Starting phenix.real_space_refine
on Wed Apr 30 14:50:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w4a_37264/04_2025/8w4a_37264.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w4a_37264/04_2025/8w4a_37264.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w4a_37264/04_2025/8w4a_37264.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w4a_37264/04_2025/8w4a_37264.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w4a_37264/04_2025/8w4a_37264.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w4a_37264/04_2025/8w4a_37264.cif"
  }
  resolution = 2.69
  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=   0.035
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       6      5.49       5
     S      40      5.16       5
     C    6612      2.51       5
     N    1382      2.21       5
     O    1548      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 9588
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "B"
      Number of atoms: 4230
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 4230
          Classifications: {'peptide': 533}
          Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 506}
          Chain breaks: 2
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 4230
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 4230
          Classifications: {'peptide': 533}
          Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 506}
          Chain breaks: 2
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 508
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 508
          Unusual residues: {'ACO': 1, 'C14': 12, 'CLR': 2, 'D10': 1, 'D12': 3, 'HP6': 1, 'NAG': 1, 'OCT': 16, 'R16': 1, 'UV6': 1}
          Classifications: {'undetermined': 39}
          Link IDs: {None: 38}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ACO:plan-1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "A"
      Number of atoms: 508
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 508
          Unusual residues: {'ACO': 1, 'C14': 12, 'CLR': 2, 'D10': 1, 'D12': 3, 'HP6': 1, 'NAG': 1, 'OCT': 16, 'R16': 1, 'UV6': 1}
          Classifications: {'undetermined': 39}
          Link IDs: {None: 38}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ACO:plan-1': 1}
          Unresolved non-hydrogen planarities: 3
  Time building chain proxies: 7.60, per 1000 atoms: 0.79
  Number of scatterers: 9588
  At special positions: 0
  Unit cell: (108.73, 87.98, 107.07, 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      40     16.00
     P       6     15.00
     O    1548      8.00
     N    1382      7.00
     C    6612      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 104 " - pdb=" SG  CYS B 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 151 " - pdb=" SG  CYS B 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 443 " - pdb=" SG  CYS B 462 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 104 " - pdb=" SG  CYS A 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 151 " - pdb=" SG  CYS A 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 443 " - pdb=" SG  CYS A 462 " distance=2.03

  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
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG A 804 " - " ASN A  94 "
      " NAG B 803 " - " ASN B  94 "
      " NAG C   1 " - " ASN B 142 "
      " NAG D   1 " - " ASN B 162 "
      " NAG E   1 " - " ASN A 142 "
      " NAG F   1 " - " ASN A 162 "
  Time building additional restraints: 2.68
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1964

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 4 sheets defined
      55.9% alpha, 9.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'B' and resid 191 through 215
    Processing helix  chain 'B' and resid 268 through 287
      removed outlier: 3.517A  pdb=" N   ASP B 272 " --> pdb=" O   LEU B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 296
      removed outlier: 3.577A  pdb=" N   TYR B 292 " --> pdb=" O   GLY B 289 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   TRP B 293 " --> pdb=" O   GLY B 290 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   TYR B 294 " --> pdb=" O   LYS B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 332
      removed outlier: 3.522A  pdb=" N   TRP B 312 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   SER B 327 " --> pdb=" O   LEU B 323 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLY B 332 " --> pdb=" O   ILE B 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 356
    Processing helix  chain 'B' and resid 367 through 371
    Processing helix  chain 'B' and resid 375 through 394
    Processing helix  chain 'B' and resid 411 through 416
      removed outlier: 3.697A  pdb=" N   SER B 416 " --> pdb=" O   ARG B 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 438
      removed outlier: 3.561A  pdb=" N   LEU B 438 " --> pdb=" O   LEU B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 454 through 458
    Processing helix  chain 'B' and resid 465 through 475
      removed outlier: 3.540A  pdb=" N   ASP B 471 " --> pdb=" O   ALA B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 480
    Processing helix  chain 'B' and resid 484 through 488
      removed outlier: 3.941A  pdb=" N   VAL B 488 " --> pdb=" O   SER B 485 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 503 through 524
    Processing helix  chain 'B' and resid 527 through 551
    Processing helix  chain 'B' and resid 567 through 590
      Proline residue:  B 587  - end of helix
