Starting phenix.real_space_refine
on Fri Jun 13 03:39:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8euc_28611/06_2025/8euc_28611_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8euc_28611/06_2025/8euc_28611.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8euc_28611/06_2025/8euc_28611.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8euc_28611/06_2025/8euc_28611.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8euc_28611/06_2025/8euc_28611_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8euc_28611/06_2025/8euc_28611_neut.cif"
  }
  resolution = 3.61
  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=   0.006 sd=   0.077
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    9491      2.51       5
     N    2369      2.21       5
     O    2630      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 163 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: 14560
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3634
      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: 3692
    Chain: "B"
      Number of atoms: 3555
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 434, 3555
          Classifications: {'peptide': 434}
          Link IDs: {'PTRANS': 14, 'TRANS': 419}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 3681
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 452, 3681
          Classifications: {'peptide': 452}
          Link IDs: {'PTRANS': 14, 'TRANS': 437}
    Chain: "D"
      Number of atoms: 3556
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 434, 3556
          Classifications: {'peptide': 434}
          Link IDs: {'PTRANS': 12, 'TRANS': 421}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 37
          Unusual residues: {'NAG': 1, 'PCG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 37
          Unusual residues: {'NAG': 1, 'PCG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 37
          Unusual residues: {'NAG': 1, 'PCG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Unusual residues: {'PCG': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  APHE A 392 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 392 " occ=0.50
  Time building chain proxies: 10.07, per 1000 atoms: 0.69
  Number of scatterers: 14560
  At special positions: 0
  Unit cell: (132.25, 108.974, 104.742, 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    2630      8.00
     N    2369      7.00
     C    9491      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: 3.13
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

  3502 Ramachandran restraints generated.
    1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3350

  Finding SS restraints...
    Secondary structure from input PDB file:
      73 helices and 12 sheets defined
      67.8% alpha, 5.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 166 through 192
      Proline residue:  A 178  - end of helix
    Processing helix  chain 'A' and resid 192 through 199
    Processing helix  chain 'A' and resid 200 through 222
    Processing helix  chain 'A' and resid 235 through 245
    Processing helix  chain 'A' and resid 247 through 255
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 3.776A  pdb=" N   VAL A 273 " --> pdb=" O   TYR A 270 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ARG A 274 " --> pdb=" O   PRO A 271 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   PHE A 275 " --> pdb=" O   GLU A 272 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   ASN A 276 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 295
      removed outlier: 4.059A  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: 3.825A  pdb=" N   ALA A 393 " --> pdb=" O   VAL A 389 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   GLY A 397 " --> pdb=" O   ALA A 393 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ASN A 398 " --> pdb=" O   THR A 394 " (cutoff:3.500A)
      removed outlier: 5.317A  pdb=" N   SER A 409 " --> pdb=" O   ASN A 405 " (cutoff:3.500A)
      removed outlier: 5.911A  pdb=" N   ARG A 410 " --> pdb=" O   MET A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 448
    Processing helix  chain 'A' and resid 452 through 457
    Processing helix  chain 'A' and resid 461 through 473
    Processing helix  chain 'A' and resid 487 through 498
    Processing helix  chain 'A' and resid 549 through 554
    Processing helix  chain 'A' and resid 581 through 589
    Processing helix  chain 'A' and resid 592 through 609
    Processing helix  chain 'B' and resid 166 through 193
      Proline residue:  B 178  - end of helix
      removed outlier: 3.780A  pdb=" N   TYR B 184 " --> pdb=" O   PHE B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 199
      removed outlier: 3.796A  pdb=" N   TYR B 199 " --> pdb=" O   LEU B 195 " (cutoff:3.500A)
    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: 3.923A  pdb=" N   LYS B 250 " --> pdb=" O   THR B 246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 279
      removed outlier: 4.089A  pdb=" N   VAL B 273 " --> pdb=" O   TYR B 270 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ARG B 274 " --> pdb=" O   PRO B 271 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   PHE B 275 " --> pdb=" O   GLU B 272 " (cutoff:3.500A)
      removed outlier: 5.049A  pdb=" N   ASN B 276 " --> pdb=" O   VAL B 273 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   LEU B 278 " --> pdb=" O   PHE B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 295
      removed outlier: 4.220A  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 428
      removed outlier: 5.617A  pdb=" N   SER B 409 " --> pdb=" O   ASN B 405 " (cutoff:3.500A)
      removed outlier: 5.692A  pdb=" N   ARG B 410 " --> pdb=" O   MET B 406 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 430 through 448
    Processing helix  chain 'B' and resid 452 through 457
    Processing helix  chain 'B' and resid 458 through 460
      No H-bonds generated for 'chain 'B' and resid 458 through 460'
    Processing helix  chain 'B' and resid 461 through 478
      removed outlier: 3.811A  pdb=" N   ILE B 468 " --> pdb=" O   LEU B 464 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA B 469 " --> pdb=" O   LYS B 465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 487 through 497
    Processing helix  chain 'B' and resid 580 through 588
      removed outlier: 3.773A  pdb=" N   LEU B 584 " --> pdb=" O   SER B 580 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 591 through 610
      removed outlier: 4.104A  pdb=" N   LYS B 595 " --> pdb=" O   TYR B 591 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 165 through 193
      Proline residue:  C 178  - end of helix
      removed outlier: 3.745A  pdb=" N   ASP C 193 " --> pdb=" O   ARG C 189 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 194 through 199
      removed outlier: 3.928A  pdb=" N   TYR C 199 " --> pdb=" O   LEU C 195 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 199 through 222
    Processing helix  chain 'C' and resid 235 through 245
    Processing helix  chain 'C' and resid 246 through 256
      removed outlier: 3.741A  pdb=" N   LYS C 250 " --> pdb=" O   THR C 246 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 259 through 267
    Processing helix  chain 'C' and resid 271 through 275
    Processing helix  chain 'C' and resid 276 through 279
      removed outlier: 3.558A  pdb=" N   LEU C 279 " --> pdb=" O   ASN C 276 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 276 through 279'
    Processing helix  chain 'C' and resid 280 through 295
    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 427
      removed outlier: 3.503A  pdb=" N   ASN C 407 " --> pdb=" O   ILE C 403 " (cutoff:3.500A)
      removed outlier: 5.778A  pdb=" N   SER C 409 " --> pdb=" O   ASN C 405 " (cutoff:3.500A)
      removed outlier: 5.937A  pdb=" N   ARG C 410 " --> pdb=" O   MET C 406 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 430 through 447
    Processing helix  chain 'C' and resid 452 through 457
    Processing helix  chain 'C' and resid 461 through 478
      removed outlier: 5.532A  pdb=" N   ASP C 475 " --> pdb=" O   ASN C 471 " (cutoff:3.500A)
      removed outlier: 4.898A  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 549 through 553
      removed outlier: 4.006A  pdb=" N   ILE C 552 " --> pdb=" O   GLU C 549 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   LEU C 553 " --> pdb=" O   ILE C 550 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 549 through 553'
    Processing helix  chain 'C' and resid 581 through 588
    Processing helix  chain 'C' and resid 592 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: 3.685A  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: 3.916A  pdb=" N   GLN D 301 " --> pdb=" O   SER D 297 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 309 through 312
    Processing helix  chain 'D' and resid 313 through 318
    Processing helix  chain 'D' and resid 322 through 329
      removed outlier: 3.600A  pdb=" N   ALA D 325 " --> pdb=" O   MET D 322 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   ASN D 326 " --> pdb=" O   PHE D 323 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 331 through 345
    Processing helix  chain 'D' and resid 347 through 379
      removed outlier: 4.245A  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 469
      removed outlier: 3.900A  pdb=" N   PHE D 432 " --> pdb=" O   PHE D 428 " (cutoff:3.500A)
      removed outlier: 5.798A  pdb=" N   ASN D 451 " --> pdb=" O   ALA D 447 " (cutoff:3.500A)
      removed outlier: 5.863A  pdb=" N   GLN D 452 " --> pdb=" O   ALA D 448 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 472 through 490
    Processing helix  chain 'D' and resid 494 through 500
      removed outlier: 4.001A  pdb=" N   LEU D 498 " --> pdb=" O   ASP D 494 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 503 through 522
      removed outlier: 5.589A  pdb=" N   SER D 517 " --> pdb=" O   ASP D 513 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   ILE D 518 " --> pdb=" O   VAL D 514 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 523 through 526
      removed outlier: 3.739A  pdb=" N   LYS D 526 " --> pdb=" O   ASP D 523 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 523 through 526'
    Processing helix  chain 'D' and resid 529 through 539
    Processing helix  chain 'D' and resid 592 through 596
      removed outlier: 4.126A  pdb=" N   LEU D 596 " --> pdb=" O   ILE D 593 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 621 through 629
    Processing helix  chain 'D' and resid 631 through 643
    Processing sheet with id=AA1, first strand: chain 'A' and resid 227 through 228
      removed outlier: 3.643A  pdb=" N   GLU A 228 " --> pdb=" O   LEU A 231 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 499 through 503
      removed outlier: 3.796A  pdb=" N   ASP A 575 " --> pdb=" O   ASN A 523 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 508 through 510
      removed outlier: 6.347A  pdb=" N   ILE A 568 " --> pdb=" O   ILE A 509 " (cutoff:3.500A)
      removed outlier: 3.913A  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
      removed outlier: 3.661A  pdb=" N   GLU B 228 " --> pdb=" O   LEU B 231 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 499 through 503
      removed outlier: 3.565A  pdb=" N   ARG B 499 " --> pdb=" O   CYS B 578 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 540 through 541
    Processing sheet with id=AA7, first strand: chain 'C' and resid 227 through 228
    Processing sheet with id=AA8, first strand: chain 'C' and resid 499 through 502
      removed outlier: 3.612A  pdb=" N   ARG C 499 " --> pdb=" O   CYS C 578 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 540 through 541
      removed outlier: 3.569A  pdb=" N   ASN C 567 " --> pdb=" O   VAL C 530 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 277 through 279
      removed outlier: 4.263A  pdb=" N   PHE D 277 " --> pdb=" O   ILE D 284 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ASP D 282 " --> pdb=" O   ARG D 279 " (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: 6.272A  pdb=" N   PHE D 550 " --> pdb=" O   ALA D 610 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   ALA D 610 " --> pdb=" O   PHE D 550 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   CYS D 552 " --> pdb=" O   VAL D 608 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   VAL D 569 " --> pdb=" O   LEU D 584 " (cutoff:3.500A)

