Starting phenix.real_space_refine
on Fri Jul 25 18:02:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zt8_60453/07_2025/8zt8_60453.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zt8_60453/07_2025/8zt8_60453.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.34
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zt8_60453/07_2025/8zt8_60453.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zt8_60453/07_2025/8zt8_60453.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zt8_60453/07_2025/8zt8_60453.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zt8_60453/07_2025/8zt8_60453.cif"
  }
  resolution = 2.34
  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=   0.000 sd=   0.050
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: 7
    Type Number    sf(0)   Gaussians
     Ca      3      9.91       5
     P       9      5.49       5
     Mg      3      5.21       5
     S      45      5.16       5
     C    5118      2.51       5
     N    1359      2.21       5
     O    1459      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7996
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 2588
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 330, 2588
          Classifications: {'peptide': 330}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 314}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 2588
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 330, 2588
          Classifications: {'peptide': 330}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 314}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "C"
      Number of atoms: 2588
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 330, 2588
          Classifications: {'peptide': 330}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 314}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "A"
      Number of atoms: 76
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 76
          Unusual residues: {' CA': 2, ' MG': 1, 'ATP': 1, 'NAG': 3}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "B"
      Number of atoms: 74
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 74
          Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 3}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "C"
      Number of atoms: 75
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 75
          Unusual residues: {' CA': 1, ' MG': 1, 'ATP': 1, 'NAG': 3}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.23, per 1000 atoms: 0.65
  Number of scatterers: 7996
  At special positions: 0
  Unit cell: (87.6, 85.41, 120.45, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Ca      3     19.99
     S      45     16.00
     P       9     15.00
     Mg      3     11.99
     O    1459      8.00
     N    1359      7.00
     C    5118      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 117 " - pdb=" SG  CYS A 165 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 126 " - pdb=" SG  CYS A 149 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 217 " - pdb=" SG  CYS A 227 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 117 " - pdb=" SG  CYS B 165 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 126 " - pdb=" SG  CYS B 149 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 217 " - pdb=" SG  CYS B 227 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 117 " - pdb=" SG  CYS C 165 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 126 " - pdb=" SG  CYS C 149 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 217 " - pdb=" SG  CYS C 227 " 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
    NAG-ASN
      " NAG A 402 " - " ASN A 210 "
      " NAG A 403 " - " ASN A 153 "
      " NAG A 404 " - " ASN A 184 "
      " NAG B 503 " - " ASN B 210 "
      " NAG B 504 " - " ASN B 153 "
      " NAG B 505 " - " ASN B 184 "
      " NAG C 503 " - " ASN C 210 "
      " NAG C 504 " - " ASN C 153 "
      " NAG C 505 " - " ASN C 184 "
  Time building additional restraints: 1.88
  Conformation dependent library (CDL) restraints added in 846.5 milliseconds
  

