Starting phenix.real_space_refine
on Thu Oct 22 23:49:05 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/21ny_67856/10_2026/21ny_67856.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/21ny_67856/10_2026/21ny_67856.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.39
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/21ny_67856/10_2026/21ny_67856.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/21ny_67856/10_2026/21ny_67856.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/21ny_67856/10_2026/21ny_67856.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/21ny_67856/10_2026/21ny_67856.cif"
  }
  resolution = 3.39
  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=   0.032
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: 4
    Type Number    sf(0)   Gaussians
     S      28      5.16       5
     C    4223      2.51       5
     N    1147      2.21       5
     O    1302      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6700
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1373
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 170, 1373
          Classifications: {'peptide': 170}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 162}
    Chain: "B"
      Number of atoms: 2556
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 314, 2556
          Classifications: {'peptide': 314}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 294}
    Chain: "C"
      Number of atoms: 2556
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 314, 2556
          Classifications: {'peptide': 314}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 294}
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          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: 81
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 81
          Unusual residues: {'BMA': 1, 'NAG': 5}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
    Chain: "B"
      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: "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
  Time building chain proxies: 1.56, per 1000 atoms: 0.23
  Number of scatterers: 6700
  At special positions: 0
  Unit cell: (76.95, 103.55, 123.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      28     16.00
     O    1302      8.00
     N    1147      7.00
     C    4223      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  59 " - pdb=" SG  CYS A 101 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 140 " - pdb=" SG  CYS A 184 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 125 " - pdb=" SG  CYS B 184 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 200 " - pdb=" SG  CYS C 112 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 230 " - pdb=" SG  CYS B 289 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 334 " - pdb=" SG  CYS B 396 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 125 " - pdb=" SG  CYS C 184 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 230 " - pdb=" SG  CYS C 289 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 334 " - pdb=" SG  CYS C 396 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG A 301 " - " NAG A 302 "
      " NAG A 302 " - " BMA A 303 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
    NAG-ASN
      " NAG A 301 " - " ASN A  75 "
      " NAG A 304 " - " ASN A  86 "
      " NAG A 305 " - " ASN A 168 "
      " NAG A 306 " - " ASN A  94 "
      " NAG B 501 " - " ASN B 170 "
      " NAG B 502 " - " ASN B 240 "
      " NAG C 501 " - " ASN C 170 "
      " NAG C 502 " - " ASN C 240 "
      " NAG D   1 " - " ASN B 265 "
      " NAG E   1 " - " ASN C 265 "
  Time building additional restraints: 0.53
  Conformation dependent library (CDL) restraints added in 325.8 milliseconds
  

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1538

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 23 sheets defined
      7.3% alpha, 44.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'B' and resid 173 through 178
    Processing helix  chain 'B' and resid 204 through 208
      removed outlier: 3.515A  pdb=" N   GLY B 207 " --> pdb=" O   GLU B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 222
    Processing helix  chain 'B' and resid 277 through 284
      removed outlier: 3.522A  pdb=" N   TRP B 281 " --> pdb=" O   ASP B 277 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   GLU B 283 " --> pdb=" O   LYS B 279 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   GLY B 284 " --> pdb=" O   ASP B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 389
    Processing helix  chain 'C' and resid 173 through 177
    Processing helix  chain 'C' and resid 216 through 222
    Processing helix  chain 'C' and resid 277 through 284
      removed outlier: 3.864A  pdb=" N   GLU C 283 " --> pdb=" O   LYS C 279 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   GLY C 284 " --> pdb=" O   ASP C 280 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 385 through 391
    Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 43
      removed outlier: 3.633A  pdb=" N   THR A  56 " --> pdb=" O   GLU A  43 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU A  57 " --> pdb=" O   TYR A  87 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   TYR A  87 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 50
      removed outlier: 6.313A  pdb=" N   VAL A  49 " --> pdb=" O   ILE A 117 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 79
