Starting phenix.real_space_refine
on Fri Jun 13 01:19:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8evc_28626/06_2025/8evc_28626_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8evc_28626/06_2025/8evc_28626.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.33
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8evc_28626/06_2025/8evc_28626.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8evc_28626/06_2025/8evc_28626.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8evc_28626/06_2025/8evc_28626_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8evc_28626/06_2025/8evc_28626_neut.cif"
  }
  resolution = 3.33
  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=   0.001 sd=   0.034
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      65      5.16       5
     C    9470      2.51       5
     N    2369      2.21       5
     O    2623      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 166 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 14531
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 446, 3632
          Classifications: {'peptide': 446}
          Link IDs: {'PTRANS': 14, 'TRANS': 431}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3565
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 436, 3565
          Classifications: {'peptide': 436}
          Link IDs: {'PTRANS': 13, 'TRANS': 422}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 3598
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 441, 3598
          Classifications: {'peptide': 441}
          Link IDs: {'PTRANS': 14, 'TRANS': 426}
          Chain breaks: 1
    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: 8.63, per 1000 atoms: 0.59
  Number of scatterers: 14531
  At special positions: 0
  Unit cell: (104.58, 108.73, 124.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      65     16.00
     P       4     15.00
     O    2623      8.00
     N    2369      7.00
     C    9470      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: 3.46
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3496 Ramachandran restraints generated.
    1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3340

  Finding SS restraints...
    Secondary structure from input PDB file:
      69 helices and 13 sheets defined
      65.7% alpha, 5.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 166 through 192
      Proline residue:  A 178  - end of helix
      removed outlier: 5.453A  pdb=" N   ILE A 187 " --> pdb=" O   TRP A 183 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   CYS A 188 " --> pdb=" O   TYR A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 198
      removed outlier: 3.971A  pdb=" N   GLN A 196 " --> pdb=" O   PHE A 192 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   SER A 197 " --> pdb=" O   ASP A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 222
    Processing helix  chain 'A' and resid 235 through 246
      removed outlier: 4.197A  pdb=" N   THR A 246 " --> pdb=" O   HIS A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 255
    Processing helix  chain 'A' and resid 271 through 278
      removed outlier: 3.688A  pdb=" N   PHE A 275 " --> pdb=" O   GLU A 272 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   ASN A 276 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ARG A 277 " --> pdb=" O   ARG A 274 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   LEU A 278 " --> pdb=" O   PHE A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 295
    Processing helix  chain 'A' and resid 297 through 329
    Processing helix  chain 'A' and resid 347 through 364
    Processing helix  chain 'A' and resid 374 through 428
      removed outlier: 4.099A  pdb=" N   MET A 406 " --> pdb=" O   MET A 402 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ASN A 407 " --> pdb=" O   ILE A 403 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   SER A 409 " --> pdb=" O   ASN A 405 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   ARG A 410 " --> pdb=" O   MET A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 447
    Processing helix  chain 'A' and resid 452 through 457
    Processing helix  chain 'A' and resid 461 through 473
    Processing helix  chain 'A' and resid 473 through 478
    Processing helix  chain 'A' and resid 487 through 498
    Processing helix  chain 'A' and resid 548 through 553
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 591 through 609
      removed outlier: 3.862A  pdb=" N   LYS A 595 " --> pdb=" O   TYR A 591 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 193
      Proline residue:  B 178  - end of helix
    Processing helix  chain 'B' and resid 194 through 199
    Processing helix  chain 'B' and resid 199 through 223
      removed outlier: 3.947A  pdb=" N   TRP B 203 " --> pdb=" O   TYR B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 245
    Processing helix  chain 'B' and resid 246 through 255
    Processing helix  chain 'B' and resid 273 through 279
      removed outlier: 3.884A  pdb=" N   ASN B 276 " --> pdb=" O   VAL B 273 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   LEU B 278 " --> pdb=" O   PHE B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 295
      removed outlier: 4.259A  pdb=" N   LEU B 284 " --> pdb=" O   LYS B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 329
    Processing helix  chain 'B' and resid 347 through 364
    Processing helix  chain 'B' and resid 374 through 406
    Processing helix  chain 'B' and resid 408 through 427
    Processing helix  chain 'B' and resid 430 through 447
    Processing helix  chain 'B' and resid 452 through 457
    Processing helix  chain 'B' and resid 461 through 478
      removed outlier: 5.756A  pdb=" N   ASP B 475 " --> pdb=" O   ASN B 471 " (cutoff:3.500A)
      removed outlier: 5.441A  pdb=" N   THR B 476 " --> pdb=" O   VAL B 472 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 491 through 496
      removed outlier: 3.985A  pdb=" N   VAL B 495 " --> pdb=" O   LEU B 491 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   LEU B 496 " --> pdb=" O   VAL B 492 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 491 through 496'
    Processing helix  chain 'B' and resid 581 through 587
    Processing helix  chain 'B' and resid 591 through 610
      removed outlier: 4.214A  pdb=" N   LYS B 595 " --> pdb=" O   TYR B 591 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 165 through 190
      Proline residue:  C 178  - end of helix
    Processing helix  chain 'C' and resid 192 through 199
      removed outlier: 3.982A  pdb=" N   GLN C 196 " --> pdb=" O   PHE C 192 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 199 through 223
    Processing helix  chain 'C' and resid 235 through 245
    Processing helix  chain 'C' and resid 247 through 255
    Processing helix  chain 'C' and resid 274 through 279
      removed outlier: 3.842A  pdb=" N   LEU C 278 " --> pdb=" O   PHE C 275 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 281 through 295
    Processing helix  chain 'C' and resid 297 through 329
    Processing helix  chain 'C' and resid 347 through 364
    Processing helix  chain 'C' and resid 374 through 427
      removed outlier: 5.240A  pdb=" N   SER C 409 " --> pdb=" O   ASN C 405 " (cutoff:3.500A)
      removed outlier: 5.949A  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 453 through 460
    Processing helix  chain 'C' and resid 461 through 479
      removed outlier: 5.107A  pdb=" N   ASP C 475 " --> pdb=" O   ASN C 471 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   THR C 476 " --> pdb=" O   VAL C 472 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   LYS C 479 " --> pdb=" O   ASP C 475 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 488 through 497
    Processing helix  chain 'C' and resid 580 through 588
    Processing helix  chain 'C' and resid 592 through 607
    Processing helix  chain 'D' and resid 215 through 242
      removed outlier: 3.522A  pdb=" N   ALA D 228 " --> pdb=" O   LEU D 224 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   TRP D 231 " --> pdb=" O   LEU D 227 " (cutoff:3.500A)
      Proline residue:  D 237  - end of helix
    Processing helix  chain 'D' and resid 249 through 272
    Processing helix  chain 'D' and resid 273 through 275
      No H-bonds generated for 'chain 'D' and resid 273 through 275'
    Processing helix  chain 'D' and resid 286 through 296
    Processing helix  chain 'D' and resid 298 through 307
    Processing helix  chain 'D' and resid 310 through 318
      removed outlier: 4.163A  pdb=" N   LEU D 315 " --> pdb=" O   ASP D 311 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   PHE D 316 " --> pdb=" O   ILE D 312 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 330 through 345
    Processing helix  chain 'D' and resid 347 through 379
      removed outlier: 4.353A  pdb=" N   TYR D 351 " --> pdb=" O   LYS D 347 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 394 through 406
      removed outlier: 3.805A  pdb=" N   TRP D 400 " --> pdb=" O   ARG D 396 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 416 through 449
      removed outlier: 4.072A  pdb=" N   THR D 449 " --> pdb=" O   ILE D 445 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 449 through 469
    Processing helix  chain 'D' and resid 472 through 490
    Processing helix  chain 'D' and resid 494 through 499
      removed outlier: 3.850A  pdb=" N   LEU D 498 " --> pdb=" O   ASP D 494 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 503 through 522
    Processing helix  chain 'D' and resid 529 through 540
    Processing helix  chain 'D' and resid 592 through 600
      removed outlier: 4.044A  pdb=" N   LEU D 595 " --> pdb=" O   GLU D 592 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   LEU D 596 " --> pdb=" O   ILE D 593 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   ALA D 597 " --> pdb=" O   SER D 594 " (cutoff:3.500A)
      removed outlier: 4.856A  pdb=" N   ALA D 598 " --> pdb=" O   LEU D 595 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 620 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: 3.597A  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
    Processing sheet with id=AA3, first strand: chain 'A' and resid 507 through 510
      removed outlier: 3.949A  pdb=" N   ASP A 507 " --> pdb=" O   SER A 570 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   ILE A 568 " --> pdb=" O   ILE A 509 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   ASN A 567 " --> pdb=" O   VAL A 530 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 227 through 228
    Processing sheet with id=AA5, first strand: chain 'B' and resid 499 through 503
    Processing sheet with id=AA6, first strand: chain 'B' and resid 507 through 508
      removed outlier: 3.579A  pdb=" N   ASP B 507 " --> pdb=" O   SER B 570 " (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 501 through 503
    Processing sheet with id=AA9, first strand: chain 'C' and resid 508 through 510
      removed outlier: 6.882A  pdb=" N   TYR C 508 " --> pdb=" O   SER C 570 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   SER C 570 " --> pdb=" O   TYR C 508 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   CYS C 510 " --> pdb=" O   ILE C 568 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ASN C 567 " --> pdb=" O   VAL C 530 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 520 through 521
    Processing sheet with id=AB2, first strand: chain 'D' and resid 277 through 279
      removed outlier: 4.014A  pdb=" N   PHE D 277 " --> pdb=" O   ILE D 284 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ASP D 282 " --> pdb=" O   ARG D 279 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 541 through 545
      removed outlier: 3.555A  pdb=" N   SER D 588 " --> pdb=" O   ILE D 564 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 550 through 552
      removed outlier: 6.934A  pdb=" N   VAL D 608 " --> pdb=" O   VAL D 551 " (cutoff:3.500A)
      removed outlier: 4.784A  pdb=" N   VAL D 582 " --> pdb=" O   VAL D 571 " (cutoff:3.500A)