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1776

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 15 sheets defined
      28.0% alpha, 23.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 47
    Processing helix  chain 'A' and resid 86 through 91
      removed outlier: 3.566A  pdb=" N   TYR A  90 " --> pdb=" O   ASP A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 185
      removed outlier: 3.521A  pdb=" N   GLU A 183 " --> pdb=" O   HIS A 180 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ASN A 184 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   PHE A 185 " --> pdb=" O   ALA A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 216
      removed outlier: 3.848A  pdb=" N   LYS A 216 " --> pdb=" O   THR A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 239
    Processing helix  chain 'A' and resid 242 through 250
      removed outlier: 3.556A  pdb=" N   LEU A 246 " --> pdb=" O   ASP A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 270
    Processing helix  chain 'A' and resid 327 through 355
      removed outlier: 3.658A  pdb=" N   THR A 331 " --> pdb=" O   ASP A 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 27 through 47
    Processing helix  chain 'B' and resid 86 through 91
    Processing helix  chain 'B' and resid 179 through 183
      removed outlier: 3.542A  pdb=" N   GLU B 183 " --> pdb=" O   HIS B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 217
      removed outlier: 4.264A  pdb=" N   LYS B 216 " --> pdb=" O   THR B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 239
    Processing helix  chain 'B' and resid 242 through 250
      removed outlier: 3.895A  pdb=" N   LYS B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 270
    Processing helix  chain 'B' and resid 327 through 355
      removed outlier: 3.619A  pdb=" N   THR B 331 " --> pdb=" O   ASP B 327 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   HIS B 355 " --> pdb=" O   LEU B 351 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 47
    Processing helix  chain 'C' and resid 86 through 91
    Processing helix  chain 'C' and resid 179 through 184
      removed outlier: 3.867A  pdb=" N   ASN C 184 " --> pdb=" O   GLU C 181 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 210 through 217
      removed outlier: 3.661A  pdb=" N   LYS C 215 " --> pdb=" O   GLY C 211 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   LYS C 216 " --> pdb=" O   THR C 212 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 232 through 240
    Processing helix  chain 'C' and resid 242 through 250
      removed outlier: 3.571A  pdb=" N   LEU C 246 " --> pdb=" O   ASP C 242 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 266 through 270
    Processing helix  chain 'C' and resid 327 through 355
      removed outlier: 3.628A  pdb=" N   THR C 331 " --> pdb=" O   ASP C 327 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 59
      removed outlier: 3.934A  pdb=" N   SER A  59 " --> pdb=" O   ALA A 323 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   ALA A 323 " --> pdb=" O   SER A  59 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   CYS A 261 " --> pdb=" O   GLY A 324 " (cutoff:3.500A)
      removed outlier: 9.459A  pdb=" N   PHE A 326 " --> pdb=" O   CYS A 261 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 70
      removed outlier: 3.731A  pdb=" N   THR A 186 " --> pdb=" O   LYS A  70 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 76
    Processing sheet with id=AA4, first strand: chain 'A' and resid 99 through 105
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 99 through 105
    current: chain 'A' and resid 273 through 279
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 273 through 279
    current: chain 'A' and resid 302 through 320
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 114 through 118
    Processing sheet with id=AA6, first strand: chain 'A' and resid 135 through 136
    Processing sheet with id=AA7, first strand: chain 'B' and resid 56 through 57
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 56 through 57
    current: chain 'B' and resid 273 through 279
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 273 through 279
    current: chain 'B' and resid 302 through 326
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 62 through 70
      removed outlier: 4.101A  pdb=" N   THR B 186 " --> pdb=" O   LYS B  70 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL B 200 " --> pdb=" O   PHE B 195 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 73 through 75
    Processing sheet with id=AB1, first strand: chain 'B' and resid 114 through 118
      removed outlier: 5.098A  pdb=" N   ASN B 148 " --> pdb=" O   GLU B 160 " (cutoff:3.500A)
      removed outlier: 8.752A  pdb=" N   PHE B 162 " --> pdb=" O   THR B 146 " (cutoff:3.500A)
      removed outlier: 8.130A  pdb=" N   THR B 146 " --> pdb=" O   PHE B 162 " (cutoff:3.500A)
      removed outlier: 9.223A  pdb=" N   TRP B 164 " --> pdb=" O   ILE B 144 " (cutoff:3.500A)
      removed outlier: 9.579A  pdb=" N   ILE B 144 " --> pdb=" O   TRP B 164 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 56 through 59
      removed outlier: 3.537A  pdb=" N   LYS C 325 " --> pdb=" O   THR C  57 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   SER C  59 " --> pdb=" O   ALA C 323 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   ALA C 323 " --> pdb=" O   SER C  59 " (cutoff:3.500A)
      removed outlier: 7.529A  pdb=" N   CYS C 261 " --> pdb=" O   GLY C 324 " (cutoff:3.500A)
      removed outlier: 9.560A  pdb=" N   PHE C 326 " --> pdb=" O   CYS C 261 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 62 through 70
      removed outlier: 3.929A  pdb=" N   THR C 186 " --> pdb=" O   LYS C  70 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL C 200 " --> pdb=" O   PHE C 195 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 73 through 76
    Processing sheet with id=AB5, first strand: chain 'C' and resid 100 through 105
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 100 through 105
    current: chain 'C' and resid 273 through 279
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 273 through 279
    current: chain 'C' and resid 302 through 320
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'C' and resid 114 through 118
      removed outlier: 5.114A  pdb=" N   ASN C 148 " --> pdb=" O   GLU C 160 " (cutoff:3.500A)
      removed outlier: 8.653A  pdb=" N   PHE C 162 " --> pdb=" O   THR C 146 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   THR C 146 " --> pdb=" O   PHE C 162 " (cutoff:3.500A)
      removed outlier: 9.302A  pdb=" N   TRP C 164 " --> pdb=" O   ILE C 144 " (cutoff:3.500A)
      removed outlier: 9.392A  pdb=" N   ILE C 144 " --> pdb=" O   TRP C 164 " (cutoff:3.500A)

    244 hydrogen bonds defined for protein.
    669 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: 1.85

