Starting phenix.real_space_refine
on Fri Jul  3 15:32:10 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7rhs_24468/07_2026/7rhs_24468.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rhs_24468/07_2026/7rhs_24468.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rhs_24468/07_2026/7rhs_24468.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rhs_24468/07_2026/7rhs_24468.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7rhs_24468/07_2026/7rhs_24468.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7rhs_24468/07_2026/7rhs_24468.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rhs_24468/07_2026/7rhs_24468.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rhs_24468/07_2026/7rhs_24468.cif"
  }
  resolution = 2.93
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.070
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
     S      66      5.16       5
     Na      1      4.78       5
     C    9644      2.51       5
     N    2398      2.21       5
     O    2658      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 151 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 14767
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3725
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 456, 3717
          Classifications: {'peptide': 456}
          Link IDs: {'PTRANS': 14, 'TRANS': 441}
      Conformer: "B"
        Number of residues, atoms: 456, 3717
          Classifications: {'peptide': 456}
          Link IDs: {'PTRANS': 14, 'TRANS': 441}
          bond proxies already assigned to first conformer: 3791
    Chain: "B"
      Number of atoms: 3692
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 453, 3692
          Classifications: {'peptide': 453}
          Link IDs: {'PTRANS': 14, 'TRANS': 438}
    Chain: "C"
      Number of atoms: 3697
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 454, 3697
          Classifications: {'peptide': 454}
          Link IDs: {'PTRANS': 14, 'TRANS': 439}
    Chain: "D"
      Number of atoms: 3610
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 441, 3602
          Classifications: {'peptide': 441}
          Link IDs: {'PTRANS': 13, 'TRANS': 427}
      Conformer: "B"
        Number of residues, atoms: 441, 3602
          Classifications: {'peptide': 441}
          Link IDs: {'PTRANS': 13, 'TRANS': 427}
          bond proxies already assigned to first conformer: 3684
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' NA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.80, per 1000 atoms: 0.26
  Number of scatterers: 14767
  At special positions: 0
  Unit cell: (129.478, 118.757, 109.685, 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
     Na      1     11.00
     O    2658      8.00
     N    2398      7.00
     C    9644      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 801 " - " ASN A 339 "
      " NAG B 801 " - " ASN B 339 "
      " NAG C 801 " - " ASN C 339 "
  Time building additional restraints: 1.09
  Conformation dependent library (CDL) restraints added in 774.3 milliseconds
  

  3596 Ramachandran restraints generated.
    1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3420

  Finding SS restraints...
    Secondary structure from input PDB file:
      78 helices and 12 sheets defined
      67.5% alpha, 6.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 166 through 193
      Proline residue:  A 178  - end of helix
      removed outlier: 3.955A  pdb=" N   ASP A 193 " --> pdb=" O   ARG A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 199
    Processing helix  chain 'A' and resid 199 through 222
    Processing helix  chain 'A' and resid 235 through 245
    Processing helix  chain 'A' and resid 246 through 256
      removed outlier: 4.093A  pdb=" N   LYS A 250 " --> pdb=" O   THR A 246 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LEU A 251 " --> pdb=" O   THR A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 261
      removed outlier: 3.767A  pdb=" N   LEU A 261 " --> pdb=" O   PRO A 258 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 258 through 261'
    Processing helix  chain 'A' and resid 262 through 267
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 3.980A  pdb=" N   VAL A 273 " --> pdb=" O   TYR A 270 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   ASN A 276 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 295
      removed outlier: 4.266A  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
      removed outlier: 3.648A  pdb=" N   THR A 364 " --> pdb=" O   THR A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 407
    Processing helix  chain 'A' and resid 407 through 427
    Processing helix  chain 'A' and resid 430 through 447
    Processing helix  chain 'A' and resid 452 through 457
    Processing helix  chain 'A' and resid 461 through 471
    Processing helix  chain 'A' and resid 473 through 478
    Processing helix  chain 'A' and resid 487 through 497
    Processing helix  chain 'A' and resid 548 through 554
      removed outlier: 3.700A  pdb=" N   ILE A 552 " --> pdb=" O   GLY A 548 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 591 through 610
    Processing helix  chain 'B' and resid 165 through 193
      removed outlier: 3.718A  pdb=" N   TYR B 169 " --> pdb=" O   SER B 165 " (cutoff:3.500A)
      Proline residue:  B 178  - end of helix
      removed outlier: 3.939A  pdb=" N   ASP B 193 " --> pdb=" O   ARG B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 199
    Processing helix  chain 'B' and resid 199 through 223
    Processing helix  chain 'B' and resid 235 through 245
    Processing helix  chain 'B' and resid 246 through 256
      removed outlier: 3.913A  pdb=" N   LYS B 250 " --> pdb=" O   THR B 246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 261
      removed outlier: 3.692A  pdb=" N   LEU B 261 " --> pdb=" O   PRO B 258 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 258 through 261'
    Processing helix  chain 'B' and resid 262 through 267
    Processing helix  chain 'B' and resid 270 through 279
      removed outlier: 4.002A  pdb=" N   VAL B 273 " --> pdb=" O   TYR B 270 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   PHE B 275 " --> pdb=" O   GLU B 272 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   ASN B 276 " --> pdb=" O   VAL B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 295
      removed outlier: 4.371A  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 407
    Processing helix  chain 'B' and resid 407 through 427
    Processing helix  chain 'B' and resid 430 through 447
    Processing helix  chain 'B' and resid 452 through 457
    Processing helix  chain 'B' and resid 461 through 478
      removed outlier: 6.421A  pdb=" N   ASP B 475 " --> pdb=" O   ASN B 471 " (cutoff:3.500A)
      removed outlier: 4.858A  pdb=" N   THR B 476 " --> pdb=" O   VAL B 472 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 487 through 497
    Processing helix  chain 'B' and resid 581 through 588
    Processing helix  chain 'B' and resid 591 through 610
    Processing helix  chain 'C' and resid 165 through 193
      removed outlier: 3.758A  pdb=" N   TYR C 169 " --> pdb=" O   SER C 165 " (cutoff:3.500A)
      Proline residue:  C 178  - end of helix
      removed outlier: 3.852A  pdb=" N   ASP C 193 " --> pdb=" O   ARG C 189 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 193 through 199
      removed outlier: 3.721A  pdb=" N   SER C 197 " --> pdb=" O   ASP C 193 " (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: 3.959A  pdb=" N   LYS C 250 " --> pdb=" O   THR C 246 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU C 251 " --> pdb=" O   THR C 247 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 259 through 266
    Processing helix  chain 'C' and resid 270 through 279
      removed outlier: 4.212A  pdb=" N   VAL C 273 " --> pdb=" O   TYR C 270 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   ASN C 276 " --> pdb=" O   VAL C 273 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 280 through 295
      removed outlier: 4.052A  pdb=" N   LEU C 284 " --> pdb=" O   LYS C 280 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 297 through 329
    Processing helix  chain 'C' and resid 347 through 364
    Processing helix  chain 'C' and resid 374 through 407
    Processing helix  chain 'C' and resid 407 through 427
    Processing helix  chain 'C' and resid 430 through 447
    Processing helix  chain 'C' and resid 452 through 457
    Processing helix  chain 'C' and resid 458 through 460
      No H-bonds generated for 'chain 'C' and resid 458 through 460'
    Processing helix  chain 'C' and resid 461 through 478
      removed outlier: 6.710A  pdb=" N   ASP C 475 " --> pdb=" O   ASN C 471 " (cutoff:3.500A)
      removed outlier: 5.053A  pdb=" N   THR C 476 " --> pdb=" O   VAL C 472 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 487 through 497
    Processing helix  chain 'C' and resid 581 through 588
    Processing helix  chain 'C' and resid 591 through 610
    Processing helix  chain 'D' and resid 215 through 242
      removed outlier: 3.722A  pdb=" N   LEU D 219 " --> pdb=" O   ASP D 215 " (cutoff:3.500A)
      Proline residue:  D 237  - end of helix
    Processing helix  chain 'D' and resid 249 through 271
      removed outlier: 3.513A  pdb=" N   TRP D 253 " --> pdb=" O   ASN D 249 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ILE D 271 " --> pdb=" O   ASP D 267 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 272 through 275
      removed outlier: 3.767A  pdb=" N   LEU D 275 " --> pdb=" O   GLN D 272 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 272 through 275'
    Processing helix  chain 'D' and resid 286 through 296
    Processing helix  chain 'D' and resid 298 through 307
      removed outlier: 3.830A  pdb=" N   LEU D 302 " --> pdb=" O   THR D 298 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 309 through 315
      removed outlier: 3.824A  pdb=" N   ILE D 312 " --> pdb=" O   PRO D 309 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU D 315 " --> pdb=" O   ILE D 312 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 320 through 329
      removed outlier: 4.490A  pdb=" N   ASN D 326 " --> pdb=" O   PHE D 323 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 330 through 345
      removed outlier: 4.140A  pdb=" N   PHE D 334 " --> pdb=" O   LYS D 330 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 347 through 379
      removed outlier: 4.385A  pdb=" N   TYR D 351 " --> pdb=" O   LYS D 347 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 392 through 406
    Processing helix  chain 'D' and resid 416 through 449
    Processing helix  chain 'D' and resid 449 through 469
    Processing helix  chain 'D' and resid 472 through 490
    Processing helix  chain 'D' and resid 495 through 500
    Processing helix  chain 'D' and resid 503 through 521
      removed outlier: 3.617A  pdb=" N   VAL D 514 " --> pdb=" O   LEU D 510 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   SER D 517 " --> pdb=" O   ASP D 513 " (cutoff:3.500A)
      removed outlier: 5.415A  pdb=" N   ILE D 518 " --> pdb=" O   VAL D 514 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 529 through 539
    Processing helix  chain 'D' and resid 592 through 596
      removed outlier: 3.504A  pdb=" N   LEU D 595 " --> pdb=" O   GLU D 592 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 621 through 629
    Processing helix  chain 'D' and resid 631 through 646
    Processing sheet with id=AA1, first strand: chain 'A' and resid 227 through 228
    Processing sheet with id=AA2, first strand: chain 'A' and resid 499 through 503
      removed outlier: 3.585A  pdb=" N   ASN A 523 " --> pdb=" O   ASP A 575 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 508 through 510
      removed outlier: 6.837A  pdb=" N   ILE A 568 " --> pdb=" O   ILE A 509 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   ASN A 567 " --> pdb=" O   VAL A 530 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   VAL A 539 " --> pdb=" O   VAL A 529 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 227 through 228
    Processing sheet with id=AA5, first strand: chain 'B' and resid 499 through 503
    Processing sheet with id=AA6, first strand: chain 'B' and resid 508 through 510
      removed outlier: 6.567A  pdb=" N   TYR B 508 " --> pdb=" O   SER B 570 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   SER B 570 " --> pdb=" O   TYR B 508 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   CYS B 510 " --> pdb=" O   ILE B 568 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   ASN B 567 " --> pdb=" O   VAL B 530 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   LEU B 527 " --> pdb=" O   VAL B 540 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   VAL B 540 " --> pdb=" O   LEU B 527 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   VAL B 529 " --> pdb=" O   PHE B 538 " (cutoff:3.500A)
    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 503
    Processing sheet with id=AA9, first strand: chain 'C' and resid 508 through 510
      removed outlier: 6.791A  pdb=" N   ILE C 568 " --> pdb=" O   ILE C 509 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ASN C 567 " --> pdb=" O   VAL C 530 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   VAL C 539 " --> pdb=" O   VAL C 529 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 277 through 279
      removed outlier: 4.098A  pdb=" N   PHE D 277 " --> pdb=" O   ILE D 284 " (cutoff:3.500A)
      removed outlier: 3.950A  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 545
      removed outlier: 3.628A  pdb=" N   SER D 588 " --> pdb=" O   ILE D 564 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 550 through 552
      removed outlier: 6.687A  pdb=" N   PHE D 550 " --> pdb=" O   ALA D 610 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   ALA D 610 " --> pdb=" O   PHE D 550 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ASN D 607 " --> pdb=" O   LEU D 572 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   VAL D 582 " --> pdb=" O   VAL D 571 " (cutoff:3.500A)