    908 hydrogen bonds defined for protein.
    2652 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: 4.88

  Time building geometry restraints manager: 4.11 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4302
        1.34 -     1.46: 3330
        1.46 -     1.58: 7142
        1.58 -     1.70: 0
        1.70 -     1.82: 104
  Bond restraints: 14878
  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 3.42e+01
  bond pdb=" O5' PCG C 802 "
       pdb=" PA  PCG C 802 "
    ideal  model  delta    sigma   weight residual
    1.606  1.489  0.117 2.00e-02 2.50e+03 3.40e+01
  bond pdb=" O5' PCG B 802 "
       pdb=" PA  PCG B 802 "
    ideal  model  delta    sigma   weight residual
    1.606  1.490  0.116 2.00e-02 2.50e+03 3.37e+01
  bond pdb=" O5' PCG A 802 "
       pdb=" PA  PCG A 802 "
    ideal  model  delta    sigma   weight residual
    1.606  1.490  0.116 2.00e-02 2.50e+03 3.35e+01
  bond pdb=" O3' PCG B 802 "
       pdb=" PA  PCG B 802 "
    ideal  model  delta    sigma   weight residual
    1.617  1.513  0.104 2.00e-02 2.50e+03 2.69e+01
  ... (remaining 14873 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.66: 19963
        3.66 -     7.31: 167
        7.31 -    10.97: 48
       10.97 -    14.62: 4
       14.62 -    18.28: 12
  Bond angle restraints: 20194
  Sorted by residual:
  angle pdb=" C3' PCG B 802 "
        pdb=" C4' PCG B 802 "
        pdb=" C5' PCG B 802 "
      ideal   model   delta    sigma   weight residual
     109.85  128.13  -18.28 3.00e+00 1.11e-01 3.71e+01
  angle pdb=" C3' PCG D 901 "
        pdb=" C4' PCG D 901 "
        pdb=" C5' PCG D 901 "
      ideal   model   delta    sigma   weight residual
     109.85  128.12  -18.27 3.00e+00 1.11e-01 3.71e+01
  angle pdb=" C3' PCG C 802 "
        pdb=" C4' PCG C 802 "
        pdb=" C5' PCG C 802 "
      ideal   model   delta    sigma   weight residual
     109.85  128.11  -18.26 3.00e+00 1.11e-01 3.71e+01
  angle pdb=" C3' PCG A 802 "
        pdb=" C4' PCG A 802 "
        pdb=" C5' PCG A 802 "
      ideal   model   delta    sigma   weight residual
     109.85  128.07  -18.22 3.00e+00 1.11e-01 3.69e+01
  angle pdb=" O1A PCG C 802 "
        pdb=" PA  PCG C 802 "
        pdb=" O5' PCG C 802 "
      ideal   model   delta    sigma   weight residual
     102.28  117.92  -15.64 3.00e+00 1.11e-01 2.72e+01
  ... (remaining 20189 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.94: 8383
       25.94 -    51.88: 461
       51.88 -    77.81: 33
       77.81 -   103.75: 13
      103.75 -   129.69: 16
  Dihedral angle restraints: 8906
    sinusoidal: 3709
      harmonic: 5197
  Sorted by residual:
  dihedral pdb=" CA  THR A 245 "
           pdb=" C   THR A 245 "
           pdb=" N   THR A 246 "
           pdb=" CA  THR A 246 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.91  -28.09     0      5.00e+00 4.00e-02 3.16e+01
  dihedral pdb=" N   SER C 558 "
           pdb=" C   SER C 558 "
           pdb=" CA  SER C 558 "
           pdb=" CB  SER C 558 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  135.17  -12.37     0      2.50e+00 1.60e-01 2.45e+01
  dihedral pdb=" C   THR B 536 "
           pdb=" N   THR B 536 "
           pdb=" CA  THR B 536 "
           pdb=" CB  THR B 536 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -133.71   11.71     0      2.50e+00 1.60e-01 2.20e+01
  ... (remaining 8903 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.356: 2289
       0.356 -    0.712: 4
       0.712 -    1.069: 0
       1.069 -    1.425: 0
       1.425 -    1.781: 4
  Chirality restraints: 2297
  Sorted by residual:
  chirality pdb=" C4' PCG C 802 "
            pdb=" C3' PCG C 802 "
            pdb=" C5' PCG C 802 "
            pdb=" O4' PCG C 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -0.72   -1.78 2.00e-01 2.50e+01 7.93e+01
  chirality pdb=" C4' PCG D 901 "
            pdb=" C3' PCG D 901 "
            pdb=" C5' PCG D 901 "
            pdb=" O4' PCG D 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -0.72   -1.78 2.00e-01 2.50e+01 7.92e+01
  chirality pdb=" C4' PCG B 802 "
            pdb=" C3' PCG B 802 "
            pdb=" C5' PCG B 802 "
            pdb=" O4' PCG B 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -0.72   -1.78 2.00e-01 2.50e+01 7.90e+01
  ... (remaining 2294 not shown)