    922 hydrogen bonds defined for protein.
    2691 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: 4.26

  Time building geometry restraints manager: 3.79 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 2298
        1.32 -     1.44: 4199
        1.44 -     1.57: 8306
        1.57 -     1.70: 2
        1.70 -     1.82: 105
  Bond restraints: 14910
  Sorted by residual:
  bond pdb=" O5' PCG D 901 "
       pdb=" PA  PCG D 901 "
    ideal  model  delta    sigma   weight residual
    1.606  1.489  0.117 2.00e-02 2.50e+03 3.44e+01
  bond pdb=" O5' PCG B 802 "
       pdb=" PA  PCG B 802 "
    ideal  model  delta    sigma   weight residual
    1.606  1.489  0.117 2.00e-02 2.50e+03 3.41e+01
  bond pdb=" O5' PCG C 802 "
       pdb=" PA  PCG C 802 "
    ideal  model  delta    sigma   weight residual
    1.606  1.489  0.117 2.00e-02 2.50e+03 3.40e+01
  bond pdb=" O5' PCG A 802 "
       pdb=" PA  PCG A 802 "
    ideal  model  delta    sigma   weight residual
    1.606  1.489  0.117 2.00e-02 2.50e+03 3.40e+01
  bond pdb=" O3' PCG D 901 "
       pdb=" PA  PCG D 901 "
    ideal  model  delta    sigma   weight residual
    1.617  1.513  0.104 2.00e-02 2.50e+03 2.70e+01
  ... (remaining 14905 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.65: 20027
        3.65 -     7.30: 152
        7.30 -    10.95: 46
       10.95 -    14.60: 6
       14.60 -    18.26: 10
  Bond angle restraints: 20241
  Sorted by residual:
  angle pdb=" N   GLY A 397 "
        pdb=" CA  GLY A 397 "
        pdb=" C   GLY A 397 "
      ideal   model   delta    sigma   weight residual
     112.77  103.87    8.90 1.28e+00 6.10e-01 4.83e+01
  angle pdb=" N   THR B 565 "
        pdb=" CA  THR B 565 "
        pdb=" C   THR B 565 "
      ideal   model   delta    sigma   weight residual
     111.37  121.98  -10.61 1.64e+00 3.72e-01 4.19e+01
  angle pdb=" N   ILE A 391 "
        pdb=" CA  ILE A 391 "
        pdb=" C   ILE A 391 "
      ideal   model   delta    sigma   weight residual
     110.36  116.77   -6.41 1.05e+00 9.07e-01 3.72e+01
  angle pdb=" C3' PCG C 802 "
        pdb=" C4' PCG C 802 "
        pdb=" C5' PCG C 802 "
      ideal   model   delta    sigma   weight residual
     109.85  128.11  -18.26 3.00e+00 1.11e-01 3.70e+01
  angle pdb=" C3' PCG D 901 "
        pdb=" C4' PCG D 901 "
        pdb=" C5' PCG D 901 "
      ideal   model   delta    sigma   weight residual
     109.85  128.09  -18.24 3.00e+00 1.11e-01 3.70e+01
  ... (remaining 20236 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.93: 8356
       25.93 -    51.86: 526
       51.86 -    77.78: 32
       77.78 -   103.71: 6
      103.71 -   129.64: 8
  Dihedral angle restraints: 8928
    sinusoidal: 3718
      harmonic: 5210
  Sorted by residual:
  dihedral pdb=" N   ILE A 395 "
           pdb=" C   ILE A 395 "
           pdb=" CA  ILE A 395 "
           pdb=" CB  ILE A 395 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  136.70  -13.30     0      2.50e+00 1.60e-01 2.83e+01
  dihedral pdb=" C   ILE A 395 "
           pdb=" N   ILE A 395 "
           pdb=" CA  ILE A 395 "
           pdb=" CB  ILE A 395 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -134.32   12.32     0      2.50e+00 1.60e-01 2.43e+01
  dihedral pdb=" CA  ASP D 286 "
           pdb=" C   ASP D 286 "
           pdb=" N   SER D 287 "
           pdb=" CA  SER D 287 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.92  -22.08     0      5.00e+00 4.00e-02 1.95e+01
  ... (remaining 8925 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.356: 2296
       0.356 -    0.711: 1
       0.711 -    1.067: 0
       1.067 -    1.422: 0
       1.422 -    1.778: 4
  Chirality restraints: 2301
  Sorted by residual:
  chirality pdb=" C4' PCG A 802 "
            pdb=" C3' PCG A 802 "
            pdb=" C5' PCG A 802 "
            pdb=" O4' PCG A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -0.72   -1.78 2.00e-01 2.50e+01 7.90e+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   -0.72   -1.78 2.00e-01 2.50e+01 7.90e+01
  chirality pdb=" C4' PCG C 802 "
            pdb=" C3' PCG C 802 "
            pdb=" C5' PCG C 802 "
            pdb=" O4' PCG C 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -0.72   -1.78 2.00e-01 2.50e+01 7.89e+01
  ... (remaining 2298 not shown)