    Processing helix  chain 'B' and resid 600 through 605
    Processing helix  chain 'B' and resid 606 through 617
    Processing helix  chain 'B' and resid 632 through 657
    Processing helix  chain 'A' and resid 191 through 215
    Processing helix  chain 'A' and resid 268 through 287
      removed outlier: 3.501A  pdb=" N   ASP A 272 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 296
      removed outlier: 3.503A  pdb=" N   TYR A 292 " --> pdb=" O   GLY A 289 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   TRP A 293 " --> pdb=" O   GLY A 290 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   TYR A 294 " --> pdb=" O   LYS A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 307
    Processing helix  chain 'A' and resid 308 through 332
      removed outlier: 3.607A  pdb=" N   TRP A 312 " --> pdb=" O   LEU A 308 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLY A 332 " --> pdb=" O   ILE A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 356
    Processing helix  chain 'A' and resid 367 through 371
    Processing helix  chain 'A' and resid 375 through 394
    Processing helix  chain 'A' and resid 411 through 416
      removed outlier: 3.694A  pdb=" N   SER A 416 " --> pdb=" O   ARG A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 438
      removed outlier: 3.638A  pdb=" N   LEU A 438 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 458
    Processing helix  chain 'A' and resid 465 through 475
    Processing helix  chain 'A' and resid 476 through 480
    Processing helix  chain 'A' and resid 484 through 488
      removed outlier: 3.947A  pdb=" N   VAL A 488 " --> pdb=" O   SER A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 524
    Processing helix  chain 'A' and resid 527 through 551
      removed outlier: 3.539A  pdb=" N   ILE A 531 " --> pdb=" O   ARG A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 590
      Proline residue:  A 587  - end of helix
    Processing helix  chain 'A' and resid 600 through 605
    Processing helix  chain 'A' and resid 606 through 617
    Processing helix  chain 'A' and resid 632 through 657
    Processing sheet with id=AA1, first strand: chain 'B' and resid 125 through 132
      removed outlier: 9.013A  pdb=" N   TYR B 163 " --> pdb=" O   GLN B  81 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   LEU B  83 " --> pdb=" O   TYR B 163 " (cutoff:3.500A)
      removed outlier: 7.468A  pdb=" N   LEU B 165 " --> pdb=" O   LEU B  83 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   LEU B  85 " --> pdb=" O   LEU B 165 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   VAL B 167 " --> pdb=" O   LEU B  85 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   HIS B  87 " --> pdb=" O   VAL B 167 " (cutoff:3.500A)
      removed outlier: 8.308A  pdb=" N   ASN B 169 " --> pdb=" O   HIS B  87 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   ASN B 162 " --> pdb=" O   ASN B 184 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 110 through 115
      removed outlier: 6.893A  pdb=" N   VAL B  97 " --> pdb=" O   LEU B 112 " (cutoff:3.500A)
      removed outlier: 4.891A  pdb=" N   ASN B 114 " --> pdb=" O   LEU B  95 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   LEU B  95 " --> pdb=" O   ASN B 114 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   SER B 137 " --> pdb=" O   GLU B 154 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   GLU B 154 " --> pdb=" O   SER B 137 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   LEU B 139 " --> pdb=" O   ARG B 152 " (cutoff:3.500A)
      removed outlier: 4.745A  pdb=" N   ARG B 152 " --> pdb=" O   LEU B 139 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   LEU B 141 " --> pdb=" O   VAL B 150 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LYS B 148 " --> pdb=" O   ASP B 143 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 132
      removed outlier: 8.947A  pdb=" N   TYR A 163 " --> pdb=" O   GLN A  81 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   LEU A  83 " --> pdb=" O   TYR A 163 " (cutoff:3.500A)
      removed outlier: 7.474A  pdb=" N   LEU A 165 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   LEU A  85 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 7.315A  pdb=" N   VAL A 167 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   HIS A  87 " --> pdb=" O   VAL A 167 " (cutoff:3.500A)
      removed outlier: 8.301A  pdb=" N   ASN A 169 " --> pdb=" O   HIS A  87 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ASN A 162 " --> pdb=" O   ASN A 184 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 115
      removed outlier: 6.906A  pdb=" N   VAL A  97 " --> pdb=" O   LEU A 112 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   ASN A 114 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   LEU A  95 " --> pdb=" O   ASN A 114 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   SER A 137 " --> pdb=" O   GLU A 154 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   GLU A 154 " --> pdb=" O   SER A 137 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   LEU A 139 " --> pdb=" O   ARG A 152 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   ARG A 152 " --> pdb=" O   LEU A 139 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   LEU A 141 " --> pdb=" O   VAL A 150 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LYS A 148 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)

    476 hydrogen bonds defined for protein.