    945 hydrogen bonds defined for protein.
    2722 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.33

  Time building geometry restraints manager: 1.43 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3105
        1.33 -     1.45: 3524
        1.45 -     1.57: 8377
        1.57 -     1.69: 1
        1.69 -     1.81: 105
  Bond restraints: 15112
  Sorted by residual:
  bond pdb=" N   PRO B 163 "
       pdb=" CD  PRO B 163 "
    ideal  model  delta    sigma   weight residual
    1.473  1.354  0.119 1.40e-02 5.10e+03 7.24e+01
  bond pdb=" C   ARG D 442 "
       pdb=" O   ARG D 442 "
    ideal  model  delta    sigma   weight residual
    1.237  1.315 -0.079 1.17e-02 7.31e+03 4.52e+01
  bond pdb=" C   PHE A 392 "
       pdb=" O   PHE A 392 "
    ideal  model  delta    sigma   weight residual
    1.236  1.310 -0.074 1.25e-02 6.40e+03 3.53e+01
  bond pdb=" N   PRO D 309 "
       pdb=" CD  PRO D 309 "
    ideal  model  delta    sigma   weight residual
    1.473  1.413  0.060 1.40e-02 5.10e+03 1.82e+01
  bond pdb=" C   PHE A 392 "
       pdb=" CA APHE A 392 "
    ideal  model  delta    sigma   weight residual
    1.522  1.577 -0.055 1.39e-02 5.18e+03 1.58e+01
  ... (remaining 15107 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.66: 19987
        2.66 -     5.31: 453
        5.31 -     7.97: 45
        7.97 -    10.63: 12
       10.63 -    13.28: 2
  Bond angle restraints: 20499
  Sorted by residual:
  angle pdb=" O   PHE A 392 "
        pdb=" C   PHE A 392 "
        pdb=" CA BPHE A 392 "
      ideal   model   delta    sigma   weight residual
     120.10  129.67   -9.57 1.13e+00 7.83e-01 7.17e+01
  angle pdb=" O   ARG D 442 "
        pdb=" C   ARG D 442 "
        pdb=" CA BARG D 442 "
      ideal   model   delta    sigma   weight residual
     120.55  129.48   -8.93 1.06e+00 8.90e-01 7.10e+01
  angle pdb=" O   ARG D 442 "
        pdb=" C   ARG D 442 "
        pdb=" CA AARG D 442 "
      ideal   model   delta    sigma   weight residual
     120.55  129.46   -8.91 1.06e+00 8.90e-01 7.07e+01
  angle pdb=" N   SER B 560 "
        pdb=" CA  SER B 560 "
        pdb=" C   SER B 560 "
      ideal   model   delta    sigma   weight residual
     111.14  120.19   -9.05 1.08e+00 8.57e-01 7.02e+01
  angle pdb=" N   PHE A 392 "
        pdb=" CA BPHE A 392 "
        pdb=" C   PHE A 392 "
      ideal   model   delta    sigma   weight residual
     111.71  118.98   -7.27 1.15e+00 7.56e-01 3.99e+01
  ... (remaining 20494 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.38: 7930
       16.38 -    32.75: 825
       32.75 -    49.13: 140
       49.13 -    65.51: 23
       65.51 -    81.89: 13
  Dihedral angle restraints: 8931
    sinusoidal: 3603
      harmonic: 5328
  Sorted by residual:
  dihedral pdb=" CA  ILE B 366 "
           pdb=" C   ILE B 366 "
           pdb=" N   GLY B 367 "
           pdb=" CA  GLY B 367 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.95   23.05     0      5.00e+00 4.00e-02 2.13e+01
  dihedral pdb=" CA  MET A 607 "
           pdb=" C   MET A 607 "
           pdb=" N   LYS A 608 "
           pdb=" CA  LYS A 608 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.16   22.84     0      5.00e+00 4.00e-02 2.09e+01
  dihedral pdb=" CA  LEU B 227 "
           pdb=" C   LEU B 227 "
           pdb=" N   GLU B 228 "
           pdb=" CA  GLU B 228 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.23   22.77     0      5.00e+00 4.00e-02 2.07e+01
  ... (remaining 8928 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1971
       0.073 -    0.147: 299
       0.147 -    0.220: 52
       0.220 -    0.293: 9
       0.293 -    0.367: 1
  Chirality restraints: 2332
  Sorted by residual:
  chirality pdb=" CB  ILE D 564 "
            pdb=" CA  ILE D 564 "
            pdb=" CG1 ILE D 564 "
            pdb=" CG2 ILE D 564 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.28    0.37 2.00e-01 2.50e+01 3.36e+00
  chirality pdb=" CB  ILE B 303 "
            pdb=" CA  ILE B 303 "
            pdb=" CG1 ILE B 303 "
            pdb=" CG2 ILE B 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.28 2.00e-01 2.50e+01 2.03e+00
  chirality pdb=" CB  ILE C 159 "
            pdb=" CA  ILE C 159 "
            pdb=" CG1 ILE C 159 "
            pdb=" CG2 ILE C 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.28 2.00e-01 2.50e+01 1.91e+00
  ... (remaining 2329 not shown)