  Planarity restraints: 2490
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN D 272 "    0.052 5.00e-02 4.00e+02   7.84e-02 9.84e+00
        pdb=" N   PRO D 273 "   -0.136 5.00e-02 4.00e+02
        pdb=" CA  PRO D 273 "    0.039 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   ARG B 499 "    0.044 5.00e-02 4.00e+02   6.64e-02 7.06e+00
        pdb=" N   PRO B 500 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO B 500 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 500 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 187 "    0.012 2.00e-02 2.50e+03   2.39e-02 5.73e+00
        pdb=" C   ILE B 187 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   ILE B 187 "    0.015 2.00e-02 2.50e+03
        pdb=" N   CYS B 188 "    0.014 2.00e-02 2.50e+03
  ... (remaining 2487 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1719
        2.75 -     3.29: 14094
        3.29 -     3.82: 24849
        3.82 -     4.36: 27258
        4.36 -     4.90: 47404
  Nonbonded interactions: 115324
  Sorted by model distance:
  nonbonded pdb=" N   THR D 605 "
            pdb=" O1A PCG D 901 "
     model   vdw
     2.211 3.120
  nonbonded pdb=" O   PHE D 516 "
            pdb=" OG  SER D 520 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OH  TYR B 243 "
            pdb=" OD2 ASP B 252 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" OG1 THR B 565 "
            pdb=" N2  PCG B 802 "
     model   vdw
     2.286 3.120
  nonbonded pdb=" O   ARG A 603 "
            pdb=" CG  LEU A 606 "
     model   vdw
     2.306 3.470
  ... (remaining 115319 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 258 or resid 270 through 391 or resid 393 thro \ 
ugh 554 or resid 562 through 609 or resid 801 through 802))
  selection = (chain 'B' and (resid 159 through 391 or resid 393 through 609 or resid 801 thro \ 
ugh 802))
  selection = (chain 'C' and (resid 159 through 258 or resid 270 through 391 or resid 393 thro \ 
ugh 554 or resid 562 through 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=0.50 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:             2.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.570
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     34.620
  Find NCS groups from input model:        0.850
  Set up NCS constraints:                  0.060
  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:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
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   0.117  14913  Z= 0.329
  Angle     :  1.044  18.256  20250  Z= 0.535
  Chirality :  0.095   1.778   2301
  Planarity :  0.007   0.078   2487
  Dihedral  : 15.994 129.641   5578
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  8.25 %
    Favored  : 91.43 %
  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: -4.03 (0.15), residues: 1751
  helix: -2.41 (0.10), residues: 1160
  sheet: -2.80 (0.45), residues: 94
  loop : -2.74 (0.23), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 171 
 HIS   0.005   0.001   HIS D 293 
 PHE   0.023   0.002   PHE A 483 
 TYR   0.017   0.002   TYR A 352 
 ARG   0.008   0.001   ARG D 603 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00427 (    3)
  link_NAG-ASN         : angle       2.13071 (    9)
  hydrogen bonds       : bond        0.12584 (  922)
  hydrogen bonds       : angle       5.94078 ( 2691)
  covalent geometry    : bond        0.00691 (14910)
  covalent geometry    : angle       1.04349 (20241)

