Starting phenix.real_space_refine
on Sat Aug 23 04:07:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jl4_36388/08_2025/8jl4_36388.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jl4_36388/08_2025/8jl4_36388.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jl4_36388/08_2025/8jl4_36388.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jl4_36388/08_2025/8jl4_36388.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jl4_36388/08_2025/8jl4_36388.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jl4_36388/08_2025/8jl4_36388.map"
  }
  resolution = 2.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.039
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 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9588
  Number of models: 1
  Model: ""
    Number of chains: 8
    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: "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: "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: "A"
      Number of atoms: 508
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 508
          Unusual residues: {'C14': 12, 'CLR': 2, 'COA': 1, '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: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 508
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 508
          Unusual residues: {'C14': 12, 'CLR': 2, 'COA': 1, '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: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.23, per 1000 atoms: 0.23
  Number of scatterers: 9588
  At special positions: 0
  Unit cell: (108.73, 86.32, 106.24, 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 A 104 " - pdb=" SG  CYS A 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 151 " - pdb=" SG  CYS A 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 443 " - pdb=" SG  CYS A 462 " distance=2.04
    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=2.04

  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 803 " - " ASN A  94 "
      " NAG B 804 " - " ASN B  94 "
      " NAG C   1 " - " ASN A 142 "
      " NAG D   1 " - " ASN A 162 "
      " NAG E   1 " - " ASN B 142 "
      " NAG F   1 " - " ASN B 162 "
  Time building additional restraints: 1.89
  Conformation dependent library (CDL) restraints added in 432.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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:
      40 helices and 4 sheets defined
      56.1% alpha, 9.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 191 through 214
    Processing helix  chain 'A' and resid 268 through 287
      removed outlier: 3.500A  pdb=" N   ASP A 272 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 296
      removed outlier: 3.599A  pdb=" N   TYR A 292 " --> pdb=" O   GLY A 289 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   TRP A 293 " --> pdb=" O   GLY A 290 " (cutoff:3.500A)
      removed outlier: 6.590A  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 331
      removed outlier: 3.548A  pdb=" N   TRP A 312 " --> pdb=" O   LEU A 308 " (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
      removed outlier: 3.557A  pdb=" N   PHE A 394 " --> pdb=" O   LEU A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 416
    Processing helix  chain 'A' and resid 417 through 438
      removed outlier: 3.651A  pdb=" N   LEU A 438 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 458
      removed outlier: 3.690A  pdb=" N   PHE A 456 " --> pdb=" O   ILE A 453 " (cutoff:3.500A)
    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: 4.045A  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
    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 helix  chain 'B' and resid 191 through 214
    Processing helix  chain 'B' and resid 268 through 287
    Processing helix  chain 'B' and resid 288 through 296
      removed outlier: 3.599A  pdb=" N   TYR B 292 " --> pdb=" O   GLY B 289 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   TRP B 293 " --> pdb=" O   GLY B 290 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   TYR B 294 " --> pdb=" O   LYS B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 307
    Processing helix  chain 'B' and resid 308 through 331
      removed outlier: 3.549A  pdb=" N   TRP B 312 " --> pdb=" O   LEU B 308 " (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
      removed outlier: 3.556A  pdb=" N   PHE B 394 " --> pdb=" O   LEU B 390 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 416
    Processing helix  chain 'B' and resid 417 through 438
      removed outlier: 3.651A  pdb=" N   LEU B 438 " --> pdb=" O   LEU B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 458
      removed outlier: 3.689A  pdb=" N   PHE B 456 " --> pdb=" O   ILE B 453 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 465 through 475
    Processing helix  chain 'B' and resid 476 through 480
    Processing helix  chain 'B' and resid 484 through 488
      removed outlier: 4.045A  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 sheet with id=AA1, first strand: chain 'A' and resid 125 through 132
      removed outlier: 8.929A  pdb=" N   TYR A 163 " --> pdb=" O   GLN A  81 " (cutoff:3.500A)
      removed outlier: 6.074A  pdb=" N   LEU A  83 " --> pdb=" O   TYR A 163 " (cutoff:3.500A)
      removed outlier: 7.356A  pdb=" N   LEU A 165 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   LEU A  85 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 7.394A  pdb=" N   VAL A 167 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   HIS A  87 " --> pdb=" O   VAL A 167 " (cutoff:3.500A)
      removed outlier: 8.372A  pdb=" N   ASN A 169 " --> pdb=" O   HIS A  87 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ASN A 162 " --> pdb=" O   ASN A 184 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LYS A 168 " --> pdb=" O   ALA A 178 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 115
      removed outlier: 6.946A  pdb=" N   VAL A  97 " --> pdb=" O   LEU A 112 " (cutoff:3.500A)
      removed outlier: 5.020A  pdb=" N   ASN A 114 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   LEU A  95 " --> pdb=" O   ASN A 114 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   CYS A 151 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   ASP A 143 " --> pdb=" O   GLU A 149 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   GLU A 149 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 125 through 132
      removed outlier: 8.929A  pdb=" N   TYR B 163 " --> pdb=" O   GLN B  81 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   LEU B  83 " --> pdb=" O   TYR B 163 " (cutoff:3.500A)
      removed outlier: 7.356A  pdb=" N   LEU B 165 " --> pdb=" O   LEU B  83 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   LEU B  85 " --> pdb=" O   LEU B 165 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   VAL B 167 " --> pdb=" O   LEU B  85 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   HIS B  87 " --> pdb=" O   VAL B 167 " (cutoff:3.500A)
      removed outlier: 8.372A  pdb=" N   ASN B 169 " --> pdb=" O   HIS B  87 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ASN B 162 " --> pdb=" O   ASN B 184 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LYS B 168 " --> pdb=" O   ALA B 178 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 110 through 115
      removed outlier: 6.947A  pdb=" N   VAL B  97 " --> pdb=" O   LEU B 112 " (cutoff:3.500A)
      removed outlier: 5.019A  pdb=" N   ASN B 114 " --> pdb=" O   LEU B  95 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   LEU B  95 " --> pdb=" O   ASN B 114 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   CYS B 151 " --> pdb=" O   LEU B 141 " (cutoff:3.500A)
      removed outlier: 6.026A  pdb=" N   ASP B 143 " --> pdb=" O   GLU B 149 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   GLU B 149 " --> pdb=" O   ASP B 143 " (cutoff:3.500A)