  Time building geometry restraints manager: 2.25 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2522
        1.34 -     1.46: 1965
        1.46 -     1.58: 3631
        1.58 -     1.70: 15
        1.70 -     1.82: 57
  Bond restraints: 8190
  Sorted by residual:
  bond pdb=" C4  ATP C 502 "
       pdb=" C5  ATP C 502 "
    ideal  model  delta    sigma   weight residual
    1.388  1.466 -0.078 1.00e-02 1.00e+04 6.09e+01
  bond pdb=" C4  ATP B 502 "
       pdb=" C5  ATP B 502 "
    ideal  model  delta    sigma   weight residual
    1.388  1.466 -0.078 1.00e-02 1.00e+04 6.08e+01
  bond pdb=" C4  ATP A 401 "
       pdb=" C5  ATP A 401 "
    ideal  model  delta    sigma   weight residual
    1.388  1.465 -0.077 1.00e-02 1.00e+04 5.88e+01
  bond pdb=" C5  ATP A 401 "
       pdb=" C6  ATP A 401 "
    ideal  model  delta    sigma   weight residual
    1.409  1.479 -0.070 1.00e-02 1.00e+04 4.89e+01
  bond pdb=" C5  ATP C 502 "
       pdb=" C6  ATP C 502 "
    ideal  model  delta    sigma   weight residual
    1.409  1.479 -0.070 1.00e-02 1.00e+04 4.87e+01
  ... (remaining 8185 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.37: 11036
        3.37 -     6.74: 66
        6.74 -    10.11: 13
       10.11 -    13.49: 0
       13.49 -    16.86: 6
  Bond angle restraints: 11121
  Sorted by residual:
  angle pdb=" PB  ATP B 502 "
        pdb=" O3B ATP B 502 "
        pdb=" PG  ATP B 502 "
      ideal   model   delta    sigma   weight residual
     139.87  123.01   16.86 1.00e+00 1.00e+00 2.84e+02
  angle pdb=" PB  ATP C 502 "
        pdb=" O3B ATP C 502 "
        pdb=" PG  ATP C 502 "
      ideal   model   delta    sigma   weight residual
     139.87  123.03   16.84 1.00e+00 1.00e+00 2.83e+02
  angle pdb=" PB  ATP A 401 "
        pdb=" O3B ATP A 401 "
        pdb=" PG  ATP A 401 "
      ideal   model   delta    sigma   weight residual
     139.87  123.86   16.01 1.00e+00 1.00e+00 2.56e+02
  angle pdb=" PA  ATP A 401 "
        pdb=" O3A ATP A 401 "
        pdb=" PB  ATP A 401 "
      ideal   model   delta    sigma   weight residual
     136.83  122.42   14.41 1.00e+00 1.00e+00 2.08e+02
  angle pdb=" PA  ATP C 502 "
        pdb=" O3A ATP C 502 "
        pdb=" PB  ATP C 502 "
      ideal   model   delta    sigma   weight residual
     136.83  122.83   14.00 1.00e+00 1.00e+00 1.96e+02
  ... (remaining 11116 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.46: 4696
       15.46 -    30.92: 177
       30.92 -    46.38: 42
       46.38 -    61.84: 27
       61.84 -    77.30: 5
  Dihedral angle restraints: 4947
    sinusoidal: 2157
      harmonic: 2790
  Sorted by residual:
  dihedral pdb=" C   VAL B  44 "
           pdb=" N   VAL B  44 "
           pdb=" CA  VAL B  44 "
           pdb=" CB  VAL B  44 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -130.50    8.50     0      2.50e+00 1.60e-01 1.16e+01
  dihedral pdb=" C   VAL C  40 "
           pdb=" N   VAL C  40 "
           pdb=" CA  VAL C  40 "
           pdb=" CB  VAL C  40 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -130.21    8.21     0      2.50e+00 1.60e-01 1.08e+01
  dihedral pdb=" C   VAL B  39 "
           pdb=" N   VAL B  39 "
           pdb=" CA  VAL B  39 "
           pdb=" CB  VAL B  39 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -129.98    7.98     0      2.50e+00 1.60e-01 1.02e+01
  ... (remaining 4944 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1017
       0.055 -    0.110: 172
       0.110 -    0.165: 38
       0.165 -    0.220: 8
       0.220 -    0.275: 7
  Chirality restraints: 1242
  Sorted by residual:
  chirality pdb=" C1  NAG C 505 "
            pdb=" ND2 ASN C 184 "
            pdb=" C2  NAG C 505 "
            pdb=" O5  NAG C 505 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.12   -0.28 2.00e-01 2.50e+01 1.89e+00
  chirality pdb=" C1  NAG A 404 "
            pdb=" ND2 ASN A 184 "
            pdb=" C2  NAG A 404 "
            pdb=" O5  NAG A 404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.13   -0.27 2.00e-01 2.50e+01 1.85e+00
  chirality pdb=" C1  NAG B 505 "
            pdb=" ND2 ASN B 184 "
            pdb=" C2  NAG B 505 "
            pdb=" O5  NAG B 505 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.13   -0.27 2.00e-01 2.50e+01 1.85e+00
  ... (remaining 1239 not shown)