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

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

  3502 Ramachandran restraints generated.
    1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3502 Ramachandran restraints generated.
    1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 281
  time to evaluate  : 1.692 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.6758 (mmm) cc_final: 0.6290 (mpp)
REVERT: A  297 TYR cc_start: 0.6889 (m-80) cc_final: 0.6668 (m-80)
REVERT: A  389 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.8114 (p)
REVERT: A  498 LEU cc_start: 0.8704 (mt) cc_final: 0.8485 (mt)
REVERT: B  201 MET cc_start: 0.6987 (ppp) cc_final: 0.6664 (ppp)
REVERT: B  425 GLN cc_start: 0.7710 (mt0) cc_final: 0.7471 (mt0)
REVERT: B  434 GLU cc_start: 0.7235 (tp30) cc_final: 0.6430 (tp30)
REVERT: B  497 LYS cc_start: 0.7442 (mtmm) cc_final: 0.7200 (mmmt)
REVERT: B  524 GLU cc_start: 0.7415 (tt0) cc_final: 0.7209 (tt0)
REVERT: B  547 PHE cc_start: 0.8751 (p90) cc_final: 0.8400 (p90)
REVERT: C  353 ILE cc_start: 0.8968 (mm) cc_final: 0.8676 (mt)
REVERT: D  316 PHE cc_start: 0.8225 (m-80) cc_final: 0.7778 (m-10)
REVERT: D  619 LEU cc_start: 0.7295 (tp) cc_final: 0.7090 (tp)
  outliers start: 4
  outliers final: 1
  residues processed: 285
  average time/residue: 0.2782
  time to fit residues: 113.8372
Evaluate side-chains
  187 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 185
  time to evaluate  : 1.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain C residue  563 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 147 optimal weight:    0.5980
   chunk 132 optimal weight:    4.9990
   chunk 73 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 89 optimal weight:    0.9980
   chunk 70 optimal weight:    5.9990
   chunk 137 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   chunk 83 optimal weight:    2.9990
   chunk 102 optimal weight:    0.8980
   chunk 158 optimal weight:    4.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
A 299 ASN
** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 345 HIS
A 405 ASN
A 471 ASN
B 196 GLN
B 407 ASN
B 414 GLN
C 242 HIS
C 317 ASN
C 414 GLN
** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 604 GLN
D 340 HIS
D 365 HIS
D 367 ASN
D 426 ASN
D 531 GLN
D 566 HIS
D 570 GLN
** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 19

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.151243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.120770 restraints weight = 31369.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.120522 restraints weight = 37853.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.122215 restraints weight = 31521.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3558
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3558 r_free = 0.3558    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3558 r_free = 0.3558    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3558
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.1755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  14913  Z= 0.139
  Angle     :  0.594  10.987  20250  Z= 0.311
  Chirality :  0.041   0.157   2301
  Planarity :  0.005   0.064   2487
  Dihedral  : 10.395 152.841   2144
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 14.68 %
    Favored  : 83.74 %
  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 (0.19), residues: 1751
  helix: -0.15 (0.14), residues: 1157
  sheet: -1.71 (0.57), residues: 73
  loop : -2.22 (0.26), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP C 440 
 HIS   0.003   0.001   HIS B 473 
 PHE   0.013   0.001   PHE B 413 
 TYR   0.017   0.001   TYR A 443 
 ARG   0.007   0.000   ARG A 564 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01049 (    3)
  link_NAG-ASN         : angle       3.15164 (    9)
  hydrogen bonds       : bond        0.04372 (  922)
  hydrogen bonds       : angle       4.49837 ( 2691)
  covalent geometry    : bond        0.00310 (14910)
  covalent geometry    : angle       0.59018 (20241)

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

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

  3502 Ramachandran restraints generated.
    1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3502 Ramachandran restraints generated.
    1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 212
  time to evaluate  : 1.758 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  591 TYR cc_start: 0.7348 (m-80) cc_final: 0.7070 (m-80)
REVERT: C  217 ASP cc_start: 0.7111 (t70) cc_final: 0.6520 (t70)
REVERT: C  311 LEU cc_start: 0.8764 (tp) cc_final: 0.8475 (tt)
REVERT: D  210 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8481 (mt)
REVERT: D  316 PHE cc_start: 0.8309 (m-80) cc_final: 0.7921 (m-10)
REVERT: D  398 TYR cc_start: 0.8453 (t80) cc_final: 0.8205 (t80)
REVERT: D  561 MET cc_start: 0.7482 (tpp) cc_final: 0.7071 (tpp)
  outliers start: 24
  outliers final: 13
  residues processed: 229
  average time/residue: 0.2398
  time to fit residues: 84.5312
Evaluate side-chains
  192 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 178
  time to evaluate  : 1.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 CYS
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  406 MET
Chi-restraints excluded: chain B residue  535 VAL
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  495 VAL
Chi-restraints excluded: chain C residue  535 VAL
Chi-restraints excluded: chain C residue  553 LEU
Chi-restraints excluded: chain D residue  210 ILE
Chi-restraints excluded: chain D residue  303 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 154 optimal weight:    0.9980
   chunk 39 optimal weight:    9.9990
   chunk 156 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 160 optimal weight:    0.3980
   chunk 64 optimal weight:    0.0070
   chunk 82 optimal weight:    9.9990
   chunk 129 optimal weight:    0.9990
   chunk 9 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 97 optimal weight:    9.9990
   overall best weight:    0.6398

-------------------------------------------------------------------------------
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 447 ASN
** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 301 GLN
** D 607 ASN ** 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 = 0.3945 r_free = 0.3945 target = 0.152395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.122002 restraints weight = 31644.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.122853 restraints weight = 35349.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.124055 restraints weight = 31486.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3579
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3579 r_free = 0.3579    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3579 r_free = 0.3579    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3579
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.2225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14913  Z= 0.121
  Angle     :  0.550   9.389  20250  Z= 0.287
  Chirality :  0.040   0.158   2301
  Planarity :  0.004   0.055   2487
  Dihedral  : 10.097 152.880   2139
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 16.26 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.19 (0.20), residues: 1751
  helix:  0.77 (0.15), residues: 1151
  sheet: -1.32 (0.59), residues: 73
  loop : -1.91 (0.26), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP C 440 
 HIS   0.005   0.001   HIS C 242 
 PHE   0.013   0.001   PHE D 590 
 TYR   0.022   0.001   TYR A 423 
 ARG   0.008   0.000   ARG A 274 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00486 (    3)
  link_NAG-ASN         : angle       3.09627 (    9)
  hydrogen bonds       : bond        0.03994 (  922)
  hydrogen bonds       : angle       4.22984 ( 2691)
  covalent geometry    : bond        0.00261 (14910)
  covalent geometry    : angle       0.54643 (20241)