    483 hydrogen bonds defined for protein.
    1365 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: 1.63

  Time building geometry restraints manager: 1.38 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 1300
        1.30 -     1.43: 2566
        1.43 -     1.56: 5852
        1.56 -     1.69: 10
        1.69 -     1.82: 52
  Bond restraints: 9780
  Sorted by residual:
  bond pdb=" C13 UV6 A 801 "
       pdb=" O7  UV6 A 801 "
    ideal  model  delta    sigma   weight residual
    1.351  1.497 -0.146 2.00e-02 2.50e+03 5.35e+01
  bond pdb=" C13 UV6 B 802 "
       pdb=" O7  UV6 B 802 "
    ideal  model  delta    sigma   weight residual
    1.351  1.497 -0.146 2.00e-02 2.50e+03 5.33e+01
  bond pdb=" C8  UV6 A 801 "
       pdb=" N9  UV6 A 801 "
    ideal  model  delta    sigma   weight residual
    1.351  1.476 -0.125 2.00e-02 2.50e+03 3.89e+01
  bond pdb=" C8  UV6 B 802 "
       pdb=" N9  UV6 B 802 "
    ideal  model  delta    sigma   weight residual
    1.351  1.476 -0.125 2.00e-02 2.50e+03 3.88e+01
  bond pdb=" C4' UV6 B 802 "
       pdb=" O5  UV6 B 802 "
    ideal  model  delta    sigma   weight residual
    1.419  1.541 -0.122 2.00e-02 2.50e+03 3.74e+01
  ... (remaining 9775 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.48: 12826
        2.48 -     4.95: 204
        4.95 -     7.43: 26
        7.43 -     9.90: 6
        9.90 -    12.38: 4
  Bond angle restraints: 13066
  Sorted by residual:
  angle pdb=" P1A COA A 802 "
        pdb=" O3A COA A 802 "
        pdb=" P2A COA A 802 "
      ideal   model   delta    sigma   weight residual
     135.11  122.73   12.38 3.00e+00 1.11e-01 1.70e+01
  angle pdb=" P1A COA B 803 "
        pdb=" O3A COA B 803 "
        pdb=" P2A COA B 803 "
      ideal   model   delta    sigma   weight residual
     135.11  122.87   12.24 3.00e+00 1.11e-01 1.66e+01
  angle pdb=" C18 UV6 A 801 "
        pdb=" C17 UV6 A 801 "
        pdb=" C5  UV6 A 801 "
      ideal   model   delta    sigma   weight residual
     110.11  120.89  -10.78 3.00e+00 1.11e-01 1.29e+01
  angle pdb=" C18 UV6 B 802 "
        pdb=" C17 UV6 B 802 "
        pdb=" C5  UV6 B 802 "
      ideal   model   delta    sigma   weight residual
     110.11  120.88  -10.77 3.00e+00 1.11e-01 1.29e+01
  angle pdb=" C2' UV6 B 802 "
        pdb=" C1' UV6 B 802 "
        pdb=" N9  UV6 B 802 "
      ideal   model   delta    sigma   weight residual
     112.50  102.86    9.64 3.00e+00 1.11e-01 1.03e+01
  ... (remaining 13061 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.97: 5605
       18.97 -    37.95: 451
       37.95 -    56.92: 128
       56.92 -    75.90: 32
       75.90 -    94.87: 8
  Dihedral angle restraints: 6224
    sinusoidal: 3152
      harmonic: 3072
  Sorted by residual:
  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  165.67  -72.67     1      1.00e+01 1.00e-02 6.74e+01
  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  165.63  -72.63     1      1.00e+01 1.00e-02 6.73e+01
  dihedral pdb=" CB  CYS B 151 "
           pdb=" SG  CYS B 151 "
           pdb=" SG  CYS B 179 "
           pdb=" CB  CYS B 179 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  136.62  -43.62     1      1.00e+01 1.00e-02 2.65e+01
  ... (remaining 6221 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.366: 1464
       0.366 -    0.733: 0
       0.733 -    1.099: 0
       1.099 -    1.466: 0
       1.466 -    1.832: 2
  Chirality restraints: 1466
  Sorted by residual:
  chirality pdb=" C17 UV6 B 802 "
            pdb=" C12 UV6 B 802 "
            pdb=" C18 UV6 B 802 "
            pdb=" C5  UV6 B 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.54    0.71    1.83 2.00e-01 2.50e+01 8.39e+01
  chirality pdb=" C17 UV6 A 801 "
            pdb=" C12 UV6 A 801 "
            pdb=" C18 UV6 A 801 "
            pdb=" C5  UV6 A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.54    0.71    1.83 2.00e-01 2.50e+01 8.36e+01
  chirality pdb=" C4' UV6 B 802 "
            pdb=" C3' UV6 B 802 "
            pdb=" C5' UV6 B 802 "
            pdb=" O5  UV6 B 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.25   -2.56    0.31 2.00e-01 2.50e+01 2.37e+00
  ... (remaining 1463 not shown)

