Starting phenix.real_space_refine
on Fri Jun 13 09:43:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8etp_28595/06_2025/8etp_28595_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8etp_28595/06_2025/8etp_28595.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8etp_28595/06_2025/8etp_28595.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8etp_28595/06_2025/8etp_28595.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8etp_28595/06_2025/8etp_28595_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8etp_28595/06_2025/8etp_28595_neut.cif"
  }
  resolution = 3.52
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.077
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      66      5.16       5
     C    9652      2.51       5
     N    2410      2.21       5
     O    2677      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 164 residue(s): 0.08s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 14809
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3692
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 452, 3684
          Classifications: {'peptide': 452}
          Link IDs: {'PTRANS': 14, 'TRANS': 437}
      Conformer: "B"
        Number of residues, atoms: 452, 3684
          Classifications: {'peptide': 452}
          Link IDs: {'PTRANS': 14, 'TRANS': 437}
          bond proxies already assigned to first conformer: 3758
    Chain: "B"
      Number of atoms: 3684
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 452, 3684
          Classifications: {'peptide': 452}
          Link IDs: {'PTRANS': 14, 'TRANS': 437}
    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: 3602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 441, 3602
          Classifications: {'peptide': 441}
          Link IDs: {'PTRANS': 13, 'TRANS': 427}
    Chain: "A"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 37
          Unusual residues: {'NAG': 1, 'PCG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 37
          Unusual residues: {'NAG': 1, 'PCG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 37
          Unusual residues: {'NAG': 1, 'PCG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Unusual residues: {'PCG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 13.26, per 1000 atoms: 0.90
  Number of scatterers: 14809
  At special positions: 0
  Unit cell: (132.25, 118.496, 106.858, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      66     16.00
     P       4     15.00
     O    2677      8.00
     N    2410      7.00
     C    9652      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 801 " - " ASN A 339 "
      " NAG B 801 " - " ASN B 339 "
      " NAG C 801 " - " ASN C 339 "
  Time building additional restraints: 3.95
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3408

  Finding SS restraints...
    Secondary structure from input PDB file:
      76 helices and 12 sheets defined
      67.3% alpha, 5.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 165 through 193
      removed outlier: 3.917A  pdb=" N   TYR A 169 " --> pdb=" O   SER A 165 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
      removed outlier: 3.766A  pdb=" N   ASP A 193 " --> pdb=" O   ARG A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 222
      removed outlier: 3.662A  pdb=" N   TRP A 203 " --> pdb=" O   TYR A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 245
    Processing helix  chain 'A' and resid 246 through 256
      removed outlier: 4.065A  pdb=" N   LYS A 250 " --> pdb=" O   THR A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 261
      removed outlier: 3.840A  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: 3.958A  pdb=" N   VAL A 273 " --> pdb=" O   TYR A 270 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   ASN A 276 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LEU A 278 " --> pdb=" O   PHE A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 295
      removed outlier: 4.232A  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: 3.644A  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 549 through 554
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 591 through 609
    Processing helix  chain 'B' and resid 165 through 193
      removed outlier: 3.816A  pdb=" N   TYR B 169 " --> pdb=" O   SER B 165 " (cutoff:3.500A)
      Proline residue:  B 178  - end of helix
      removed outlier: 3.901A  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: 3.971A  pdb=" N   LYS B 250 " --> pdb=" O   THR B 246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 261
      No H-bonds generated for 'chain 'B' and resid 259 through 261'
    Processing helix  chain 'B' and resid 262 through 267
    Processing helix  chain 'B' and resid 270 through 280
      removed outlier: 3.885A  pdb=" N   VAL B 273 " --> pdb=" O   TYR B 270 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   ASN B 276 " --> pdb=" O   VAL B 273 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LEU B 278 " --> pdb=" O   PHE B 275 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   LYS B 280 " --> pdb=" O   ARG B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 281 through 295
    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 427
      removed outlier: 5.280A  pdb=" N   SER B 409 " --> pdb=" O   ASN B 405 " (cutoff:3.500A)
      removed outlier: 5.566A  pdb=" N   ARG B 410 " --> pdb=" O   MET B 406 " (cutoff:3.500A)
    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: 5.979A  pdb=" N   ASP B 475 " --> pdb=" O   ASN B 471 " (cutoff:3.500A)
      removed outlier: 4.981A  pdb=" N   THR B 476 " --> pdb=" O   VAL B 472 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 479 through 484
      removed outlier: 6.240A  pdb=" N   ILE B 482 " --> pdb=" O   LYS B 479 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   GLN B 484 " --> pdb=" O   ARG B 481 " (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: 3.743A  pdb=" N   TYR C 169 " --> pdb=" O   SER C 165 " (cutoff:3.500A)
      Proline residue:  C 178  - end of helix
      removed outlier: 4.008A  pdb=" N   ASP C 193 " --> pdb=" O   ARG C 189 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 194 through 199
    Processing helix  chain 'C' and resid 199 through 222
    Processing helix  chain 'C' and resid 235 through 245
    Processing helix  chain 'C' and resid 246 through 256
      removed outlier: 3.774A  pdb=" N   LYS C 250 " --> pdb=" O   THR C 246 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 259 through 266
    Processing helix  chain 'C' and resid 272 through 279
      removed outlier: 3.553A  pdb=" N   PHE C 275 " --> pdb=" O   GLU C 272 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   ASN C 276 " --> pdb=" O   VAL C 273 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   LEU C 278 " --> pdb=" O   PHE C 275 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU C 279 " --> pdb=" O   ASN C 276 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 280 through 295
      removed outlier: 3.532A  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 427
      removed outlier: 5.701A  pdb=" N   SER C 409 " --> pdb=" O   ASN C 405 " (cutoff:3.500A)
      removed outlier: 5.595A  pdb=" N   ARG C 410 " --> pdb=" O   MET C 406 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 430 through 447
    Processing helix  chain 'C' and resid 452 through 457
    Processing helix  chain 'C' and resid 461 through 478
      removed outlier: 6.114A  pdb=" N   ASP C 475 " --> pdb=" O   ASN C 471 " (cutoff:3.500A)
      removed outlier: 4.838A  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: 3.658A  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: 3.633A  pdb=" N   TRP D 253 " --> pdb=" O   ASN D 249 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ILE D 271 " --> pdb=" O   ASP D 267 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 272 through 275
      removed outlier: 3.920A  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: 3.625A  pdb=" N   LEU D 302 " --> pdb=" O   THR D 298 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 309 through 312
      removed outlier: 3.633A  pdb=" N   ILE D 312 " --> pdb=" O   PRO D 309 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 309 through 312'
    Processing helix  chain 'D' and resid 313 through 318
    Processing helix  chain 'D' and resid 320 through 329
      removed outlier: 3.502A  pdb=" N   PHE D 323 " --> pdb=" O   ASN D 320 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   ASN D 326 " --> pdb=" O   PHE D 323 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   MET D 328 " --> pdb=" O   ALA D 325 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 330 through 345
      removed outlier: 4.298A  pdb=" N   PHE D 334 " --> pdb=" O   LYS D 330 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 347 through 379
      removed outlier: 4.313A  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: 3.856A  pdb=" N   VAL D 514 " --> pdb=" O   LEU D 510 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   SER D 517 " --> pdb=" O   ASP D 513 " (cutoff:3.500A)
      removed outlier: 5.385A  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 591 through 596
      removed outlier: 3.595A  pdb=" N   SER D 594 " --> pdb=" O   GLY D 591 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU D 595 " --> pdb=" O   GLU D 592 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   LEU D 596 " --> pdb=" O   ILE D 593 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 591 through 596'
    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
      removed outlier: 3.745A  pdb=" N   LEU A 231 " --> pdb=" O   GLU A 228 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 499 through 503
      removed outlier: 3.768A  pdb=" N   ASP A 575 " --> pdb=" O   ASN A 523 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 508 through 510
      removed outlier: 6.694A  pdb=" N   TYR A 508 " --> pdb=" O   SER A 570 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   SER A 570 " --> pdb=" O   TYR A 508 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   ASN A 567 " --> pdb=" O   VAL A 530 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ALA A 528 " --> pdb=" O   ARG A 569 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 227 through 228
      removed outlier: 3.642A  pdb=" N   GLU B 228 " --> pdb=" O   LEU B 231 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 500 through 503
      removed outlier: 3.558A  pdb=" N   ILE B 521 " --> pdb=" O   PHE B 577 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 508 through 510
      removed outlier: 7.161A  pdb=" N   ILE B 568 " --> pdb=" O   ILE B 509 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ASN B 567 " --> pdb=" O   VAL B 530 " (cutoff:3.500A)
      removed outlier: 6.249A  pdb=" N   LEU B 527 " --> pdb=" O   VAL B 540 " (cutoff:3.500A)
      removed outlier: 4.702A  pdb=" N   VAL B 540 " --> pdb=" O   LEU B 527 " (cutoff:3.500A)
      removed outlier: 6.523A  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 502
    Processing sheet with id=AA9, first strand: chain 'C' and resid 508 through 510
      removed outlier: 7.060A  pdb=" N   ILE C 568 " --> pdb=" O   ILE C 509 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ASN C 567 " --> pdb=" O   VAL C 530 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   LEU C 527 " --> pdb=" O   VAL C 540 " (cutoff:3.500A)
      removed outlier: 5.108A  pdb=" N   VAL C 540 " --> pdb=" O   LEU C 527 " (cutoff:3.500A)
      removed outlier: 7.165A  pdb=" N   VAL C 529 " --> pdb=" O   PHE C 538 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 278 through 279
      removed outlier: 3.789A  pdb=" N   ARG D 279 " --> pdb=" O   ASP D 282 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ASP D 282 " --> pdb=" O   ARG D 279 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'D' and resid 541 through 542
      removed outlier: 3.511A  pdb=" N   ASN D 615 " --> pdb=" O   LYS D 565 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 550 through 552
      removed outlier: 7.241A  pdb=" N   VAL D 608 " --> pdb=" O   VAL D 551 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ASN D 607 " --> pdb=" O   LEU D 572 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   VAL D 571 " --> pdb=" O   VAL D 582 " (cutoff:3.500A)
      removed outlier: 4.720A  pdb=" N   VAL D 582 " --> pdb=" O   VAL D 571 " (cutoff:3.500A)

