) cc_final: 0.4993 (t0)
  outliers start: 28
  outliers final: 17
  residues processed: 256
  average time/residue: 0.2680
  time to fit residues: 101.5277
Evaluate side-chains
  244 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 226
  time to evaluate  : 1.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  473 HIS
Chi-restraints excluded: chain A residue  508 TYR
Chi-restraints excluded: chain A residue  581 LYS
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  459 SER
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  521 ILE
Chi-restraints excluded: chain B residue  539 VAL
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain C residue  311 LEU
Chi-restraints excluded: chain C residue  394 THR
Chi-restraints excluded: chain C residue  420 ILE
Chi-restraints excluded: chain C residue  486 CYS
Chi-restraints excluded: chain C residue  496 LEU
Chi-restraints excluded: chain C residue  540 VAL
Chi-restraints excluded: chain C residue  573 TYR
Chi-restraints excluded: chain D residue  350 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 43 optimal weight:   10.0000
   chunk 69 optimal weight:    0.5980
   chunk 144 optimal weight:    0.7980
   chunk 163 optimal weight:    1.9990
   chunk 110 optimal weight:    0.8980
   chunk 44 optimal weight:    4.9990
   chunk 98 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 82 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 229 GLN
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 288 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.176476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.143346 restraints weight = 22848.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.144779 restraints weight = 43794.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.146323 restraints weight = 31870.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3707
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3707 r_free = 0.3707    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3707 r_free = 0.3707    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3707
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.2401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14949  Z= 0.130
  Angle     :  0.558  10.043  20297  Z= 0.291
  Chirality :  0.040   0.164   2307
  Planarity :  0.004   0.056   2493
  Dihedral  : 10.332 173.836   2147
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 16.21 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.20), residues: 1756
  helix:  1.39 (0.15), residues: 1155
  sheet: -1.79 (0.61), residues: 69
  loop : -1.43 (0.27), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 171 
 HIS   0.010   0.001   HIS C 242 
 PHE   0.016   0.001   PHE D 310 
 TYR   0.020   0.001   TYR A 423 
 ARG   0.005   0.000   ARG A 603 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00033 (    3)
  link_NAG-ASN         : angle       1.83562 (    9)
  hydrogen bonds       : bond        0.03981 (  918)
  hydrogen bonds       : angle       4.00978 ( 2668)
  covalent geometry    : bond        0.00291 (14946)
  covalent geometry    : angle       0.55658 (20288)