    1353 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.68

  Time building geometry restraints manager: 3.11 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1302
        1.32 -     1.44: 2594
        1.44 -     1.57: 5821
        1.57 -     1.70: 11
        1.70 -     1.82: 52
  Bond restraints: 9780
  Sorted by residual:
  bond pdb=" C4' UV6 B 801 "
       pdb=" O5  UV6 B 801 "
    ideal  model  delta    sigma   weight residual
    1.419  1.560 -0.141 2.00e-02 2.50e+03 4.98e+01
  bond pdb=" C4' UV6 A 802 "
       pdb=" O5  UV6 A 802 "
    ideal  model  delta    sigma   weight residual
    1.419  1.560 -0.141 2.00e-02 2.50e+03 4.94e+01
  bond pdb=" C8  UV6 B 801 "
       pdb=" N9  UV6 B 801 "
    ideal  model  delta    sigma   weight residual
    1.351  1.477 -0.126 2.00e-02 2.50e+03 3.98e+01
  bond pdb=" C8  UV6 A 802 "
       pdb=" N9  UV6 A 802 "
    ideal  model  delta    sigma   weight residual
    1.351  1.476 -0.125 2.00e-02 2.50e+03 3.90e+01
  bond pdb=" C4' UV6 B 801 "
       pdb=" C5' UV6 B 801 "
    ideal  model  delta    sigma   weight residual
    1.527  1.419  0.108 2.00e-02 2.50e+03 2.91e+01
  ... (remaining 9775 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 12806
        1.60 -     3.21: 205
        3.21 -     4.81: 42
        4.81 -     6.42: 9
        6.42 -     8.02: 4
  Bond angle restraints: 13066
  Sorted by residual:
  angle pdb=" C9  UV6 B 801 "
        pdb=" OP3 UV6 B 801 "
        pdb=" CAA UV6 B 801 "
      ideal   model   delta    sigma   weight residual
     119.59  111.57    8.02 3.00e+00 1.11e-01 7.15e+00
  angle pdb=" C   LYS A 551 "
        pdb=" N   VAL A 552 "
        pdb=" CA  VAL A 552 "
      ideal   model   delta    sigma   weight residual
     121.97  126.63   -4.66 1.80e+00 3.09e-01 6.69e+00
  angle pdb=" C9  UV6 A 802 "
        pdb=" OP3 UV6 A 802 "
        pdb=" CAA UV6 A 802 "
      ideal   model   delta    sigma   weight residual
     119.59  111.91    7.68 3.00e+00 1.11e-01 6.55e+00
  angle pdb=" C   LYS B 551 "
        pdb=" N   VAL B 552 "
        pdb=" CA  VAL B 552 "
      ideal   model   delta    sigma   weight residual
     121.97  126.57   -4.60 1.80e+00 3.09e-01 6.53e+00
  angle pdb=" C2' UV6 A 802 "
        pdb=" C1' UV6 A 802 "
        pdb=" N9  UV6 A 802 "
      ideal   model   delta    sigma   weight residual
     112.50  105.68    6.82 3.00e+00 1.11e-01 5.16e+00
  ... (remaining 13061 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.05: 5355
       16.05 -    32.09: 618
       32.09 -    48.14: 158
       48.14 -    64.18: 61
       64.18 -    80.23: 12
  Dihedral angle restraints: 6204
    sinusoidal: 3132
      harmonic: 3072
  Sorted by residual:
  dihedral pdb=" CB  CYS B 443 "
           pdb=" SG  CYS B 443 "
           pdb=" SG  CYS B 462 "
           pdb=" CB  CYS B 462 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  169.66  -76.66     1      1.00e+01 1.00e-02 7.38e+01
  dihedral pdb=" CB  CYS A 443 "
           pdb=" SG  CYS A 443 "
           pdb=" SG  CYS A 462 "
           pdb=" CB  CYS A 462 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  168.30  -75.30     1      1.00e+01 1.00e-02 7.16e+01
  dihedral pdb=" CA  LEU A 308 "
           pdb=" C   LEU A 308 "
           pdb=" N   VAL A 309 "
           pdb=" CA  VAL A 309 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.36  -18.64     0      5.00e+00 4.00e-02 1.39e+01
  ... (remaining 6201 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1348
       0.070 -    0.141: 114
       0.141 -    0.211: 0
       0.211 -    0.282: 2
       0.282 -    0.352: 2
  Chirality restraints: 1466
  Sorted by residual:
  chirality pdb=" C4' UV6 A 802 "
            pdb=" C3' UV6 A 802 "
            pdb=" C5' UV6 A 802 "
            pdb=" O5  UV6 A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.25   -2.60    0.35 2.00e-01 2.50e+01 3.10e+00
  chirality pdb=" C4' UV6 B 801 "
            pdb=" C3' UV6 B 801 "
            pdb=" C5' UV6 B 801 "
            pdb=" O5  UV6 B 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.25   -2.59    0.34 2.00e-01 2.50e+01 2.90e+00
  chirality pdb=" C17 UV6 A 802 "
            pdb=" C12 UV6 A 802 "
            pdb=" C18 UV6 A 802 "
            pdb=" C5  UV6 A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.54    2.79   -0.25 2.00e-01 2.50e+01 1.51e+00
  ... (remaining 1463 not shown)

  Planarity restraints: 1474
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 265 "    0.047 5.00e-02 4.00e+02   7.10e-02 8.07e+00
        pdb=" N   PRO B 266 "   -0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO B 266 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO B 266 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 265 "   -0.030 5.00e-02 4.00e+02   4.59e-02 3.37e+00
        pdb=" N   PRO A 266 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A 266 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 266 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 481 "    0.014 2.00e-02 2.50e+03   1.07e-02 2.28e+00
        pdb=" CG  TYR B 481 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 481 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 481 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 481 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 481 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 481 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR B 481 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1471 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 929
        2.75 -     3.29: 8399
        3.29 -     3.82: 15220
        3.82 -     4.36: 19875
        4.36 -     4.90: 33489