  Planarity restraints: 2483
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 389 "   -0.016 2.00e-02 2.50e+03   3.16e-02 9.96e+00
        pdb=" C   VAL A 389 "    0.055 2.00e-02 2.50e+03
        pdb=" O   VAL A 389 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   LEU A 390 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE D 512 "   -0.015 2.00e-02 2.50e+03   3.03e-02 9.20e+00
        pdb=" C   ILE D 512 "    0.052 2.00e-02 2.50e+03
        pdb=" O   ILE D 512 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ASP D 513 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET D 268 "   -0.015 2.00e-02 2.50e+03   3.01e-02 9.07e+00
        pdb=" C   MET D 268 "    0.052 2.00e-02 2.50e+03
        pdb=" O   MET D 268 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   LEU D 269 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 2480 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 2073
        2.76 -     3.30: 13460
        3.30 -     3.83: 24620
        3.83 -     4.37: 27484
        4.37 -     4.90: 48265
  Nonbonded interactions: 115902
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS B 512 "
            pdb=" O   THR B 565 "
     model   vdw
     2.228 3.120
  nonbonded pdb=" O   THR C 360 "
            pdb=" OG1 THR C 364 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" NH1 ARG B 564 "
            pdb=" O2A PCG B 802 "
     model   vdw
     2.304 3.120
  nonbonded pdb=" OG1 THR A 476 "
            pdb=" OD1 ASN A 523 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" O   TYR D 294 "
            pdb=" OG  SER D 297 "
     model   vdw
     2.331 3.040
  ... (remaining 115897 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 159 through 257 or resid 269 through 483 or resid 489 thro \ 
ugh 607 or resid 801 through 802))
  selection = (chain 'B' and (resid 159 through 607 or resid 801 through 802))
  selection = (chain 'C' and (resid 159 through 257 or resid 269 through 483 or resid 489 thro \ 
ugh 607 or resid 801 through 802))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.610
  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:          0.600
  Check model and map are aligned:         0.110
  Set scattering table:                    0.140
  Process input model:                     33.090
  Find NCS groups from input model:        0.640
  Set up NCS constraints:                  0.080
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
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  14881  Z= 0.316
  Angle     :  1.073  18.281  20203  Z= 0.538
  Chirality :  0.094   1.781   2297
  Planarity :  0.008   0.069   2480
  Dihedral  : 16.450 129.691   5566
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  4.29 %
    Favored  : 94.76 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.28 (0.14), residues: 1748
  helix: -2.78 (0.10), residues: 1115
  sheet: -2.84 (0.48), residues: 74
  loop : -2.49 (0.22), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP C 240 
 HIS   0.007   0.002   HIS B 473 
 PHE   0.043   0.002   PHE D 427 
 TYR   0.039   0.002   TYR D 314 
 ARG   0.015   0.001   ARG D 324 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00435 (    3)
  link_NAG-ASN         : angle       2.72301 (    9)
  hydrogen bonds       : bond        0.10910 (  908)
  hydrogen bonds       : angle       6.34087 ( 2652)
  covalent geometry    : bond        0.00649 (14878)
  covalent geometry    : angle       1.07134 (20194)

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

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

  3496 Ramachandran restraints generated.
    1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3496 Ramachandran restraints generated.
    1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 238
  time to evaluate  : 1.698 
Fit side-chains
   revert: symmetry clash
REVERT: A  175 ILE cc_start: 0.8563 (tp) cc_final: 0.8358 (tp)
REVERT: B  175 ILE cc_start: 0.8695 (tp) cc_final: 0.8349 (tp)
REVERT: B  445 TRP cc_start: 0.8669 (t-100) cc_final: 0.8377 (t-100)
REVERT: B  526 LYS cc_start: 0.8231 (mmmt) cc_final: 0.7898 (mmtm)
REVERT: C  184 TYR cc_start: 0.7581 (m-80) cc_final: 0.7080 (m-80)
REVERT: C  407 ASN cc_start: 0.7542 (t0) cc_final: 0.6957 (t0)
REVERT: D  532 MET cc_start: 0.4701 (tmm) cc_final: 0.4458 (tmm)
REVERT: D  608 VAL cc_start: 0.7484 (OUTLIER) cc_final: 0.7235 (p)
REVERT: D  639 MET cc_start: 0.6085 (mmp) cc_final: 0.4718 (mtt)
  outliers start: 15
  outliers final: 3
  residues processed: 253
  average time/residue: 0.3253
  time to fit residues: 120.9724
Evaluate side-chains
  158 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 154
  time to evaluate  : 1.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 LYS
Chi-restraints excluded: chain C residue  342 ILE
Chi-restraints excluded: chain C residue  396 VAL
Chi-restraints excluded: chain D residue  608 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 147 optimal weight:    0.9980
   chunk 132 optimal weight:    0.9980
   chunk 73 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 89 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 137 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 83 optimal weight:    4.9990
   chunk 102 optimal weight:    0.6980
   chunk 158 optimal weight:    3.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A 414 GLN
** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 196 GLN
B 317 ASN
B 407 ASN
** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 537 GLN
C 229 GLN
C 317 ASN
C 414 GLN
C 425 GLN
D 340 HIS
D 423 GLN
D 468 ASN
D 607 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.164016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.124093 restraints weight = 19445.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 2.07
r_work: 0.3384 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3249 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.1402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  14881  Z= 0.133
  Angle     :  0.551   8.143  20203  Z= 0.294
  Chirality :  0.041   0.273   2297
  Planarity :  0.005   0.048   2480
  Dihedral  : 13.110 149.593   2144
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  8.90 %
    Favored  : 89.65 %
  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: -1.66 (0.18), residues: 1748
  helix: -0.45 (0.14), residues: 1118
  sheet: -2.67 (0.50), residues: 75
  loop : -2.01 (0.24), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 171 
 HIS   0.005   0.001   HIS A 315 
 PHE   0.017   0.001   PHE C 547 
 TYR   0.015   0.001   TYR D 314 
 ARG   0.008   0.001   ARG B 439 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00211 (    3)
  link_NAG-ASN         : angle       2.83517 (    9)
  hydrogen bonds       : bond        0.04431 (  908)
  hydrogen bonds       : angle       4.70854 ( 2652)
  covalent geometry    : bond        0.00286 (14878)
  covalent geometry    : angle       0.54761 (20194)