      removed outlier: 4.160A  pdb=" N   TRP A  72 " --> pdb=" O   ILE A  79 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 124
    Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 130
      removed outlier: 4.669A  pdb=" N   TYR A 187 " --> pdb=" O   LYS A 150 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   LYS A 150 " --> pdb=" O   TYR A 187 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   VAL A 151 " --> pdb=" O   TYR A 162 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   TYR A 162 " --> pdb=" O   VAL A 151 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   LEU A 153 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 129 through 130
    Processing sheet with id=AA7, first strand: chain 'A' and resid 136 through 137
    Processing sheet with id=AA8, first strand: chain 'B' and resid 104 through 109
      removed outlier: 3.762A  pdb=" N   SER B 167 " --> pdb=" O   CYS B 125 " (cutoff:3.500A)
      removed outlier: 5.249A  pdb=" N   ALA B 163 " --> pdb=" O   GLY B 129 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   LEU B 162 " --> pdb=" O   GLU B 158 " (cutoff:3.500A)
      removed outlier: 5.127A  pdb=" N   GLU B 158 " --> pdb=" O   LEU B 162 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   SER B 164 " --> pdb=" O   ILE B 156 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 137 through 141
      removed outlier: 3.520A  pdb=" N   ALA B 195 " --> pdb=" O   CYS B 184 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 209 through 213
      removed outlier: 3.544A  pdb=" N   THR B 229 " --> pdb=" O   ILE B 213 " (cutoff:3.500A)
      removed outlier: 5.858A  pdb=" N   THR B 229 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
      removed outlier: 7.253A  pdb=" N   LEU B 274 " --> pdb=" O   THR B 229 " (cutoff:3.500A)
      removed outlier: 5.526A  pdb=" N   LEU B 231 " --> pdb=" O   SER B 272 " (cutoff:3.500A)
      removed outlier: 7.508A  pdb=" N   SER B 272 " --> pdb=" O   LEU B 231 " (cutoff:3.500A)
      removed outlier: 5.361A  pdb=" N   LEU B 233 " --> pdb=" O   ILE B 270 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   ILE B 270 " --> pdb=" O   LEU B 233 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 242 through 247
      removed outlier: 3.568A  pdb=" N   THR B 242 " --> pdb=" O   ASP B 292 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ARG B 302 " --> pdb=" O   CYS B 289 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 315 through 319
      removed outlier: 4.140A  pdb=" N   THR B 333 " --> pdb=" O   PHE B 319 " (cutoff:3.500A)
      removed outlier: 6.169A  pdb=" N   PHE B 375 " --> pdb=" O   ASN B 338 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 315 through 319
      removed outlier: 4.140A  pdb=" N   THR B 333 " --> pdb=" O   PHE B 319 " (cutoff:3.500A)
      removed outlier: 6.169A  pdb=" N   PHE B 375 " --> pdb=" O   ASN B 338 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 353 through 354
    Processing sheet with id=AB6, first strand: chain 'C' and resid 106 through 109
      removed outlier: 5.541A  pdb=" N   ALA C 163 " --> pdb=" O   GLY C 129 " (cutoff:3.500A)
      removed outlier: 7.698A  pdb=" N   LEU C 162 " --> pdb=" O   GLU C 158 " (cutoff:3.500A)
      removed outlier: 5.585A  pdb=" N   GLU C 158 " --> pdb=" O   LEU C 162 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   SER C 164 " --> pdb=" O   ILE C 156 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 106 through 109
    Processing sheet with id=AB8, first strand: chain 'C' and resid 144 through 145
      removed outlier: 3.535A  pdb=" N   THR C 197 " --> pdb=" O   PHE C 182 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 209 through 213
      removed outlier: 3.562A  pdb=" N   THR C 229 " --> pdb=" O   ILE C 213 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   SER C 272 " --> pdb=" O   CYS C 230 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   ASP C 234 " --> pdb=" O   THR C 268 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   THR C 268 " --> pdb=" O   ASP C 234 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 209 through 213
      removed outlier: 3.562A  pdb=" N   THR C 229 " --> pdb=" O   ILE C 213 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   SER C 272 " --> pdb=" O   CYS C 230 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   ASP C 234 " --> pdb=" O   THR C 268 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   THR C 268 " --> pdb=" O   ASP C 234 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 245 through 246
    Processing sheet with id=AC3, first strand: chain 'C' and resid 315 through 319
      removed outlier: 3.917A  pdb=" N   THR C 333 " --> pdb=" O   PHE C 319 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   PHE C 375 " --> pdb=" O   ASN C 338 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'C' and resid 315 through 319
      removed outlier: 3.917A  pdb=" N   THR C 333 " --> pdb=" O   PHE C 319 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   PHE C 375 " --> pdb=" O   ASN C 338 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'C' and resid 345 through 350
      removed outlier: 3.535A  pdb=" N   ARG C 411 " --> pdb=" O   CYS C 396 " (cutoff:3.500A)

    235 hydrogen bonds defined for protein.