  Nonbonded interactions: 77912
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 652 "
            pdb=" NH2 ARG A 656 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" ND2 ASN A 506 "
            pdb=" O   TRP A 566 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" OH  TYR B 652 "
            pdb=" NH2 ARG B 656 "
     model   vdw
     2.312 3.120
  nonbonded pdb=" OH  TYR A 447 "
            pdb=" OD2 ASP A 455 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" O   ILE B 355 "
            pdb=" OH  TYR B 361 "
     model   vdw
     2.332 3.040
  ... (remaining 77907 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: 0.04
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 75 through 663 or resid 805 through 807 or resid 814 or re \ 
sid 819 through 820 or resid 824 or resid 829 through 830 or resid 832 or resid  \ 
835 through 838))
  selection = (chain 'B' and (resid 75 through 663 or resid 805 through 807 or resid 814 or re \ 
sid 819 through 820 or resid 824 or resid 829 through 830 or resid 832 or resid  \ 
835 through 838))
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             5.070
  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:          0.420
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     26.180
  Find NCS groups from input model:        0.520
  Set up NCS constraints:                  0.050
  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:15.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
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   0.141   9796  Z= 0.295
  Angle     :  0.575   8.020  13108  Z= 0.264
  Chirality :  0.043   0.352   1466
  Planarity :  0.004   0.071   1468
  Dihedral  : 14.929  80.225   4222
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    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:  1.30 (0.25), residues: 1054
  helix:  1.47 (0.22), residues: 506
  sheet:  1.29 (0.44), residues: 128
  loop :  0.08 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 418 
 HIS   0.007   0.001   HIS B 614 
 PHE   0.020   0.001   PHE B 274 
 TYR   0.026   0.001   TYR B 481 
 ARG   0.005   0.001   ARG B 337 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00051 (    6)
  link_NAG-ASN         : angle       1.78339 (   18)
  link_BETA1-4         : bond        0.00430 (    4)
  link_BETA1-4         : angle       0.84279 (   12)
  hydrogen bonds       : bond        0.18678 (  476)
  hydrogen bonds       : angle       5.94964 ( 1353)
  SS BOND              : bond        0.00307 (    6)
  SS BOND              : angle       1.05544 (   12)
  covalent geometry    : bond        0.00612 ( 9780)
  covalent geometry    : angle       0.57020 (13066)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.970 
Fit side-chains
REVERT: B  471 ASP cc_start: 0.8312 (m-30) cc_final: 0.7991 (m-30)
REVERT: B  628 LYS cc_start: 0.8068 (tttp) cc_final: 0.7804 (tttp)
REVERT: A  125 SER cc_start: 0.8571 (m) cc_final: 0.8357 (m)
REVERT: A  471 ASP cc_start: 0.7679 (m-30) cc_final: 0.7419 (m-30)
REVERT: A  546 SER cc_start: 0.8313 (m) cc_final: 0.8059 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 1.2073
  time to fit residues: 139.1729
Evaluate side-chains
  94 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    0.7980
   chunk 80 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0980
   chunk 54 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0060
   chunk 96 optimal weight:    0.9980
   overall best weight:    0.9798

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

Flipped N/Q/H residues before XYZ refinement:
B 286 ASN
B 358 ASN
B 624 GLN
A 114 ASN
A 286 ASN
A 330 GLN
A 358 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.141178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.108570 restraints weight = 10290.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 1.61
r_work: 0.3166 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3058 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.0833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9796  Z= 0.163
  Angle     :  0.540   6.531  13108  Z= 0.274
  Chirality :  0.042   0.137   1466
  Planarity :  0.004   0.054   1468
  Dihedral  : 12.809  72.066   2312
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  :  7.03 %
    Favored  : 91.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    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:  1.97 (0.25), residues: 1054
  helix:  2.49 (0.22), residues: 496
  sheet:  1.49 (0.42), residues: 126
  loop : -0.14 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 647 
 HIS   0.007   0.001   HIS B 614 
 PHE   0.022   0.001   PHE B 274 
 TYR   0.024   0.002   TYR B 481 
 ARG   0.004   0.000   ARG B 337 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00283 (    6)
  link_NAG-ASN         : angle       1.61426 (   18)
  link_BETA1-4         : bond        0.00442 (    4)
  link_BETA1-4         : angle       1.11813 (   12)
  hydrogen bonds       : bond        0.05737 (  476)
  hydrogen bonds       : angle       4.13831 ( 1353)
  SS BOND              : bond        0.00215 (    6)
  SS BOND              : angle       0.78807 (   12)
  covalent geometry    : bond        0.00387 ( 9780)
  covalent geometry    : angle       0.53568 (13066)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 1.062 
Fit side-chains
REVERT: B  471 ASP cc_start: 0.8188 (m-30) cc_final: 0.7899 (m-30)
REVERT: B  556 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6697 (mm-30)
REVERT: A  471 ASP cc_start: 0.7781 (m-30) cc_final: 0.7500 (m-30)
REVERT: A  546 SER cc_start: 0.8278 (m) cc_final: 0.7994 (m)
  outliers start: 13
  outliers final: 4