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

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

  3496 Ramachandran restraints generated.
    1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3496 Ramachandran restraints generated.
    1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 176
  time to evaluate  : 1.510 
Fit side-chains
REVERT: A  175 ILE cc_start: 0.8597 (tp) cc_final: 0.8390 (tp)
REVERT: A  524 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7140 (mm-30)
REVERT: B  175 ILE cc_start: 0.8815 (tp) cc_final: 0.8536 (tp)
REVERT: B  193 ASP cc_start: 0.8595 (t0) cc_final: 0.8393 (t0)
REVERT: B  418 ASP cc_start: 0.8407 (t0) cc_final: 0.8070 (m-30)
REVERT: C  184 TYR cc_start: 0.7924 (m-80) cc_final: 0.7372 (m-80)
REVERT: C  237 ASN cc_start: 0.7989 (m-40) cc_final: 0.7786 (t0)
REVERT: C  274 ARG cc_start: 0.7563 (mmt-90) cc_final: 0.6831 (mpt180)
REVERT: C  511 LYS cc_start: 0.7336 (mmmt) cc_final: 0.7127 (mmmt)
REVERT: C  604 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.6579 (mp10)
REVERT: D  270 PHE cc_start: 0.8058 (m-10) cc_final: 0.7795 (m-10)
REVERT: D  322 MET cc_start: 0.6485 (ttt) cc_final: 0.5206 (tmm)
REVERT: D  532 MET cc_start: 0.4698 (tmm) cc_final: 0.4352 (ppp)
  outliers start: 23
  outliers final: 13
  residues processed: 194
  average time/residue: 0.2183
  time to fit residues: 66.0221
Evaluate side-chains
  171 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 157
  time to evaluate  : 1.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  562 ASN
Chi-restraints excluded: chain A residue  571 ILE
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  576 LEU
Chi-restraints excluded: chain C residue  312 ILE
Chi-restraints excluded: chain C residue  342 ILE
Chi-restraints excluded: chain C residue  527 LEU
Chi-restraints excluded: chain C residue  604 GLN
Chi-restraints excluded: chain D residue  313 CYS
Chi-restraints excluded: chain D residue  582 VAL
Chi-restraints excluded: chain D residue  608 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 130 optimal weight:    9.9990
   chunk 33 optimal weight:    0.4980
   chunk 127 optimal weight:   10.0000
   chunk 64 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 156 optimal weight:    3.9990
   chunk 145 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 158 optimal weight:    2.9990
   chunk 89 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   overall best weight:    1.0186

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

Flipped N/Q/H residues before XYZ refinement:
B 345 HIS
B 407 ASN
** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.161936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.122316 restraints weight = 19445.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3495 rms_B_bonded: 2.06
r_work: 0.3369 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3234 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.1764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  14881  Z= 0.130
  Angle     :  0.511   7.011  20203  Z= 0.271
  Chirality :  0.040   0.221   2297
  Planarity :  0.004   0.045   2480
  Dihedral  : 12.894 155.786   2139
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 10.73 %
    Favored  : 87.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.20), residues: 1748
  helix:  0.65 (0.15), residues: 1110
  sheet: -2.24 (0.55), residues: 67
  loop : -1.78 (0.25), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 171 
 HIS   0.003   0.001   HIS A 315 
 PHE   0.023   0.001   PHE C 547 
 TYR   0.017   0.001   TYR B 297 
 ARG   0.005   0.000   ARG B 439 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00094 (    3)
  link_NAG-ASN         : angle       2.64790 (    9)
  hydrogen bonds       : bond        0.04148 (  908)
  hydrogen bonds       : angle       4.44313 ( 2652)
  covalent geometry    : bond        0.00289 (14878)
  covalent geometry    : angle       0.50853 (20194)

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

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

  3496 Ramachandran restraints generated.
    1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3496 Ramachandran restraints generated.
    1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 173
  time to evaluate  : 1.674 
Fit side-chains
REVERT: A  421 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7801 (mtmt)
REVERT: A  493 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6487 (tm-30)
REVERT: A  524 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7219 (tt0)
REVERT: B  199 TYR cc_start: 0.7943 (OUTLIER) cc_final: 0.7306 (p90)
REVERT: B  418 ASP cc_start: 0.8387 (t0) cc_final: 0.8024 (m-30)
REVERT: C  184 TYR cc_start: 0.7875 (m-80) cc_final: 0.7421 (m-80)
REVERT: C  274 ARG cc_start: 0.7548 (mmt-90) cc_final: 0.6763 (mpt180)
REVERT: C  511 LYS cc_start: 0.7321 (mmmt) cc_final: 0.7094 (mmmt)
REVERT: C  546 TYR cc_start: 0.7892 (p90) cc_final: 0.7492 (p90)
REVERT: C  604 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.6745 (mp10)
REVERT: D  270 PHE cc_start: 0.8126 (m-10) cc_final: 0.7918 (m-10)
REVERT: D  322 MET cc_start: 0.6573 (ttt) cc_final: 0.5298 (tmm)
REVERT: D  532 MET cc_start: 0.4657 (tmm) cc_final: 0.4355 (ppp)
REVERT: D  639 MET cc_start: 0.6147 (mmp) cc_final: 0.4627 (mtt)
  outliers start: 32
  outliers final: 22
  residues processed: 198
  average time/residue: 0.2576
  time to fit residues: 79.9775
Evaluate side-chains
  187 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 161
  time to evaluate  : 2.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 LYS
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  519 MET
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  562 ASN
Chi-restraints excluded: chain A residue  571 ILE
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain B residue  199 TYR
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  462 ASP
Chi-restraints excluded: chain B residue  501 THR
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  529 VAL
Chi-restraints excluded: chain B residue  576 LEU
Chi-restraints excluded: chain C residue  218 VAL
Chi-restraints excluded: chain C residue  342 ILE
Chi-restraints excluded: chain C residue  396 VAL
Chi-restraints excluded: chain C residue  527 LEU
Chi-restraints excluded: chain C residue  604 GLN
Chi-restraints excluded: chain D residue  564 ILE
Chi-restraints excluded: chain D residue  580 VAL
Chi-restraints excluded: chain D residue  608 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 109 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9980
   chunk 112 optimal weight:    0.7980
   chunk 154 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 159 optimal weight:    0.0060
   chunk 153 optimal weight:    0.9990
   chunk 171 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    0.6998

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

Flipped N/Q/H residues before XYZ refinement:
A 422 GLN
B 407 ASN
** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 537 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 = 0.3971 r_free = 0.3971 target = 0.163226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.125589 restraints weight = 19259.103|
|-----------------------------------------------------------------------------|
r_work (start): 0.3532 rms_B_bonded: 2.04
r_work: 0.3391 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3257 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.1983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.058  14881  Z= 0.112
  Angle     :  0.486   6.818  20203  Z= 0.257
  Chirality :  0.039   0.183   2297
  Planarity :  0.004   0.043   2480
  Dihedral  : 12.712 153.637   2139
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 12.31 %
    Favored  : 85.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.23 (0.20), residues: 1748
  helix:  1.18 (0.16), residues: 1107
  sheet: -1.84 (0.55), residues: 72
  loop : -1.61 (0.26), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 171 
 HIS   0.002   0.001   HIS D 251 
 PHE   0.015   0.001   PHE C 547 
 TYR   0.016   0.001   TYR D 377 
 ARG   0.004   0.000   ARG A 569 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00113 (    3)
  link_NAG-ASN         : angle       2.53118 (    9)
  hydrogen bonds       : bond        0.03862 (  908)
  hydrogen bonds       : angle       4.28530 ( 2652)
  covalent geometry    : bond        0.00242 (14878)
  covalent geometry    : angle       0.48335 (20194)