    579 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: 0.95

  Time building geometry restraints manager: 0.68 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1326
        1.33 -     1.45: 1709
        1.45 -     1.57: 3797
        1.57 -     1.70: 0
        1.70 -     1.82: 35
  Bond restraints: 6867
  Sorted by residual:
  bond pdb=" CA  PHE C 296 "
       pdb=" C   PHE C 296 "
    ideal  model  delta    sigma   weight residual
    1.524  1.488  0.036 8.10e-03 1.52e+04 2.01e+01
  bond pdb=" CA  PRO C 297 "
       pdb=" CB  PRO C 297 "
    ideal  model  delta    sigma   weight residual
    1.533  1.478  0.055 1.59e-02 3.96e+03 1.19e+01
  bond pdb=" CA  LYS A 150 "
       pdb=" C   LYS A 150 "
    ideal  model  delta    sigma   weight residual
    1.528  1.487  0.041 1.25e-02 6.40e+03 1.06e+01
  bond pdb=" CA  PRO C 297 "
       pdb=" C   PRO C 297 "
    ideal  model  delta    sigma   weight residual
    1.519  1.473  0.045 1.46e-02 4.69e+03 9.67e+00
  bond pdb=" N   PRO C 297 "
       pdb=" CA  PRO C 297 "
    ideal  model  delta    sigma   weight residual
    1.473  1.437  0.035 1.33e-02 5.65e+03 7.12e+00
  ... (remaining 6862 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.96: 9084
        1.96 -     3.92: 206
        3.92 -     5.89: 31
        5.89 -     7.85: 8
        7.85 -     9.81: 2
  Bond angle restraints: 9331
  Sorted by residual:
  angle pdb=" C   PRO C 299 "
        pdb=" CA  PRO C 299 "
        pdb=" CB  PRO C 299 "
      ideal   model   delta    sigma   weight residual
     111.56  101.75    9.81 1.65e+00 3.67e-01 3.54e+01
  angle pdb=" N   PRO C 299 "
        pdb=" CA  PRO C 299 "
        pdb=" C   PRO C 299 "
      ideal   model   delta    sigma   weight residual
     112.47  121.90   -9.43 2.06e+00 2.36e-01 2.10e+01
  angle pdb=" C   PRO C 297 "
        pdb=" CA  PRO C 297 "
        pdb=" CB  PRO C 297 "
      ideal   model   delta    sigma   weight residual
     113.20  106.26    6.94 1.69e+00 3.50e-01 1.69e+01
  angle pdb=" C   ILE C 300 "
        pdb=" CA  ILE C 300 "
        pdb=" CB  ILE C 300 "
      ideal   model   delta    sigma   weight residual
     111.59  117.24   -5.65 1.63e+00 3.76e-01 1.20e+01
  angle pdb=" N   PHE C 296 "
        pdb=" CA  PHE C 296 "
        pdb=" C   PHE C 296 "
      ideal   model   delta    sigma   weight residual
     108.45  102.49    5.96 1.93e+00 2.68e-01 9.54e+00
  ... (remaining 9326 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.27: 4032
       22.27 -    44.55: 260
       44.55 -    66.82: 38
       66.82 -    89.09: 28
       89.09 -   111.37: 13
  Dihedral angle restraints: 4371
    sinusoidal: 2011
      harmonic: 2360
  Sorted by residual:
  dihedral pdb=" CB  CYS B 230 "
           pdb=" SG  CYS B 230 "
           pdb=" SG  CYS B 289 "
           pdb=" CB  CYS B 289 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  161.34  -68.34     1      1.00e+01 1.00e-02 6.06e+01
  dihedral pdb=" CB  CYS B 334 "
           pdb=" SG  CYS B 334 "
           pdb=" SG  CYS B 396 "
           pdb=" CB  CYS B 396 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  159.92  -66.92     1      1.00e+01 1.00e-02 5.84e+01
  dihedral pdb=" CB  CYS A  59 "
           pdb=" SG  CYS A  59 "
           pdb=" SG  CYS A 101 "
           pdb=" CB  CYS A 101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -147.48   61.48     1      1.00e+01 1.00e-02 5.02e+01