    920 hydrogen bonds defined for protein.
    2690 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.59

  Time building geometry restraints manager: 4.36 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 2339
        1.31 -     1.44: 4238
        1.44 -     1.56: 8474
        1.56 -     1.69: 10
        1.69 -     1.82: 105
  Bond restraints: 15166
  Sorted by residual:
  bond pdb=" O5' PCG D 901 "
       pdb=" PA  PCG D 901 "
    ideal  model  delta    sigma   weight residual
    1.606  1.489  0.117 2.00e-02 2.50e+03 3.45e+01
  bond pdb=" O5' PCG C 802 "
       pdb=" PA  PCG C 802 "
    ideal  model  delta    sigma   weight residual
    1.606  1.489  0.117 2.00e-02 2.50e+03 3.44e+01
  bond pdb=" O5' PCG A 802 "
       pdb=" PA  PCG A 802 "
    ideal  model  delta    sigma   weight residual
    1.606  1.489  0.117 2.00e-02 2.50e+03 3.41e+01
  bond pdb=" O5' PCG B 802 "
       pdb=" PA  PCG B 802 "
    ideal  model  delta    sigma   weight residual
    1.606  1.489  0.117 2.00e-02 2.50e+03 3.40e+01
  bond pdb=" O3' PCG C 802 "
       pdb=" PA  PCG C 802 "
    ideal  model  delta    sigma   weight residual
    1.617  1.512  0.105 2.00e-02 2.50e+03 2.74e+01
  ... (remaining 15161 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.67: 20392
        3.67 -     7.35: 134
        7.35 -    11.02: 52
       11.02 -    14.70: 7
       14.70 -    18.37: 9
  Bond angle restraints: 20594
  Sorted by residual:
  angle pdb=" C3' PCG D 901 "
        pdb=" C4' PCG D 901 "
        pdb=" C5' PCG D 901 "
      ideal   model   delta    sigma   weight residual
     109.85  128.22  -18.37 3.00e+00 1.11e-01 3.75e+01
  angle pdb=" C3' PCG B 802 "
        pdb=" C4' PCG B 802 "
        pdb=" C5' PCG B 802 "
      ideal   model   delta    sigma   weight residual
     109.85  128.05  -18.20 3.00e+00 1.11e-01 3.68e+01
  angle pdb=" C3' PCG A 802 "
        pdb=" C4' PCG A 802 "
        pdb=" C5' PCG A 802 "
      ideal   model   delta    sigma   weight residual
     109.85  127.89  -18.04 3.00e+00 1.11e-01 3.62e+01
  angle pdb=" C3' PCG C 802 "
        pdb=" C4' PCG C 802 "
        pdb=" C5' PCG C 802 "
      ideal   model   delta    sigma   weight residual
     109.85  127.84  -17.99 3.00e+00 1.11e-01 3.60e+01
  angle pdb=" O1A PCG A 802 "
        pdb=" PA  PCG A 802 "
        pdb=" O5' PCG A 802 "
      ideal   model   delta    sigma   weight residual
     102.28  117.95  -15.67 3.00e+00 1.11e-01 2.73e+01
  ... (remaining 20589 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.76: 8758
       31.76 -    63.51: 293
       63.51 -    95.27: 26
       95.27 -   127.03: 3
      127.03 -   158.78: 3
  Dihedral angle restraints: 9083
    sinusoidal: 3774
      harmonic: 5309
  Sorted by residual:
  dihedral pdb=" C   ALA A 566 "
           pdb=" N   ALA A 566 "
           pdb=" CA  ALA A 566 "
           pdb=" CB  ALA A 566 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.31   11.71     0      2.50e+00 1.60e-01 2.19e+01
  dihedral pdb=" N   ALA A 566 "
           pdb=" C   ALA A 566 "
           pdb=" CA  ALA A 566 "
           pdb=" CB  ALA A 566 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.90  134.59  -11.69     0      2.50e+00 1.60e-01 2.19e+01
  dihedral pdb=" C5' PCG C 802 "
           pdb=" O5' PCG C 802 "
           pdb=" PA  PCG C 802 "
           pdb=" O2A PCG C 802 "
      ideal   model   delta sinusoidal    sigma   weight residual
      81.13  -77.65  158.78     1      3.00e+01 1.11e-03 2.06e+01
  ... (remaining 9080 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.353: 2338
       0.353 -    0.706: 1
       0.706 -    1.058: 0
       1.058 -    1.411: 0
       1.411 -    1.764: 4
  Chirality restraints: 2343
  Sorted by residual:
  chirality pdb=" C4' PCG B 802 "
            pdb=" C3' PCG B 802 "
            pdb=" C5' PCG B 802 "
            pdb=" O4' PCG B 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -0.73   -1.76 2.00e-01 2.50e+01 7.78e+01
  chirality pdb=" C4' PCG D 901 "
            pdb=" C3' PCG D 901 "
            pdb=" C5' PCG D 901 "
            pdb=" O4' PCG D 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -0.74   -1.76 2.00e-01 2.50e+01 7.74e+01
  chirality pdb=" C4' PCG A 802 "
            pdb=" C3' PCG A 802 "
            pdb=" C5' PCG A 802 "
            pdb=" O4' PCG A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -0.81   -1.68 2.00e-01 2.50e+01 7.09e+01
  ... (remaining 2340 not shown)