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

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

  3496 Ramachandran restraints generated.
    1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3496 Ramachandran restraints generated.
    1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 174
  time to evaluate  : 1.969 
Fit side-chains
REVERT: A  421 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7741 (mtmt)
REVERT: A  493 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6508 (tm-30)
REVERT: A  524 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7138 (tt0)
REVERT: A  607 MET cc_start: 0.7581 (mmp) cc_final: 0.7359 (mmp)
REVERT: B  199 TYR cc_start: 0.7999 (OUTLIER) cc_final: 0.7401 (p90)
REVERT: B  418 ASP cc_start: 0.8364 (t0) cc_final: 0.8013 (m-30)
REVERT: B  514 ASP cc_start: 0.8215 (t0) cc_final: 0.7704 (t0)
REVERT: C  184 TYR cc_start: 0.7810 (m-80) cc_final: 0.7338 (m-80)
REVERT: C  274 ARG cc_start: 0.7451 (mmt-90) cc_final: 0.6739 (mpt180)
REVERT: C  508 TYR cc_start: 0.8820 (m-80) cc_final: 0.8160 (m-10)
REVERT: C  511 LYS cc_start: 0.7258 (mmmt) cc_final: 0.6410 (mptt)
REVERT: C  519 MET cc_start: 0.7882 (mmm) cc_final: 0.7642 (tpp)
REVERT: C  546 TYR cc_start: 0.8001 (p90) cc_final: 0.7503 (p90)
REVERT: D  322 MET cc_start: 0.6610 (ttt) cc_final: 0.5381 (tmm)
REVERT: D  377 TYR cc_start: 0.8805 (t80) cc_final: 0.8567 (t80)
REVERT: D  532 MET cc_start: 0.4660 (tmm) cc_final: 0.4381 (ppp)
  outliers start: 34
  outliers final: 21
  residues processed: 201
  average time/residue: 0.3191
  time to fit residues: 101.2694
Evaluate side-chains
  179 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 155
  time to evaluate  : 1.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  421 LYS
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  562 ASN
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain B residue  199 TYR
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain B residue  462 ASP
Chi-restraints excluded: chain B residue  501 THR
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  529 VAL
Chi-restraints excluded: chain B residue  576 LEU
Chi-restraints excluded: chain C residue  342 ILE
Chi-restraints excluded: chain C residue  396 VAL
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  480 VAL
Chi-restraints excluded: chain C residue  527 LEU
Chi-restraints excluded: chain D residue  564 ILE
Chi-restraints excluded: chain D residue  580 VAL
Chi-restraints excluded: chain D residue  608 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 71 optimal weight:    6.9990
   chunk 20 optimal weight:    0.0170
   chunk 127 optimal weight:    9.9990
   chunk 119 optimal weight:    6.9990
   chunk 154 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 65 optimal weight:    0.5980
   chunk 138 optimal weight:    0.1980
   chunk 37 optimal weight:    7.9990
   chunk 28 optimal weight:    0.0170
   chunk 96 optimal weight:    0.0070
   overall best weight:    0.1674

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

Flipped N/Q/H residues before XYZ refinement:
B 407 ASN
** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 425 GLN
** C 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.166571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.127290 restraints weight = 19400.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 2.06
r_work: 0.3435 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3301 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.067  14881  Z= 0.098
  Angle     :  0.466   6.913  20203  Z= 0.246
  Chirality :  0.038   0.168   2297
  Planarity :  0.003   0.042   2480
  Dihedral  : 12.584 153.370   2139
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 13.01 %
    Favored  : 84.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.21), residues: 1748
  helix:  1.50 (0.16), residues: 1111
  sheet: -1.62 (0.56), residues: 72
  loop : -1.53 (0.26), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 221 
 HIS   0.004   0.001   HIS C 473 
 PHE   0.018   0.001   PHE C 547 
 TYR   0.013   0.001   TYR D 377 
 ARG   0.004   0.000   ARG A 569 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00118 (    3)
  link_NAG-ASN         : angle       2.45791 (    9)
  hydrogen bonds       : bond        0.03604 (  908)
  hydrogen bonds       : angle       4.16709 ( 2652)
  covalent geometry    : bond        0.00199 (14878)
  covalent geometry    : angle       0.46343 (20194)

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

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

  3496 Ramachandran restraints generated.
    1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3496 Ramachandran restraints generated.
    1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 184
  time to evaluate  : 1.548 
Fit side-chains
   revert: symmetry clash
REVERT: A  421 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7767 (mtmt)
REVERT: A  493 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6516 (tm-30)
REVERT: A  607 MET cc_start: 0.7523 (mmp) cc_final: 0.7302 (mmp)
REVERT: B  418 ASP cc_start: 0.8340 (t0) cc_final: 0.8044 (m-30)
REVERT: B  514 ASP cc_start: 0.8274 (t0) cc_final: 0.7728 (t0)
REVERT: C  184 TYR cc_start: 0.7737 (m-80) cc_final: 0.7291 (m-80)
REVERT: C  352 TYR cc_start: 0.8285 (t80) cc_final: 0.8081 (t80)
REVERT: C  414 GLN cc_start: 0.8373 (tp-100) cc_final: 0.8154 (tp40)
REVERT: C  508 TYR cc_start: 0.8795 (m-80) cc_final: 0.8071 (m-10)
REVERT: C  511 LYS cc_start: 0.7061 (mmmt) cc_final: 0.6377 (mptt)
REVERT: C  519 MET cc_start: 0.7902 (mmm) cc_final: 0.7664 (tpp)
REVERT: C  546 TYR cc_start: 0.7962 (p90) cc_final: 0.7477 (p90)
REVERT: C  604 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7125 (mp10)
REVERT: D  322 MET cc_start: 0.6533 (ttt) cc_final: 0.5349 (tmm)
REVERT: D  377 TYR cc_start: 0.8786 (t80) cc_final: 0.8450 (t80)
REVERT: D  532 MET cc_start: 0.4609 (tmm) cc_final: 0.4362 (ppp)
REVERT: D  538 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8299 (tp)
REVERT: D  556 GLU cc_start: 0.8230 (pt0) cc_final: 0.8029 (pm20)
REVERT: D  639 MET cc_start: 0.6133 (mmp) cc_final: 0.4691 (mtt)
  outliers start: 32
  outliers final: 18
  residues processed: 209
  average time/residue: 0.2295
  time to fit residues: 76.5303
Evaluate side-chains
  185 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 163
  time to evaluate  : 1.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 LYS
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  562 ASN
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain B residue  199 TYR
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain B residue  462 ASP
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  576 LEU
Chi-restraints excluded: chain C residue  402 MET
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  480 VAL
Chi-restraints excluded: chain C residue  527 LEU
Chi-restraints excluded: chain C residue  604 GLN
Chi-restraints excluded: chain D residue  405 LEU
Chi-restraints excluded: chain D residue  538 LEU
Chi-restraints excluded: chain D residue  564 ILE
Chi-restraints excluded: chain D residue  580 VAL
Chi-restraints excluded: chain D residue  582 VAL
Chi-restraints excluded: chain D residue  608 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 171 optimal weight:    3.9990
   chunk 69 optimal weight:    0.2980
   chunk 54 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   chunk 150 optimal weight:    3.9990
   chunk 162 optimal weight:    1.9990
   chunk 1 optimal weight:    0.4980
   chunk 43 optimal weight:   10.0000
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B 407 ASN
** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 425 GLN
** C 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.163360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.123533 restraints weight = 19485.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.3508 rms_B_bonded: 2.06
r_work: 0.3385 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.2329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.085  14881  Z= 0.120
  Angle     :  0.480   6.788  20203  Z= 0.254
  Chirality :  0.039   0.178   2297
  Planarity :  0.003   0.041   2480
  Dihedral  : 12.495 152.850   2137
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 13.19 %
    Favored  : 84.47 %
  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:  0.77 (0.21), residues: 1748
  helix:  1.58 (0.16), residues: 1109
  sheet: -1.54 (0.61), residues: 62
  loop : -1.40 (0.26), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 171 
 HIS   0.003   0.001   HIS C 473 
 PHE   0.015   0.001   PHE C 547 
 TYR   0.012   0.001   TYR D 377 
 ARG   0.005   0.000   ARG A 569 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00061 (    3)
  link_NAG-ASN         : angle       2.34983 (    9)
  hydrogen bonds       : bond        0.03780 (  908)
  hydrogen bonds       : angle       4.15873 ( 2652)
  covalent geometry    : bond        0.00272 (14878)
  covalent geometry    : angle       0.47706 (20194)