  ... (remaining 4368 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 910
       0.063 -    0.126: 154
       0.126 -    0.189: 14
       0.189 -    0.252: 2
       0.252 -    0.315: 4
  Chirality restraints: 1084
  Sorted by residual:
  chirality pdb=" C1  NAG C 502 "
            pdb=" ND2 ASN C 240 "
            pdb=" C2  NAG C 502 "
            pdb=" O5  NAG C 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.09   -0.31 2.00e-01 2.50e+01 2.48e+00
  chirality pdb=" CB  ILE C 253 "
            pdb=" CA  ILE C 253 "
            pdb=" CG1 ILE C 253 "
            pdb=" CG2 ILE C 253 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.28 2.00e-01 2.50e+01 2.03e+00
  chirality pdb=" C5  BMA D   3 "
            pdb=" C4  BMA D   3 "
            pdb=" C6  BMA D   3 "
            pdb=" O5  BMA D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.27 2.00e-01 2.50e+01 1.86e+00
  ... (remaining 1081 not shown)

  Planarity restraints: 1174
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE C 304 "   -0.021 2.00e-02 2.50e+03   4.28e-02 1.83e+01
        pdb=" C   ILE C 304 "    0.074 2.00e-02 2.50e+03
        pdb=" O   ILE C 304 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   THR C 305 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 304 "    0.021 2.00e-02 2.50e+03   4.27e-02 1.82e+01
        pdb=" C   ILE B 304 "   -0.074 2.00e-02 2.50e+03
        pdb=" O   ILE B 304 "    0.028 2.00e-02 2.50e+03
        pdb=" N   THR B 305 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS C 293 "   -0.032 5.00e-02 4.00e+02   4.86e-02 3.78e+00
        pdb=" N   PRO C 294 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO C 294 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO C 294 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 1171 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 876
        2.76 -     3.30: 5820
        3.30 -     3.83: 9972
        3.83 -     4.37: 11296
        4.37 -     4.90: 20942
  Nonbonded interactions: 48906
  Sorted by model distance:
  nonbonded pdb=" O   PRO A  36 "
            pdb=" OG1 THR A 106 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" O   GLU A  43 "
            pdb=" OG1 THR A  56 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" NH1 ARG C 206 "
            pdb=" O7  NAG E   1 "
     model   vdw
     2.244 3.120
  nonbonded pdb=" OD1 ASP A  95 "
            pdb=" OH  TYR A  99 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" OD1 ASN A  94 "
            pdb=" O3  NAG A 301 "
     model   vdw
     2.263 3.040
  ... (remaining 48901 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 'B'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
}

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:             1.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.910
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  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:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
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   0.055   6892  Z= 0.229
  Angle     :  0.724   9.812   9397  Z= 0.353
  Chirality :  0.050   0.315   1084
  Planarity :  0.004   0.049   1164
  Dihedral  : 17.062 111.368   2806
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.08 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  0.27 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.13 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 are not related in a simple way.