  Planarity restraints: 2536
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 562 "    0.020 2.00e-02 2.50e+03   4.04e-02 1.63e+01
        pdb=" C   ASN A 562 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   ASN A 562 "    0.027 2.00e-02 2.50e+03
        pdb=" N   ARG A 563 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN D 272 "    0.049 5.00e-02 4.00e+02   7.38e-02 8.73e+00
        pdb=" N   PRO D 273 "   -0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO D 273 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO D 273 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C 504 "   -0.046 5.00e-02 4.00e+02   7.00e-02 7.83e+00
        pdb=" N   PRO C 505 "    0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO C 505 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO C 505 "   -0.038 5.00e-02 4.00e+02
  ... (remaining 2533 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.85: 4934
        2.85 -     3.36: 13261
        3.36 -     3.87: 25023
        3.87 -     4.39: 27322
        4.39 -     4.90: 47477
  Nonbonded interactions: 118017
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 504 "
            pdb=" OD1 ASP C 507 "
     model   vdw
     2.332 3.040
  nonbonded pdb=" O   PHE D 516 "
            pdb=" OG  SER D 520 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" O   ALA B 415 "
            pdb=" OG  SER B 419 "
     model   vdw
     2.342 3.040
  nonbonded pdb=" OG1 THR A 430 "
            pdb=" OD1 ASP A 432 "
     model   vdw
     2.370 3.040
  nonbonded pdb=" OE1 GLU D 560 "
            pdb=" OH  TYR D 562 "
     model   vdw
     2.371 3.040
  ... (remaining 118012 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 610 or resid 801 thro \ 
ugh 802))
  selection = (chain 'B' and (resid 159 through 391 or resid 393 through 610 or resid 801 thro \ 
ugh 802))
  selection = (chain 'C' and (resid 159 through 391 or resid 393 through 610 or resid 801 thro \ 
ugh 802))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.790
  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:          0.790
  Check model and map are aligned:         0.140
  Set scattering table:                    0.190
  Process input model:                     40.410
  Find NCS groups from input model:        0.750
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
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   0.117  15169  Z= 0.309
  Angle     :  1.012  18.372  20603  Z= 0.509
  Chirality :  0.090   1.764   2343
  Planarity :  0.007   0.074   2533
  Dihedral  : 16.202 158.782   5675
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  5.76 %
    Favored  : 94.18 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.88 (0.14), residues: 1792
  helix: -2.65 (0.09), residues: 1166
  sheet: -2.64 (0.57), residues: 63
  loop : -1.87 (0.23), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 203 
 HIS   0.005   0.001   HIS A 315 
 PHE   0.024   0.002   PHE C 180 
 TYR   0.026   0.002   TYR C 184 
 ARG   0.013   0.000   ARG A 603 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00174 (    3)
  link_NAG-ASN         : angle       2.10437 (    9)
  hydrogen bonds       : bond        0.10687 (  920)
  hydrogen bonds       : angle       5.77819 ( 2690)
  covalent geometry    : bond        0.00599 (15166)
  covalent geometry    : angle       1.01137 (20594)