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

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

  3496 Ramachandran restraints generated.
    1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3496 Ramachandran restraints generated.
    1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 163
  time to evaluate  : 1.421 
Fit side-chains
   revert: symmetry clash
REVERT: A  254 LEU cc_start: 0.8330 (mp) cc_final: 0.8121 (mp)
REVERT: A  421 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7814 (mtmt)
REVERT: A  427 ARG cc_start: 0.7232 (mtt180) cc_final: 0.6899 (mtt180)
REVERT: A  524 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7141 (tt0)
REVERT: A  607 MET cc_start: 0.7536 (mmp) cc_final: 0.7285 (mmp)
REVERT: B  418 ASP cc_start: 0.8349 (t0) cc_final: 0.8058 (m-30)
REVERT: B  514 ASP cc_start: 0.8258 (t0) cc_final: 0.7780 (t0)
REVERT: C  184 TYR cc_start: 0.7811 (m-80) cc_final: 0.7360 (m-80)
REVERT: C  274 ARG cc_start: 0.7470 (mmt-90) cc_final: 0.6733 (mpt180)
REVERT: C  352 TYR cc_start: 0.8374 (t80) cc_final: 0.8174 (t80)
REVERT: C  511 LYS cc_start: 0.6977 (mmmt) cc_final: 0.6752 (mmmt)
REVERT: C  546 TYR cc_start: 0.8041 (p90) cc_final: 0.7554 (p90)
REVERT: C  604 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7406 (mp10)
REVERT: D  310 PHE cc_start: 0.5839 (m-80) cc_final: 0.5625 (m-80)
REVERT: D  322 MET cc_start: 0.6610 (ttt) cc_final: 0.5450 (tmm)
REVERT: D  377 TYR cc_start: 0.8807 (t80) cc_final: 0.8530 (t80)
REVERT: D  532 MET cc_start: 0.4656 (tmm) cc_final: 0.4403 (ppp)
REVERT: D  639 MET cc_start: 0.6126 (mmp) cc_final: 0.4684 (mtt)
  outliers start: 37
  outliers final: 24
  residues processed: 190
  average time/residue: 0.2775
  time to fit residues: 81.9794
Evaluate side-chains
  188 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 162
  time to evaluate  : 1.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  421 LYS
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  519 MET
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  562 ASN
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain B residue  199 TYR
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain B residue  501 THR
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  576 LEU
Chi-restraints excluded: chain C residue  396 VAL
Chi-restraints excluded: chain C residue  402 MET
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  480 VAL
Chi-restraints excluded: chain C residue  527 LEU
Chi-restraints excluded: chain C residue  604 GLN
Chi-restraints excluded: chain D residue  405 LEU
Chi-restraints excluded: chain D residue  564 ILE
Chi-restraints excluded: chain D residue  580 VAL
Chi-restraints excluded: chain D residue  582 VAL
Chi-restraints excluded: chain D residue  608 VAL
Chi-restraints excluded: chain D residue  644 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 132 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 99 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 104 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 116 optimal weight:    0.8980
   chunk 125 optimal weight:    8.9990
   chunk 59 optimal weight:    0.7980
   chunk 88 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
B 407 ASN
** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 425 GLN
** C 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 272 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.161736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.121747 restraints weight = 19496.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 2.05
r_work: 0.3360 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.2391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.095  14881  Z= 0.134
  Angle     :  0.498   7.162  20203  Z= 0.264
  Chirality :  0.040   0.163   2297
  Planarity :  0.003   0.040   2480
  Dihedral  : 12.474 153.673   2137
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 13.83 %
    Favored  : 83.96 %
  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 (0.21), residues: 1748
  helix:  1.62 (0.16), residues: 1110
  sheet: -1.35 (0.63), residues: 62
  loop : -1.34 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 171 
 HIS   0.002   0.001   HIS C 473 
 PHE   0.015   0.001   PHE C 180 
 TYR   0.015   0.001   TYR B 297 
 ARG   0.005   0.000   ARG A 569 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00093 (    3)
  link_NAG-ASN         : angle       2.28870 (    9)
  hydrogen bonds       : bond        0.03880 (  908)
  hydrogen bonds       : angle       4.18506 ( 2652)
  covalent geometry    : bond        0.00310 (14878)
  covalent geometry    : angle       0.49530 (20194)

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

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

  3496 Ramachandran restraints generated.
    1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3496 Ramachandran restraints generated.
    1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 168
  time to evaluate  : 1.664 
Fit side-chains
REVERT: A  219 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8262 (tt)
REVERT: A  254 LEU cc_start: 0.8349 (mp) cc_final: 0.8120 (mp)
REVERT: A  421 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7857 (mtmt)
REVERT: A  427 ARG cc_start: 0.7326 (mtt180) cc_final: 0.6999 (mtt180)
REVERT: A  493 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6412 (tm-30)
REVERT: A  524 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7163 (tt0)
REVERT: B  418 ASP cc_start: 0.8356 (t0) cc_final: 0.8061 (m-30)
REVERT: B  425 GLN cc_start: 0.8395 (tp40) cc_final: 0.7668 (mp10)
REVERT: B  514 ASP cc_start: 0.8240 (t0) cc_final: 0.7761 (t0)
REVERT: C  184 TYR cc_start: 0.7838 (m-80) cc_final: 0.7422 (m-80)
REVERT: C  274 ARG cc_start: 0.7526 (mmt-90) cc_final: 0.6755 (mpt180)
REVERT: C  414 GLN cc_start: 0.8387 (tp-100) cc_final: 0.8172 (tp40)
REVERT: C  508 TYR cc_start: 0.8902 (m-80) cc_final: 0.8134 (m-10)
REVERT: C  511 LYS cc_start: 0.6945 (mmmt) cc_final: 0.6282 (mptt)
REVERT: C  546 TYR cc_start: 0.8113 (p90) cc_final: 0.7562 (p90)
REVERT: D  322 MET cc_start: 0.6725 (ttt) cc_final: 0.5567 (tmm)
REVERT: D  532 MET cc_start: 0.4680 (tmm) cc_final: 0.4455 (ppp)
REVERT: D  556 GLU cc_start: 0.8333 (pt0) cc_final: 0.8087 (pm20)
  outliers start: 35
  outliers final: 23
  residues processed: 197
  average time/residue: 0.2254
  time to fit residues: 69.4632
Evaluate side-chains
  184 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 158
  time to evaluate  : 1.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  421 LYS
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  519 MET
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  562 ASN
Chi-restraints excluded: chain B residue  199 TYR
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain B residue  501 THR
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  576 LEU
Chi-restraints excluded: chain C residue  396 VAL
Chi-restraints excluded: chain C residue  402 MET
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  480 VAL
Chi-restraints excluded: chain C residue  527 LEU
Chi-restraints excluded: chain D residue  313 CYS
Chi-restraints excluded: chain D residue  405 LEU
Chi-restraints excluded: chain D residue  564 ILE
Chi-restraints excluded: chain D residue  580 VAL
Chi-restraints excluded: chain D residue  582 VAL
Chi-restraints excluded: chain D residue  608 VAL
Chi-restraints excluded: chain D residue  644 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 87 optimal weight:    6.9990
   chunk 127 optimal weight:    9.9990
   chunk 111 optimal weight:    7.9990
   chunk 53 optimal weight:    1.9990
   chunk 59 optimal weight:    0.5980
   chunk 152 optimal weight:    0.5980
   chunk 77 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0050
   chunk 131 optimal weight:   10.0000
   chunk 100 optimal weight:    2.9990
   overall best weight:    1.0398