  Planarity restraints: 1474
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C7P COA B 803 "   -0.270 2.00e-02 2.50e+03   2.22e-01 6.17e+02
        pdb=" C9P COA B 803 "    0.078 2.00e-02 2.50e+03
        pdb=" CAP COA B 803 "   -0.185 2.00e-02 2.50e+03
        pdb=" N8P COA B 803 "    0.366 2.00e-02 2.50e+03
        pdb=" O9P COA B 803 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C7P COA A 802 "    0.246 2.00e-02 2.50e+03   2.02e-01 5.11e+02
        pdb=" C9P COA A 802 "   -0.071 2.00e-02 2.50e+03
        pdb=" CAP COA A 802 "    0.174 2.00e-02 2.50e+03
        pdb=" N8P COA A 802 "   -0.329 2.00e-02 2.50e+03
        pdb=" O9P COA A 802 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 373 "   -0.031 5.00e-02 4.00e+02   4.57e-02 3.35e+00
        pdb=" N   PRO A 374 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A 374 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 374 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1471 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2563
        2.82 -     3.34: 8120
        3.34 -     3.86: 15385
        3.86 -     4.38: 19408
        4.38 -     4.90: 32858
  Nonbonded interactions: 78334
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN B 506 "
            pdb=" O   TRP B 566 "
     model   vdw
     2.302 3.120
  nonbonded pdb=" ND2 ASN A 506 "
            pdb=" O   TRP A 566 "
     model   vdw
     2.302 3.120
  nonbonded pdb=" O   LYS B 296 "
            pdb=" OG1 THR B 304 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" O   LYS A 296 "
            pdb=" OG1 THR A 304 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" ND2 ASN A 286 "
            pdb=" O1  UV6 A 801 "
     model   vdw
     2.334 3.120
  ... (remaining 78329 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: 0.02
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:             5.190
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.410
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.020
  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:7.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
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      :  0.008   0.146   9796  Z= 0.377
  Angle     :  0.784  12.378  13108  Z= 0.345
  Chirality :  0.083   1.832   1466
  Planarity :  0.009   0.222   1468
  Dihedral  : 14.992  94.870   4242
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.43 (0.26), residues: 1054
  helix:  1.80 (0.22), residues: 516
  sheet:  1.63 (0.48), residues: 128
  loop : -0.35 (0.29), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 472 
 TYR   0.010   0.002   TYR B 481 
 PHE   0.015   0.002   PHE B 315 
 TRP   0.015   0.002   TRP B 647 
 HIS   0.007   0.001   HIS A 633 

Details of bonding type rmsd
  covalent geometry    : bond        0.00830 ( 9780)
  covalent geometry    : angle       0.77420 (13066)
  SS BOND              : bond        0.00410 (    6)
  SS BOND              : angle       2.31395 (   12)
  hydrogen bonds       : bond        0.15813 (  483)
  hydrogen bonds       : angle       5.58046 ( 1365)
  link_BETA1-4         : bond        0.00316 (    4)
  link_BETA1-4         : angle       0.92453 (   12)
  link_NAG-ASN         : bond        0.00195 (    6)
  link_NAG-ASN         : angle       2.84542 (   18)