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

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

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 319
  time to evaluate  : 1.487 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  198 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7377 (pt0)
REVERT: A  228 GLU cc_start: 0.8451 (tm-30) cc_final: 0.7999 (tm-30)
REVERT: A  241 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7443 (mm-40)
REVERT: A  271 PRO cc_start: 0.8637 (Cg_endo) cc_final: 0.8349 (Cg_exo)
REVERT: A  581 LYS cc_start: 0.8792 (tttm) cc_final: 0.8502 (tptt)
REVERT: B  263 TYR cc_start: 0.7835 (m-10) cc_final: 0.7578 (m-80)
REVERT: B  271 PRO cc_start: 0.7872 (Cg_endo) cc_final: 0.7617 (Cg_exo)
REVERT: B  305 ASN cc_start: 0.8387 (t0) cc_final: 0.8184 (t0)
REVERT: B  422 GLN cc_start: 0.8427 (tt0) cc_final: 0.8002 (tt0)
REVERT: B  524 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6687 (tm-30)
REVERT: B  551 SER cc_start: 0.7782 (p) cc_final: 0.7479 (t)
REVERT: C  240 TRP cc_start: 0.8072 (t-100) cc_final: 0.7556 (t60)
REVERT: C  311 LEU cc_start: 0.8326 (mt) cc_final: 0.7733 (tt)
REVERT: C  439 ARG cc_start: 0.7932 (ttt90) cc_final: 0.7505 (ttt90)
REVERT: C  497 LYS cc_start: 0.9232 (mmtp) cc_final: 0.8684 (mmmm)
REVERT: C  607 MET cc_start: 0.6645 (mtp) cc_final: 0.6284 (mtm)
REVERT: D  267 ASP cc_start: 0.8362 (t70) cc_final: 0.7492 (t0)
REVERT: D  441 MET cc_start: 0.8447 (mmt) cc_final: 0.8065 (mmt)
REVERT: D  466 MET cc_start: 0.8371 (mtm) cc_final: 0.8155 (mtp)
REVERT: D  500 LYS cc_start: 0.8513 (pttp) cc_final: 0.8311 (pttm)
REVERT: D  534 TYR cc_start: 0.8043 (m-10) cc_final: 0.7790 (m-10)
REVERT: D  641 LYS cc_start: 0.7271 (mttt) cc_final: 0.6894 (tppt)
  outliers start: 1
  outliers final: 0
  residues processed: 320
  average time/residue: 0.3003
  time to fit residues: 137.9162
Evaluate side-chains
  215 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 1.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 151 optimal weight:    1.9990
   chunk 135 optimal weight:    4.9990
   chunk 75 optimal weight:    6.9990
   chunk 46 optimal weight:    0.7980
   chunk 91 optimal weight:    0.8980
   chunk 72 optimal weight:    0.4980
   chunk 140 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   chunk 162 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 166 ASN
A 414 GLN
A 562 ASN
A 567 ASN
B 196 GLN
B 276 ASN
B 317 ASN
B 471 ASN
C 237 ASN
C 407 ASN
C 425 GLN
D 365 HIS
D 423 GLN
D 440 GLN
D 607 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.152641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.122307 restraints weight = 23048.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.124812 restraints weight = 16688.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.126185 restraints weight = 11569.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3467
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3467 r_free = 0.3467    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3467 r_free = 0.3467    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3467
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.1628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15169  Z= 0.128
  Angle     :  0.529   8.378  20603  Z= 0.280
  Chirality :  0.040   0.156   2343
  Planarity :  0.005   0.055   2533
  Dihedral  : 10.594 178.905   2180
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 12.27 %
    Favored  : 85.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.18), residues: 1792
  helix: -0.08 (0.14), residues: 1156
  sheet: -1.43 (0.65), residues: 55
  loop : -1.24 (0.25), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 231 
 HIS   0.006   0.001   HIS A 242 
 PHE   0.013   0.001   PHE D 516 
 TYR   0.014   0.001   TYR C 357 
 ARG   0.006   0.000   ARG D 636 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00122 (    3)
  link_NAG-ASN         : angle       2.18122 (    9)
  hydrogen bonds       : bond        0.03888 (  920)
  hydrogen bonds       : angle       4.14571 ( 2690)
  covalent geometry    : bond        0.00282 (15166)
  covalent geometry    : angle       0.52699 (20594)

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

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

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 244
  time to evaluate  : 1.864 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7781 (tm-30)
REVERT: A  240 TRP cc_start: 0.8311 (t-100) cc_final: 0.7658 (t60)
REVERT: A  241 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7576 (mm110)
REVERT: A  352 TYR cc_start: 0.8713 (t80) cc_final: 0.8464 (t80)
REVERT: A  395 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7203 (mt)
REVERT: A  422 GLN cc_start: 0.7986 (tm-30) cc_final: 0.7564 (tm-30)
REVERT: A  581 LYS cc_start: 0.8543 (tttm) cc_final: 0.8292 (tptt)
REVERT: A  583 ASP cc_start: 0.6291 (m-30) cc_final: 0.6023 (m-30)
REVERT: B  418 ASP cc_start: 0.7398 (m-30) cc_final: 0.7144 (m-30)
REVERT: B  422 GLN cc_start: 0.8286 (tt0) cc_final: 0.7792 (mt0)
REVERT: B  524 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6895 (tm-30)
REVERT: B  551 SER cc_start: 0.8078 (p) cc_final: 0.7787 (t)
REVERT: B  575 ASP cc_start: 0.7475 (t0) cc_final: 0.7079 (t0)
REVERT: C  311 LEU cc_start: 0.8281 (mt) cc_final: 0.7914 (tt)
REVERT: C  376 GLU cc_start: 0.8184 (pm20) cc_final: 0.7781 (tt0)
REVERT: C  422 GLN cc_start: 0.8584 (tp40) cc_final: 0.8330 (tp-100)
REVERT: C  439 ARG cc_start: 0.7865 (ttt90) cc_final: 0.7521 (ttt90)
REVERT: C  604 GLN cc_start: 0.8321 (mm-40) cc_final: 0.8090 (mm-40)
REVERT: D  267 ASP cc_start: 0.8073 (t70) cc_final: 0.7179 (t0)
REVERT: D  268 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7851 (mtp)
  outliers start: 29
  outliers final: 14
  residues processed: 260
  average time/residue: 0.3235
  time to fit residues: 129.5522
Evaluate side-chains
  220 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 204
  time to evaluate  : 1.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  268 THR
Chi-restraints excluded: chain A residue  360 THR
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  272 GLU
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  474 LEU
Chi-restraints excluded: chain C residue  177 LEU
Chi-restraints excluded: chain D residue  254 LEU
Chi-restraints excluded: chain D residue  268 MET
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  608 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 171 optimal weight:    9.9990
   chunk 140 optimal weight:    0.9990
   chunk 92 optimal weight:    0.7980
   chunk 148 optimal weight:    4.9990
   chunk 138 optimal weight:    0.0870
   chunk 70 optimal weight:    1.9990
   chunk 95 optimal weight:    0.6980
   chunk 112 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 152 optimal weight:    0.2980
   chunk 10 optimal weight:   10.0000
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
A 166 ASN
B 473 HIS
C 305 ASN
C 425 GLN
** D 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 566 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.153412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.126213 restraints weight = 29880.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.128422 restraints weight = 22587.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.128919 restraints weight = 19258.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3483
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3483 r_free = 0.3483    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3483 r_free = 0.3483    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3483
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.1979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  15169  Z= 0.109
  Angle     :  0.486   8.253  20603  Z= 0.257
  Chirality :  0.040   0.150   2343
  Planarity :  0.004   0.055   2533
  Dihedral  : 10.236 178.012   2180
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 14.81 %
    Favored  : 83.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.20), residues: 1792
  helix:  0.96 (0.15), residues: 1167
  sheet: -0.90 (0.64), residues: 51
  loop : -0.91 (0.26), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP B 316 
 HIS   0.005   0.001   HIS A 242 
 PHE   0.012   0.001   PHE D 270 
 TYR   0.013   0.001   TYR C 357 
 ARG   0.004   0.000   ARG D 636 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00066 (    3)
  link_NAG-ASN         : angle       2.18793 (    9)
  hydrogen bonds       : bond        0.03630 (  920)
  hydrogen bonds       : angle       3.83747 ( 2690)
  covalent geometry    : bond        0.00235 (15166)
  covalent geometry    : angle       0.48396 (20594)