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

Flipped N/Q/H residues before XYZ refinement:
A 422 GLN
** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 407 ASN
** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 425 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.160631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.124462 restraints weight = 19071.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 1.85
r_work: 0.3386 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3259 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.2459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.116  14881  Z= 0.130
  Angle     :  0.493   7.269  20203  Z= 0.262
  Chirality :  0.040   0.158   2297
  Planarity :  0.003   0.039   2480
  Dihedral  : 12.448 153.820   2137
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 13.89 %
    Favored  : 83.65 %
  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:  0.90 (0.21), residues: 1748
  helix:  1.65 (0.16), residues: 1110
  sheet: -1.30 (0.64), residues: 62
  loop : -1.29 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 171 
 HIS   0.002   0.001   HIS C 473 
 PHE   0.015   0.001   PHE C 180 
 TYR   0.021   0.001   TYR D 377 
 ARG   0.007   0.000   ARG A 569 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00080 (    3)
  link_NAG-ASN         : angle       2.26934 (    9)
  hydrogen bonds       : bond        0.03844 (  908)
  hydrogen bonds       : angle       4.17785 ( 2652)
  covalent geometry    : bond        0.00305 (14878)
  covalent geometry    : angle       0.49093 (20194)

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

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

  3496 Ramachandran restraints generated.
    1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3496 Ramachandran restraints generated.
    1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 167
  time to evaluate  : 1.603 
Fit side-chains
REVERT: A  219 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8227 (tt)
REVERT: A  254 LEU cc_start: 0.8327 (mp) cc_final: 0.8087 (mp)
REVERT: A  421 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7867 (mtmt)
REVERT: A  427 ARG cc_start: 0.7332 (mtt180) cc_final: 0.7016 (mtt180)
REVERT: A  493 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6439 (tm-30)
REVERT: A  524 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7160 (tt0)
REVERT: B  418 ASP cc_start: 0.8307 (t0) cc_final: 0.8036 (m-30)
REVERT: B  514 ASP cc_start: 0.8191 (t0) cc_final: 0.7785 (t0)
REVERT: B  519 MET cc_start: 0.8195 (ttt) cc_final: 0.7915 (ttt)
REVERT: C  184 TYR cc_start: 0.7793 (m-80) cc_final: 0.7404 (m-80)
REVERT: C  274 ARG cc_start: 0.7488 (mmt-90) cc_final: 0.6757 (mpt180)
REVERT: C  310 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8602 (mt)
REVERT: C  511 LYS cc_start: 0.6887 (mmmt) cc_final: 0.6660 (mmmt)
REVERT: C  546 TYR cc_start: 0.8108 (p90) cc_final: 0.7582 (p90)
REVERT: C  604 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7319 (mp10)
REVERT: D  322 MET cc_start: 0.6702 (ttt) cc_final: 0.5577 (tmm)
REVERT: D  532 MET cc_start: 0.4639 (tmm) cc_final: 0.4403 (ppp)
REVERT: D  639 MET cc_start: 0.6310 (mmp) cc_final: 0.4863 (mtt)
  outliers start: 39
  outliers final: 28
  residues processed: 196
  average time/residue: 0.2289
  time to fit residues: 70.1387
Evaluate side-chains
  193 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 160
  time to evaluate  : 1.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  300 MET
Chi-restraints excluded: chain A residue  421 LYS
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  519 MET
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain B residue  199 TYR
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain B residue  407 ASN
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  501 THR
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  576 LEU
Chi-restraints excluded: chain C residue  310 ILE
Chi-restraints excluded: chain C residue  361 LEU
Chi-restraints excluded: chain C residue  396 VAL
Chi-restraints excluded: chain C residue  402 MET
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  480 VAL
Chi-restraints excluded: chain C residue  527 LEU
Chi-restraints excluded: chain C residue  604 GLN
Chi-restraints excluded: chain D residue  313 CYS
Chi-restraints excluded: chain D residue  405 LEU
Chi-restraints excluded: chain D residue  564 ILE
Chi-restraints excluded: chain D residue  580 VAL
Chi-restraints excluded: chain D residue  582 VAL
Chi-restraints excluded: chain D residue  608 VAL
Chi-restraints excluded: chain D residue  644 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 95 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 115 optimal weight:    7.9990
   chunk 50 optimal weight:    6.9990
   chunk 32 optimal weight:    9.9990
   chunk 13 optimal weight:    0.0970
   chunk 134 optimal weight:    0.8980
   chunk 110 optimal weight:    0.8980
   chunk 153 optimal weight:    0.8980
   overall best weight:    1.3580

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

Flipped N/Q/H residues before XYZ refinement:
** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 414 GLN
C 425 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.159385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.120699 restraints weight = 19211.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 1.92
r_work: 0.3357 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.2508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.105  14881  Z= 0.150
  Angle     :  0.520   8.518  20203  Z= 0.274
  Chirality :  0.041   0.158   2297
  Planarity :  0.004   0.039   2480
  Dihedral  : 12.469 154.424   2137
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 14.14 %
    Favored  : 83.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.20), residues: 1748
  helix:  1.61 (0.16), residues: 1111
  sheet: -1.18 (0.65), residues: 62
  loop : -1.29 (0.26), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 171 
 HIS   0.002   0.001   HIS D 365 
 PHE   0.015   0.001   PHE C 180 
 TYR   0.022   0.001   TYR B 297 
 ARG   0.008   0.000   ARG A 410 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00118 (    3)
  link_NAG-ASN         : angle       2.24554 (    9)
  hydrogen bonds       : bond        0.03987 (  908)
  hydrogen bonds       : angle       4.22602 ( 2652)
  covalent geometry    : bond        0.00356 (14878)
  covalent geometry    : angle       0.51833 (20194)