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

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

  3502 Ramachandran restraints generated.
    1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3502 Ramachandran restraints generated.
    1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 194
  time to evaluate  : 1.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  524 GLU cc_start: 0.6975 (tt0) cc_final: 0.6769 (tt0)
REVERT: C  217 ASP cc_start: 0.7008 (t70) cc_final: 0.6489 (t70)
REVERT: C  311 LEU cc_start: 0.8749 (tp) cc_final: 0.8459 (tt)
REVERT: D  210 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8408 (mt)
REVERT: D  398 TYR cc_start: 0.8435 (t80) cc_final: 0.8219 (t80)
REVERT: D  561 MET cc_start: 0.7312 (tpp) cc_final: 0.7089 (tpp)
  outliers start: 29
  outliers final: 18
  residues processed: 216
  average time/residue: 0.2345
  time to fit residues: 78.7457
Evaluate side-chains
  195 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 176
  time to evaluate  : 1.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  406 MET
Chi-restraints excluded: chain B residue  535 VAL
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  444 LEU
Chi-restraints excluded: chain C residue  495 VAL
Chi-restraints excluded: chain C residue  502 VAL
Chi-restraints excluded: chain C residue  535 VAL
Chi-restraints excluded: chain C residue  540 VAL
Chi-restraints excluded: chain C residue  553 LEU
Chi-restraints excluded: chain D residue  210 ILE
Chi-restraints excluded: chain D residue  538 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 74 optimal weight:    7.9990
   chunk 95 optimal weight:    1.9990
   chunk 98 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 155 optimal weight:    0.7980
   chunk 88 optimal weight:    2.9990
   chunk 165 optimal weight:    1.9990
   chunk 166 optimal weight:    2.9990
   chunk 170 optimal weight:    3.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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**
C 229 GLN
** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.149399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.112419 restraints weight = 37665.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.115360 restraints weight = 29878.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.116092 restraints weight = 16208.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3483
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3483 r_free = 0.3483    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3483 r_free = 0.3483    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3483
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.2422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14913  Z= 0.155
  Angle     :  0.568   8.387  20250  Z= 0.295
  Chirality :  0.041   0.158   2301
  Planarity :  0.004   0.050   2487
  Dihedral  :  9.994 155.572   2139
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 17.45 %
    Favored  : 80.15 %
  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:  0.12 (0.20), residues: 1751
  helix:  1.04 (0.15), residues: 1151
  sheet: -1.37 (0.61), residues: 68
  loop : -1.83 (0.26), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C 440 
 HIS   0.005   0.001   HIS C 242 
 PHE   0.015   0.001   PHE C 301 
 TYR   0.019   0.002   TYR B 423 
 ARG   0.006   0.000   ARG C 499 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00471 (    3)
  link_NAG-ASN         : angle       3.05068 (    9)
  hydrogen bonds       : bond        0.04144 (  922)
  hydrogen bonds       : angle       4.16149 ( 2691)
  covalent geometry    : bond        0.00351 (14910)
  covalent geometry    : angle       0.56417 (20241)

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

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

  3502 Ramachandran restraints generated.
    1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3502 Ramachandran restraints generated.
    1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 184
  time to evaluate  : 1.577 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  360 THR cc_start: 0.8699 (OUTLIER) cc_final: 0.8275 (m)
REVERT: B  524 GLU cc_start: 0.7250 (tt0) cc_final: 0.6987 (tt0)
REVERT: C  217 ASP cc_start: 0.7242 (t70) cc_final: 0.6814 (t70)
REVERT: C  311 LEU cc_start: 0.8868 (tp) cc_final: 0.8584 (tt)
REVERT: C  608 LYS cc_start: 0.4781 (pttp) cc_final: 0.4440 (mmtm)
REVERT: D  210 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8519 (mt)
REVERT: D  426 ASN cc_start: 0.9064 (OUTLIER) cc_final: 0.8809 (t0)
  outliers start: 37
  outliers final: 23
  residues processed: 209
  average time/residue: 0.2213
  time to fit residues: 72.0600
Evaluate side-chains
  200 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 174
  time to evaluate  : 1.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  360 THR
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  406 MET
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  535 VAL
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  444 LEU
Chi-restraints excluded: chain C residue  495 VAL
Chi-restraints excluded: chain C residue  502 VAL
Chi-restraints excluded: chain C residue  535 VAL
Chi-restraints excluded: chain C residue  540 VAL
Chi-restraints excluded: chain C residue  553 LEU
Chi-restraints excluded: chain D residue  210 ILE
Chi-restraints excluded: chain D residue  328 MET
Chi-restraints excluded: chain D residue  404 THR
Chi-restraints excluded: chain D residue  426 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 138 optimal weight:    0.3980
   chunk 67 optimal weight:    0.9990
   chunk 83 optimal weight:   10.0000
   chunk 12 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 71 optimal weight:    5.9990
   chunk 90 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0670
   chunk 134 optimal weight:    0.6980
   chunk 128 optimal weight:    7.9990
   chunk 166 optimal weight:    0.0770
   overall best weight:    0.3676

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

Flipped N/Q/H residues before XYZ refinement:
A 317 ASN
** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.153491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.123321 restraints weight = 37749.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.126783 restraints weight = 41388.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.128256 restraints weight = 22621.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3615
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3615 r_free = 0.3615    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3615 r_free = 0.3615    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3615
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  14913  Z= 0.108
  Angle     :  0.526   8.168  20250  Z= 0.273
  Chirality :  0.039   0.154   2301
  Planarity :  0.004   0.091   2487
  Dihedral  :  9.883 153.524   2139
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 18.21 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.48 (0.21), residues: 1751
  helix:  1.28 (0.15), residues: 1158
  sheet: -1.36 (0.63), residues: 61
  loop : -1.63 (0.27), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.001   TRP C 440 
 HIS   0.004   0.001   HIS C 242 
 PHE   0.013   0.001   PHE D 590 
 TYR   0.013   0.001   TYR C 573 
 ARG   0.009   0.000   ARG A 427 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00365 (    3)
  link_NAG-ASN         : angle       2.79333 (    9)
  hydrogen bonds       : bond        0.03704 (  922)
  hydrogen bonds       : angle       4.02997 ( 2691)
  covalent geometry    : bond        0.00226 (14910)
  covalent geometry    : angle       0.52320 (20241)