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

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

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 227
  time to evaluate  : 1.909 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7795 (tm-30)
REVERT: A  240 TRP cc_start: 0.8244 (t-100) cc_final: 0.7669 (t60)
REVERT: A  241 GLN cc_start: 0.7866 (mm-40) cc_final: 0.7513 (mm110)
REVERT: A  395 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7138 (mt)
REVERT: A  422 GLN cc_start: 0.7808 (tm-30) cc_final: 0.7328 (tm-30)
REVERT: A  482 ILE cc_start: 0.7982 (pt) cc_final: 0.7599 (mt)
REVERT: A  583 ASP cc_start: 0.6278 (m-30) cc_final: 0.6063 (m-30)
REVERT: A  607 MET cc_start: 0.7857 (mmt) cc_final: 0.7241 (mmm)
REVERT: B  422 GLN cc_start: 0.8165 (tt0) cc_final: 0.7700 (mt0)
REVERT: B  551 SER cc_start: 0.7928 (p) cc_final: 0.7658 (t)
REVERT: B  575 ASP cc_start: 0.7537 (t0) cc_final: 0.7111 (t0)
REVERT: C  311 LEU cc_start: 0.8249 (mt) cc_final: 0.7975 (tt)
REVERT: C  376 GLU cc_start: 0.8222 (pm20) cc_final: 0.7818 (tt0)
REVERT: C  439 ARG cc_start: 0.7778 (ttt90) cc_final: 0.7540 (ttt90)
REVERT: D  267 ASP cc_start: 0.7919 (t70) cc_final: 0.7112 (t0)
  outliers start: 25
  outliers final: 13
  residues processed: 240
  average time/residue: 0.3608
  time to fit residues: 135.4307
Evaluate side-chains
  221 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 207
  time to evaluate  : 2.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  424 MET
Chi-restraints excluded: chain B residue  474 LEU
Chi-restraints excluded: chain C residue  177 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain D residue  254 LEU
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  405 LEU
Chi-restraints excluded: chain D residue  458 CYS
Chi-restraints excluded: chain D residue  608 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0670
   chunk 170 optimal weight:    4.9990
   chunk 63 optimal weight:    6.9990
   chunk 146 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9980
   chunk 103 optimal weight:    0.8980
   chunk 47 optimal weight:    0.8980
   chunk 142 optimal weight:    0.0670
   chunk 137 optimal weight:    0.7980
   chunk 90 optimal weight:    2.9990
   overall best weight:    0.5456

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

Flipped N/Q/H residues before XYZ refinement:
A 554 ASN
B 484 GLN
C 299 ASN
C 422 GLN
C 425 GLN
** D 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.152844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.124109 restraints weight = 23209.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.124634 restraints weight = 19043.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.126509 restraints weight = 16005.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3477
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3477 r_free = 0.3477    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3477 r_free = 0.3477    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3477
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  15169  Z= 0.108
  Angle     :  0.489   7.921  20603  Z= 0.259
  Chirality :  0.040   0.152   2343
  Planarity :  0.004   0.048   2533
  Dihedral  : 10.062 177.930   2180
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 16.05 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.20), residues: 1792
  helix:  1.46 (0.15), residues: 1164
  sheet: -0.60 (0.69), residues: 46
  loop : -0.62 (0.27), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.001   TRP B 316 
 HIS   0.005   0.001   HIS A 242 
 PHE   0.012   0.001   PHE B 547 
 TYR   0.013   0.001   TYR C 357 
 ARG   0.007   0.000   ARG A 603 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00043 (    3)
  link_NAG-ASN         : angle       2.17690 (    9)
  hydrogen bonds       : bond        0.03573 (  920)
  hydrogen bonds       : angle       3.72145 ( 2690)
  covalent geometry    : bond        0.00234 (15166)
  covalent geometry    : angle       0.48748 (20594)

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

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

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 223
  time to evaluate  : 1.727 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7776 (tm-30)
REVERT: A  240 TRP cc_start: 0.8277 (t-100) cc_final: 0.7679 (t60)
REVERT: A  241 GLN cc_start: 0.7857 (mm-40) cc_final: 0.7499 (mm110)
REVERT: A  395 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7062 (mt)
REVERT: A  405 ASN cc_start: 0.7909 (t0) cc_final: 0.7464 (t0)
REVERT: A  422 GLN cc_start: 0.7820 (tm-30) cc_final: 0.7337 (tm-30)
REVERT: A  482 ILE cc_start: 0.8035 (pt) cc_final: 0.7608 (mt)
REVERT: A  583 ASP cc_start: 0.6315 (m-30) cc_final: 0.6103 (m-30)
REVERT: B  316 TRP cc_start: 0.8596 (m100) cc_final: 0.8345 (m100)
REVERT: B  418 ASP cc_start: 0.7205 (t70) cc_final: 0.6983 (t0)
REVERT: B  422 GLN cc_start: 0.8087 (tt0) cc_final: 0.7675 (mt0)
REVERT: B  551 SER cc_start: 0.7873 (p) cc_final: 0.7533 (t)
REVERT: B  575 ASP cc_start: 0.7551 (t0) cc_final: 0.7222 (t0)
REVERT: C  241 GLN cc_start: 0.7955 (mp10) cc_final: 0.7427 (mp10)
REVERT: C  311 LEU cc_start: 0.8201 (mt) cc_final: 0.7970 (tt)
REVERT: C  376 GLU cc_start: 0.8120 (pm20) cc_final: 0.7821 (tt0)
REVERT: C  439 ARG cc_start: 0.7789 (ttt90) cc_final: 0.7507 (ttt90)
REVERT: D  267 ASP cc_start: 0.7882 (t70) cc_final: 0.7112 (t0)
REVERT: D  339 HIS cc_start: 0.6974 (t-90) cc_final: 0.6704 (t-90)
  outliers start: 24
  outliers final: 15
  residues processed: 239
  average time/residue: 0.3558
  time to fit residues: 128.9394
Evaluate side-chains
  219 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 203
  time to evaluate  : 1.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  424 MET
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  474 LEU
Chi-restraints excluded: chain C residue  177 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain D residue  254 LEU
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  405 LEU
Chi-restraints excluded: chain D residue  608 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 71 optimal weight:    0.8980
   chunk 93 optimal weight:    0.8980
   chunk 85 optimal weight:    9.9990
   chunk 95 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 96 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 177 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 484 GLN
C 425 GLN
C 484 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.150521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.122480 restraints weight = 30111.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.123771 restraints weight = 24061.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.125338 restraints weight = 20603.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3453
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3453 r_free = 0.3453    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3453 r_free = 0.3453    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3453
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.2403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  15169  Z= 0.134
  Angle     :  0.507   8.327  20603  Z= 0.269
  Chirality :  0.041   0.158   2343
  Planarity :  0.004   0.048   2533
  Dihedral  :  9.962 177.717   2180
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 16.42 %
    Favored  : 81.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.20), residues: 1792
  helix:  1.61 (0.15), residues: 1165
  sheet: -0.57 (0.70), residues: 46
  loop : -0.57 (0.27), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B 316 
 HIS   0.004   0.001   HIS A 242 
 PHE   0.012   0.001   PHE C 301 
 TYR   0.015   0.001   TYR D 351 
 ARG   0.004   0.000   ARG D 239 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00062 (    3)
  link_NAG-ASN         : angle       2.16408 (    9)
  hydrogen bonds       : bond        0.03699 (  920)
  hydrogen bonds       : angle       3.72271 ( 2690)
  covalent geometry    : bond        0.00306 (15166)
  covalent geometry    : angle       0.50555 (20594)