*********************** 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
  103 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
REVERT: A  478 ASP cc_start: 0.8236 (m-30) cc_final: 0.8029 (m-30)
REVERT: B  185 GLU cc_start: 0.7850 (tt0) cc_final: 0.7599 (tt0)
REVERT: B  412 ARG cc_start: 0.7583 (ptt-90) cc_final: 0.6596 (mtt-85)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.7406
  time to fit residues: 80.8782
Evaluate side-chains
  78 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A  87 HIS
A 286 ASN
A 358 ASN
A 491 HIS
A 624 GLN
B  87 HIS
B 286 ASN
B 358 ASN
B 491 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.144676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.110100 restraints weight = 8979.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 1.36
r_work: 0.3037 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2909 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.1095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9796  Z= 0.163
  Angle     :  0.599   6.644  13108  Z= 0.292
  Chirality :  0.043   0.137   1466
  Planarity :  0.004   0.046   1468
  Dihedral  : 13.102  82.533   2332
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  6.82 %
    Favored  : 91.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.86 (0.26), residues: 1054
  helix:  2.43 (0.23), residues: 502
  sheet:  1.61 (0.47), residues: 128
  loop : -0.38 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 152 
 TYR   0.014   0.002   TYR A 570 
 PHE   0.017   0.002   PHE B 315 
 TRP   0.012   0.001   TRP B 647 
 HIS   0.006   0.001   HIS B 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 9780)
  covalent geometry    : angle       0.59287 (13066)
  SS BOND              : bond        0.00250 (    6)
  SS BOND              : angle       1.09348 (   12)
  hydrogen bonds       : bond        0.05647 (  483)
  hydrogen bonds       : angle       4.19156 ( 1365)
  link_BETA1-4         : bond        0.00356 (    4)
  link_BETA1-4         : angle       1.27620 (   12)
  link_NAG-ASN         : bond        0.00199 (    6)
  link_NAG-ASN         : angle       2.14860 (   18)

*********************** 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
  101 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: A  148 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7069 (tmtt)
REVERT: A  180 ASP cc_start: 0.8283 (p0) cc_final: 0.8046 (p0)
REVERT: A  478 ASP cc_start: 0.8184 (m-30) cc_final: 0.7975 (m-30)
REVERT: A  628 LYS cc_start: 0.7853 (mttt) cc_final: 0.6875 (mmtt)
REVERT: B  185 GLU cc_start: 0.8132 (tt0) cc_final: 0.7813 (tt0)
  outliers start: 14
  outliers final: 2
  residues processed: 93
  average time/residue: 0.6237
  time to fit residues: 62.2259
Evaluate side-chains
  82 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 79
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 LYS
Chi-restraints excluded: chain A residue  186 ASP
Chi-restraints excluded: chain A residue  204 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 100 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 114 ASN
B 117 GLN
B 184 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.142240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.107731 restraints weight = 9058.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.3047 rms_B_bonded: 1.38
r_work: 0.2929 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2798 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
moved from start:          0.1331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.068   9796  Z= 0.226
  Angle     :  0.653   8.760  13108  Z= 0.317
  Chirality :  0.046   0.166   1466
  Planarity :  0.005   0.047   1468
  Dihedral  : 13.433  85.054   2332
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  :  8.01 %
    Favored  : 89.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.69 (0.25), residues: 1054
  helix:  2.26 (0.22), residues: 502
  sheet:  1.46 (0.45), residues: 128
  loop : -0.39 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 152 
 TYR   0.014   0.002   TYR A 570 
 PHE   0.017   0.002   PHE B 315 
 TRP   0.014   0.002   TRP B 647 
 HIS   0.006   0.001   HIS A 633 

Details of bonding type rmsd
  covalent geometry    : bond        0.00557 ( 9780)
  covalent geometry    : angle       0.64597 (13066)
  SS BOND              : bond        0.00215 (    6)
  SS BOND              : angle       1.10247 (   12)
  hydrogen bonds       : bond        0.06340 (  483)
  hydrogen bonds       : angle       4.26495 ( 1365)
  link_BETA1-4         : bond        0.00315 (    4)
  link_BETA1-4         : angle       1.47795 (   12)
  link_NAG-ASN         : bond        0.00156 (    6)
  link_NAG-ASN         : angle       2.37792 (   18)

*********************** 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
  101 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
REVERT: A  148 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.6987 (tmtt)
REVERT: A  152 ARG cc_start: 0.8067 (ttt-90) cc_final: 0.7781 (ttt-90)
REVERT: A  180 ASP cc_start: 0.8228 (p0) cc_final: 0.7979 (p0)
REVERT: A  478 ASP cc_start: 0.8270 (m-30) cc_final: 0.8060 (m-30)
REVERT: B  185 GLU cc_start: 0.8183 (tt0) cc_final: 0.7803 (tt0)
REVERT: B  410 SER cc_start: 0.9060 (t) cc_final: 0.8757 (t)
REVERT: B  663 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7844 (pt)
  outliers start: 19
  outliers final: 3
  residues processed: 89
  average time/residue: 0.6673
  time to fit residues: 63.5278
Evaluate side-chains
  85 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 LYS
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain B residue  663 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 95 optimal weight:    0.0170
   chunk 79 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 62 optimal weight:    6.9990
   chunk 3 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 69 optimal weight:    0.6980
   chunk 102 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.9220