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

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

  3512 Ramachandran restraints generated.
    1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3512 Ramachandran restraints generated.
    1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 236
  time to evaluate  : 1.644 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 ASP cc_start: 0.7890 (m-30) cc_final: 0.7662 (m-30)
REVERT: A  410 ARG cc_start: 0.7035 (tpm170) cc_final: 0.6704 (tpp-160)
REVERT: A  473 HIS cc_start: 0.6163 (OUTLIER) cc_final: 0.5745 (t-90)
REVERT: A  478 LYS cc_start: 0.6768 (ptmt) cc_final: 0.6434 (tppt)
REVERT: B  175 ILE cc_start: 0.9035 (tp) cc_final: 0.8696 (tp)
REVERT: B  254 LEU cc_start: 0.8434 (tp) cc_final: 0.8112 (tp)
REVERT: B  425 GLN cc_start: 0.8360 (tp40) cc_final: 0.8008 (tp-100)
REVERT: C  200 LEU cc_start: 0.9033 (tp) cc_final: 0.8735 (tp)
REVERT: C  232 MET cc_start: 0.7978 (tpp) cc_final: 0.7683 (tpp)
REVERT: C  422 GLN cc_start: 0.8463 (tp40) cc_final: 0.8186 (tp40)
REVERT: C  490 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6789 (mm)
REVERT: C  509 ILE cc_start: 0.8244 (mm) cc_final: 0.7942 (mt)
REVERT: C  580 SER cc_start: 0.8153 (OUTLIER) cc_final: 0.7918 (p)
REVERT: D  210 ILE cc_start: 0.8361 (mm) cc_final: 0.8052 (mm)
REVERT: D  248 ASP cc_start: 0.5278 (t0) cc_final: 0.5007 (t0)
  outliers start: 25
  outliers final: 17
  residues processed: 253
  average time/residue: 0.2708
  time to fit residues: 102.7140
Evaluate side-chains
  247 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 227
  time to evaluate  : 1.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  473 HIS
Chi-restraints excluded: chain A residue  508 TYR
Chi-restraints excluded: chain A residue  581 LYS
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  539 VAL
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain C residue  311 LEU
Chi-restraints excluded: chain C residue  420 ILE
Chi-restraints excluded: chain C residue  462 ASP
Chi-restraints excluded: chain C residue  490 LEU
Chi-restraints excluded: chain C residue  496 LEU
Chi-restraints excluded: chain C residue  540 VAL
Chi-restraints excluded: chain C residue  580 SER
Chi-restraints excluded: chain D residue  213 TYR
Chi-restraints excluded: chain D residue  350 ILE
Chi-restraints excluded: chain D residue  506 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 90 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0870
   chunk 33 optimal weight:    5.9990
   chunk 106 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 120 optimal weight:    6.9990
   chunk 140 optimal weight:    0.8980
   chunk 96 optimal weight:    0.7980
   chunk 66 optimal weight:    1.9990
   chunk 148 optimal weight:    0.6980
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 604 GLN
D 272 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.176544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.150402 restraints weight = 28366.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.151698 restraints weight = 53649.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.150968 restraints weight = 20942.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3752
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3752 r_free = 0.3752    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3752 r_free = 0.3752    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3752
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.2520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14949  Z= 0.133
  Angle     :  0.583  14.643  20297  Z= 0.298
  Chirality :  0.040   0.163   2307
  Planarity :  0.004   0.057   2493
  Dihedral  : 10.230 172.993   2147
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 16.90 %
    Favored  : 81.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.20), residues: 1756
  helix:  1.44 (0.15), residues: 1155
  sheet: -1.70 (0.62), residues: 69
  loop : -1.37 (0.27), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 171 
 HIS   0.010   0.001   HIS C 242 
 PHE   0.024   0.001   PHE C 226 
 TYR   0.023   0.001   TYR C 591 
 ARG   0.004   0.000   ARG C 410 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00038 (    3)
  link_NAG-ASN         : angle       1.79380 (    9)
  hydrogen bonds       : bond        0.03986 (  918)
  hydrogen bonds       : angle       4.02415 ( 2668)
  covalent geometry    : bond        0.00297 (14946)
  covalent geometry    : angle       0.58162 (20288)

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

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

  3512 Ramachandran restraints generated.
    1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3512 Ramachandran restraints generated.
    1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 234
  time to evaluate  : 1.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  473 HIS cc_start: 0.5943 (OUTLIER) cc_final: 0.5645 (t-90)
REVERT: B  254 LEU cc_start: 0.8459 (tp) cc_final: 0.8108 (tp)
REVERT: B  425 GLN cc_start: 0.8355 (tp40) cc_final: 0.8008 (tp-100)
REVERT: B  464 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7406 (mm)
REVERT: C  200 LEU cc_start: 0.9026 (tp) cc_final: 0.8729 (tp)
REVERT: C  232 MET cc_start: 0.8025 (tpp) cc_final: 0.7796 (tpp)
REVERT: C  422 GLN cc_start: 0.8535 (tp40) cc_final: 0.8278 (tp40)
REVERT: C  509 ILE cc_start: 0.8220 (mm) cc_final: 0.7846 (mt)
REVERT: C  580 SER cc_start: 0.8162 (OUTLIER) cc_final: 0.7893 (p)
REVERT: D  210 ILE cc_start: 0.8321 (mm) cc_final: 0.8106 (mm)
REVERT: D  248 ASP cc_start: 0.5278 (t0) cc_final: 0.5033 (t0)
REVERT: D  286 ASP cc_start: 0.7289 (p0) cc_final: 0.6635 (p0)
REVERT: D  289 GLU cc_start: 0.7280 (mp0) cc_final: 0.6880 (mp0)
  outliers start: 28
  outliers final: 16
  residues processed: 253
  average time/residue: 0.2557
  time to fit residues: 96.9070
Evaluate side-chains
  237 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 218
  time to evaluate  : 1.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  473 HIS
Chi-restraints excluded: chain A residue  508 TYR
Chi-restraints excluded: chain A residue  581 LYS
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  359 SER
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  539 VAL
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain C residue  311 LEU
Chi-restraints excluded: chain C residue  420 ILE
Chi-restraints excluded: chain C residue  444 LEU
Chi-restraints excluded: chain C residue  462 ASP
Chi-restraints excluded: chain C residue  540 VAL
Chi-restraints excluded: chain C residue  580 SER
Chi-restraints excluded: chain D residue  350 ILE
Chi-restraints excluded: chain D residue  506 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 124 optimal weight:    0.9980
   chunk 41 optimal weight:    0.2980
   chunk 16 optimal weight:    2.9990
   chunk 141 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 86 optimal weight:    4.9990
   chunk 74 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9980
   chunk 122 optimal weight:    3.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 272 GLN
D 288 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.174448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.141598 restraints weight = 22372.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.143386 restraints weight = 40555.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.143930 restraints weight = 31368.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3689
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3689 r_free = 0.3689    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3689 r_free = 0.3689    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3689
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.2597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  14949  Z= 0.173
  Angle     :  0.611  16.254  20297  Z= 0.312
  Chirality :  0.041   0.170   2307
  Planarity :  0.004   0.058   2493
  Dihedral  : 10.188 172.428   2147
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 17.59 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.20), residues: 1756
  helix:  1.36 (0.15), residues: 1155
  sheet: -1.68 (0.62), residues: 69
  loop : -1.29 (0.27), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 171 
 HIS   0.007   0.001   HIS A 473 
 PHE   0.034   0.001   PHE C 226 
 TYR   0.021   0.001   TYR A 423 
 ARG   0.004   0.000   ARG C 410 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00076 (    3)
  link_NAG-ASN         : angle       1.81597 (    9)
  hydrogen bonds       : bond        0.04149 (  918)
  hydrogen bonds       : angle       4.08808 ( 2668)
  covalent geometry    : bond        0.00400 (14946)
  covalent geometry    : angle       0.61005 (20288)