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

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

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 207
  time to evaluate  : 1.608 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 GLU cc_start: 0.8343 (tm-30) cc_final: 0.7867 (tm-30)
REVERT: A  241 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7520 (mm110)
REVERT: A  395 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7192 (mt)
REVERT: A  422 GLN cc_start: 0.7968 (tm-30) cc_final: 0.7478 (tm-30)
REVERT: A  493 GLU cc_start: 0.7316 (tp30) cc_final: 0.6410 (tp30)
REVERT: A  583 ASP cc_start: 0.6518 (m-30) cc_final: 0.6280 (m-30)
REVERT: B  305 ASN cc_start: 0.8471 (t0) cc_final: 0.8208 (t0)
REVERT: B  418 ASP cc_start: 0.7504 (t70) cc_final: 0.7210 (t0)
REVERT: B  422 GLN cc_start: 0.8225 (tt0) cc_final: 0.7843 (mt0)
REVERT: B  575 ASP cc_start: 0.7583 (t0) cc_final: 0.7248 (t0)
REVERT: C  241 GLN cc_start: 0.8029 (mp10) cc_final: 0.7543 (mp10)
REVERT: C  311 LEU cc_start: 0.8177 (mt) cc_final: 0.7773 (tt)
REVERT: C  439 ARG cc_start: 0.7934 (ttt90) cc_final: 0.7601 (ttt90)
REVERT: C  484 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7842 (mp10)
REVERT: D  267 ASP cc_start: 0.8029 (t70) cc_final: 0.7225 (t0)
REVERT: D  339 HIS cc_start: 0.7161 (t-90) cc_final: 0.6897 (t-90)
  outliers start: 30
  outliers final: 21
  residues processed: 224
  average time/residue: 0.2281
  time to fit residues: 80.3994
Evaluate side-chains
  222 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 199
  time to evaluate  : 1.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  424 MET
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  474 LEU
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  177 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  349 SER
Chi-restraints excluded: chain C residue  434 GLU
Chi-restraints excluded: chain C residue  484 GLN
Chi-restraints excluded: chain D residue  254 LEU
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  290 LEU
Chi-restraints excluded: chain D residue  405 LEU
Chi-restraints excluded: chain D residue  431 VAL
Chi-restraints excluded: chain D residue  458 CYS
Chi-restraints excluded: chain D residue  608 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 73 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 114 optimal weight:    0.9980
   chunk 95 optimal weight:    1.9990
   chunk 43 optimal weight:    7.9990
   chunk 89 optimal weight:    4.9990
   chunk 177 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 39 optimal weight:    4.9990
   chunk 47 optimal weight:    0.8980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B 484 GLN
C 422 GLN
C 425 GLN
** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.150432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.120821 restraints weight = 23986.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.121804 restraints weight = 18069.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.122964 restraints weight = 15056.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3430
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3430 r_free = 0.3430    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3430 r_free = 0.3430    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3430
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  15169  Z= 0.130
  Angle     :  0.504   8.491  20603  Z= 0.266
  Chirality :  0.041   0.169   2343
  Planarity :  0.004   0.048   2533
  Dihedral  :  9.871 178.073   2180
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 17.10 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.21), residues: 1792
  helix:  1.73 (0.15), residues: 1165
  sheet: -0.53 (0.70), residues: 46
  loop : -0.49 (0.28), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.001   TRP B 316 
 HIS   0.003   0.001   HIS A 242 
 PHE   0.013   0.001   PHE C 483 
 TYR   0.014   0.001   TYR C 357 
 ARG   0.003   0.000   ARG C 223 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00046 (    3)
  link_NAG-ASN         : angle       2.12129 (    9)
  hydrogen bonds       : bond        0.03700 (  920)
  hydrogen bonds       : angle       3.69579 ( 2690)
  covalent geometry    : bond        0.00294 (15166)
  covalent geometry    : angle       0.50229 (20594)

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

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

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 207
  time to evaluate  : 1.712 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7818 (tm-30)
REVERT: A  241 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7512 (mm110)
REVERT: A  395 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7169 (mt)
REVERT: A  422 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7383 (tm-30)
REVERT: A  583 ASP cc_start: 0.6399 (m-30) cc_final: 0.6167 (m-30)
REVERT: B  305 ASN cc_start: 0.8388 (t0) cc_final: 0.8172 (t0)
REVERT: B  418 ASP cc_start: 0.7217 (t70) cc_final: 0.6954 (t0)
REVERT: B  422 GLN cc_start: 0.8089 (tt0) cc_final: 0.7705 (mt0)
REVERT: B  575 ASP cc_start: 0.7567 (t0) cc_final: 0.7262 (t0)
REVERT: C  241 GLN cc_start: 0.7943 (mp10) cc_final: 0.7537 (mp10)
REVERT: C  311 LEU cc_start: 0.8224 (mt) cc_final: 0.7951 (tp)
REVERT: C  439 ARG cc_start: 0.7892 (ttt90) cc_final: 0.7570 (ttt90)
REVERT: C  480 VAL cc_start: 0.8712 (t) cc_final: 0.8359 (t)
REVERT: D  267 ASP cc_start: 0.7864 (t70) cc_final: 0.7017 (t0)
  outliers start: 30
  outliers final: 21
  residues processed: 224
  average time/residue: 0.2884
  time to fit residues: 100.8654
Evaluate side-chains
  222 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 200
  time to evaluate  : 1.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  586 GLU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  417 ILE
Chi-restraints excluded: chain B residue  424 MET
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  474 LEU
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  177 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  349 SER
Chi-restraints excluded: chain D residue  254 LEU
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  290 LEU
Chi-restraints excluded: chain D residue  405 LEU
Chi-restraints excluded: chain D residue  431 VAL
Chi-restraints excluded: chain D residue  608 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 173 optimal weight:    4.9990
   chunk 105 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 167 optimal weight:    0.0030
   chunk 90 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 102 optimal weight:    0.6980
   chunk 30 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 156 optimal weight:    0.6980
   overall best weight:    0.5990

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

Flipped N/Q/H residues before XYZ refinement:
B 484 GLN
C 425 GLN
D 453 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.151735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.121588 restraints weight = 21076.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.123339 restraints weight = 15992.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.123763 restraints weight = 11948.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3440
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3440 r_free = 0.3440    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3440 r_free = 0.3440    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3440
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.2612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  15169  Z= 0.113
  Angle     :  0.505   7.979  20603  Z= 0.266
  Chirality :  0.040   0.183   2343
  Planarity :  0.003   0.049   2533
  Dihedral  :  9.767 178.852   2180
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 18.09 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.21), residues: 1792
  helix:  1.83 (0.15), residues: 1167
  sheet: -0.47 (0.70), residues: 46
  loop : -0.42 (0.28), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.059   0.001   TRP B 316 
 HIS   0.003   0.001   HIS A 242 
 PHE   0.016   0.001   PHE C 483 
 TYR   0.012   0.001   TYR C 357 
 ARG   0.005   0.000   ARG A 499 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00016 (    3)
  link_NAG-ASN         : angle       2.07554 (    9)
  hydrogen bonds       : bond        0.03556 (  920)
  hydrogen bonds       : angle       3.65499 ( 2690)
  covalent geometry    : bond        0.00247 (15166)
  covalent geometry    : angle       0.50310 (20594)