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

Flipped N/Q/H residues before XYZ refinement:
B 117 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.144044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.109589 restraints weight = 9097.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 1.37
r_work: 0.2966 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2835 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.1472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9796  Z= 0.149
  Angle     :  0.548   6.613  13108  Z= 0.270
  Chirality :  0.042   0.128   1466
  Planarity :  0.004   0.043   1468
  Dihedral  : 12.805  84.343   2332
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  :  9.20 %
    Favored  : 88.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.95 (0.25), residues: 1054
  helix:  2.57 (0.22), residues: 502
  sheet:  1.48 (0.44), residues: 128
  loop : -0.37 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 152 
 TYR   0.013   0.002   TYR A 570 
 PHE   0.016   0.001   PHE A 315 
 TRP   0.012   0.001   TRP B 647 
 HIS   0.006   0.001   HIS B 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 9780)
  covalent geometry    : angle       0.54058 (13066)
  SS BOND              : bond        0.00191 (    6)
  SS BOND              : angle       0.82123 (   12)
  hydrogen bonds       : bond        0.05142 (  483)
  hydrogen bonds       : angle       3.98913 ( 1365)
  link_BETA1-4         : bond        0.00293 (    4)
  link_BETA1-4         : angle       1.40209 (   12)
  link_NAG-ASN         : bond        0.00192 (    6)
  link_NAG-ASN         : angle       2.11002 (   18)

*********************** 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
  93 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
REVERT: A  148 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.6942 (tmtt)
REVERT: A  152 ARG cc_start: 0.8075 (ttt-90) cc_final: 0.7790 (ttt-90)
REVERT: A  478 ASP cc_start: 0.8230 (m-30) cc_final: 0.8027 (m-30)
REVERT: A  493 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6594 (mp0)
REVERT: B  170 ILE cc_start: 0.7002 (OUTLIER) cc_final: 0.6287 (tt)
REVERT: B  185 GLU cc_start: 0.8190 (tt0) cc_final: 0.7944 (tt0)
REVERT: B  410 SER cc_start: 0.9016 (t) cc_final: 0.8763 (t)
REVERT: B  663 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7803 (pt)
  outliers start: 20
  outliers final: 6
  residues processed: 80
  average time/residue: 0.6566
  time to fit residues: 56.3157
Evaluate side-chains
  78 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 LYS
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  186 ASP
Chi-restraints excluded: chain A residue  330 GLN
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  630 ASN
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  330 GLN
Chi-restraints excluded: chain B residue  663 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 69 optimal weight:    0.0570
   chunk 70 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9980
   chunk 94 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 63 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   overall best weight:    1.0100

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

Flipped N/Q/H residues before XYZ refinement:
B 117 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 = 0.143667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.109285 restraints weight = 9101.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 1.36
r_work: 0.3028 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2899 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.1551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9796  Z= 0.159
  Angle     :  0.556   6.956  13108  Z= 0.274
  Chirality :  0.042   0.129   1466
  Planarity :  0.004   0.046   1468
  Dihedral  : 12.563  80.371   2332
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  :  9.96 %
    Favored  : 87.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.94 (0.25), residues: 1054
  helix:  2.57 (0.22), residues: 502
  sheet:  1.47 (0.44), residues: 128
  loop : -0.37 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 152 
 TYR   0.013   0.002   TYR A 570 
 PHE   0.016   0.001   PHE B 315 
 TRP   0.012   0.001   TRP B 647 
 HIS   0.007   0.001   HIS A 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 9780)
  covalent geometry    : angle       0.54939 (13066)
  SS BOND              : bond        0.00205 (    6)
  SS BOND              : angle       0.83397 (   12)
  hydrogen bonds       : bond        0.05248 (  483)
  hydrogen bonds       : angle       3.97901 ( 1365)
  link_BETA1-4         : bond        0.00366 (    4)
  link_BETA1-4         : angle       1.40310 (   12)
  link_NAG-ASN         : bond        0.00189 (    6)
  link_NAG-ASN         : angle       2.11835 (   18)