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

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

  3512 Ramachandran restraints generated.
    1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3512 Ramachandran restraints generated.
    1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 233
  time to evaluate  : 1.694 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  473 HIS cc_start: 0.5925 (OUTLIER) cc_final: 0.5725 (t-90)
REVERT: B  175 ILE cc_start: 0.9061 (tp) cc_final: 0.8687 (tp)
REVERT: B  254 LEU cc_start: 0.8509 (tp) cc_final: 0.8143 (tp)
REVERT: B  464 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7463 (mm)
REVERT: C  200 LEU cc_start: 0.9056 (tp) cc_final: 0.8748 (tp)
REVERT: C  353 ILE cc_start: 0.8683 (mm) cc_final: 0.8376 (mt)
REVERT: C  422 GLN cc_start: 0.8541 (tp40) cc_final: 0.8279 (tp40)
REVERT: C  509 ILE cc_start: 0.8224 (mm) cc_final: 0.7956 (mt)
REVERT: C  580 SER cc_start: 0.8108 (OUTLIER) cc_final: 0.7881 (p)
REVERT: D  210 ILE cc_start: 0.8368 (mm) cc_final: 0.8155 (mm)
REVERT: D  248 ASP cc_start: 0.5377 (t0) cc_final: 0.5108 (t0)
  outliers start: 23
  outliers final: 17
  residues processed: 247
  average time/residue: 0.2547
  time to fit residues: 94.5389
Evaluate side-chains
  239 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 219
  time to evaluate  : 1.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  473 HIS
Chi-restraints excluded: chain A residue  508 TYR
Chi-restraints excluded: chain A residue  581 LYS
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  359 SER
Chi-restraints excluded: chain B residue  459 SER
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  539 VAL
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain C residue  311 LEU
Chi-restraints excluded: chain C residue  420 ILE
Chi-restraints excluded: chain C residue  444 LEU
Chi-restraints excluded: chain C residue  462 ASP
Chi-restraints excluded: chain C residue  540 VAL
Chi-restraints excluded: chain C residue  580 SER
Chi-restraints excluded: chain D residue  350 ILE
Chi-restraints excluded: chain D residue  506 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 110 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 114 optimal weight:    0.1980
   chunk 6 optimal weight:    1.9990
   chunk 170 optimal weight:    0.0170
   chunk 99 optimal weight:    0.8980
   chunk 147 optimal weight:    0.5980
   chunk 115 optimal weight:    0.9990
   chunk 32 optimal weight:    7.9990
   chunk 61 optimal weight:    0.1980
   overall best weight:    0.3218