  whole: -1.63 (0.29), residues: 792
  helix: -0.83 (0.68), residues: 48
  sheet: -0.31 (0.31), residues: 323
  loop : -1.77 (0.27), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 161 
 TYR   0.011   0.001   TYR C 166 
 PHE   0.015   0.002   PHE B 339 
 TRP   0.022   0.001   TRP A 143 
 HIS   0.005   0.001   HIS C 150 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00436 /  0.23 ( 6867)
  covalent geometry    : angle       0.69612 /  0.35 ( 9331)
  SS BOND              : bond        0.00215 /  0.08 (    9)
  SS BOND              : angle       0.60288 /  0.51 (   18)
  hydrogen bonds       : bond        0.25246 / 16.35 (  188)
  hydrogen bonds       : angle       9.46514 /  6.62 (  579)
  link_BETA1-4         : bond        0.00522 /  0.27 (    6)
  link_BETA1-4         : angle       1.39408 /  0.83 (   18)
  link_NAG-ASN         : bond        0.00349 /  0.23 (   10)
  link_NAG-ASN         : angle       3.46953 /  2.05 (   30)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 93
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  297 PRO cc_start: 0.9066 (Cg_exo) cc_final: 0.8839 (Cg_endo)
  outliers start: 2
  outliers final: 1
  residues processed: 95
  average time/residue: 0.0589
  time to fit residues: 8.3120
Evaluate side-chains
  82 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  299 PRO
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74]
   chunk 49 optimal weight:    0.0980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 150 HIS
** C 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 390 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.161129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.118140 restraints weight = 8194.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 3.00
r_work: 0.3069 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.0982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6892  Z= 0.124
  Angle     :  0.637   8.002   9397  Z= 0.312
  Chirality :  0.048   0.324   1084
  Planarity :  0.004   0.049   1164
  Dihedral  : 10.282  73.942   1196
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  :  5.67 %
    Favored  : 93.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 are not related in a simple way.
  whole: -1.75 (0.29), residues: 792
  helix: -0.70 (0.62), residues: 56
  sheet: -0.29 (0.29), residues: 338
  loop : -2.05 (0.28), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 161 
 TYR   0.013   0.001   TYR A 183 
 PHE   0.013   0.002   PHE C 376 
 TRP   0.013   0.001   TRP A 143 
 HIS   0.005   0.001   HIS C 118 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.12 ( 6867)
  covalent geometry    : angle       0.60457 /  0.31 ( 9331)
  SS BOND              : bond        0.00390 /  0.19 (    9)
  SS BOND              : angle       0.82081 /  0.72 (   18)
  hydrogen bonds       : bond        0.03925 /  2.45 (  188)
  hydrogen bonds       : angle       6.02542 /  4.25 (  579)
  link_BETA1-4         : bond        0.00470 /  0.24 (    6)
  link_BETA1-4         : angle       2.39138 /  1.67 (   18)
  link_NAG-ASN         : bond        0.00273 /  0.19 (   10)
  link_NAG-ASN         : angle       3.06843 /  1.83 (   30)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7523 (tp30)
REVERT: A  164 HIS cc_start: 0.7953 (p-80) cc_final: 0.7506 (p-80)
REVERT: B  409 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8517 (tt)
REVERT: C  206 ARG cc_start: 0.8214 (mtm180) cc_final: 0.7857 (ptp-170)
REVERT: C  253 ILE cc_start: 0.7501 (tp) cc_final: 0.7221 (tp)
  outliers start: 9
  outliers final: 7
  residues processed: 90
  average time/residue: 0.0575
  time to fit residues: 7.7940
Evaluate side-chains
  84 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  285 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks: [72, 4, 62, 31, 26, 35, 20, 23, 57, 29, 5]
   chunk 72 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0570
   chunk 62 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 20 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9990
   chunk 57 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.9904

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 196 HIS
** C 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.161697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.119358 restraints weight = 8116.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 3.03
r_work: 0.3077 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.1184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6892  Z= 0.148
  Angle     :  0.625   7.846   9397  Z= 0.305
  Chirality :  0.047   0.320   1084
  Planarity :  0.004   0.049   1164
  Dihedral  :  8.172  61.906   1193
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  :  8.77 %
    Favored  : 89.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 are not related in a simple way.