*********************** 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
  91 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
REVERT: A  148 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.6951 (tmtt)
REVERT: A  152 ARG cc_start: 0.8074 (ttt-90) cc_final: 0.7850 (ttt-90)
REVERT: A  478 ASP cc_start: 0.8228 (m-30) cc_final: 0.8023 (m-30)
REVERT: A  493 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6677 (mp0)
REVERT: B  185 GLU cc_start: 0.8202 (tt0) cc_final: 0.7988 (tt0)
REVERT: B  410 SER cc_start: 0.9036 (t) cc_final: 0.8757 (t)
REVERT: B  663 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7763 (pt)
  outliers start: 19
  outliers final: 7
  residues processed: 79
  average time/residue: 0.6365
  time to fit residues: 54.0446
Evaluate side-chains
  81 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 LYS
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  186 ASP
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain A residue  630 ASN
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  663 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 57 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 54 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   overall best weight:    1.7986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.141587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.107300 restraints weight = 9141.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3127 rms_B_bonded: 1.37
r_work: 0.3010 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2882 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.1576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.074   9796  Z= 0.249
  Angle     :  0.667   9.242  13108  Z= 0.322
  Chirality :  0.047   0.164   1466
  Planarity :  0.005   0.044   1468
  Dihedral  : 13.239  83.180   2332
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 10.50 %
    Favored  : 87.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.64 (0.25), residues: 1054
  helix:  2.21 (0.22), residues: 502
  sheet:  1.47 (0.45), residues: 128
  loop : -0.42 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 372 
 TYR   0.015   0.002   TYR A 570 
 PHE   0.016   0.002   PHE B 315 
 TRP   0.015   0.002   TRP B 647 
 HIS   0.008   0.001   HIS A 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00620 ( 9780)
  covalent geometry    : angle       0.65958 (13066)
  SS BOND              : bond        0.00260 (    6)
  SS BOND              : angle       1.11456 (   12)
  hydrogen bonds       : bond        0.06385 (  483)
  hydrogen bonds       : angle       4.20958 ( 1365)
  link_BETA1-4         : bond        0.00292 (    4)
  link_BETA1-4         : angle       1.46212 (   12)
  link_NAG-ASN         : bond        0.00175 (    6)
  link_NAG-ASN         : angle       2.48258 (   18)

*********************** 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
  99 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
REVERT: A  148 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.6914 (tmtt)
REVERT: A  152 ARG cc_start: 0.8087 (ttt-90) cc_final: 0.7866 (ttt-90)
REVERT: A  478 ASP cc_start: 0.8257 (m-30) cc_final: 0.8045 (m-30)
REVERT: A  556 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6896 (mm-30)
REVERT: B  170 ILE cc_start: 0.7103 (OUTLIER) cc_final: 0.6642 (mm)
REVERT: B  185 GLU cc_start: 0.8184 (tt0) cc_final: 0.7952 (tt0)
REVERT: B  410 SER cc_start: 0.9056 (t) cc_final: 0.8637 (t)
REVERT: B  412 ARG cc_start: 0.7883 (ptt90) cc_final: 0.7524 (mtm180)
REVERT: B  663 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7745 (pt)
  outliers start: 20
  outliers final: 8
  residues processed: 89
  average time/residue: 0.6644
  time to fit residues: 63.3623
Evaluate side-chains
  89 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 LYS
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  186 ASP
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  556 GLU
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain A residue  628 LYS
Chi-restraints excluded: chain A residue  630 ASN
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  422 LEU
Chi-restraints excluded: chain B residue  663 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 93 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 104 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 12 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 60 optimal weight:    6.9990
   chunk 17 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.143600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.109418 restraints weight = 9094.308|
|-----------------------------------------------------------------------------|
r_work (start): 0.3069 rms_B_bonded: 1.36
r_work: 0.2953 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.2823 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.1642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9796  Z= 0.145
  Angle     :  0.543   6.832  13108  Z= 0.268
  Chirality :  0.042   0.137   1466
  Planarity :  0.004   0.042   1468
  Dihedral  : 12.649  81.035   2332
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 11.69 %
    Favored  : 86.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.97 (0.25), residues: 1054
  helix:  2.64 (0.22), residues: 498
  sheet:  1.45 (0.44), residues: 128
  loop : -0.38 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 152 
 TYR   0.013   0.002   TYR A 570 
 PHE   0.016   0.001   PHE A 315 
 TRP   0.012   0.001   TRP B 647 
 HIS   0.007   0.001   HIS A 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 9780)
  covalent geometry    : angle       0.53552 (13066)
  SS BOND              : bond        0.00353 (    6)
  SS BOND              : angle       0.77279 (   12)
  hydrogen bonds       : bond        0.05113 (  483)
  hydrogen bonds       : angle       3.96783 ( 1365)
  link_BETA1-4         : bond        0.00295 (    4)
  link_BETA1-4         : angle       1.39754 (   12)
  link_NAG-ASN         : bond        0.00185 (    6)
  link_NAG-ASN         : angle       2.17245 (   18)