  Planarity restraints: 1407
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A  92 "    0.020 5.00e-02 4.00e+02   3.03e-02 1.46e+00
        pdb=" N   PRO A  93 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A  93 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A  93 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C  92 "    0.020 5.00e-02 4.00e+02   2.98e-02 1.42e+00
        pdb=" N   PRO C  93 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO C  93 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C  93 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B  92 "   -0.019 5.00e-02 4.00e+02   2.87e-02 1.32e+00
        pdb=" N   PRO B  93 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO B  93 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B  93 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 1404 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 177
        2.68 -     3.24: 7357
        3.24 -     3.79: 12669
        3.79 -     4.35: 16931
        4.35 -     4.90: 28137
  Nonbonded interactions: 65271
  Sorted by model distance:
  nonbonded pdb=" O3G ATP B 502 "
            pdb="MG    MG C 501 "
     model   vdw
     2.127 2.170
  nonbonded pdb="MG    MG A 405 "
            pdb=" O3G ATP C 502 "
     model   vdw
     2.210 2.170
  nonbonded pdb=" O3G ATP A 401 "
            pdb="MG    MG B 501 "
     model   vdw
     2.237 2.170
  nonbonded pdb=" OD1 ASP C 170 "
            pdb="MG    MG C 501 "
     model   vdw
     2.307 2.170
  nonbonded pdb=" OG  SER B  63 "
            pdb=" OD1 ASN B 191 "
     model   vdw
     2.313 3.040
  ... (remaining 65266 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 26 through 355 or resid 403 through 404))
  selection = (chain 'B' and (resid 26 through 355 or resid 503 through 504))
  selection = (chain 'C' and (resid 26 through 355 or resid 503 through 504))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.360
  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:          0.330
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.230
  Find NCS groups from input model:        0.370
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6754
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      :  0.004   0.078   8208  Z= 0.327
  Angle     :  0.779  16.858  11166  Z= 0.568
  Chirality :  0.051   0.275   1242
  Planarity :  0.003   0.030   1398
  Dihedral  :  9.783  77.302   3144
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  :  2.96 %
    Favored  : 94.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.26), residues: 984
  helix:  1.11 (0.33), residues: 267
  sheet:  0.90 (0.32), residues: 258
  loop : -1.95 (0.24), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  47 
 HIS   0.002   0.000   HIS C 306 
 PHE   0.011   0.001   PHE B  49 
 TYR   0.012   0.001   TYR A  55 
 ARG   0.002   0.000   ARG A  34 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00836 (    9)
  link_NAG-ASN         : angle       3.15802 (   27)
  hydrogen bonds       : bond        0.22888 (  244)
  hydrogen bonds       : angle       7.39474 (  669)
  SS BOND              : bond        0.00206 (    9)
  SS BOND              : angle       0.76840 (   18)
  covalent geometry    : bond        0.00424 ( 8190)
  covalent geometry    : angle       0.76432 (11121)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 227
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  341 ILE cc_start: 0.7691 (mt) cc_final: 0.7470 (mt)
  outliers start: 19
  outliers final: 0
  residues processed: 243
  average time/residue: 1.2212
  time to fit residues: 313.6717
Evaluate side-chains
  116 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.851 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    5.9990
   chunk 75 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    0.3980
   chunk 40 optimal weight:    0.7980
   chunk 77 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9990
   chunk 89 optimal weight:    3.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 112 GLN
A 180 HIS
A 191 ASN
A 220 HIS
B  37 GLN
B  56 GLN
B 191 ASN
B 220 HIS
C 191 ASN
C 220 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.127533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.100957 restraints weight = 11963.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 2.53
r_work: 0.3310 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3209 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.2780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8208  Z= 0.139
  Angle     :  0.597   9.266  11166  Z= 0.298
  Chirality :  0.048   0.339   1242
  Planarity :  0.004   0.036   1398
  Dihedral  :  8.840  84.040   1347
  Min Nonbonded Distance : 1.858

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 15.01 %
    Favored  : 82.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.27), residues: 984
  helix:  0.79 (0.33), residues: 291
  sheet:  1.43 (0.34), residues: 222
  loop : -1.21 (0.26), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  47 
 HIS   0.004   0.001   HIS B 306 
 PHE   0.042   0.001   PHE B  33 
 TYR   0.028   0.002   TYR B  90 
 ARG   0.008   0.001   ARG B 244 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01199 (    9)
  link_NAG-ASN         : angle       3.44942 (   27)
  hydrogen bonds       : bond        0.03739 (  244)
  hydrogen bonds       : angle       5.13599 (  669)
  SS BOND              : bond        0.00256 (    9)
  SS BOND              : angle       2.38505 (   18)
  covalent geometry    : bond        0.00318 ( 8190)
  covalent geometry    : angle       0.56527 (11121)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 114
  time to evaluate  : 0.957 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  181 GLU cc_start: 0.8155 (mp0) cc_final: 0.7827 (mm-30)
REVERT: A  341 ILE cc_start: 0.7627 (mt) cc_final: 0.7416 (mt)
REVERT: B  138 GLU cc_start: 0.8333 (pm20) cc_final: 0.8087 (mp0)
REVERT: B  265 TRP cc_start: 0.8430 (m100) cc_final: 0.7609 (m-10)
REVERT: C  275 GLN cc_start: 0.8463 (mm-40) cc_final: 0.8245 (mt0)
REVERT: C  322 LYS cc_start: 0.8175 (ttmt) cc_final: 0.7882 (ptmm)
  outliers start: 24
  outliers final: 10
  residues processed: 129
  average time/residue: 1.0859
  time to fit residues: 150.0420
Evaluate side-chains
  106 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  284 ASN
Chi-restraints excluded: chain B residue  172 LYS
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   63 SER
Chi-restraints excluded: chain C residue  258 ASP
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  347 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 68 optimal weight:    6.9990
   chunk 28 optimal weight:    5.9990
   chunk 83 optimal weight:    3.9990
   chunk 91 optimal weight:    0.0070
   chunk 63 optimal weight:    0.0980
   chunk 57 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 16 optimal weight:    6.9990
   chunk 42 optimal weight:    0.0670
   overall best weight:    0.8138