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
A 414 GLN
** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.174212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.139614 restraints weight = 19682.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.138197 restraints weight = 31018.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.139703 restraints weight = 28854.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3645
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3645 r_free = 0.3645    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3645 r_free = 0.3645    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3645
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.2625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.195  14949  Z= 0.238
  Angle     :  0.817  59.200  20297  Z= 0.468
  Chirality :  0.042   0.259   2307
  Planarity :  0.004   0.062   2493
  Dihedral  : 10.187 172.415   2147
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 17.78 %
    Favored  : 80.72 %
  Cbeta Deviations :  0.06 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.20), residues: 1756
  helix:  1.39 (0.15), residues: 1155
  sheet: -1.67 (0.62), residues: 69
  loop : -1.30 (0.27), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 171 
 HIS   0.008   0.001   HIS A 473 
 PHE   0.034   0.001   PHE C 226 
 TYR   0.089   0.002   TYR D 294 
 ARG   0.009   0.000   ARG C 410 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00057 (    3)
  link_NAG-ASN         : angle       1.82008 (    9)
  hydrogen bonds       : bond        0.04170 (  918)
  hydrogen bonds       : angle       4.10169 ( 2668)
  covalent geometry    : bond        0.00497 (14946)
  covalent geometry    : angle       0.81622 (20288)

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

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

  3512 Ramachandran restraints generated.
    1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3512 Ramachandran restraints generated.
    1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 219
  time to evaluate  : 1.790 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  269 ASN cc_start: 0.7405 (OUTLIER) cc_final: 0.6785 (t0)
REVERT: A  473 HIS cc_start: 0.6520 (OUTLIER) cc_final: 0.6171 (t-90)
REVERT: A  478 LYS cc_start: 0.6724 (ptmt) cc_final: 0.6493 (tppt)
REVERT: B  175 ILE cc_start: 0.9063 (tp) cc_final: 0.8724 (tp)
REVERT: B  254 LEU cc_start: 0.8641 (tp) cc_final: 0.8302 (tp)
REVERT: B  464 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7758 (mm)
REVERT: C  200 LEU cc_start: 0.9080 (tp) cc_final: 0.8797 (tp)
REVERT: C  353 ILE cc_start: 0.8787 (mm) cc_final: 0.8462 (mt)
REVERT: C  422 GLN cc_start: 0.8693 (tp40) cc_final: 0.8376 (tp40)
REVERT: C  509 ILE cc_start: 0.8313 (mm) cc_final: 0.8028 (mt)
REVERT: C  580 SER cc_start: 0.8221 (OUTLIER) cc_final: 0.7903 (p)
REVERT: D  248 ASP cc_start: 0.5588 (t0) cc_final: 0.5208 (t0)
  outliers start: 24
  outliers final: 18
  residues processed: 234
  average time/residue: 0.2436
  time to fit residues: 86.2336
Evaluate side-chains
  240 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 218
  time to evaluate  : 1.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  473 HIS
Chi-restraints excluded: chain A residue  508 TYR
Chi-restraints excluded: chain A residue  581 LYS
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  359 SER
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  539 VAL
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain C residue  311 LEU
Chi-restraints excluded: chain C residue  420 ILE
Chi-restraints excluded: chain C residue  444 LEU
Chi-restraints excluded: chain C residue  462 ASP
Chi-restraints excluded: chain C residue  496 LEU
Chi-restraints excluded: chain C residue  510 CYS
Chi-restraints excluded: chain C residue  540 VAL
Chi-restraints excluded: chain C residue  580 SER
Chi-restraints excluded: chain D residue  506 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 141 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 153 optimal weight:    0.8980
   chunk 166 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0970
   chunk 37 optimal weight:    0.0670
   chunk 31 optimal weight:    0.0020
   chunk 112 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 80 optimal weight:    3.9990
   chunk 82 optimal weight:    5.9990
   overall best weight:    0.4124