  Planarity restraints: 2541
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN D 272 "    0.052 5.00e-02 4.00e+02   7.83e-02 9.80e+00
        pdb=" N   PRO D 273 "   -0.135 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   SER C 504 "   -0.045 5.00e-02 4.00e+02   6.77e-02 7.33e+00
        pdb=" N   PRO C 505 "    0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO C 505 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO C 505 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 546 "   -0.044 5.00e-02 4.00e+02   6.55e-02 6.86e+00
        pdb=" N   PRO D 547 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO D 547 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO D 547 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 2538 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 4773
        2.83 -     3.35: 13251
        3.35 -     3.87: 25562
        3.87 -     4.38: 29160
        4.38 -     4.90: 50341
  Nonbonded interactions: 123087
  Sorted by model distance:
  nonbonded pdb=" O   TRP A 358 "
            pdb=" OG1 THR A 362 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" O   LYS A 431 "
            pdb=" OG1 THR A 435 "
     model   vdw
     2.332 3.040
  nonbonded pdb=" O   TRP D 482 "
            pdb=" OG1 THR D 486 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" O   LEU D 222 "
            pdb=" OG1 THR D 226 "
     model   vdw
     2.342 3.040
  nonbonded pdb=" O   THR B 360 "
            pdb=" OG1 THR B 364 "
     model   vdw
     2.343 3.040
  ... (remaining 123082 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 391 or resid 393 through 611 or resid 801))
  selection = (chain 'B' and (resid 159 through 391 or resid 393 through 801))
  selection = (chain 'C' and (resid 159 through 391 or resid 393 through 801))
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.970
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.940
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
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      :  0.006   0.119  15115  Z= 0.307
  Angle     :  0.956  13.282  20508  Z= 0.563
  Chirality :  0.057   0.367   2332
  Planarity :  0.008   0.078   2538
  Dihedral  : 13.586  81.887   5511
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  4.94 %
    Favored  : 95.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.90 (0.15), residues: 1798
  helix: -3.08 (0.09), residues: 1122
  sheet: -1.39 (0.64), residues: 53
  loop : -1.22 (0.24), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 294 
 TYR   0.025   0.002   TYR D 351 
 PHE   0.025   0.002   PHE C 301 
 TRP   0.028   0.003   TRP B 171 
 HIS   0.007   0.002   HIS D 365 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00630 /  0.31 (15112)
  covalent geometry    : angle       0.95532 /  0.56 (20499)
  hydrogen bonds       : bond        0.13565 /  8.73 (  945)
  hydrogen bonds       : angle       6.95709 /  4.87 ( 2722)
  link_NAG-ASN         : bond        0.00393 /  0.18 (    3)
  link_NAG-ASN         : angle       2.17965 /  1.15 (    9)

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

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

  3596 Ramachandran restraints generated.
    1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3596 Ramachandran restraints generated.
    1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 284
  time to evaluate  : 0.530 
Fit side-chains
REVERT: A  265 LYS cc_start: 0.7604 (tmtt) cc_final: 0.7390 (tptt)
REVERT: A  302 ARG cc_start: 0.7693 (mtm-85) cc_final: 0.7283 (mtp-110)
REVERT: A  418 ASP cc_start: 0.8259 (m-30) cc_final: 0.7812 (m-30)
REVERT: A  455 GLU cc_start: 0.7869 (mp0) cc_final: 0.7563 (mp0)
REVERT: A  458 LYS cc_start: 0.8601 (ttpp) cc_final: 0.8090 (pttm)
REVERT: A  535 VAL cc_start: 0.8420 (m) cc_final: 0.8162 (t)
REVERT: A  556 LYS cc_start: 0.8154 (mtmm) cc_final: 0.7876 (mtmp)
REVERT: A  603 ARG cc_start: 0.7206 (ttt-90) cc_final: 0.6864 (ttm-80)
REVERT: B  228 GLU cc_start: 0.7687 (pp20) cc_final: 0.7424 (pp20)
REVERT: B  499 ARG cc_start: 0.7704 (ttp80) cc_final: 0.7417 (ttp-110)
REVERT: B  575 ASP cc_start: 0.7963 (t0) cc_final: 0.7653 (t0)
REVERT: C  193 ASP cc_start: 0.8105 (t0) cc_final: 0.7850 (t0)
REVERT: C  217 ASP cc_start: 0.8689 (t70) cc_final: 0.8457 (t0)
REVERT: C  467 GLU cc_start: 0.7397 (tp30) cc_final: 0.7073 (tp30)
REVERT: C  499 ARG cc_start: 0.7814 (ptt90) cc_final: 0.7423 (ptt90)
REVERT: C  514 ASP cc_start: 0.7675 (m-30) cc_final: 0.7162 (m-30)
REVERT: C  542 SER cc_start: 0.8342 (p) cc_final: 0.8009 (m)
REVERT: D  268 MET cc_start: 0.8890 (mtp) cc_final: 0.8674 (mtp)
REVERT: D  316 PHE cc_start: 0.8672 (m-80) cc_final: 0.8344 (m-10)
REVERT: D  443 ASP cc_start: 0.8163 (t70) cc_final: 0.7907 (t70)
REVERT: D  452 GLN cc_start: 0.7638 (tp-100) cc_final: 0.7282 (tm-30)
REVERT: D  468 ASN cc_start: 0.8957 (t0) cc_final: 0.8733 (t0)
REVERT: D  477 LYS cc_start: 0.7785 (tttm) cc_final: 0.7325 (tppt)
REVERT: D  513 ASP cc_start: 0.8006 (t0) cc_final: 0.7706 (t0)
REVERT: D  593 ILE cc_start: 0.9134 (tp) cc_final: 0.8837 (mt)
  outliers start: 1
  outliers final: 2
  residues processed: 284
  average time/residue: 0.5726
  time to fit residues: 178.5537
Evaluate side-chains
  180 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 178
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  519 MET
Chi-restraints excluded: chain D residue  259 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    0.0270
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    0.0040
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    0.8980
   overall best weight:    0.5650

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 166 ASN
A 229 GLN
A 241 GLN
A 248 GLN
** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 473 HIS
A 554 ASN
A 604 GLN
B 196 GLN
B 229 GLN
B 248 GLN
C 241 GLN
C 248 GLN
C 398 ASN
C 407 ASN
C 422 GLN
C 425 GLN
C 473 HIS
** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 232 ASN
D 340 HIS
D 365 HIS

Total number of N/Q/H flips: 20

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.125329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.102703 restraints weight = 36201.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 2.84
r_work: 0.3116 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3137
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3137 r_free = 0.3137    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3136 r_free = 0.3136    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (7 function evaluations)
r_final: 0.3136
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.1631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  15115  Z= 0.130
  Angle     :  0.542   7.844  20508  Z= 0.292
  Chirality :  0.041   0.190   2332
  Planarity :  0.005   0.049   2538
  Dihedral  :  4.606  29.068   2006
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 11.98 %
    Favored  : 85.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.83 (0.18), residues: 1798
  helix: -0.44 (0.13), residues: 1134
  sheet: -1.08 (0.64), residues: 60
  loop : -0.38 (0.26), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 279 
 TYR   0.014   0.001   TYR C 263 
 PHE   0.015   0.001   PHE B 192 
 TRP   0.014   0.001   TRP B 171 
 HIS   0.003   0.001   HIS D 365 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.13 (15112)
  covalent geometry    : angle       0.53995 /  0.29 (20499)
  hydrogen bonds       : bond        0.04124 /  2.62 (  945)
  hydrogen bonds       : angle       4.52394 /  3.18 ( 2722)
  link_NAG-ASN         : bond        0.00039 /  0.02 (    3)
  link_NAG-ASN         : angle       2.26892 /  1.19 (    9)