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

Flipped N/Q/H residues before XYZ refinement:
A 290 ASN
C  83 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.121394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.093926 restraints weight = 12063.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 2.54
r_work: 0.3224 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3122 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.3403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8208  Z= 0.129
  Angle     :  0.586  10.929  11166  Z= 0.288
  Chirality :  0.049   0.388   1242
  Planarity :  0.004   0.032   1398
  Dihedral  :  8.731  87.483   1347
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 15.72 %
    Favored  : 81.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.28), residues: 984
  helix:  0.89 (0.34), residues: 291
  sheet:  1.59 (0.32), residues: 252
  loop : -0.78 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  47 
 HIS   0.003   0.001   HIS B 306 
 PHE   0.020   0.001   PHE B  33 
 TYR   0.017   0.001   TYR C  90 
 ARG   0.010   0.001   ARG B 244 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00809 (    9)
  link_NAG-ASN         : angle       3.77449 (   27)
  hydrogen bonds       : bond        0.03245 (  244)
  hydrogen bonds       : angle       4.72223 (  669)
  SS BOND              : bond        0.00358 (    9)
  SS BOND              : angle       2.30694 (   18)
  covalent geometry    : bond        0.00290 ( 8190)
  covalent geometry    : angle       0.54951 (11121)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 CYS cc_start: 0.5965 (p) cc_final: 0.5442 (m)
REVERT: A  181 GLU cc_start: 0.8278 (mp0) cc_final: 0.8060 (mm-30)
REVERT: A  341 ILE cc_start: 0.7764 (mt) cc_final: 0.7553 (mt)
REVERT: B  265 TRP cc_start: 0.8582 (m100) cc_final: 0.7768 (m-10)
REVERT: C  108 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8092 (ttp)
REVERT: C  275 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8285 (mt0)
REVERT: C  322 LYS cc_start: 0.8384 (ttmt) cc_final: 0.8093 (ptmm)
  outliers start: 23
  outliers final: 8
  residues processed: 116
  average time/residue: 1.0752
  time to fit residues: 133.6197
Evaluate side-chains
  100 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  172 LYS
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  267 VAL
Chi-restraints excluded: chain C residue   41 LEU
Chi-restraints excluded: chain C residue   63 SER
Chi-restraints excluded: chain C residue  108 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 67 optimal weight:    6.9990
   chunk 11 optimal weight:    7.9990
   chunk 87 optimal weight:    0.8980
   chunk 72 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 29 optimal weight:    6.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 127 GLN
C 114 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.109935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.080593 restraints weight = 11936.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 2.54
r_work: 0.2958 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2852 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8683
moved from start:          0.4613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074   8208  Z= 0.231
  Angle     :  0.745  17.281  11166  Z= 0.365
  Chirality :  0.054   0.473   1242
  Planarity :  0.004   0.040   1398
  Dihedral  :  9.793  86.162   1347
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 16.67 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.28), residues: 984
  helix:  1.37 (0.35), residues: 267
  sheet:  1.26 (0.31), residues: 282
  loop : -0.47 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  47 
 HIS   0.005   0.001   HIS C 116 
 PHE   0.034   0.002   PHE C  92 
 TYR   0.022   0.002   TYR C  90 
 ARG   0.010   0.001   ARG B 244 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01185 (    9)
  link_NAG-ASN         : angle       6.14361 (   27)
  hydrogen bonds       : bond        0.03728 (  244)
  hydrogen bonds       : angle       4.65795 (  669)
  SS BOND              : bond        0.00464 (    9)
  SS BOND              : angle       3.00018 (   18)
  covalent geometry    : bond        0.00534 ( 8190)
  covalent geometry    : angle       0.67171 (11121)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.827 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 ARG cc_start: 0.8970 (ttm-80) cc_final: 0.8685 (ttt-90)
REVERT: B  261 CYS cc_start: 0.8685 (p) cc_final: 0.8456 (m)
REVERT: B  265 TRP cc_start: 0.8765 (m100) cc_final: 0.7955 (m-10)
REVERT: C  260 GLU cc_start: 0.7654 (mp0) cc_final: 0.7399 (mm-30)
REVERT: C  275 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8192 (mt0)
  outliers start: 19
  outliers final: 8
  residues processed: 115
  average time/residue: 1.1618
  time to fit residues: 142.1733
Evaluate side-chains
  93 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  172 LYS
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   63 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 38 optimal weight:    0.0470
   chunk 26 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 92 optimal weight:    0.9980
   chunk 79 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   chunk 97 optimal weight:    3.9990
   chunk 55 optimal weight:    0.0370
   chunk 9 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9980
   overall best weight:    0.4956