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

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

  3496 Ramachandran restraints generated.
    1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3496 Ramachandran restraints generated.
    1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 161
  time to evaluate  : 1.825 
Fit side-chains
REVERT: A  219 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8259 (tt)
REVERT: A  254 LEU cc_start: 0.8352 (mp) cc_final: 0.8104 (mp)
REVERT: A  421 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7902 (mtmt)
REVERT: A  427 ARG cc_start: 0.7345 (mtt180) cc_final: 0.7016 (mtt180)
REVERT: A  491 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8341 (tp)
REVERT: A  493 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6445 (tm-30)
REVERT: A  524 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7183 (tt0)
REVERT: B  418 ASP cc_start: 0.8345 (t0) cc_final: 0.8068 (m-30)
REVERT: B  514 ASP cc_start: 0.8174 (t0) cc_final: 0.7764 (t0)
REVERT: B  519 MET cc_start: 0.8202 (ttt) cc_final: 0.7925 (ttt)
REVERT: C  184 TYR cc_start: 0.7818 (m-80) cc_final: 0.7411 (m-80)
REVERT: C  274 ARG cc_start: 0.7558 (mmt-90) cc_final: 0.6926 (mpt180)
REVERT: C  414 GLN cc_start: 0.8398 (tp40) cc_final: 0.8177 (tp40)
REVERT: C  511 LYS cc_start: 0.6951 (mmmt) cc_final: 0.6709 (mmmt)
REVERT: C  546 TYR cc_start: 0.8142 (p90) cc_final: 0.7618 (p90)
REVERT: C  604 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.7304 (mp10)
REVERT: D  322 MET cc_start: 0.6744 (ttt) cc_final: 0.5617 (tmm)
REVERT: D  532 MET cc_start: 0.4717 (tmm) cc_final: 0.4434 (ppp)
REVERT: D  639 MET cc_start: 0.6277 (mmp) cc_final: 0.4795 (mtt)
  outliers start: 35
  outliers final: 27
  residues processed: 187
  average time/residue: 0.2214
  time to fit residues: 65.4956
Evaluate side-chains
  187 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 155
  time to evaluate  : 1.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  300 MET
Chi-restraints excluded: chain A residue  421 LYS
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  519 MET
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain B residue  199 TYR
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  462 ASP
Chi-restraints excluded: chain B residue  501 THR
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  576 LEU
Chi-restraints excluded: chain C residue  361 LEU
Chi-restraints excluded: chain C residue  396 VAL
Chi-restraints excluded: chain C residue  402 MET
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  480 VAL
Chi-restraints excluded: chain C residue  527 LEU
Chi-restraints excluded: chain C residue  604 GLN
Chi-restraints excluded: chain D residue  313 CYS
Chi-restraints excluded: chain D residue  405 LEU
Chi-restraints excluded: chain D residue  564 ILE
Chi-restraints excluded: chain D residue  580 VAL
Chi-restraints excluded: chain D residue  582 VAL
Chi-restraints excluded: chain D residue  608 VAL
Chi-restraints excluded: chain D residue  644 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 117 optimal weight:    7.9990
   chunk 83 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 120 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 62 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 115 optimal weight:    0.0570
   chunk 173 optimal weight:    3.9990
   chunk 48 optimal weight:    0.0040
   overall best weight:    0.5110

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

Flipped N/Q/H residues before XYZ refinement:
A 422 GLN
** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 425 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.164415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.124670 restraints weight = 19276.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 2.06
r_work: 0.3406 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3272 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.2618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.089  14881  Z= 0.106
  Angle     :  0.488   8.883  20203  Z= 0.257
  Chirality :  0.039   0.147   2297
  Planarity :  0.003   0.041   2480
  Dihedral  : 12.386 153.845   2137
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 14.90 %
    Favored  : 83.40 %
  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:  0.99 (0.21), residues: 1748
  helix:  1.72 (0.16), residues: 1121
  sheet: -0.99 (0.66), residues: 62
  loop : -1.35 (0.26), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 171 
 HIS   0.003   0.001   HIS C 473 
 PHE   0.015   0.001   PHE C 547 
 TYR   0.023   0.001   TYR D 377 
 ARG   0.007   0.000   ARG A 410 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00074 (    3)
  link_NAG-ASN         : angle       2.27746 (    9)
  hydrogen bonds       : bond        0.03619 (  908)
  hydrogen bonds       : angle       4.11167 ( 2652)
  covalent geometry    : bond        0.00234 (14878)
  covalent geometry    : angle       0.48553 (20194)

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

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

  3496 Ramachandran restraints generated.
    1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3496 Ramachandran restraints generated.
    1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 175
  time to evaluate  : 1.707 
Fit side-chains
REVERT: A  198 GLU cc_start: 0.8143 (tt0) cc_final: 0.7761 (tt0)
REVERT: A  219 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8229 (tt)
REVERT: A  254 LEU cc_start: 0.8301 (mp) cc_final: 0.8049 (mp)
REVERT: A  421 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7888 (mtmt)
REVERT: A  493 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6399 (tm-30)
REVERT: A  524 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7089 (tt0)
REVERT: B  418 ASP cc_start: 0.8344 (t0) cc_final: 0.8065 (m-30)
REVERT: B  425 GLN cc_start: 0.8373 (tp40) cc_final: 0.7669 (mp10)
REVERT: B  514 ASP cc_start: 0.8156 (t0) cc_final: 0.7744 (t0)
REVERT: B  518 GLU cc_start: 0.8077 (pt0) cc_final: 0.7717 (pt0)
REVERT: B  519 MET cc_start: 0.8153 (ttt) cc_final: 0.7902 (ttt)
REVERT: C  184 TYR cc_start: 0.7753 (m-80) cc_final: 0.7374 (m-80)
REVERT: C  274 ARG cc_start: 0.7565 (mmt-90) cc_final: 0.6750 (mpt180)
REVERT: C  310 ILE cc_start: 0.8871 (mm) cc_final: 0.8585 (mt)
REVERT: C  414 GLN cc_start: 0.8292 (tp40) cc_final: 0.8011 (tp40)
REVERT: C  511 LYS cc_start: 0.6894 (mmmt) cc_final: 0.6658 (mmmt)
REVERT: C  546 TYR cc_start: 0.8103 (p90) cc_final: 0.7631 (p90)
REVERT: C  604 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7310 (mp10)
REVERT: D  322 MET cc_start: 0.6654 (ttt) cc_final: 0.5556 (tmm)
REVERT: D  532 MET cc_start: 0.4609 (tmm) cc_final: 0.4360 (ppp)
REVERT: D  639 MET cc_start: 0.6303 (mmp) cc_final: 0.4827 (mtt)
  outliers start: 27
  outliers final: 20
  residues processed: 195
  average time/residue: 0.2180
  time to fit residues: 66.6144
Evaluate side-chains
  184 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 160
  time to evaluate  : 1.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  421 LYS
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  519 MET
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain B residue  199 TYR
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  576 LEU
Chi-restraints excluded: chain C residue  396 VAL
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  480 VAL
Chi-restraints excluded: chain C residue  527 LEU
Chi-restraints excluded: chain C residue  604 GLN
Chi-restraints excluded: chain D residue  405 LEU
Chi-restraints excluded: chain D residue  564 ILE
Chi-restraints excluded: chain D residue  580 VAL
Chi-restraints excluded: chain D residue  582 VAL
Chi-restraints excluded: chain D residue  608 VAL
Chi-restraints excluded: chain D residue  644 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 171 optimal weight:    2.9990
   chunk 116 optimal weight:    0.4980
   chunk 42 optimal weight:    3.9990
   chunk 163 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 29 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 166 optimal weight:    3.9990
   chunk 40 optimal weight:    8.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    2.4986

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.159038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.117697 restraints weight = 19754.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 2.08
r_work: 0.3298 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3162 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.2634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.083  14881  Z= 0.233
  Angle     :  0.610   9.615  20203  Z= 0.317
  Chirality :  0.044   0.164   2297
  Planarity :  0.004   0.038   2480
  Dihedral  : 12.546 155.677   2137
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 14.96 %
    Favored  : 83.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.64 (0.20), residues: 1748
  helix:  1.40 (0.15), residues: 1115
  sheet: -0.71 (0.66), residues: 67
  loop : -1.40 (0.26), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 171 
 HIS   0.004   0.001   HIS B 473 
 PHE   0.017   0.002   PHE C 180 
 TYR   0.022   0.002   TYR B 297 
 ARG   0.007   0.000   ARG A 410 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00283 (    3)
  link_NAG-ASN         : angle       2.30591 (    9)
  hydrogen bonds       : bond        0.04565 (  908)
  hydrogen bonds       : angle       4.38021 ( 2652)
  covalent geometry    : bond        0.00555 (14878)
  covalent geometry    : angle       0.60840 (20194)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8485.02 seconds
wall clock time: 150 minutes 19.48 seconds (9019.48 seconds total)