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

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

  3596 Ramachandran restraints generated.
    1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3596 Ramachandran restraints generated.
    1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 199
  time to evaluate  : 0.603 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  302 ARG cc_start: 0.7962 (mtm-85) cc_final: 0.7438 (mtp-110)
REVERT: A  405 ASN cc_start: 0.8239 (t0) cc_final: 0.7971 (m-40)
REVERT: A  425 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.6646 (mp-120)
REVERT: A  455 GLU cc_start: 0.8243 (mp0) cc_final: 0.7934 (mp0)
REVERT: A  458 LYS cc_start: 0.8727 (ttpp) cc_final: 0.8201 (pttm)
REVERT: A  481 ARG cc_start: 0.8720 (mtm180) cc_final: 0.8340 (mtm180)
REVERT: A  535 VAL cc_start: 0.8503 (m) cc_final: 0.8281 (t)
REVERT: A  556 LYS cc_start: 0.8104 (mtmm) cc_final: 0.7776 (mtmp)
REVERT: A  581 LYS cc_start: 0.8559 (tttt) cc_final: 0.8350 (tttm)
REVERT: A  603 ARG cc_start: 0.7125 (ttt-90) cc_final: 0.6743 (ttm-80)
REVERT: B  418 ASP cc_start: 0.8176 (m-30) cc_final: 0.7803 (m-30)
REVERT: B  425 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.6981 (mp-120)
REVERT: B  499 ARG cc_start: 0.8308 (ttp80) cc_final: 0.7863 (ttp-110)
REVERT: B  575 ASP cc_start: 0.8285 (t0) cc_final: 0.8000 (t0)
REVERT: C  193 ASP cc_start: 0.8457 (t0) cc_final: 0.8184 (t0)
REVERT: C  481 ARG cc_start: 0.8926 (mtm110) cc_final: 0.8694 (mtp180)
REVERT: C  514 ASP cc_start: 0.7816 (m-30) cc_final: 0.7213 (m-30)
REVERT: C  539 VAL cc_start: 0.8587 (t) cc_final: 0.8255 (p)
REVERT: C  542 SER cc_start: 0.8332 (p) cc_final: 0.8034 (m)
REVERT: D  316 PHE cc_start: 0.8635 (m-80) cc_final: 0.8262 (m-10)
REVERT: D  378 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7862 (mt-10)
REVERT: D  452 GLN cc_start: 0.8039 (tp-100) cc_final: 0.7679 (tm-30)
REVERT: D  477 LYS cc_start: 0.8200 (tttm) cc_final: 0.7722 (tppt)
REVERT: D  513 ASP cc_start: 0.8478 (t0) cc_final: 0.8168 (t0)
REVERT: D  593 ILE cc_start: 0.9046 (tp) cc_final: 0.8635 (mt)
REVERT: D  636 ARG cc_start: 0.7832 (mtm110) cc_final: 0.7589 (mtm110)
  outliers start: 33
  outliers final: 8
  residues processed: 219
  average time/residue: 0.5535
  time to fit residues: 134.1462
Evaluate side-chains
  184 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 174
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 MET
Chi-restraints excluded: chain A residue  425 GLN
Chi-restraints excluded: chain A residue  599 GLU
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  425 GLN
Chi-restraints excluded: chain B residue  454 LYS
Chi-restraints excluded: chain B residue  459 SER
Chi-restraints excluded: chain B residue  496 LEU
Chi-restraints excluded: chain C residue  159 ILE
Chi-restraints excluded: chain C residue  161 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 142 optimal weight:    5.9990
   chunk 156 optimal weight:    0.7980
   chunk 71 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   chunk 56 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 158 optimal weight:    0.8980
   chunk 146 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 248 GLN
A 405 ASN
** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 GLN
C 241 GLN
C 248 GLN
C 407 ASN
** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 453 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.123809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.100876 restraints weight = 41515.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 2.95
r_work: 0.3084 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3089
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3089 r_free = 0.3089    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3089 r_free = 0.3089    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (9 function evaluations)
r_final: 0.3089
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8710
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15115  Z= 0.145
  Angle     :  0.526   8.186  20508  Z= 0.281
  Chirality :  0.041   0.201   2332
  Planarity :  0.004   0.042   2538
  Dihedral  :  4.228  17.642   2001
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 13.27 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.49 (0.19), residues: 1798
  helix:  0.72 (0.15), residues: 1128
  sheet: -0.28 (0.68), residues: 50
  loop : -0.17 (0.26), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 279 
 TYR   0.014   0.001   TYR C 263 
 PHE   0.016   0.001   PHE B 192 
 TRP   0.014   0.001   TRP D 373 
 HIS   0.004   0.001   HIS D 365 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.14 (15112)
  covalent geometry    : angle       0.52434 /  0.28 (20499)
  hydrogen bonds       : bond        0.03992 /  2.52 (  945)
  hydrogen bonds       : angle       4.16933 /  2.94 ( 2722)
  link_NAG-ASN         : bond        0.00067 /  0.03 (    3)
  link_NAG-ASN         : angle       2.17076 /  1.13 (    9)

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

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

  3596 Ramachandran restraints generated.
    1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3596 Ramachandran restraints generated.
    1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 189
  time to evaluate  : 0.495 
Fit side-chains
REVERT: A  302 ARG cc_start: 0.8087 (mtm-85) cc_final: 0.7599 (mtp-110)
REVERT: A  422 GLN cc_start: 0.8789 (tm-30) cc_final: 0.8585 (tt0)
REVERT: A  425 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.6677 (mp-120)
REVERT: A  455 GLU cc_start: 0.8288 (mp0) cc_final: 0.7990 (mp0)
REVERT: A  458 LYS cc_start: 0.8762 (ttpp) cc_final: 0.8241 (pttm)
REVERT: A  481 ARG cc_start: 0.8778 (mtm180) cc_final: 0.8364 (mtm180)
REVERT: A  556 LYS cc_start: 0.7922 (mtmm) cc_final: 0.7624 (mtmp)
REVERT: A  599 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.5726 (mp0)
REVERT: A  603 ARG cc_start: 0.7345 (ttt-90) cc_final: 0.6943 (ttm-80)
REVERT: B  418 ASP cc_start: 0.8191 (m-30) cc_final: 0.7823 (m-30)
REVERT: B  425 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7002 (mp-120)
REVERT: B  499 ARG cc_start: 0.8370 (ttp80) cc_final: 0.8066 (ttp-110)
REVERT: B  559 LYS cc_start: 0.8365 (mtpp) cc_final: 0.7748 (mmtt)
REVERT: C  193 ASP cc_start: 0.8369 (t0) cc_final: 0.8005 (t0)
REVERT: C  514 ASP cc_start: 0.7828 (m-30) cc_final: 0.7264 (m-30)
REVERT: C  542 SER cc_start: 0.8439 (p) cc_final: 0.8186 (m)
REVERT: D  301 GLN cc_start: 0.8612 (mp-120) cc_final: 0.8299 (mm-40)
REVERT: D  316 PHE cc_start: 0.8641 (m-80) cc_final: 0.8317 (m-10)
REVERT: D  452 GLN cc_start: 0.8161 (tp-100) cc_final: 0.7795 (tm-30)
REVERT: D  477 LYS cc_start: 0.8307 (tttm) cc_final: 0.7889 (tppt)
REVERT: D  513 ASP cc_start: 0.8410 (t0) cc_final: 0.8128 (t0)
REVERT: D  593 ILE cc_start: 0.9131 (tp) cc_final: 0.8753 (mt)
REVERT: D  636 ARG cc_start: 0.7927 (mtm110) cc_final: 0.7707 (mtm110)
  outliers start: 32
  outliers final: 8
  residues processed: 205
  average time/residue: 0.5676
  time to fit residues: 128.2029
Evaluate side-chains
  179 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 168
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  425 GLN
Chi-restraints excluded: chain A residue  519 MET
Chi-restraints excluded: chain A residue  599 GLU
Chi-restraints excluded: chain B residue  425 GLN
Chi-restraints excluded: chain B residue  454 LYS
Chi-restraints excluded: chain B residue  459 SER
Chi-restraints excluded: chain B residue  496 LEU
Chi-restraints excluded: chain C residue  159 ILE
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  539 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 150 optimal weight:    0.5980
   chunk 83 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 62 optimal weight:    0.4980
   chunk 15 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 140 optimal weight:    0.7980
   chunk 12 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 69 optimal weight:    0.6980
   overall best weight:    0.7182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 248 GLN
A 554 ASN
B 317 ASN
C 248 GLN
C 407 ASN
** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 423 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.124423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.102078 restraints weight = 32986.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 2.63
r_work: 0.3109 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3140
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3140
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8685
moved from start:          0.2249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  15115  Z= 0.128
  Angle     :  0.505   8.911  20508  Z= 0.267
  Chirality :  0.041   0.183   2332
  Planarity :  0.004   0.053   2538
  Dihedral  :  3.996  15.289   2001
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 13.40 %
    Favored  : 84.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.20), residues: 1798
  helix:  1.33 (0.15), residues: 1121
  sheet: -0.12 (0.68), residues: 50
  loop :  0.03 (0.26), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 279 
 TYR   0.011   0.001   TYR C 263 
 PHE   0.013   0.001   PHE C 301 
 TRP   0.013   0.001   TRP B 171 
 HIS   0.003   0.001   HIS D 365 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.13 (15112)
  covalent geometry    : angle       0.50324 /  0.27 (20499)
  hydrogen bonds       : bond        0.03765 /  2.38 (  945)
  hydrogen bonds       : angle       3.95395 /  2.80 ( 2722)
  link_NAG-ASN         : bond        0.00056 /  0.03 (    3)
  link_NAG-ASN         : angle       1.98316 /  1.03 (    9)