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

Flipped N/Q/H residues before XYZ refinement:
C  83 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.112834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.083336 restraints weight = 12012.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3123 rms_B_bonded: 2.58
r_work: 0.3026 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2922 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8642
moved from start:          0.4583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   8208  Z= 0.127
  Angle     :  0.662  12.399  11166  Z= 0.318
  Chirality :  0.051   0.687   1242
  Planarity :  0.004   0.043   1398
  Dihedral  : 10.304  88.223   1347
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 17.85 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.28), residues: 984
  helix:  1.09 (0.34), residues: 285
  sheet:  1.36 (0.32), residues: 267
  loop : -0.53 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 164 
 HIS   0.002   0.000   HIS B 306 
 PHE   0.020   0.001   PHE A  92 
 TYR   0.020   0.001   TYR B  90 
 ARG   0.010   0.001   ARG B 244 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.02034 (    9)
  link_NAG-ASN         : angle       4.48988 (   27)
  hydrogen bonds       : bond        0.02858 (  244)
  hydrogen bonds       : angle       4.52254 (  669)
  SS BOND              : bond        0.00492 (    9)
  SS BOND              : angle       2.58691 (   18)
  covalent geometry    : bond        0.00280 ( 8190)
  covalent geometry    : angle       0.61616 (11121)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 ARG cc_start: 0.8954 (ttm-80) cc_final: 0.8666 (ttt-90)
REVERT: B  265 TRP cc_start: 0.8723 (m100) cc_final: 0.7871 (m-10)
REVERT: C  258 ASP cc_start: 0.8785 (t70) cc_final: 0.8470 (t70)
REVERT: C  275 GLN cc_start: 0.8546 (mm-40) cc_final: 0.8217 (mt0)
  outliers start: 17
  outliers final: 8
  residues processed: 106
  average time/residue: 1.1739
  time to fit residues: 132.4739
Evaluate side-chains
  94 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  221 LYS
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  267 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue  146 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 73 optimal weight:    5.9990
   chunk 63 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 88 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 3 optimal weight:    5.9990
   chunk 86 optimal weight:    0.8980
   chunk 85 optimal weight:    3.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 114 GLN
B 116 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.104269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.074141 restraints weight = 11218.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.2922 rms_B_bonded: 2.56
r_work: 0.2794 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2670 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.4762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077   8208  Z= 0.165
  Angle     :  0.670  11.788  11166  Z= 0.329
  Chirality :  0.049   0.381   1242
  Planarity :  0.004   0.047   1398
  Dihedral  : 10.295  82.878   1347
  Min Nonbonded Distance : 1.858

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 17.61 %
    Favored  : 79.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.28), residues: 984
  helix:  1.16 (0.34), residues: 285
  sheet:  1.31 (0.30), residues: 294
  loop : -0.57 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  85 
 HIS   0.003   0.001   HIS B 306 
 PHE   0.028   0.001   PHE C  92 
 TYR   0.018   0.002   TYR C  90 
 ARG   0.011   0.001   ARG B 244 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00939 (    9)
  link_NAG-ASN         : angle       3.51220 (   27)
  hydrogen bonds       : bond        0.03095 (  244)
  hydrogen bonds       : angle       4.44930 (  669)
  SS BOND              : bond        0.00383 (    9)
  SS BOND              : angle       3.44913 (   18)
  covalent geometry    : bond        0.00383 ( 8190)
  covalent geometry    : angle       0.63336 (11121)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 ARG cc_start: 0.8961 (ttm-80) cc_final: 0.8668 (ttt-90)
REVERT: B  221 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8637 (mtpp)
REVERT: B  265 TRP cc_start: 0.8684 (m100) cc_final: 0.7812 (m-10)
REVERT: C  260 GLU cc_start: 0.7666 (mp0) cc_final: 0.7326 (mp0)
REVERT: C  275 GLN cc_start: 0.8438 (mm-40) cc_final: 0.8046 (mt0)
  outliers start: 22
  outliers final: 11
  residues processed: 105
  average time/residue: 1.1023
  time to fit residues: 123.7108
Evaluate side-chains
  97 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  221 LYS
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  275 GLN
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  337 SER
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   63 SER
Chi-restraints excluded: chain C residue  245 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 45 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 14 optimal weight:    0.7980
   chunk 97 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 85 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
B 116 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.109071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.080208 restraints weight = 12045.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.3042 rms_B_bonded: 2.52
r_work: 0.2939 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2833 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8700
moved from start:          0.4959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   8208  Z= 0.195
  Angle     :  0.673   9.949  11166  Z= 0.333
  Chirality :  0.050   0.403   1242
  Planarity :  0.004   0.050   1398
  Dihedral  : 10.360  76.759   1347
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 18.20 %
    Favored  : 79.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.28), residues: 984
  helix:  1.58 (0.35), residues: 267
  sheet:  1.17 (0.30), residues: 312
  loop : -0.52 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 259 
 HIS   0.003   0.001   HIS B 306 
 PHE   0.031   0.002   PHE A  92 
 TYR   0.019   0.002   TYR C  90 
 ARG   0.012   0.001   ARG B 244 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00718 (    9)
  link_NAG-ASN         : angle       3.50213 (   27)
  hydrogen bonds       : bond        0.03202 (  244)
  hydrogen bonds       : angle       4.41548 (  669)
  SS BOND              : bond        0.00390 (    9)
  SS BOND              : angle       3.07954 (   18)
  covalent geometry    : bond        0.00455 ( 8190)
  covalent geometry    : angle       0.64031 (11121)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 0.877 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 ARG cc_start: 0.8984 (ttm-80) cc_final: 0.8723 (ttt-90)
REVERT: B  221 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8710 (mtpp)
REVERT: B  265 TRP cc_start: 0.8787 (m100) cc_final: 0.7939 (m-10)
REVERT: C  260 GLU cc_start: 0.7711 (mp0) cc_final: 0.7371 (mp0)
REVERT: C  275 GLN cc_start: 0.8559 (mm-40) cc_final: 0.8211 (mt0)
  outliers start: 23
  outliers final: 12
  residues processed: 107
  average time/residue: 1.0673
  time to fit residues: 122.4022
Evaluate side-chains
  95 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  221 LYS
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  337 SER
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   63 SER
Chi-restraints excluded: chain C residue  156 VAL
Chi-restraints excluded: chain C residue  245 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0030
   chunk 88 optimal weight:    3.9990
   chunk 64 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9990
   chunk 65 optimal weight:   20.0000
   chunk 46 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    1.1596