  whole: -1.70 (0.28), residues: 792
  helix: -0.59 (0.62), residues: 55
  sheet: -0.32 (0.29), residues: 346
  loop : -1.99 (0.28), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 161 
 TYR   0.013   0.001   TYR A 183 
 PHE   0.015   0.002   PHE B 339 
 TRP   0.006   0.001   TRP A  46 
 HIS   0.005   0.001   HIS C 118 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00370 /  0.15 ( 6867)
  covalent geometry    : angle       0.59453 /  0.30 ( 9331)
  SS BOND              : bond        0.00339 /  0.15 (    9)
  SS BOND              : angle       0.81813 /  0.74 (   18)
  hydrogen bonds       : bond        0.03815 /  2.45 (  188)
  hydrogen bonds       : angle       5.43023 /  3.85 (  579)
  link_BETA1-4         : bond        0.00434 /  0.22 (    6)
  link_BETA1-4         : angle       2.16510 /  1.40 (   18)
  link_NAG-ASN         : bond        0.00320 /  0.20 (   10)
  link_NAG-ASN         : angle       3.04817 /  1.79 (   30)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7473 (tp30)
REVERT: B  409 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8546 (tt)
  outliers start: 12
  outliers final: 11
  residues processed: 83
  average time/residue: 0.0516
  time to fit residues: 6.6916
Evaluate side-chains
  82 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain B residue  178 SER
Chi-restraints excluded: chain B residue  242 THR
Chi-restraints excluded: chain B residue  331 THR
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  143 ASP
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  285 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks: [7, 23, 67, 73, 57, 76, 9, 66, 41, 40, 64]
   chunk 7 optimal weight:    5.9990
   chunk 23 optimal weight:    6.9990
   chunk 67 optimal weight:    0.8980
   chunk 73 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9990
   chunk 41 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 293 HIS
** C 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.161396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.118908 restraints weight = 8249.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 3.06
r_work: 0.3072 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.1368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6892  Z= 0.135
  Angle     :  0.591   7.357   9397  Z= 0.291
  Chirality :  0.046   0.328   1084
  Planarity :  0.004   0.050   1164
  Dihedral  :  6.701  52.499   1193
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 10.39 %
    Favored  : 87.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 are not related in a simple way.
  whole: -1.65 (0.28), residues: 792
  helix: -0.54 (0.63), residues: 55
  sheet: -0.27 (0.28), residues: 346
  loop : -1.97 (0.27), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 161 
 TYR   0.013   0.001   TYR A 183 
 PHE   0.014   0.002   PHE B 339 
 TRP   0.016   0.001   TRP B 194 
 HIS   0.005   0.001   HIS A 164 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00338 /  0.14 ( 6867)
  covalent geometry    : angle       0.56175 /  0.28 ( 9331)
  SS BOND              : bond        0.00344 /  0.14 (    9)
  SS BOND              : angle       0.80267 /  0.71 (   18)
  hydrogen bonds       : bond        0.03284 /  2.06 (  188)
  hydrogen bonds       : angle       5.12100 /  3.65 (  579)
  link_BETA1-4         : bond        0.00410 /  0.21 (    6)
  link_BETA1-4         : angle       1.99546 /  1.27 (   18)
  link_NAG-ASN         : bond        0.00285 /  0.18 (   10)
  link_NAG-ASN         : angle       2.91941 /  1.74 (   30)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7512 (tp30)
REVERT: B  409 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8525 (tt)
  outliers start: 12
  outliers final: 10
  residues processed: 86
  average time/residue: 0.0552
  time to fit residues: 7.3306
Evaluate side-chains
  83 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  143 ASP
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  285 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks: [15, 16, 40, 11, 78, 52, 8, 20, 21, 65, 75]
   chunk 15 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 78 optimal weight:    5.9990
   chunk 52 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 20 optimal weight:    9.9990
   chunk 21 optimal weight:    0.0670
   chunk 65 optimal weight:    0.3980
   chunk 75 optimal weight:    0.7980
   overall best weight:    0.5718

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 350 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.162440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.120069 restraints weight = 8198.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 3.09
r_work: 0.3096 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.1488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6892  Z= 0.104
  Angle     :  0.554   6.573   9397  Z= 0.275
  Chirality :  0.045   0.301   1084
  Planarity :  0.004   0.049   1164
  Dihedral  :  5.273  39.988   1193
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 10.53 %
    Favored  : 87.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 are not related in a simple way.