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

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

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 209
  time to evaluate  : 1.556 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7804 (tm-30)
REVERT: A  241 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7500 (mm110)
REVERT: A  395 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7054 (mt)
REVERT: A  422 GLN cc_start: 0.7733 (tm-30) cc_final: 0.7328 (tm-30)
REVERT: A  579 LEU cc_start: 0.7980 (tp) cc_final: 0.7763 (tt)
REVERT: A  583 ASP cc_start: 0.6474 (m-30) cc_final: 0.6227 (m-30)
REVERT: B  418 ASP cc_start: 0.7218 (t70) cc_final: 0.6951 (t0)
REVERT: B  422 GLN cc_start: 0.8057 (tt0) cc_final: 0.7676 (mt0)
REVERT: B  575 ASP cc_start: 0.7532 (t0) cc_final: 0.7267 (t0)
REVERT: C  311 LEU cc_start: 0.8250 (mt) cc_final: 0.7997 (tt)
REVERT: C  439 ARG cc_start: 0.7884 (ttt90) cc_final: 0.7543 (ttt90)
REVERT: D  267 ASP cc_start: 0.7874 (t70) cc_final: 0.7014 (t0)
  outliers start: 26
  outliers final: 18
  residues processed: 226
  average time/residue: 0.2215
  time to fit residues: 78.8117
Evaluate side-chains
  221 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 202
  time to evaluate  : 1.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  424 MET
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  474 LEU
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  177 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  349 SER
Chi-restraints excluded: chain D residue  254 LEU
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  290 LEU
Chi-restraints excluded: chain D residue  405 LEU
Chi-restraints excluded: chain D residue  431 VAL
Chi-restraints excluded: chain D residue  608 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 44 optimal weight:    4.9990
   chunk 154 optimal weight:    2.9990
   chunk 90 optimal weight:    0.0370
   chunk 10 optimal weight:    8.9990
   chunk 60 optimal weight:    0.5980
   chunk 132 optimal weight:    4.9990
   chunk 174 optimal weight:    6.9990
   chunk 155 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9980
   chunk 162 optimal weight:    0.8980
   overall best weight:    0.6658

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

Flipped N/Q/H residues before XYZ refinement:
B 484 GLN
C 229 GLN
C 422 GLN
C 425 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.151580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.121579 restraints weight = 20893.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.122890 restraints weight = 16199.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.124420 restraints weight = 12469.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3437
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3437 r_free = 0.3437    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3437 r_free = 0.3437    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3437
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.2691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  15169  Z= 0.117
  Angle     :  0.518   9.974  20603  Z= 0.270
  Chirality :  0.040   0.191   2343
  Planarity :  0.004   0.050   2533
  Dihedral  :  9.666 179.040   2180
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 18.71 %
    Favored  : 79.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.21), residues: 1792
  helix:  1.90 (0.15), residues: 1167
  sheet: -0.47 (0.70), residues: 46
  loop : -0.40 (0.27), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.001   TRP B 316 
 HIS   0.003   0.001   HIS A 242 
 PHE   0.013   0.001   PHE C 180 
 TYR   0.013   0.001   TYR C 357 
 ARG   0.005   0.000   ARG A 499 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00016 (    3)
  link_NAG-ASN         : angle       2.07780 (    9)
  hydrogen bonds       : bond        0.03563 (  920)
  hydrogen bonds       : angle       3.62834 ( 2690)
  covalent geometry    : bond        0.00259 (15166)
  covalent geometry    : angle       0.51661 (20594)

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

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

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 211
  time to evaluate  : 1.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7815 (tm-30)
REVERT: A  395 ILE cc_start: 0.7712 (OUTLIER) cc_final: 0.7082 (mt)
REVERT: A  422 GLN cc_start: 0.7730 (tm-30) cc_final: 0.7381 (tm-30)
REVERT: A  583 ASP cc_start: 0.6403 (m-30) cc_final: 0.6132 (m-30)
REVERT: B  418 ASP cc_start: 0.7260 (t70) cc_final: 0.7005 (t0)
REVERT: B  422 GLN cc_start: 0.8082 (tt0) cc_final: 0.7712 (mt0)
REVERT: B  575 ASP cc_start: 0.7601 (t0) cc_final: 0.7312 (t0)
REVERT: C  241 GLN cc_start: 0.7954 (mp10) cc_final: 0.7520 (mp10)
REVERT: C  311 LEU cc_start: 0.8258 (mt) cc_final: 0.7930 (tp)
REVERT: C  439 ARG cc_start: 0.7884 (ttt90) cc_final: 0.7546 (ttt90)
  outliers start: 25
  outliers final: 21
  residues processed: 228
  average time/residue: 0.2244
  time to fit residues: 79.8509
Evaluate side-chains
  221 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 199
  time to evaluate  : 1.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  539 VAL
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  424 MET
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  474 LEU
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  177 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  349 SER
Chi-restraints excluded: chain D residue  254 LEU
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  290 LEU
Chi-restraints excluded: chain D residue  405 LEU
Chi-restraints excluded: chain D residue  431 VAL
Chi-restraints excluded: chain D residue  458 CYS
Chi-restraints excluded: chain D residue  608 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 48 optimal weight:    0.3980
   chunk 132 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 119 optimal weight:    3.9990
   chunk 131 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 125 optimal weight:    2.9990
   chunk 93 optimal weight:    0.8980
   chunk 67 optimal weight:    0.7980
   chunk 3 optimal weight:    0.1980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 241 GLN
B 422 GLN
C 425 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.151753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.121856 restraints weight = 23732.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.123394 restraints weight = 17386.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.124419 restraints weight = 14072.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3454
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3454 r_free = 0.3454    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3454 r_free = 0.3454    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3454
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.2752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  15169  Z= 0.114
  Angle     :  0.516  10.132  20603  Z= 0.268
  Chirality :  0.040   0.204   2343
  Planarity :  0.004   0.051   2533
  Dihedral  :  9.594 179.417   2180
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 19.14 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.20), residues: 1792
  helix:  2.00 (0.15), residues: 1153
  sheet: -0.45 (0.70), residues: 46
  loop : -0.28 (0.27), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.001   TRP B 316 
 HIS   0.003   0.001   HIS A 242 
 PHE   0.012   0.001   PHE B 547 
 TYR   0.012   0.001   TYR C 357 
 ARG   0.006   0.000   ARG A 499 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00017 (    3)
  link_NAG-ASN         : angle       2.08558 (    9)
  hydrogen bonds       : bond        0.03527 (  920)
  hydrogen bonds       : angle       3.62176 ( 2690)
  covalent geometry    : bond        0.00253 (15166)
  covalent geometry    : angle       0.51468 (20594)