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

Flipped N/Q/H residues before XYZ refinement:
B 116 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.109893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.081113 restraints weight = 12128.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 2.51
r_work: 0.2978 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2873 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8688
moved from start:          0.4985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8208  Z= 0.150
  Angle     :  0.656  10.204  11166  Z= 0.321
  Chirality :  0.049   0.535   1242
  Planarity :  0.004   0.057   1398
  Dihedral  : 10.436  72.462   1347
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 19.03 %
    Favored  : 78.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.28), residues: 984
  helix:  1.16 (0.34), residues: 285
  sheet:  1.23 (0.30), residues: 294
  loop : -0.57 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 259 
 HIS   0.003   0.001   HIS B 306 
 PHE   0.026   0.001   PHE A  92 
 TYR   0.018   0.002   TYR B  90 
 ARG   0.013   0.001   ARG B 244 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00918 (    9)
  link_NAG-ASN         : angle       3.73259 (   27)
  hydrogen bonds       : bond        0.02926 (  244)
  hydrogen bonds       : angle       4.37132 (  669)
  SS BOND              : bond        0.00337 (    9)
  SS BOND              : angle       2.62618 (   18)
  covalent geometry    : bond        0.00347 ( 8190)
  covalent geometry    : angle       0.62211 (11121)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 ARG cc_start: 0.8975 (ttm-80) cc_final: 0.8729 (ttt-90)
REVERT: B  216 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8559 (pptt)
REVERT: B  221 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8731 (mtpp)
REVERT: B  265 TRP cc_start: 0.8775 (m100) cc_final: 0.7931 (m-10)
REVERT: C  258 ASP cc_start: 0.8811 (t70) cc_final: 0.8361 (t70)
REVERT: C  260 GLU cc_start: 0.7678 (mp0) cc_final: 0.7398 (mp0)
REVERT: C  275 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8208 (mt0)
  outliers start: 17
  outliers final: 12
  residues processed: 104
  average time/residue: 1.0638
  time to fit residues: 118.3836
Evaluate side-chains
  97 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 1.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  216 LYS
Chi-restraints excluded: chain B residue  221 LYS
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  337 SER
Chi-restraints excluded: chain C residue   63 SER
Chi-restraints excluded: chain C residue  245 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 93 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 3 optimal weight:    4.9990
   chunk 46 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 92 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 38 optimal weight:    8.9990
   chunk 66 optimal weight:   20.0000
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.3536 r_free = 0.3536 target = 0.109812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.080927 restraints weight = 12218.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 2.53
r_work: 0.2955 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2848 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8667
moved from start:          0.5039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   8208  Z= 0.153
  Angle     :  0.660  10.089  11166  Z= 0.325
  Chirality :  0.049   0.514   1242
  Planarity :  0.004   0.059   1398
  Dihedral  : 10.276  69.206   1347
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 19.98 %
    Favored  : 78.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.28), residues: 984
  helix:  1.13 (0.34), residues: 285
  sheet:  1.21 (0.30), residues: 294
  loop : -0.57 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 259 
 HIS   0.003   0.001   HIS B 306 
 PHE   0.026   0.001   PHE A  92 
 TYR   0.017   0.002   TYR C  90 
 ARG   0.014   0.001   ARG B 244 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00992 (    9)
  link_NAG-ASN         : angle       3.64859 (   27)
  hydrogen bonds       : bond        0.02892 (  244)
  hydrogen bonds       : angle       4.38476 (  669)
  SS BOND              : bond        0.00352 (    9)
  SS BOND              : angle       3.04459 (   18)
  covalent geometry    : bond        0.00356 ( 8190)
  covalent geometry    : angle       0.62504 (11121)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 ARG cc_start: 0.8972 (ttm-80) cc_final: 0.8725 (ttt-90)
REVERT: B  216 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8534 (pptt)
REVERT: B  221 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8725 (mtpp)
REVERT: B  265 TRP cc_start: 0.8764 (m100) cc_final: 0.7910 (m-10)
REVERT: C  260 GLU cc_start: 0.7625 (mp0) cc_final: 0.7418 (mp0)
REVERT: C  275 GLN cc_start: 0.8523 (mm-40) cc_final: 0.8175 (mt0)
  outliers start: 16