  residues processed: 99
  average time/residue: 1.1021
  time to fit residues: 118.4658
Evaluate side-chains
  91 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 86
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   79 MET
Chi-restraints excluded: chain B residue  202 LEU
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  556 GLU
Chi-restraints excluded: chain B residue  618 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 9 optimal weight:    9.9990
   chunk 2 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
B 624 GLN
A 114 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.138754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.106283 restraints weight = 10480.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3203 rms_B_bonded: 1.60
r_work: 0.3120 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3010 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.1131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.069   9796  Z= 0.282
  Angle     :  0.658   7.638  13108  Z= 0.324
  Chirality :  0.047   0.174   1466
  Planarity :  0.005   0.051   1468
  Dihedral  : 13.203  73.379   2312
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  :  9.74 %
    Favored  : 88.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    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:  1.63 (0.25), residues: 1054
  helix:  2.19 (0.22), residues: 496
  sheet:  1.29 (0.42), residues: 126
  loop : -0.28 (0.28), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 647 
 HIS   0.009   0.002   HIS A 614 
 PHE   0.019   0.002   PHE B 315 
 TYR   0.024   0.002   TYR B 481 
 ARG   0.006   0.001   ARG A 267 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00245 (    6)
  link_NAG-ASN         : angle       1.92926 (   18)
  link_BETA1-4         : bond        0.00457 (    4)
  link_BETA1-4         : angle       1.47338 (   12)
  hydrogen bonds       : bond        0.06529 (  476)
  hydrogen bonds       : angle       4.24279 ( 1353)
  SS BOND              : bond        0.00210 (    6)
  SS BOND              : angle       1.08095 (   12)
  covalent geometry    : bond        0.00706 ( 9780)
  covalent geometry    : angle       0.65289 (13066)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.925 
Fit side-chains
REVERT: B  471 ASP cc_start: 0.8269 (m-30) cc_final: 0.7987 (m-30)
REVERT: B  556 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6759 (mm-30)
REVERT: A  529 LYS cc_start: 0.7853 (tmmt) cc_final: 0.7643 (tttm)
  outliers start: 16
  outliers final: 7
  residues processed: 92
  average time/residue: 1.1200
  time to fit residues: 111.6905
Evaluate side-chains
  89 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 81
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   79 MET
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue  552 VAL
Chi-restraints excluded: chain B residue  556 GLU
Chi-restraints excluded: chain B residue  618 GLU
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain A residue  618 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 95 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 0 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0980
   chunk 40 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0970
   chunk 3 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 624 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.141675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.109244 restraints weight = 10324.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 1.60
r_work: 0.3180 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.1174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9796  Z= 0.122
  Angle     :  0.491   6.374  13108  Z= 0.249
  Chirality :  0.040   0.127   1466
  Planarity :  0.004   0.042   1468
  Dihedral  : 12.033  73.267   2312
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 11.47 %
    Favored  : 87.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    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:  2.13 (0.25), residues: 1054
  helix:  2.77 (0.22), residues: 496
  sheet:  1.40 (0.43), residues: 126
  loop : -0.21 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 647 
 HIS   0.005   0.001   HIS B 614 
 PHE   0.016   0.001   PHE A 315 
 TYR   0.014   0.001   TYR B 570 
 ARG   0.004   0.000   ARG B 412 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00221 (    6)
  link_NAG-ASN         : angle       1.64004 (   18)
  link_BETA1-4         : bond        0.00412 (    4)
  link_BETA1-4         : angle       1.19586 (   12)
  hydrogen bonds       : bond        0.04619 (  476)
  hydrogen bonds       : angle       3.82632 ( 1353)
  SS BOND              : bond        0.00175 (    6)
  SS BOND              : angle       0.58802 (   12)
  covalent geometry    : bond        0.00276 ( 9780)
  covalent geometry    : angle       0.48606 (13066)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.920 
Fit side-chains
REVERT: B  471 ASP cc_start: 0.8227 (m-30) cc_final: 0.7967 (m-30)
REVERT: B  556 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6655 (mm-30)
REVERT: A  546 SER cc_start: 0.8241 (m) cc_final: 0.7998 (m)
  outliers start: 12
  outliers final: 1
  residues processed: 90
  average time/residue: 1.0261
  time to fit residues: 100.7761
Evaluate side-chains
  85 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 83
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  556 GLU
Chi-restraints excluded: chain B residue  618 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 79 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 58 optimal weight:    4.9990