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

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

  3596 Ramachandran restraints generated.
    1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3596 Ramachandran restraints generated.
    1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 189
  time to evaluate  : 0.575 
Fit side-chains
   revert: symmetry clash
REVERT: A  302 ARG cc_start: 0.8049 (mtm-85) cc_final: 0.7572 (mtp-110)
REVERT: A  422 GLN cc_start: 0.8789 (tm-30) cc_final: 0.8583 (tt0)
REVERT: A  425 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.6592 (mp-120)
REVERT: A  431 LYS cc_start: 0.8567 (mppt) cc_final: 0.8247 (tppp)
REVERT: A  455 GLU cc_start: 0.8301 (mp0) cc_final: 0.7941 (mp0)
REVERT: A  458 LYS cc_start: 0.8781 (ttpp) cc_final: 0.8256 (pttm)
REVERT: A  599 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.5661 (mp0)
REVERT: B  418 ASP cc_start: 0.8222 (m-30) cc_final: 0.7858 (m-30)
REVERT: B  425 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.6940 (mp-120)
REVERT: B  499 ARG cc_start: 0.8343 (ttp80) cc_final: 0.8142 (ttp-110)
REVERT: B  607 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7356 (mtm)
REVERT: C  193 ASP cc_start: 0.8283 (t0) cc_final: 0.7893 (t0)
REVERT: C  514 ASP cc_start: 0.7854 (m-30) cc_final: 0.7292 (m-30)
REVERT: C  542 SER cc_start: 0.8419 (p) cc_final: 0.8187 (m)
REVERT: D  301 GLN cc_start: 0.8596 (mp-120) cc_final: 0.8276 (mm-40)
REVERT: D  316 PHE cc_start: 0.8611 (m-80) cc_final: 0.8312 (m-10)
REVERT: D  452 GLN cc_start: 0.8069 (tp-100) cc_final: 0.7752 (tm-30)
REVERT: D  477 LYS cc_start: 0.8283 (tttm) cc_final: 0.7863 (tppt)
REVERT: D  513 ASP cc_start: 0.8489 (t0) cc_final: 0.8227 (t0)
REVERT: D  593 ILE cc_start: 0.9101 (tp) cc_final: 0.8717 (mt)
REVERT: D  636 ARG cc_start: 0.7916 (mtm110) cc_final: 0.7685 (mtm110)
  outliers start: 37
  outliers final: 13
  residues processed: 212
  average time/residue: 0.5159
  time to fit residues: 121.5019
Evaluate side-chains
  188 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 171
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain A residue  425 GLN
Chi-restraints excluded: chain A residue  519 MET
Chi-restraints excluded: chain A residue  599 GLU
Chi-restraints excluded: chain B residue  359 SER
Chi-restraints excluded: chain B residue  425 GLN
Chi-restraints excluded: chain B residue  454 LYS
Chi-restraints excluded: chain B residue  496 LEU
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  536 THR
Chi-restraints excluded: chain B residue  607 MET
Chi-restraints excluded: chain C residue  159 ILE
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  381 VAL
Chi-restraints excluded: chain D residue  208 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 97 optimal weight:    5.9990
   chunk 84 optimal weight:    0.0040
   chunk 173 optimal weight:    0.0470
   chunk 177 optimal weight:    0.1980
   chunk 149 optimal weight:    0.0270
   chunk 108 optimal weight:    0.1980
   chunk 11 optimal weight:    0.9980
   chunk 161 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 110 optimal weight:    2.9990
   overall best weight:    0.0948

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 248 GLN
** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 554 ASN
B 473 HIS
C 248 GLN
** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.128554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.106779 restraints weight = 32501.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 2.60
r_work: 0.3183 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3209
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3209 r_free = 0.3209    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3209 r_free = 0.3209    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (6 function evaluations)
r_final: 0.3209
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  15115  Z= 0.100
  Angle     :  0.473   9.700  20508  Z= 0.253
  Chirality :  0.039   0.186   2332
  Planarity :  0.003   0.048   2538
  Dihedral  :  3.771  13.943   2001
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 14.32 %
    Favored  : 83.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.66 (0.20), residues: 1798
  helix:  1.74 (0.16), residues: 1127
  sheet: -0.07 (0.70), residues: 50
  loop :  0.13 (0.27), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 603 
 TYR   0.011   0.001   TYR B 297 
 PHE   0.011   0.001   PHE C 301 
 TRP   0.012   0.001   TRP B 171 
 HIS   0.002   0.000   HIS C 473 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00199 /  0.10 (15112)
  covalent geometry    : angle       0.47189 /  0.25 (20499)
  hydrogen bonds       : bond        0.03403 /  2.17 (  945)
  hydrogen bonds       : angle       3.69277 /  2.62 ( 2722)
  link_NAG-ASN         : bond        0.00107 /  0.05 (    3)
  link_NAG-ASN         : angle       1.76726 /  0.92 (    9)