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

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

  3502 Ramachandran restraints generated.
    1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3502 Ramachandran restraints generated.
    1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 195
  time to evaluate  : 1.623 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  241 GLN cc_start: 0.7214 (OUTLIER) cc_final: 0.6683 (mt0)
REVERT: B  524 GLU cc_start: 0.6986 (tt0) cc_final: 0.6778 (tt0)
REVERT: C  217 ASP cc_start: 0.7059 (t70) cc_final: 0.6561 (t70)
REVERT: C  311 LEU cc_start: 0.8646 (tp) cc_final: 0.8402 (tt)
REVERT: C  608 LYS cc_start: 0.4916 (pttp) cc_final: 0.4615 (mmtm)
REVERT: D  426 ASN cc_start: 0.9103 (OUTLIER) cc_final: 0.8897 (t0)
  outliers start: 36
  outliers final: 19
  residues processed: 222
  average time/residue: 0.2296
  time to fit residues: 78.2133
Evaluate side-chains
  197 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 176
  time to evaluate  : 1.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  241 GLN
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  535 VAL
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  444 LEU
Chi-restraints excluded: chain C residue  495 VAL
Chi-restraints excluded: chain C residue  502 VAL
Chi-restraints excluded: chain C residue  535 VAL
Chi-restraints excluded: chain C residue  540 VAL
Chi-restraints excluded: chain C residue  553 LEU
Chi-restraints excluded: chain D residue  328 MET
Chi-restraints excluded: chain D residue  426 ASN
Chi-restraints excluded: chain D residue  582 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 75 optimal weight:    0.3980
   chunk 68 optimal weight:    0.9980
   chunk 94 optimal weight:    4.9990
   chunk 35 optimal weight:    0.0770
   chunk 79 optimal weight:    0.9980
   chunk 17 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   chunk 50 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
C 299 ASN
** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.152568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.122259 restraints weight = 28869.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.121640 restraints weight = 28431.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.122655 restraints weight = 30642.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3573
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3573 r_free = 0.3573    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3573 r_free = 0.3573    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3573
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.2852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14913  Z= 0.115
  Angle     :  0.529   8.637  20250  Z= 0.272
  Chirality :  0.039   0.156   2301
  Planarity :  0.004   0.048   2487
  Dihedral  :  9.789 154.615   2139
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 19.16 %
    Favored  : 78.51 %
  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:  0.60 (0.21), residues: 1751
  helix:  1.33 (0.15), residues: 1164
  sheet: -1.14 (0.63), residues: 61
  loop : -1.52 (0.27), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP C 440 
 HIS   0.004   0.001   HIS C 242 
 PHE   0.020   0.001   PHE B 413 
 TYR   0.013   0.001   TYR C 573 
 ARG   0.006   0.000   ARG B 221 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00376 (    3)
  link_NAG-ASN         : angle       2.75712 (    9)
  hydrogen bonds       : bond        0.03727 (  922)
  hydrogen bonds       : angle       3.97373 ( 2691)
  covalent geometry    : bond        0.00252 (14910)
  covalent geometry    : angle       0.52614 (20241)

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

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

  3502 Ramachandran restraints generated.
    1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3502 Ramachandran restraints generated.
    1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 190
  time to evaluate  : 1.772 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  241 GLN cc_start: 0.7210 (OUTLIER) cc_final: 0.6689 (mt0)
REVERT: B  603 ARG cc_start: 0.6000 (tpp80) cc_final: 0.5358 (mmt180)
REVERT: C  217 ASP cc_start: 0.6976 (t70) cc_final: 0.6498 (t70)
REVERT: C  311 LEU cc_start: 0.8817 (tp) cc_final: 0.8582 (tt)
REVERT: C  519 MET cc_start: 0.7301 (tpt) cc_final: 0.6637 (tpt)
REVERT: C  608 LYS cc_start: 0.4952 (pttp) cc_final: 0.4730 (mmtm)
REVERT: D  530 THR cc_start: 0.7429 (p) cc_final: 0.7087 (t)
  outliers start: 36
  outliers final: 26
  residues processed: 216
  average time/residue: 0.2525
  time to fit residues: 83.4078
Evaluate side-chains
  204 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 177
  time to evaluate  : 2.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  241 GLN
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  406 MET
Chi-restraints excluded: chain B residue  535 VAL
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  365 THR
Chi-restraints excluded: chain C residue  444 LEU
Chi-restraints excluded: chain C residue  495 VAL
Chi-restraints excluded: chain C residue  502 VAL
Chi-restraints excluded: chain C residue  529 VAL
Chi-restraints excluded: chain C residue  535 VAL
Chi-restraints excluded: chain C residue  540 VAL
Chi-restraints excluded: chain C residue  553 LEU
Chi-restraints excluded: chain D residue  328 MET
Chi-restraints excluded: chain D residue  582 VAL
Chi-restraints excluded: chain D residue  608 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 87 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   chunk 125 optimal weight:   10.0000
   chunk 146 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 128 optimal weight:    1.9990
   chunk 137 optimal weight:    0.9980
   chunk 80 optimal weight:    0.5980
   chunk 111 optimal weight:    3.9990
   chunk 70 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 426 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.150276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.119234 restraints weight = 29329.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.118596 restraints weight = 27750.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.119873 restraints weight = 22123.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3538
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3538 r_free = 0.3538    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3538 r_free = 0.3538    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3538
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.2912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14913  Z= 0.140
  Angle     :  0.545   8.735  20250  Z= 0.281
  Chirality :  0.040   0.156   2301
  Planarity :  0.004   0.050   2487
  Dihedral  :  9.754 155.294   2139
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 19.47 %
    Favored  : 77.76 %
  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:  0.60 (0.21), residues: 1751
  helix:  1.33 (0.15), residues: 1163
  sheet: -1.19 (0.62), residues: 61
  loop : -1.49 (0.27), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP C 440 
 HIS   0.004   0.001   HIS C 242 
 PHE   0.014   0.001   PHE A 483 
 TYR   0.016   0.001   TYR C 573 
 ARG   0.005   0.000   ARG A 427 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00423 (    3)
  link_NAG-ASN         : angle       2.76077 (    9)
  hydrogen bonds       : bond        0.03871 (  922)
  hydrogen bonds       : angle       3.98670 ( 2691)
  covalent geometry    : bond        0.00320 (14910)
  covalent geometry    : angle       0.54191 (20241)