   chunk 104 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0050
   overall best weight:    1.3400

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

Flipped N/Q/H residues before XYZ refinement:
B 624 GLN
A 330 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.140022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.107548 restraints weight = 10436.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 1.61
r_work: 0.3145 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.1212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   9796  Z= 0.202
  Angle     :  0.570   6.395  13108  Z= 0.283
  Chirality :  0.043   0.134   1466
  Planarity :  0.004   0.041   1468
  Dihedral  : 12.253  73.378   2312
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 12.45 %
    Favored  : 86.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    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:  1.94 (0.25), residues: 1054
  helix:  2.54 (0.22), residues: 498
  sheet:  1.33 (0.43), residues: 126
  loop : -0.24 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 647 
 HIS   0.009   0.001   HIS B 614 
 PHE   0.017   0.002   PHE A 322 
 TYR   0.016   0.002   TYR B 570 
 ARG   0.004   0.001   ARG A 412 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00224 (    6)
  link_NAG-ASN         : angle       1.78500 (   18)
  link_BETA1-4         : bond        0.00435 (    4)
  link_BETA1-4         : angle       1.32986 (   12)
  hydrogen bonds       : bond        0.05481 (  476)
  hydrogen bonds       : angle       3.95135 ( 1353)
  SS BOND              : bond        0.00160 (    6)
  SS BOND              : angle       0.85103 (   12)
  covalent geometry    : bond        0.00497 ( 9780)
  covalent geometry    : angle       0.56545 (13066)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.909 
Fit side-chains
REVERT: B  471 ASP cc_start: 0.8236 (m-30) cc_final: 0.7967 (m-30)
REVERT: B  556 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6746 (mm-30)
  outliers start: 10
  outliers final: 5
  residues processed: 87
  average time/residue: 1.0894
  time to fit residues: 103.0371
Evaluate side-chains
  86 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   79 MET
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  556 GLU
Chi-restraints excluded: chain B residue  618 GLU
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain A residue  663 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 80 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 10 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0270
   chunk 41 optimal weight:    1.9990
   chunk 104 optimal weight:    1.9990
   overall best weight:    0.8840

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

Flipped N/Q/H residues before XYZ refinement:
B 624 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.141061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.108607 restraints weight = 10385.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 1.60
r_work: 0.3163 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3055 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.1250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9796  Z= 0.150
  Angle     :  0.516   6.658  13108  Z= 0.258
  Chirality :  0.041   0.126   1466
  Planarity :  0.004   0.038   1468
  Dihedral  : 11.833  73.712   2312
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 13.20 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    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:  2.09 (0.25), residues: 1054
  helix:  2.71 (0.22), residues: 498
  sheet:  1.36 (0.43), residues: 126
  loop : -0.21 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 647 
 HIS   0.007   0.001   HIS B 614 
 PHE   0.017   0.001   PHE A 315 
 TYR   0.015   0.001   TYR B 570 
 ARG   0.004   0.000   ARG A 412 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00212 (    6)
  link_NAG-ASN         : angle       1.70105 (   18)
  link_BETA1-4         : bond        0.00433 (    4)
  link_BETA1-4         : angle       1.23290 (   12)
  hydrogen bonds       : bond        0.04842 (  476)
  hydrogen bonds       : angle       3.81663 ( 1353)
  SS BOND              : bond        0.00163 (    6)
  SS BOND              : angle       0.66947 (   12)
  covalent geometry    : bond        0.00359 ( 9780)
  covalent geometry    : angle       0.51073 (13066)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.924 
Fit side-chains
REVERT: B  471 ASP cc_start: 0.8228 (m-30) cc_final: 0.7962 (m-30)
REVERT: B  556 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6729 (mm-30)
  outliers start: 10
  outliers final: 4
  residues processed: 91
  average time/residue: 0.9987
  time to fit residues: 99.2947
Evaluate side-chains
  87 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 82
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   79 MET
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  556 GLU
Chi-restraints excluded: chain B residue  618 GLU
Chi-restraints excluded: chain A residue  614 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 66 optimal weight:    6.9990
   chunk 76 optimal weight:    0.4980
   chunk 64 optimal weight:    3.9990
   chunk 93 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   chunk 105 optimal weight:    1.9990
   chunk 57 optimal weight:    0.4980
   chunk 104 optimal weight:    1.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
B 140 GLN
B 624 GLN
A 330 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.140108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.107608 restraints weight = 10494.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 1.61