*********************** 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
  86 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 ARG cc_start: 0.8081 (ttt-90) cc_final: 0.7871 (ttt-90)
REVERT: A  478 ASP cc_start: 0.8217 (m-30) cc_final: 0.8013 (m-30)
REVERT: A  493 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6704 (mp0)
REVERT: B  170 ILE cc_start: 0.7050 (OUTLIER) cc_final: 0.6605 (mm)
REVERT: B  185 GLU cc_start: 0.8237 (tt0) cc_final: 0.7995 (tt0)
REVERT: B  410 SER cc_start: 0.9042 (t) cc_final: 0.8686 (t)
REVERT: B  412 ARG cc_start: 0.7819 (ptt90) cc_final: 0.7459 (mpp-170)
REVERT: B  663 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7730 (pt)
  outliers start: 14
  outliers final: 5
  residues processed: 77
  average time/residue: 0.6771
  time to fit residues: 55.9355
Evaluate side-chains
  77 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  186 ASP
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain A residue  628 LYS
Chi-restraints excluded: chain A residue  630 ASN
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  663 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 101 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    1.5788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.141988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.107748 restraints weight = 9114.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.3084 rms_B_bonded: 1.37
r_work: 0.2967 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2837 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.1637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   9796  Z= 0.222
  Angle     :  0.629   8.563  13108  Z= 0.306
  Chirality :  0.046   0.154   1466
  Planarity :  0.005   0.042   1468
  Dihedral  : 13.009  82.993   2332
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 12.01 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.72 (0.25), residues: 1054
  helix:  2.31 (0.22), residues: 502
  sheet:  1.39 (0.44), residues: 128
  loop : -0.38 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 152 
 TYR   0.014   0.002   TYR A 570 
 PHE   0.016   0.002   PHE B 315 
 TRP   0.015   0.002   TRP B 647 
 HIS   0.008   0.001   HIS A 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00549 ( 9780)
  covalent geometry    : angle       0.62142 (13066)
  SS BOND              : bond        0.00231 (    6)
  SS BOND              : angle       1.02562 (   12)
  hydrogen bonds       : bond        0.06016 (  483)
  hydrogen bonds       : angle       4.12160 ( 1365)
  link_BETA1-4         : bond        0.00303 (    4)
  link_BETA1-4         : angle       1.44003 (   12)
  link_NAG-ASN         : bond        0.00176 (    6)
  link_NAG-ASN         : angle       2.38513 (   18)

*********************** 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
  92 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 ARG cc_start: 0.8098 (ttt-90) cc_final: 0.7885 (ttt-90)
REVERT: A  478 ASP cc_start: 0.8236 (m-30) cc_final: 0.8027 (m-30)
REVERT: B  170 ILE cc_start: 0.7083 (OUTLIER) cc_final: 0.6632 (mm)
REVERT: B  185 GLU cc_start: 0.8143 (tt0) cc_final: 0.7904 (tt0)
REVERT: B  410 SER cc_start: 0.9066 (t) cc_final: 0.8670 (t)
REVERT: B  412 ARG cc_start: 0.7884 (ptt90) cc_final: 0.7493 (mpp-170)
REVERT: B  663 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7721 (pt)
  outliers start: 14
  outliers final: 7
  residues processed: 86
  average time/residue: 0.6649
  time to fit residues: 61.3157
Evaluate side-chains
  86 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  186 ASP
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain A residue  628 LYS
Chi-restraints excluded: chain A residue  630 ASN
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  663 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 84 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 98 optimal weight:    0.8980
   chunk 90 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 69 optimal weight:    0.8980
   overall best weight:    0.8980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.143747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.109614 restraints weight = 9083.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3111 rms_B_bonded: 1.35
r_work: 0.2996 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2873 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.1698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9796  Z= 0.148
  Angle     :  0.537   6.579  13108  Z= 0.266
  Chirality :  0.042   0.140   1466
  Planarity :  0.004   0.041   1468
  Dihedral  : 12.472  81.263   2332
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 12.23 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.97 (0.25), residues: 1054
  helix:  2.61 (0.22), residues: 502
  sheet:  1.41 (0.44), residues: 128
  loop : -0.35 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 152 
 TYR   0.013   0.002   TYR A 570 
 PHE   0.016   0.001   PHE A 315 
 TRP   0.012   0.001   TRP B 647 
 HIS   0.007   0.001   HIS A 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 9780)
  covalent geometry    : angle       0.53017 (13066)
  SS BOND              : bond        0.00234 (    6)
  SS BOND              : angle       0.77675 (   12)
  hydrogen bonds       : bond        0.05044 (  483)
  hydrogen bonds       : angle       3.93326 ( 1365)
  link_BETA1-4         : bond        0.00336 (    4)
  link_BETA1-4         : angle       1.37319 (   12)
  link_NAG-ASN         : bond        0.00183 (    6)
  link_NAG-ASN         : angle       2.10559 (   18)