  outliers final: 12
  residues processed: 99
  average time/residue: 1.0967
  time to fit residues: 116.5727
Evaluate side-chains
  97 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  216 LYS
Chi-restraints excluded: chain B residue  221 LYS
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  337 SER
Chi-restraints excluded: chain C residue   63 SER
Chi-restraints excluded: chain C residue  245 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 50 optimal weight:    0.2980
   chunk 84 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 95 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0570
   chunk 47 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 33 optimal weight:   30.0000
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
B 116 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.112953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.084347 restraints weight = 12107.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 2.54
r_work: 0.3014 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2908 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.4938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8208  Z= 0.114
  Angle     :  0.602   9.502  11166  Z= 0.296
  Chirality :  0.047   0.481   1242
  Planarity :  0.004   0.057   1398
  Dihedral  :  9.681  70.152   1347
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 20.33 %
    Favored  : 78.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.28), residues: 984
  helix:  1.16 (0.34), residues: 285
  sheet:  1.25 (0.30), residues: 294
  loop : -0.55 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  85 
 HIS   0.002   0.000   HIS B 306 
 PHE   0.022   0.001   PHE A  92 
 TYR   0.018   0.001   TYR C  90 
 ARG   0.015   0.001   ARG B 244 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00802 (    9)
  link_NAG-ASN         : angle       2.85906 (   27)
  hydrogen bonds       : bond        0.02545 (  244)
  hydrogen bonds       : angle       4.28195 (  669)
  SS BOND              : bond        0.00320 (    9)
  SS BOND              : angle       2.34718 (   18)
  covalent geometry    : bond        0.00263 ( 8190)
  covalent geometry    : angle       0.57930 (11121)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.829 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 HIS cc_start: 0.7342 (m-70) cc_final: 0.7066 (m-70)
REVERT: A  197 ARG cc_start: 0.8948 (ttm-80) cc_final: 0.8704 (ttt-90)
REVERT: B  216 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8558 (pptt)
REVERT: B  265 TRP cc_start: 0.8745 (m100) cc_final: 0.7918 (m-10)
REVERT: C  275 GLN cc_start: 0.8523 (mm-40) cc_final: 0.8184 (mt0)
  outliers start: 13
  outliers final: 10
  residues processed: 99
  average time/residue: 1.1137
  time to fit residues: 118.2187
Evaluate side-chains
  90 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  216 LYS
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  337 SER
Chi-restraints excluded: chain C residue  245 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 74 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0170
   chunk 48 optimal weight:    0.8980
   chunk 88 optimal weight:    0.0050
   chunk 31 optimal weight:    5.9990
   chunk 1 optimal weight:    0.2980
   chunk 27 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.3232

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

Flipped N/Q/H residues before XYZ refinement:
B 116 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.114702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.086003 restraints weight = 12167.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 2.55
r_work: 0.3065 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.4893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   8208  Z= 0.107
  Angle     :  0.595   9.644  11166  Z= 0.296
  Chirality :  0.046   0.415   1242
  Planarity :  0.004   0.062   1398
  Dihedral  :  9.365  76.258   1347
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 20.57 %
    Favored  : 78.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.28), residues: 984
  helix:  1.17 (0.34), residues: 285
  sheet:  1.29 (0.30), residues: 294
  loop : -0.55 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 164 
 HIS   0.002   0.000   HIS B 306 
 PHE   0.017   0.001   PHE A  92 
 TYR   0.023   0.001   TYR C  43 
 ARG   0.014   0.001   ARG B 244 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00792 (    9)
  link_NAG-ASN         : angle       2.67409 (   27)
  hydrogen bonds       : bond        0.02447 (  244)
  hydrogen bonds       : angle       4.30403 (  669)
  SS BOND              : bond        0.00386 (    9)
  SS BOND              : angle       3.01015 (   18)
  covalent geometry    : bond        0.00253 ( 8190)
  covalent geometry    : angle       0.56862 (11121)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7500.65 seconds
wall clock time: 128 minutes 51.29 seconds (7731.29 seconds total)