r_work: 0.3150 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3041 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8554
moved from start:          0.1289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   9796  Z= 0.185
  Angle     :  0.552   6.773  13108  Z= 0.274
  Chirality :  0.042   0.127   1466
  Planarity :  0.004   0.037   1468
  Dihedral  : 11.974  73.917   2312
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 13.74 %
    Favored  : 85.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    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:  1.98 (0.25), residues: 1054
  helix:  2.59 (0.22), residues: 498
  sheet:  1.29 (0.43), residues: 126
  loop : -0.21 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 647 
 HIS   0.008   0.001   HIS B 614 
 PHE   0.016   0.001   PHE A 315 
 TYR   0.015   0.002   TYR B 570 
 ARG   0.005   0.001   ARG A 412 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00213 (    6)
  link_NAG-ASN         : angle       1.79639 (   18)
  link_BETA1-4         : bond        0.00436 (    4)
  link_BETA1-4         : angle       1.31043 (   12)
  hydrogen bonds       : bond        0.05251 (  476)
  hydrogen bonds       : angle       3.87907 ( 1353)
  SS BOND              : bond        0.00172 (    6)
  SS BOND              : angle       0.85777 (   12)
  covalent geometry    : bond        0.00453 ( 9780)
  covalent geometry    : angle       0.54693 (13066)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 81
  time to evaluate  : 1.051 
Fit side-chains
REVERT: B  471 ASP cc_start: 0.8222 (m-30) cc_final: 0.7953 (m-30)
REVERT: B  556 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6773 (mm-30)
REVERT: A  618 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8189 (pt0)
  outliers start: 9
  outliers final: 6
  residues processed: 89
  average time/residue: 1.0883
  time to fit residues: 105.7141
Evaluate side-chains
  88 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   79 MET
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  556 GLU
Chi-restraints excluded: chain B residue  618 GLU
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain A residue  618 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 90 optimal weight:    0.5980
   chunk 24 optimal weight:    0.3980
   chunk 55 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 624 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.141762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.109198 restraints weight = 10537.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 1.62
r_work: 0.3174 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.1326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9796  Z= 0.129
  Angle     :  0.494   7.006  13108  Z= 0.248
  Chirality :  0.040   0.126   1466
  Planarity :  0.004   0.035   1468
  Dihedral  : 11.491  74.053   2312
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 13.96 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    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:  2.20 (0.25), residues: 1054
  helix:  2.83 (0.22), residues: 498
  sheet:  1.28 (0.43), residues: 128
  loop : -0.16 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 647 
 HIS   0.007   0.001   HIS B 614 
 PHE   0.016   0.001   PHE A 315 
 TYR   0.014   0.001   TYR B 570 
 ARG   0.005   0.000   ARG A 412 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00218 (    6)
  link_NAG-ASN         : angle       1.64429 (   18)
  link_BETA1-4         : bond        0.00433 (    4)
  link_BETA1-4         : angle       1.19380 (   12)
  hydrogen bonds       : bond        0.04536 (  476)
  hydrogen bonds       : angle       3.73428 ( 1353)
  SS BOND              : bond        0.00245 (    6)
  SS BOND              : angle       0.86896 (   12)
  covalent geometry    : bond        0.00302 ( 9780)
  covalent geometry    : angle       0.48847 (13066)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 1.083 
Fit side-chains
REVERT: B  471 ASP cc_start: 0.8214 (m-30) cc_final: 0.7949 (m-30)
REVERT: B  556 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6683 (mm-30)
  outliers start: 9
  outliers final: 4
  residues processed: 91
  average time/residue: 1.0309
  time to fit residues: 102.6070
Evaluate side-chains
  90 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  556 GLU
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  614 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 80 optimal weight:    0.6980
   chunk 2 optimal weight:    0.5980
   chunk 66 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 10 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
B 624 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.140794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.108416 restraints weight = 10359.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 1.60
r_work: 0.3169 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.1342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9796  Z= 0.152
  Angle     :  0.518   7.244  13108  Z= 0.259
  Chirality :  0.041   0.126   1466
  Planarity :  0.004   0.034   1468
  Dihedral  : 11.527  74.274   2312
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 14.39 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    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:  2.14 (0.25), residues: 1054
  helix:  2.76 (0.22), residues: 498
  sheet:  1.25 (0.43), residues: 128
  loop : -0.15 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 647 
 HIS   0.006   0.001   HIS B 614 
 PHE   0.016   0.001   PHE A 315 
 TYR   0.014   0.001   TYR B 570 
 ARG   0.005   0.000   ARG A 412 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00209 (    6)