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

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

  3596 Ramachandran restraints generated.
    1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3596 Ramachandran restraints generated.
    1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 208
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
REVERT: A  302 ARG cc_start: 0.8066 (mtm-85) cc_final: 0.7595 (mtp-110)
REVERT: A  425 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.6702 (mp-120)
REVERT: A  431 LYS cc_start: 0.8608 (mppt) cc_final: 0.8270 (tppp)
REVERT: A  455 GLU cc_start: 0.8255 (mp0) cc_final: 0.7857 (mp0)
REVERT: A  458 LYS cc_start: 0.8767 (ttpp) cc_final: 0.8268 (pttm)
REVERT: A  481 ARG cc_start: 0.8698 (mtm180) cc_final: 0.8401 (mtm180)
REVERT: A  537 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8295 (mt0)
REVERT: A  556 LYS cc_start: 0.8035 (mtmp) cc_final: 0.7658 (pmtt)
REVERT: A  599 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.5642 (mp0)
REVERT: B  418 ASP cc_start: 0.8144 (m-30) cc_final: 0.7808 (m-30)
REVERT: B  425 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.6963 (mp-120)
REVERT: B  496 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8179 (mm)
REVERT: C  193 ASP cc_start: 0.8017 (t0) cc_final: 0.7660 (t0)
REVERT: C  272 GLU cc_start: 0.5604 (tt0) cc_final: 0.4893 (mp0)
REVERT: C  344 GLU cc_start: 0.8271 (tp30) cc_final: 0.8036 (tp30)
REVERT: C  352 TYR cc_start: 0.8630 (t80) cc_final: 0.7909 (t80)
REVERT: C  514 ASP cc_start: 0.7804 (m-30) cc_final: 0.7207 (m-30)
REVERT: D  316 PHE cc_start: 0.8597 (m-80) cc_final: 0.8344 (m-10)
REVERT: D  452 GLN cc_start: 0.7972 (tp-100) cc_final: 0.7700 (tm-30)
REVERT: D  477 LYS cc_start: 0.8237 (tttm) cc_final: 0.7799 (tppt)
REVERT: D  513 ASP cc_start: 0.8441 (t0) cc_final: 0.8159 (t0)
REVERT: D  593 ILE cc_start: 0.9093 (tp) cc_final: 0.8693 (mt)
  outliers start: 31
  outliers final: 5
  residues processed: 229
  average time/residue: 0.4914
  time to fit residues: 125.6693
Evaluate side-chains
  186 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 176
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  425 GLN
Chi-restraints excluded: chain A residue  537 GLN
Chi-restraints excluded: chain A residue  599 GLU
Chi-restraints excluded: chain B residue  425 GLN
Chi-restraints excluded: chain B residue  496 LEU
Chi-restraints excluded: chain B residue  536 THR
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  361 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 116 optimal weight:    0.9990
   chunk 93 optimal weight:    0.9990
   chunk 38 optimal weight:    5.9990
   chunk 52 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 125 optimal weight:    4.9990
   chunk 32 optimal weight:    0.0970
   chunk 157 optimal weight:    0.8980
   chunk 127 optimal weight:    0.4980
   overall best weight:    0.6982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 562 ASN
C 241 GLN
C 248 GLN
** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 301 GLN
D 453 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.125339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.103687 restraints weight = 27941.114|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 2.38
r_work: 0.3143 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3018
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3018 r_free = 0.3018    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3018 r_free = 0.3018    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (13 function evaluations)
r_final: 0.3018
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8737
moved from start:          0.2538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15115  Z= 0.127
  Angle     :  0.502   9.493  20508  Z= 0.266
  Chirality :  0.041   0.199   2332
  Planarity :  0.004   0.047   2538
  Dihedral  :  3.769  14.859   2001
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 15.56 %
    Favored  : 82.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.81 (0.20), residues: 1798
  helix:  1.89 (0.16), residues: 1125
  sheet: -0.14 (0.69), residues: 50
  loop :  0.13 (0.27), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG D 636 
 TYR   0.011   0.001   TYR B 270 
 PHE   0.014   0.001   PHE B 192 
 TRP   0.010   0.001   TRP D 373 
 HIS   0.003   0.001   HIS D 365 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.13 (15112)
  covalent geometry    : angle       0.50111 /  0.27 (20499)
  hydrogen bonds       : bond        0.03585 /  2.26 (  945)
  hydrogen bonds       : angle       3.71581 /  2.64 ( 2722)
  link_NAG-ASN         : bond        0.00076 /  0.04 (    3)
  link_NAG-ASN         : angle       1.76679 /  0.92 (    9)

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

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

  3596 Ramachandran restraints generated.
    1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3596 Ramachandran restraints generated.
    1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 180
  time to evaluate  : 0.581 
Fit side-chains
REVERT: A  302 ARG cc_start: 0.8200 (mtm-85) cc_final: 0.7721 (mtp-110)
REVERT: A  407 ASN cc_start: 0.7888 (p0) cc_final: 0.7593 (t0)
REVERT: A  425 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.6890 (mp-120)
REVERT: A  455 GLU cc_start: 0.8453 (mp0) cc_final: 0.8051 (mp0)
REVERT: A  458 LYS cc_start: 0.8831 (ttpp) cc_final: 0.8299 (pttm)
REVERT: A  481 ARG cc_start: 0.8802 (mtm180) cc_final: 0.8341 (mtm180)
REVERT: A  556 LYS cc_start: 0.8055 (mtmp) cc_final: 0.7704 (pmtt)
REVERT: A  599 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.5773 (mp0)
REVERT: B  418 ASP cc_start: 0.8348 (m-30) cc_final: 0.7987 (m-30)
REVERT: B  425 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7192 (mp-120)
REVERT: B  559 LYS cc_start: 0.8344 (mtpp) cc_final: 0.7626 (mmtt)
REVERT: C  193 ASP cc_start: 0.8185 (t0) cc_final: 0.7669 (t0)
REVERT: C  272 GLU cc_start: 0.5665 (tt0) cc_final: 0.4878 (mp0)
REVERT: C  344 GLU cc_start: 0.8371 (tp30) cc_final: 0.8061 (tp30)
REVERT: C  514 ASP cc_start: 0.7940 (m-30) cc_final: 0.7343 (m-30)
REVERT: C  524 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7525 (tt0)
REVERT: C  542 SER cc_start: 0.8442 (p) cc_final: 0.8231 (m)
REVERT: D  316 PHE cc_start: 0.8608 (m-80) cc_final: 0.8327 (m-10)
REVERT: D  376 ASN cc_start: 0.8853 (OUTLIER) cc_final: 0.8518 (m110)
REVERT: D  452 GLN cc_start: 0.8223 (tp-100) cc_final: 0.7883 (tm-30)
REVERT: D  477 LYS cc_start: 0.8408 (tttm) cc_final: 0.7962 (tppt)
REVERT: D  513 ASP cc_start: 0.8574 (t0) cc_final: 0.8292 (t0)
REVERT: D  593 ILE cc_start: 0.9171 (tp) cc_final: 0.8772 (mt)
  outliers start: 31
  outliers final: 10
  residues processed: 199
  average time/residue: 0.5493
  time to fit residues: 121.1325
Evaluate side-chains
  187 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 173
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  425 GLN
Chi-restraints excluded: chain A residue  519 MET
Chi-restraints excluded: chain A residue  599 GLU
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  425 GLN
Chi-restraints excluded: chain B residue  459 SER
Chi-restraints excluded: chain B residue  496 LEU
Chi-restraints excluded: chain B residue  536 THR
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  582 ASP
Chi-restraints excluded: chain D residue  376 ASN
Chi-restraints excluded: chain D residue  405 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 132 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 104 optimal weight:    0.9980
   chunk 160 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 82 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0980
   chunk 178 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 554 ASN
C 248 GLN
C 407 ASN
C 425 GLN
** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.124644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.102373 restraints weight = 31172.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 2.55
r_work: 0.3120 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3111
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3111 r_free = 0.3111    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3111 r_free = 0.3111    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (9 function evaluations)
r_final: 0.3111
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8676
moved from start:          0.2592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15115  Z= 0.134
  Angle     :  0.505  11.124  20508  Z= 0.267
  Chirality :  0.041   0.198   2332
  Planarity :  0.004   0.048   2538
  Dihedral  :  3.791  14.627   2001
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 15.80 %
    Favored  : 82.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.85 (0.20), residues: 1798
  helix:  1.94 (0.16), residues: 1119
  sheet: -0.19 (0.68), residues: 50
  loop :  0.14 (0.27), residues: 629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG D 636 
 TYR   0.011   0.001   TYR C 354 
 PHE   0.013   0.001   PHE B 192 
 TRP   0.012   0.001   TRP D 373 
 HIS   0.003   0.001   HIS D 566 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.13 (15112)
  covalent geometry    : angle       0.50355 /  0.27 (20499)
  hydrogen bonds       : bond        0.03609 /  2.28 (  945)
  hydrogen bonds       : angle       3.71943 /  2.64 ( 2722)
  link_NAG-ASN         : bond        0.00064 /  0.03 (    3)
  link_NAG-ASN         : angle       1.77051 /  0.92 (    9)