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

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

  3502 Ramachandran restraints generated.
    1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3502 Ramachandran restraints generated.
    1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 182
  time to evaluate  : 1.647 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  360 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8174 (m)
REVERT: B  221 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7636 (mtt90)
REVERT: B  232 MET cc_start: 0.7444 (tpp) cc_final: 0.7044 (tpt)
REVERT: B  241 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6716 (mt0)
REVERT: C  217 ASP cc_start: 0.6958 (t70) cc_final: 0.6476 (t70)
REVERT: C  309 TYR cc_start: 0.8104 (m-10) cc_final: 0.7822 (m-80)
REVERT: C  311 LEU cc_start: 0.8848 (tp) cc_final: 0.8616 (tt)
REVERT: C  519 MET cc_start: 0.7505 (tpt) cc_final: 0.6814 (tpt)
REVERT: C  608 LYS cc_start: 0.5189 (pttp) cc_final: 0.4878 (mmtm)
REVERT: D  530 THR cc_start: 0.7429 (p) cc_final: 0.7047 (t)
REVERT: D  532 MET cc_start: 0.7175 (mmp) cc_final: 0.6935 (tpt)
  outliers start: 43
  outliers final: 32
  residues processed: 213
  average time/residue: 0.2277
  time to fit residues: 75.8946
Evaluate side-chains
  211 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 176
  time to evaluate  : 1.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  360 THR
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  221 ARG
Chi-restraints excluded: chain B residue  241 GLN
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  369 THR
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  406 MET
Chi-restraints excluded: chain B residue  476 THR
Chi-restraints excluded: chain B residue  510 CYS
Chi-restraints excluded: chain B residue  535 VAL
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  365 THR
Chi-restraints excluded: chain C residue  444 LEU
Chi-restraints excluded: chain C residue  495 VAL
Chi-restraints excluded: chain C residue  502 VAL
Chi-restraints excluded: chain C residue  529 VAL
Chi-restraints excluded: chain C residue  535 VAL
Chi-restraints excluded: chain C residue  540 VAL
Chi-restraints excluded: chain C residue  553 LEU
Chi-restraints excluded: chain D residue  328 MET
Chi-restraints excluded: chain D residue  569 VAL
Chi-restraints excluded: chain D residue  582 VAL
Chi-restraints excluded: chain D residue  608 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 99 optimal weight:    3.9990
   chunk 165 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 159 optimal weight:    0.9980
   chunk 138 optimal weight:    0.6980
   chunk 111 optimal weight:    0.7980
   chunk 86 optimal weight:    1.9990
   chunk 76 optimal weight:    8.9990
   chunk 128 optimal weight:    0.9990
   chunk 161 optimal weight:    1.9990
   chunk 97 optimal weight:    9.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 423 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.150890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.120093 restraints weight = 28324.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.119387 restraints weight = 27483.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.120649 restraints weight = 22304.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3542
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3542 r_free = 0.3542    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3542 r_free = 0.3542    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3542
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.3036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  14913  Z= 0.128
  Angle     :  0.539   9.306  20250  Z= 0.279
  Chirality :  0.040   0.155   2301
  Planarity :  0.004   0.049   2487
  Dihedral  :  9.695 154.812   2139
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 19.97 %
    Favored  : 77.50 %
  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:  0.69 (0.21), residues: 1751
  helix:  1.38 (0.15), residues: 1162
  sheet: -1.18 (0.61), residues: 61
  loop : -1.40 (0.28), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.001   TRP C 440 
 HIS   0.004   0.001   HIS C 242 
 PHE   0.028   0.001   PHE B 413 
 TYR   0.015   0.001   TYR C 573 
 ARG   0.005   0.000   ARG A 427 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00384 (    3)
  link_NAG-ASN         : angle       2.68907 (    9)
  hydrogen bonds       : bond        0.03826 (  922)
  hydrogen bonds       : angle       3.95947 ( 2691)
  covalent geometry    : bond        0.00292 (14910)
  covalent geometry    : angle       0.53659 (20241)

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

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

  3502 Ramachandran restraints generated.
    1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3502 Ramachandran restraints generated.
    1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 183
  time to evaluate  : 1.539 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  360 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.7902 (m)
REVERT: B  232 MET cc_start: 0.7520 (tpp) cc_final: 0.7156 (tpt)
REVERT: B  241 GLN cc_start: 0.7228 (OUTLIER) cc_final: 0.6742 (mt0)
REVERT: B  603 ARG cc_start: 0.6061 (tpp80) cc_final: 0.5310 (mmt180)
REVERT: C  217 ASP cc_start: 0.7071 (t70) cc_final: 0.6592 (t70)
REVERT: C  311 LEU cc_start: 0.8874 (tp) cc_final: 0.8610 (tt)
REVERT: C  519 MET cc_start: 0.7667 (tpt) cc_final: 0.7019 (tpt)
REVERT: C  608 LYS cc_start: 0.5238 (pttp) cc_final: 0.4845 (mmtm)
REVERT: D  532 MET cc_start: 0.7207 (mmp) cc_final: 0.6795 (tpt)
  outliers start: 39
  outliers final: 28
  residues processed: 207
  average time/residue: 0.2234
  time to fit residues: 72.0836
Evaluate side-chains
  203 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 173
  time to evaluate  : 1.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  360 THR
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  241 GLN
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  369 THR
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  406 MET
Chi-restraints excluded: chain B residue  476 THR
Chi-restraints excluded: chain B residue  535 VAL
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  365 THR
Chi-restraints excluded: chain C residue  444 LEU
Chi-restraints excluded: chain C residue  495 VAL
Chi-restraints excluded: chain C residue  502 VAL
Chi-restraints excluded: chain C residue  529 VAL
Chi-restraints excluded: chain C residue  535 VAL
Chi-restraints excluded: chain C residue  540 VAL
Chi-restraints excluded: chain D residue  328 MET
Chi-restraints excluded: chain D residue  582 VAL
Chi-restraints excluded: chain D residue  608 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 105 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 40 optimal weight:    7.9990
   chunk 84 optimal weight:    7.9990
   chunk 87 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 166 optimal weight:    0.9990
   chunk 131 optimal weight:    7.9990
   chunk 145 optimal weight:    0.6980
   chunk 112 optimal weight:    0.9980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.151066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.114085 restraints weight = 45560.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.117579 restraints weight = 42373.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.119060 restraints weight = 22443.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3527
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3527 r_free = 0.3527    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3527 r_free = 0.3527    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3527
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.3118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14913  Z= 0.125
  Angle     :  0.561   9.791  20250  Z= 0.288
  Chirality :  0.040   0.178   2301
  Planarity :  0.004   0.049   2487
  Dihedral  :  9.636 154.890   2139
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 20.48 %
    Favored  : 77.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.75 (0.21), residues: 1751
  helix:  1.41 (0.15), residues: 1162
  sheet: -1.07 (0.60), residues: 61
  loop : -1.36 (0.28), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.001   TRP C 440 
 HIS   0.004   0.001   HIS C 242 
 PHE   0.014   0.001   PHE D 590 
 TYR   0.015   0.001   TYR C 573 
 ARG   0.005   0.000   ARG A 427 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00364 (    3)
  link_NAG-ASN         : angle       2.65928 (    9)
  hydrogen bonds       : bond        0.03770 (  922)
  hydrogen bonds       : angle       3.94049 ( 2691)
  covalent geometry    : bond        0.00285 (14910)
  covalent geometry    : angle       0.55865 (20241)