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

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

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 209
  time to evaluate  : 1.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7843 (tm-30)
REVERT: A  395 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7056 (mt)
REVERT: A  422 GLN cc_start: 0.7791 (tm-30) cc_final: 0.7402 (tm-30)
REVERT: A  583 ASP cc_start: 0.6451 (m-30) cc_final: 0.6164 (m-30)
REVERT: B  418 ASP cc_start: 0.7485 (t70) cc_final: 0.7192 (t0)
REVERT: B  422 GLN cc_start: 0.8130 (tt0) cc_final: 0.7837 (mt0)
REVERT: B  575 ASP cc_start: 0.7731 (t0) cc_final: 0.7513 (t0)
REVERT: C  241 GLN cc_start: 0.7948 (mp10) cc_final: 0.7439 (mp10)
REVERT: C  311 LEU cc_start: 0.8264 (mt) cc_final: 0.7913 (tp)
REVERT: C  439 ARG cc_start: 0.7979 (ttt90) cc_final: 0.7588 (ttt90)
REVERT: C  591 TYR cc_start: 0.8018 (m-80) cc_final: 0.7785 (m-80)
  outliers start: 24
  outliers final: 21
  residues processed: 225
  average time/residue: 0.2233
  time to fit residues: 78.5458
Evaluate side-chains
  225 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 203
  time to evaluate  : 1.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  360 THR
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  539 VAL
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  359 SER
Chi-restraints excluded: chain B residue  424 MET
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  474 LEU
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  177 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  349 SER
Chi-restraints excluded: chain D residue  254 LEU
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  290 LEU
Chi-restraints excluded: chain D residue  405 LEU
Chi-restraints excluded: chain D residue  431 VAL
Chi-restraints excluded: chain D residue  608 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 169 optimal weight:    0.0030
   chunk 125 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 127 optimal weight:    2.9990
   chunk 121 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 137 optimal weight:    0.8980
   chunk 145 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 78 optimal weight:    0.5980
   overall best weight:    0.5990

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

Flipped N/Q/H residues before XYZ refinement:
B 484 GLN
C 422 GLN
C 425 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.152171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.124126 restraints weight = 29851.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.124205 restraints weight = 23910.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.125905 restraints weight = 23142.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3463
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3463 r_free = 0.3463    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3463 r_free = 0.3463    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3463
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.2809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  15169  Z= 0.114
  Angle     :  0.527  10.651  20603  Z= 0.271
  Chirality :  0.040   0.207   2343
  Planarity :  0.004   0.051   2533
  Dihedral  :  9.556 179.694   2180
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 19.39 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.20), residues: 1792
  helix:  2.03 (0.15), residues: 1153
  sheet: -0.41 (0.70), residues: 46
  loop : -0.27 (0.27), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.001   TRP B 316 
 HIS   0.003   0.001   HIS A 242 
 PHE   0.012   0.001   PHE B 547 
 TYR   0.025   0.001   TYR D 229 
 ARG   0.007   0.000   ARG A 499 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00012 (    3)
  link_NAG-ASN         : angle       2.04071 (    9)
  hydrogen bonds       : bond        0.03508 (  920)
  hydrogen bonds       : angle       3.60015 ( 2690)
  covalent geometry    : bond        0.00253 (15166)
  covalent geometry    : angle       0.52525 (20594)

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

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

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3584 Ramachandran restraints generated.
    1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 206
  time to evaluate  : 1.600 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7868 (tm-30)
REVERT: A  395 ILE cc_start: 0.7660 (OUTLIER) cc_final: 0.7035 (mt)
REVERT: A  497 LYS cc_start: 0.7534 (mmtp) cc_final: 0.7264 (mmmt)
REVERT: A  583 ASP cc_start: 0.6436 (m-30) cc_final: 0.6127 (m-30)
REVERT: B  418 ASP cc_start: 0.7459 (t70) cc_final: 0.7170 (t0)
REVERT: B  422 GLN cc_start: 0.8072 (tt0) cc_final: 0.7823 (mt0)
REVERT: C  241 GLN cc_start: 0.7964 (mp10) cc_final: 0.7452 (mp10)
REVERT: C  311 LEU cc_start: 0.8184 (mt) cc_final: 0.7802 (tp)
REVERT: C  439 ARG cc_start: 0.7952 (ttt90) cc_final: 0.7597 (ttt90)
  outliers start: 25
  outliers final: 23
  residues processed: 222
  average time/residue: 0.2408
  time to fit residues: 83.3552
Evaluate side-chains
  229 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 205
  time to evaluate  : 1.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  360 THR
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  539 VAL
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  359 SER
Chi-restraints excluded: chain B residue  424 MET
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  474 LEU
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  177 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  349 SER
Chi-restraints excluded: chain D residue  254 LEU
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  290 LEU
Chi-restraints excluded: chain D residue  405 LEU
Chi-restraints excluded: chain D residue  431 VAL
Chi-restraints excluded: chain D residue  458 CYS
Chi-restraints excluded: chain D residue  608 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 99 optimal weight:    4.9990
   chunk 169 optimal weight:    0.7980
   chunk 153 optimal weight:    3.9990
   chunk 108 optimal weight:    0.9990
   chunk 140 optimal weight:    3.9990
   chunk 81 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0970
   chunk 166 optimal weight:    0.9990
   chunk 91 optimal weight:    0.5980
   chunk 133 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 305 ASN
C 425 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.151972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.122064 restraints weight = 21031.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.124029 restraints weight = 15967.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.124982 restraints weight = 12231.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3460
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3460 r_free = 0.3460    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3460 r_free = 0.3460    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3460
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.2842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  15169  Z= 0.115
  Angle     :  0.534  10.937  20603  Z= 0.274
  Chirality :  0.040   0.206   2343
  Planarity :  0.004   0.051   2533
  Dihedral  :  9.545 179.824   2180
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 19.52 %
    Favored  : 78.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.20), residues: 1792
  helix:  2.04 (0.15), residues: 1148
  sheet: -0.43 (0.71), residues: 46
  loop : -0.23 (0.27), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.001   TRP B 316 
 HIS   0.003   0.001   HIS A 242 
 PHE   0.012   0.001   PHE B 547 
 TYR   0.023   0.001   TYR D 229 
 ARG   0.007   0.000   ARG A 499 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00015 (    3)
  link_NAG-ASN         : angle       2.00890 (    9)
  hydrogen bonds       : bond        0.03516 (  920)
  hydrogen bonds       : angle       3.60347 ( 2690)
  covalent geometry    : bond        0.00257 (15166)
  covalent geometry    : angle       0.53244 (20594)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5228.38 seconds
wall clock time: 94 minutes 32.61 seconds (5672.61 seconds total)