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

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

  3596 Ramachandran restraints generated.
    1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3596 Ramachandran restraints generated.
    1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 171
  time to evaluate  : 0.508 
Fit side-chains
   revert: symmetry clash
REVERT: A  302 ARG cc_start: 0.8031 (mtm-85) cc_final: 0.7579 (mtp-110)
REVERT: A  425 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.6741 (mp-120)
REVERT: A  431 LYS cc_start: 0.8698 (tppt) cc_final: 0.8431 (tppp)
REVERT: A  455 GLU cc_start: 0.8336 (mp0) cc_final: 0.7940 (mp0)
REVERT: A  458 LYS cc_start: 0.8773 (ttpp) cc_final: 0.8260 (pttm)
REVERT: A  481 ARG cc_start: 0.8682 (mtm180) cc_final: 0.8193 (mtm180)
REVERT: A  537 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8254 (mt0)
REVERT: A  556 LYS cc_start: 0.8048 (mtmp) cc_final: 0.7703 (pmtt)
REVERT: A  599 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.5606 (mp0)
REVERT: B  418 ASP cc_start: 0.8202 (m-30) cc_final: 0.7842 (m-30)
REVERT: B  425 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.6953 (mp-120)
REVERT: B  559 LYS cc_start: 0.8407 (mtpp) cc_final: 0.7651 (mmtt)
REVERT: C  272 GLU cc_start: 0.5638 (tt0) cc_final: 0.4882 (mp0)
REVERT: C  344 GLU cc_start: 0.8218 (tp30) cc_final: 0.7951 (tp30)
REVERT: C  524 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7393 (tt0)
REVERT: C  542 SER cc_start: 0.8373 (p) cc_final: 0.8155 (m)
REVERT: C  559 LYS cc_start: 0.6276 (mmtt) cc_final: 0.4854 (mtmm)
REVERT: D  316 PHE cc_start: 0.8609 (m-80) cc_final: 0.8336 (m-10)
REVERT: D  452 GLN cc_start: 0.8105 (tp-100) cc_final: 0.7752 (tm-30)
REVERT: D  477 LYS cc_start: 0.8271 (tttm) cc_final: 0.7840 (tppt)
REVERT: D  513 ASP cc_start: 0.8462 (t0) cc_final: 0.8201 (t0)
REVERT: D  537 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7917 (mp)
REVERT: D  593 ILE cc_start: 0.9149 (tp) cc_final: 0.8753 (mt)
  outliers start: 29
  outliers final: 11
  residues processed: 187
  average time/residue: 0.5372
  time to fit residues: 111.5050
Evaluate side-chains
  181 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 165
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  425 GLN
Chi-restraints excluded: chain A residue  519 MET
Chi-restraints excluded: chain A residue  537 GLN
Chi-restraints excluded: chain A residue  599 GLU
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  425 GLN
Chi-restraints excluded: chain B residue  454 LYS
Chi-restraints excluded: chain B residue  459 SER
Chi-restraints excluded: chain B residue  496 LEU
Chi-restraints excluded: chain B residue  536 THR
Chi-restraints excluded: chain C residue  159 ILE
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain D residue  405 LEU
Chi-restraints excluded: chain D residue  537 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 155 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 147 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   chunk 169 optimal weight:    0.5980
   chunk 139 optimal weight:    0.9990
   chunk 100 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9990
   chunk 153 optimal weight:    0.9990
   overall best weight:    0.8586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 554 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 = 0.3532 r_free = 0.3532 target = 0.123956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.101560 restraints weight = 35903.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 2.69
r_work: 0.3095 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3083
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3083 r_free = 0.3083    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3083 r_free = 0.3083    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3083
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8700
moved from start:          0.2636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  15115  Z= 0.140
  Angle     :  0.513  10.165  20508  Z= 0.270
  Chirality :  0.041   0.196   2332
  Planarity :  0.004   0.045   2538
  Dihedral  :  3.810  14.497   2001
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 16.30 %
    Favored  : 82.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.89 (0.20), residues: 1798
  helix:  1.97 (0.16), residues: 1119
  sheet: -0.20 (0.68), residues: 50
  loop :  0.17 (0.26), residues: 629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG D 636 
 TYR   0.011   0.001   TYR A 354 
 PHE   0.014   0.001   PHE B 192 
 TRP   0.012   0.001   TRP D 373 
 HIS   0.003   0.001   HIS D 365 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.14 (15112)
  covalent geometry    : angle       0.51146 /  0.27 (20499)
  hydrogen bonds       : bond        0.03646 /  2.30 (  945)
  hydrogen bonds       : angle       3.73551 /  2.65 ( 2722)
  link_NAG-ASN         : bond        0.00068 /  0.03 (    3)
  link_NAG-ASN         : angle       1.77747 /  0.93 (    9)

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

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

  3596 Ramachandran restraints generated.
    1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3596 Ramachandran restraints generated.
    1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 167
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  302 ARG cc_start: 0.8074 (mtm-85) cc_final: 0.7609 (mtp-110)
REVERT: A  425 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.6742 (mp-120)
REVERT: A  455 GLU cc_start: 0.8336 (mp0) cc_final: 0.7932 (mp0)
REVERT: A  458 LYS cc_start: 0.8798 (ttpp) cc_final: 0.8275 (pttm)
REVERT: A  481 ARG cc_start: 0.8684 (mtm180) cc_final: 0.8214 (mtm180)
REVERT: A  537 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8168 (mt0)
REVERT: A  556 LYS cc_start: 0.8008 (mtmp) cc_final: 0.7694 (pmtt)
REVERT: A  599 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.5639 (mp0)
REVERT: B  418 ASP cc_start: 0.8223 (m-30) cc_final: 0.7862 (m-30)
REVERT: B  425 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.6982 (mp-120)
REVERT: B  559 LYS cc_start: 0.8419 (mtpp) cc_final: 0.7676 (mmtt)
REVERT: C  193 ASP cc_start: 0.8036 (t0) cc_final: 0.7589 (t0)
REVERT: C  272 GLU cc_start: 0.5617 (tt0) cc_final: 0.4878 (mp0)
REVERT: C  344 GLU cc_start: 0.8193 (tp30) cc_final: 0.7941 (tp30)
REVERT: C  542 SER cc_start: 0.8408 (p) cc_final: 0.8194 (m)
REVERT: C  559 LYS cc_start: 0.6458 (mmtt) cc_final: 0.5149 (mtmm)
REVERT: D  316 PHE cc_start: 0.8534 (m-80) cc_final: 0.8247 (m-10)
REVERT: D  452 GLN cc_start: 0.8150 (tp-100) cc_final: 0.7782 (tm-30)
REVERT: D  477 LYS cc_start: 0.8289 (tttm) cc_final: 0.7878 (tppt)
REVERT: D  513 ASP cc_start: 0.8480 (t0) cc_final: 0.8229 (t0)
REVERT: D  537 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7945 (mp)
REVERT: D  593 ILE cc_start: 0.9182 (tp) cc_final: 0.8777 (mt)
  outliers start: 26
  outliers final: 13
  residues processed: 186
  average time/residue: 0.5593
  time to fit residues: 115.4389
Evaluate side-chains
  179 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 161
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  425 GLN
Chi-restraints excluded: chain A residue  519 MET
Chi-restraints excluded: chain A residue  537 GLN
Chi-restraints excluded: chain A residue  599 GLU
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  241 GLN
Chi-restraints excluded: chain B residue  425 GLN
Chi-restraints excluded: chain B residue  456 VAL
Chi-restraints excluded: chain B residue  459 SER
Chi-restraints excluded: chain B residue  496 LEU
Chi-restraints excluded: chain B residue  536 THR
Chi-restraints excluded: chain C residue  159 ILE
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain D residue  405 LEU
Chi-restraints excluded: chain D residue  537 LEU
Chi-restraints excluded: chain D residue  572 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 142 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   chunk 38 optimal weight:    3.9990
   chunk 136 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 116 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 108 optimal weight:    0.9990
   chunk 127 optimal weight:    5.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 407 ASN
** C 554 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 = 0.3520 r_free = 0.3520 target = 0.123020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.100387 restraints weight = 33294.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 2.65
r_work: 0.3083 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3107
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3107 r_free = 0.3107    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3107 r_free = 0.3107    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.3107
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  15115  Z= 0.155
  Angle     :  0.526  11.530  20508  Z= 0.276
  Chirality :  0.042   0.200   2332
  Planarity :  0.004   0.042   2538
  Dihedral  :  3.863  14.593   2001
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 16.85 %
    Favored  : 81.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.85 (0.20), residues: 1798
  helix:  1.94 (0.15), residues: 1119
  sheet: -0.20 (0.68), residues: 50
  loop :  0.14 (0.26), residues: 629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D 636 
 TYR   0.012   0.001   TYR A 352 
 PHE   0.015   0.001   PHE B 192 
 TRP   0.012   0.001   TRP D 373 
 HIS   0.003   0.001   HIS D 365 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00361 /  0.15 (15112)
  covalent geometry    : angle       0.52461 /  0.28 (20499)
  hydrogen bonds       : bond        0.03739 /  2.36 (  945)
  hydrogen bonds       : angle       3.78289 /  2.68 ( 2722)
  link_NAG-ASN         : bond        0.00071 /  0.03 (    3)
  link_NAG-ASN         : angle       1.82588 /  0.95 (    9)