*********************** 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
  85 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 ARG cc_start: 0.8084 (ttt-90) cc_final: 0.7874 (ttt-90)
REVERT: A  478 ASP cc_start: 0.8240 (m-30) cc_final: 0.8038 (m-30)
REVERT: B  170 ILE cc_start: 0.7174 (OUTLIER) cc_final: 0.6679 (mm)
REVERT: B  185 GLU cc_start: 0.8182 (tt0) cc_final: 0.7960 (tt0)
REVERT: B  410 SER cc_start: 0.9039 (t) cc_final: 0.8694 (t)
REVERT: B  412 ARG cc_start: 0.7836 (ptt90) cc_final: 0.7472 (mpp-170)
REVERT: B  663 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7715 (pt)
  outliers start: 13
  outliers final: 6
  residues processed: 78
  average time/residue: 0.6667
  time to fit residues: 55.7394
Evaluate side-chains
  80 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  186 ASP
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain A residue  628 LYS
Chi-restraints excluded: chain A residue  630 ASN
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  663 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 94 optimal weight:    4.9990
   chunk 74 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 184 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.143745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.109592 restraints weight = 9118.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 1.35
r_work: 0.3032 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2903 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.1730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9796  Z= 0.149
  Angle     :  0.538   6.645  13108  Z= 0.267
  Chirality :  0.042   0.130   1466
  Planarity :  0.004   0.041   1468
  Dihedral  : 12.231  81.187   2332
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 12.45 %
    Favored  : 86.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.98 (0.25), residues: 1054
  helix:  2.61 (0.22), residues: 502
  sheet:  1.40 (0.43), residues: 128
  loop : -0.33 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 152 
 TYR   0.013   0.002   TYR A 570 
 PHE   0.016   0.001   PHE B 315 
 TRP   0.012   0.001   TRP B 647 
 HIS   0.007   0.001   HIS A 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 9780)
  covalent geometry    : angle       0.53186 (13066)
  SS BOND              : bond        0.00241 (    6)
  SS BOND              : angle       0.79418 (   12)
  hydrogen bonds       : bond        0.05068 (  483)
  hydrogen bonds       : angle       3.92100 ( 1365)
  link_BETA1-4         : bond        0.00331 (    4)
  link_BETA1-4         : angle       1.34766 (   12)
  link_NAG-ASN         : bond        0.00175 (    6)
  link_NAG-ASN         : angle       2.04181 (   18)

********************** 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
  85 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
REVERT: A  184 ASN cc_start: 0.8685 (m110) cc_final: 0.8476 (m-40)
REVERT: A  478 ASP cc_start: 0.8232 (m-30) cc_final: 0.8022 (m-30)
REVERT: B  170 ILE cc_start: 0.7101 (OUTLIER) cc_final: 0.6639 (mm)
REVERT: B  185 GLU cc_start: 0.8243 (tt0) cc_final: 0.8013 (tt0)
REVERT: B  410 SER cc_start: 0.9032 (t) cc_final: 0.8662 (t)
REVERT: B  412 ARG cc_start: 0.7820 (ptt90) cc_final: 0.7442 (mpp-170)
REVERT: B  663 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7668 (pt)
  outliers start: 12
  outliers final: 8
  residues processed: 79
  average time/residue: 0.6625
  time to fit residues: 56.1174
Evaluate side-chains
  83 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  186 ASP
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain A residue  628 LYS
Chi-restraints excluded: chain A residue  630 ASN
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  663 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 85 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 102 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 94 optimal weight:    4.9990
   chunk 104 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   overall best weight:    1.5786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.141905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.107692 restraints weight = 9082.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 1.37
r_work: 0.3019 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2889 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.1706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   9796  Z= 0.222
  Angle     :  0.627   8.551  13108  Z= 0.305
  Chirality :  0.045   0.155   1466
  Planarity :  0.005   0.042   1468
  Dihedral  : 12.787  83.979   2332
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 12.66 %
    Favored  : 86.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.73 (0.25), residues: 1054
  helix:  2.32 (0.22), residues: 502
  sheet:  1.38 (0.44), residues: 128
  loop : -0.38 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 372 
 TYR   0.014   0.002   TYR A 570 
 PHE   0.016   0.002   PHE A 315 
 TRP   0.014   0.002   TRP B 647 
 HIS   0.008   0.001   HIS A 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00547 ( 9780)
  covalent geometry    : angle       0.61987 (13066)
  SS BOND              : bond        0.00244 (    6)
  SS BOND              : angle       1.04560 (   12)
  hydrogen bonds       : bond        0.06018 (  483)
  hydrogen bonds       : angle       4.11298 ( 1365)
  link_BETA1-4         : bond        0.00308 (    4)
  link_BETA1-4         : angle       1.39484 (   12)
  link_NAG-ASN         : bond        0.00173 (    6)
  link_NAG-ASN         : angle       2.34316 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3320.70 seconds
wall clock time: 57 minutes 38.75 seconds (3458.75 seconds total)