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 288 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.174164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.128584 restraints weight = 30557.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.130567 restraints weight = 34160.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.129824 restraints weight = 19086.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3535
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3535 r_free = 0.3535    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3535 r_free = 0.3535    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3535
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.2630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.196  14949  Z= 0.249
  Angle     :  0.764  47.590  20297  Z= 0.434
  Chirality :  0.042   0.259   2307
  Planarity :  0.004   0.068   2493
  Dihedral  : 10.187 172.415   2147
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 17.78 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.06 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.20), residues: 1756
  helix:  1.39 (0.15), residues: 1155
  sheet: -1.67 (0.62), residues: 69
  loop : -1.30 (0.27), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 171 
 HIS   0.008   0.001   HIS A 473 
 PHE   0.034   0.001   PHE C 226 
 TYR   0.089   0.002   TYR D 294 
 ARG   0.009   0.000   ARG C 410 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00057 (    3)
  link_NAG-ASN         : angle       1.82008 (    9)
  hydrogen bonds       : bond        0.04170 (  918)
  hydrogen bonds       : angle       4.10169 ( 2668)
  covalent geometry    : bond        0.00516 (14946)
  covalent geometry    : angle       0.76344 (20288)

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

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

  3512 Ramachandran restraints generated.
    1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3512 Ramachandran restraints generated.
    1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 218
  time to evaluate  : 1.794 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  473 HIS cc_start: 0.6531 (OUTLIER) cc_final: 0.6203 (t-90)
REVERT: A  478 LYS cc_start: 0.6744 (ptmt) cc_final: 0.6498 (tppt)
REVERT: B  175 ILE cc_start: 0.9045 (tp) cc_final: 0.8706 (tp)
REVERT: B  254 LEU cc_start: 0.8646 (tp) cc_final: 0.8298 (tp)
REVERT: B  464 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7787 (mm)
REVERT: C  200 LEU cc_start: 0.9073 (tp) cc_final: 0.8775 (tp)
REVERT: C  353 ILE cc_start: 0.8846 (mm) cc_final: 0.8542 (mt)
REVERT: C  422 GLN cc_start: 0.8705 (tp40) cc_final: 0.8401 (tp40)
REVERT: C  509 ILE cc_start: 0.8322 (mm) cc_final: 0.8034 (mt)
REVERT: C  580 SER cc_start: 0.8219 (OUTLIER) cc_final: 0.7884 (p)
REVERT: D  248 ASP cc_start: 0.5507 (t0) cc_final: 0.5150 (t0)
  outliers start: 21
  outliers final: 18
  residues processed: 230
  average time/residue: 0.2481
  time to fit residues: 86.5912
Evaluate side-chains
  239 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 218
  time to evaluate  : 1.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  473 HIS
Chi-restraints excluded: chain A residue  508 TYR
Chi-restraints excluded: chain A residue  581 LYS
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  359 SER
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  539 VAL
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain C residue  311 LEU
Chi-restraints excluded: chain C residue  420 ILE
Chi-restraints excluded: chain C residue  444 LEU
Chi-restraints excluded: chain C residue  462 ASP
Chi-restraints excluded: chain C residue  496 LEU
Chi-restraints excluded: chain C residue  510 CYS
Chi-restraints excluded: chain C residue  540 VAL
Chi-restraints excluded: chain C residue  580 SER
Chi-restraints excluded: chain D residue  506 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 141 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 125 optimal weight:    5.9990
   chunk 63 optimal weight:    0.4980
   chunk 169 optimal weight:    0.1980
   chunk 74 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 154 optimal weight:    0.5980
   chunk 102 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 288 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.176313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.138916 restraints weight = 25024.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.142304 restraints weight = 42764.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.145278 restraints weight = 20861.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3697
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3697 r_free = 0.3697    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3697 r_free = 0.3697    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3697
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
moved from start:          0.2724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  14949  Z= 0.127
  Angle     :  0.592   9.775  20297  Z= 0.306
  Chirality :  0.041   0.167   2307
  Planarity :  0.004   0.060   2493
  Dihedral  : 10.143 172.343   2147
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 17.90 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.21), residues: 1756
  helix:  1.53 (0.15), residues: 1155
  sheet: -1.64 (0.62), residues: 69
  loop : -1.21 (0.28), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 171 
 HIS   0.008   0.001   HIS A 473 
 PHE   0.039   0.001   PHE C 226 
 TYR   0.024   0.001   TYR A 423 
 ARG   0.005   0.000   ARG C 410 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00040 (    3)
  link_NAG-ASN         : angle       1.76285 (    9)
  hydrogen bonds       : bond        0.03969 (  918)
  hydrogen bonds       : angle       4.04683 ( 2668)
  covalent geometry    : bond        0.00279 (14946)
  covalent geometry    : angle       0.59056 (20288)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4943.46 seconds
wall clock time: 86 minutes 58.16 seconds (5218.16 seconds total)