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

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

  3596 Ramachandran restraints generated.
    1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3596 Ramachandran restraints generated.
    1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 162
  time to evaluate  : 0.614 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  302 ARG cc_start: 0.8062 (mtm-85) cc_final: 0.7593 (mtp-110)
REVERT: A  425 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.6711 (mp-120)
REVERT: A  455 GLU cc_start: 0.8403 (mp0) cc_final: 0.7970 (mp0)
REVERT: A  458 LYS cc_start: 0.8832 (ttpp) cc_final: 0.8276 (pttm)
REVERT: A  537 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8185 (mt0)
REVERT: A  556 LYS cc_start: 0.7992 (mtmp) cc_final: 0.7679 (pmtt)
REVERT: A  599 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.5566 (mp0)
REVERT: B  418 ASP cc_start: 0.8211 (m-30) cc_final: 0.7851 (m-30)
REVERT: B  425 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.6847 (mp-120)
REVERT: C  193 ASP cc_start: 0.8095 (t0) cc_final: 0.7639 (t0)
REVERT: C  272 GLU cc_start: 0.5599 (tt0) cc_final: 0.4815 (mp0)
REVERT: C  454 LYS cc_start: 0.8732 (mptt) cc_final: 0.8527 (mmtm)
REVERT: C  542 SER cc_start: 0.8413 (p) cc_final: 0.8183 (m)
REVERT: D  316 PHE cc_start: 0.8528 (m-80) cc_final: 0.8215 (m-10)
REVERT: D  452 GLN cc_start: 0.8146 (tp-100) cc_final: 0.7754 (tm-30)
REVERT: D  477 LYS cc_start: 0.8266 (tttm) cc_final: 0.7846 (tppt)
REVERT: D  513 ASP cc_start: 0.8495 (t0) cc_final: 0.8216 (t0)
REVERT: D  537 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7917 (mp)
REVERT: D  640 LYS cc_start: 0.7854 (ttpp) cc_final: 0.7418 (tptp)
  outliers start: 22
  outliers final: 13
  residues processed: 177
  average time/residue: 0.5839
  time to fit residues: 114.9282
Evaluate side-chains
  177 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 159
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  425 GLN
Chi-restraints excluded: chain A residue  519 MET
Chi-restraints excluded: chain A residue  537 GLN
Chi-restraints excluded: chain A residue  599 GLU
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  241 GLN
Chi-restraints excluded: chain B residue  359 SER
Chi-restraints excluded: chain B residue  425 GLN
Chi-restraints excluded: chain B residue  456 VAL
Chi-restraints excluded: chain B residue  459 SER
Chi-restraints excluded: chain B residue  496 LEU
Chi-restraints excluded: chain B residue  536 THR
Chi-restraints excluded: chain C residue  159 ILE
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain D residue  405 LEU
Chi-restraints excluded: chain D residue  537 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 176 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 126 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   chunk 106 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 160 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 554 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 = 0.3517 r_free = 0.3517 target = 0.122845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.100012 restraints weight = 38562.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3215 rms_B_bonded: 2.82
r_work: 0.3069 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3074
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3074
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8721
moved from start:          0.2674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  15115  Z= 0.157
  Angle     :  0.539  12.043  20508  Z= 0.281
  Chirality :  0.042   0.198   2332
  Planarity :  0.004   0.042   2538
  Dihedral  :  3.888  17.548   2001
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 17.28 %
    Favored  : 81.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.82 (0.20), residues: 1798
  helix:  1.91 (0.15), residues: 1119
  sheet: -0.21 (0.69), residues: 50
  loop :  0.13 (0.26), residues: 629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D 643 
 TYR   0.013   0.001   TYR A 352 
 PHE   0.015   0.001   PHE B 192 
 TRP   0.012   0.001   TRP B 171 
 HIS   0.003   0.001   HIS D 365 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00366 /  0.16 (15112)
  covalent geometry    : angle       0.53731 /  0.28 (20499)
  hydrogen bonds       : bond        0.03759 /  2.37 (  945)
  hydrogen bonds       : angle       3.81019 /  2.70 ( 2722)
  link_NAG-ASN         : bond        0.00092 /  0.04 (    3)
  link_NAG-ASN         : angle       1.84993 /  0.97 (    9)

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

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

  3596 Ramachandran restraints generated.
    1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3596 Ramachandran restraints generated.
    1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 162
  time to evaluate  : 0.632 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  302 ARG cc_start: 0.8036 (mtm-85) cc_final: 0.7597 (mtp-110)
REVERT: A  425 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.6587 (mp-120)
REVERT: A  455 GLU cc_start: 0.8390 (mp0) cc_final: 0.7961 (mp0)
REVERT: A  458 LYS cc_start: 0.8861 (ttpp) cc_final: 0.8319 (pttm)
REVERT: A  537 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8175 (mt0)
REVERT: A  556 LYS cc_start: 0.7980 (mtmp) cc_final: 0.7643 (pmtt)
REVERT: A  599 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.5613 (mp0)
REVERT: B  418 ASP cc_start: 0.8231 (m-30) cc_final: 0.7869 (m-30)
REVERT: B  425 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.6896 (mp-120)
REVERT: C  193 ASP cc_start: 0.8086 (t0) cc_final: 0.7633 (t0)
REVERT: C  272 GLU cc_start: 0.5690 (tt0) cc_final: 0.4942 (mp0)
REVERT: C  454 LYS cc_start: 0.8732 (mptt) cc_final: 0.8522 (mmtm)
REVERT: C  542 SER cc_start: 0.8435 (p) cc_final: 0.8215 (m)
REVERT: D  316 PHE cc_start: 0.8541 (m-80) cc_final: 0.8227 (m-10)
REVERT: D  452 GLN cc_start: 0.8169 (tp-100) cc_final: 0.7784 (tm-30)
REVERT: D  473 LYS cc_start: 0.8322 (mtmm) cc_final: 0.8113 (mmtm)
REVERT: D  477 LYS cc_start: 0.8291 (tttm) cc_final: 0.7891 (tppt)
REVERT: D  513 ASP cc_start: 0.8494 (t0) cc_final: 0.8224 (t0)
REVERT: D  537 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.7973 (mp)
REVERT: D  640 LYS cc_start: 0.7838 (ttpp) cc_final: 0.7436 (tptp)
  outliers start: 19
  outliers final: 14
  residues processed: 173
  average time/residue: 0.5759
  time to fit residues: 110.3049
Evaluate side-chains
  179 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 160
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  425 GLN
Chi-restraints excluded: chain A residue  519 MET
Chi-restraints excluded: chain A residue  537 GLN
Chi-restraints excluded: chain A residue  599 GLU
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  241 GLN
Chi-restraints excluded: chain B residue  425 GLN
Chi-restraints excluded: chain B residue  456 VAL
Chi-restraints excluded: chain B residue  459 SER
Chi-restraints excluded: chain B residue  496 LEU
Chi-restraints excluded: chain B residue  536 THR
Chi-restraints excluded: chain C residue  159 ILE
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  582 ASP
Chi-restraints excluded: chain D residue  246 THR
Chi-restraints excluded: chain D residue  405 LEU
Chi-restraints excluded: chain D residue  537 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 169 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9980
   chunk 174 optimal weight:    1.9990
   chunk 119 optimal weight:    0.4980
   chunk 58 optimal weight:    1.9990
   chunk 116 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 112 optimal weight:    0.5980
   chunk 132 optimal weight:    0.8980
   chunk 115 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 554 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 = 0.3534 r_free = 0.3534 target = 0.124149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.101839 restraints weight = 30890.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 2.54
r_work: 0.3110 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3154
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3154 r_free = 0.3154    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3154 r_free = 0.3154    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.3154
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8674
moved from start:          0.2700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  15115  Z= 0.131
  Angle     :  0.520  12.267  20508  Z= 0.271
  Chirality :  0.041   0.187   2332
  Planarity :  0.004   0.048   2538
  Dihedral  :  3.845  19.565   2001
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 17.22 %
    Favored  : 81.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.90 (0.20), residues: 1798
  helix:  1.96 (0.15), residues: 1119
  sheet: -0.19 (0.69), residues: 50
  loop :  0.18 (0.26), residues: 629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D 636 
 TYR   0.011   0.001   TYR A 352 
 PHE   0.012   0.001   PHE C 301 
 TRP   0.013   0.001   TRP B 171 
 HIS   0.003   0.001   HIS D 365 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.13 (15112)
  covalent geometry    : angle       0.51907 /  0.27 (20499)
  hydrogen bonds       : bond        0.03622 /  2.30 (  945)
  hydrogen bonds       : angle       3.74653 /  2.65 ( 2722)
  link_NAG-ASN         : bond        0.00070 /  0.03 (    3)
  link_NAG-ASN         : angle       1.78843 /  0.93 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4730.16 seconds
wall clock time: 81 minutes 28.82 seconds (4888.82 seconds total)