  link_NAG-ASN         : angle       1.70441 (   18)
  link_BETA1-4         : bond        0.00449 (    4)
  link_BETA1-4         : angle       1.23259 (   12)
  hydrogen bonds       : bond        0.04798 (  476)
  hydrogen bonds       : angle       3.75992 ( 1353)
  SS BOND              : bond        0.00137 (    6)
  SS BOND              : angle       0.87192 (   12)
  covalent geometry    : bond        0.00363 ( 9780)
  covalent geometry    : angle       0.51286 (13066)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.997 
Fit side-chains
REVERT: B  471 ASP cc_start: 0.8216 (m-30) cc_final: 0.7944 (m-30)
REVERT: B  556 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6764 (mm-30)
  outliers start: 7
  outliers final: 4
  residues processed: 89
  average time/residue: 1.1615
  time to fit residues: 114.6204
Evaluate side-chains
  87 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 82
  time to evaluate  : 1.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  556 GLU
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  614 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 94 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 82 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
B 624 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.139027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.106592 restraints weight = 10542.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 1.62
r_work: 0.3132 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3023 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8575
moved from start:          0.1373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   9796  Z= 0.251
  Angle     :  0.623   7.229  13108  Z= 0.306
  Chirality :  0.046   0.155   1466
  Planarity :  0.004   0.036   1468
  Dihedral  : 12.309  73.303   2312
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 14.39 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    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:  1.77 (0.25), residues: 1054
  helix:  2.36 (0.22), residues: 500
  sheet:  1.20 (0.42), residues: 126
  loop : -0.27 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 647 
 HIS   0.008   0.001   HIS B 614 
 PHE   0.018   0.002   PHE A 322 
 TYR   0.016   0.002   TYR B 570 
 ARG   0.005   0.001   ARG A 412 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00188 (    6)
  link_NAG-ASN         : angle       2.05671 (   18)
  link_BETA1-4         : bond        0.00473 (    4)
  link_BETA1-4         : angle       1.42274 (   12)
  hydrogen bonds       : bond        0.05925 (  476)
  hydrogen bonds       : angle       4.00579 ( 1353)
  SS BOND              : bond        0.00154 (    6)
  SS BOND              : angle       1.20685 (   12)
  covalent geometry    : bond        0.00624 ( 9780)
  covalent geometry    : angle       0.61689 (13066)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 79
  time to evaluate  : 0.933 
Fit side-chains
REVERT: B  471 ASP cc_start: 0.8311 (m-30) cc_final: 0.8057 (m-30)
REVERT: B  556 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.6923 (mm-30)
REVERT: A  471 ASP cc_start: 0.8214 (m-30) cc_final: 0.7956 (m-30)
REVERT: A  618 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8225 (pt0)
  outliers start: 7
  outliers final: 4
  residues processed: 86
  average time/residue: 1.0076
  time to fit residues: 94.7674
Evaluate side-chains
  84 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 78
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  556 GLU
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain A residue  618 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 76 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0570
   chunk 103 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 97 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
B 624 GLN
A 114 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.141249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.108874 restraints weight = 10436.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 1.61
r_work: 0.3171 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3064 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.1395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9796  Z= 0.128
  Angle     :  0.500   7.398  13108  Z= 0.251
  Chirality :  0.040   0.127   1466
  Planarity :  0.004   0.035   1468
  Dihedral  : 11.548  73.785   2312
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 14.18 %
    Favored  : 84.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    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:  2.13 (0.25), residues: 1054
  helix:  2.76 (0.22), residues: 498
  sheet:  1.26 (0.43), residues: 128
  loop : -0.18 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 647 
 HIS   0.005   0.001   HIS A 614 
 PHE   0.016   0.001   PHE A 315 
 TYR   0.014   0.001   TYR B 570 
 ARG   0.005   0.000   ARG A 412 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00204 (    6)
  link_NAG-ASN         : angle       1.72956 (   18)
  link_BETA1-4         : bond        0.00438 (    4)
  link_BETA1-4         : angle       1.21675 (   12)
  hydrogen bonds       : bond        0.04550 (  476)
  hydrogen bonds       : angle       3.74630 ( 1353)
  SS BOND              : bond        0.00248 (    6)
  SS BOND              : angle       0.76403 (   12)
  covalent geometry    : bond        0.00297 ( 9780)
  covalent geometry    : angle       0.49434 (13066)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6603.58 seconds
wall clock time: 113 minutes 54.48 seconds (6834.48 seconds total)