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

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

  3502 Ramachandran restraints generated.
    1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3502 Ramachandran restraints generated.
    1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 184
  time to evaluate  : 1.532 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  360 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8172 (m)
REVERT: B  241 GLN cc_start: 0.7226 (OUTLIER) cc_final: 0.6742 (mt0)
REVERT: B  413 PHE cc_start: 0.7615 (t80) cc_final: 0.7400 (t80)
REVERT: B  603 ARG cc_start: 0.6065 (tpp80) cc_final: 0.5357 (mmt180)
REVERT: C  217 ASP cc_start: 0.7087 (t70) cc_final: 0.6614 (t70)
REVERT: C  311 LEU cc_start: 0.8830 (tp) cc_final: 0.8623 (tt)
REVERT: C  519 MET cc_start: 0.7602 (tpt) cc_final: 0.6944 (tpt)
REVERT: D  532 MET cc_start: 0.7384 (mmp) cc_final: 0.7007 (tpt)
  outliers start: 35
  outliers final: 31
  residues processed: 209
  average time/residue: 0.2252
  time to fit residues: 73.0208
Evaluate side-chains
  205 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 172
  time to evaluate  : 1.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  360 THR
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  241 GLN
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  369 THR
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  406 MET
Chi-restraints excluded: chain B residue  476 THR
Chi-restraints excluded: chain B residue  535 VAL
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  365 THR
Chi-restraints excluded: chain C residue  444 LEU
Chi-restraints excluded: chain C residue  495 VAL
Chi-restraints excluded: chain C residue  502 VAL
Chi-restraints excluded: chain C residue  529 VAL
Chi-restraints excluded: chain C residue  535 VAL
Chi-restraints excluded: chain C residue  540 VAL
Chi-restraints excluded: chain D residue  328 MET
Chi-restraints excluded: chain D residue  569 VAL
Chi-restraints excluded: chain D residue  582 VAL
Chi-restraints excluded: chain D residue  608 VAL
Chi-restraints excluded: chain D residue  618 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 158 optimal weight:    1.9990
   chunk 126 optimal weight:    9.9990
   chunk 46 optimal weight:    1.9990
   chunk 163 optimal weight:    0.9980
   chunk 93 optimal weight:    7.9990
   chunk 89 optimal weight:    0.5980
   chunk 122 optimal weight:    6.9990
   chunk 139 optimal weight:    7.9990
   chunk 84 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.148760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.116913 restraints weight = 33256.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.118633 restraints weight = 35100.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.119780 restraints weight = 25852.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3517
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3517 r_free = 0.3517    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3517 r_free = 0.3517    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3517
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.3148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  14913  Z= 0.173
  Angle     :  0.612  10.292  20250  Z= 0.314
  Chirality :  0.042   0.201   2301
  Planarity :  0.004   0.050   2487
  Dihedral  :  9.661 155.777   2139
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 20.92 %
    Favored  : 76.81 %
  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:  0.67 (0.21), residues: 1751
  helix:  1.35 (0.15), residues: 1161
  sheet: -1.11 (0.58), residues: 61
  loop : -1.37 (0.28), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.001   TRP C 440 
 HIS   0.004   0.001   HIS C 242 
 PHE   0.015   0.001   PHE C 301 
 TYR   0.016   0.001   TYR C 573 
 ARG   0.010   0.000   ARG B 563 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00425 (    3)
  link_NAG-ASN         : angle       2.75338 (    9)
  hydrogen bonds       : bond        0.04064 (  922)
  hydrogen bonds       : angle       4.04015 ( 2691)
  covalent geometry    : bond        0.00403 (14910)
  covalent geometry    : angle       0.60916 (20241)

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

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

  3502 Ramachandran restraints generated.
    1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3502 Ramachandran restraints generated.
    1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 175
  time to evaluate  : 1.614 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 GLU cc_start: 0.8519 (mt-10) cc_final: 0.7790 (mp0)
REVERT: B  241 GLN cc_start: 0.7282 (OUTLIER) cc_final: 0.6802 (mt0)
REVERT: C  217 ASP cc_start: 0.7267 (t70) cc_final: 0.6803 (t70)
REVERT: C  311 LEU cc_start: 0.8735 (tp) cc_final: 0.8506 (tt)
REVERT: C  519 MET cc_start: 0.7871 (tpt) cc_final: 0.7208 (tpt)
REVERT: C  608 LYS cc_start: 0.5052 (pttp) cc_final: 0.4562 (ttpt)
REVERT: D  532 MET cc_start: 0.7431 (mmp) cc_final: 0.7132 (tpt)
  outliers start: 35
  outliers final: 31
  residues processed: 200
  average time/residue: 0.2380
  time to fit residues: 73.3489
Evaluate side-chains
  198 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 166
  time to evaluate  : 1.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  241 GLN
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  369 THR
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  406 MET
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  476 THR
Chi-restraints excluded: chain B residue  535 VAL
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  186 LEU
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  365 THR
Chi-restraints excluded: chain C residue  444 LEU
Chi-restraints excluded: chain C residue  495 VAL
Chi-restraints excluded: chain C residue  502 VAL
Chi-restraints excluded: chain C residue  529 VAL
Chi-restraints excluded: chain C residue  535 VAL
Chi-restraints excluded: chain C residue  540 VAL
Chi-restraints excluded: chain D residue  328 MET
Chi-restraints excluded: chain D residue  569 VAL
Chi-restraints excluded: chain D residue  582 VAL
Chi-restraints excluded: chain D residue  608 VAL
Chi-restraints excluded: chain D residue  618 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 145 optimal weight:    1.9990
   chunk 113 optimal weight:    0.8980
   chunk 171 optimal weight:    9.9990
   chunk 72 optimal weight:    0.7980
   chunk 79 optimal weight:    4.9990
   chunk 61 optimal weight:    0.6980
   chunk 86 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 117 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0050
   overall best weight:    0.6394

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

Flipped N/Q/H residues before XYZ refinement:
** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.151365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.121189 restraints weight = 38445.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.123759 restraints weight = 43455.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.125544 restraints weight = 24779.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3580
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3580 r_free = 0.3580    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3580 r_free = 0.3580    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3580
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.3275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14913  Z= 0.120
  Angle     :  0.582  11.482  20250  Z= 0.295
  Chirality :  0.040   0.189   2301
  Planarity :  0.003   0.049   2487
  Dihedral  :  9.592 154.293   2139
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 21.36 %
    Favored  : 76.56 %
  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: 1751
  helix:  1.50 (0.15), residues: 1161
  sheet: -1.30 (0.60), residues: 55
  loop : -1.26 (0.28), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.001   TRP C 440 
 HIS   0.005   0.001   HIS C 242 
 PHE   0.042   0.001   PHE B 413 
 TYR   0.015   0.001   TYR C 573 
 ARG   0.012   0.000   ARG B 563 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00341 (    3)
  link_NAG-ASN         : angle       2.65041 (    9)
  hydrogen bonds       : bond        0.03758 (  922)
  hydrogen bonds       : angle       3.96686 ( 2691)
  covalent geometry    : bond        0.00267 (14910)
  covalent geometry    : angle       0.57958 (20241)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4629.94 seconds
wall clock time: 82 minutes 7.19 seconds (4927.19 seconds total)