  whole: -1.52 (0.28), residues: 792
  helix: -0.44 (0.63), residues: 55
  sheet: -0.14 (0.28), residues: 345
  loop : -1.93 (0.27), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 247 
 TYR   0.010   0.001   TYR A 183 
 PHE   0.011   0.001   PHE B 339 
 TRP   0.020   0.001   TRP B 194 
 HIS   0.004   0.001   HIS C 118 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.10 ( 6867)
  covalent geometry    : angle       0.52775 /  0.27 ( 9331)
  SS BOND              : bond        0.00316 /  0.14 (    9)
  SS BOND              : angle       0.69221 /  0.64 (   18)
  hydrogen bonds       : bond        0.03011 /  1.90 (  188)
  hydrogen bonds       : angle       4.91958 /  3.51 (  579)
  link_BETA1-4         : bond        0.00458 /  0.23 (    6)
  link_BETA1-4         : angle       1.76035 /  1.11 (   18)
  link_NAG-ASN         : bond        0.00283 /  0.16 (   10)
  link_NAG-ASN         : angle       2.68599 /  1.60 (   30)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7418 (tp30)
REVERT: B  166 TYR cc_start: 0.8631 (p90) cc_final: 0.8430 (p90)
REVERT: B  200 CYS cc_start: 0.7454 (m) cc_final: 0.7200 (m)
REVERT: B  409 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8527 (tt)
  outliers start: 15
  outliers final: 12
  residues processed: 91
  average time/residue: 0.0548
  time to fit residues: 7.6582
Evaluate side-chains
  88 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  178 SER
Chi-restraints excluded: chain B residue  242 THR
Chi-restraints excluded: chain B residue  331 THR
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  143 ASP
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  285 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks: [49, 48, 55, 15, 64, 26, 56, 3, 58, 2, 9]
   chunk 49 optimal weight:    0.7980
   chunk 48 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9990
   chunk 3 optimal weight:    8.9990
   chunk 58 optimal weight:    0.0270
   chunk 2 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   overall best weight:    0.7040

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 350 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.162126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.119662 restraints weight = 8315.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 3.11
r_work: 0.3083 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.1569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6892  Z= 0.114
  Angle     :  0.558   6.323   9397  Z= 0.276
  Chirality :  0.045   0.299   1084
  Planarity :  0.004   0.049   1164
  Dihedral  :  5.181  38.591   1193
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 11.20 %
    Favored  : 86.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 are not related in a simple way.
  whole: -1.46 (0.28), residues: 792
  helix: -0.40 (0.63), residues: 55
  sheet: -0.09 (0.28), residues: 345
  loop : -1.90 (0.27), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 407 
 TYR   0.013   0.001   TYR A 187 
 PHE   0.012   0.002   PHE B 339 
 TRP   0.013   0.001   TRP B 194 
 HIS   0.005   0.001   HIS B 130 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.11 ( 6867)
  covalent geometry    : angle       0.53267 /  0.27 ( 9331)
  SS BOND              : bond        0.00323 /  0.13 (    9)
  SS BOND              : angle       0.74391 /  0.69 (   18)
  hydrogen bonds       : bond        0.03039 /  1.91 (  188)
  hydrogen bonds       : angle       4.85093 /  3.46 (  579)
  link_BETA1-4         : bond        0.00417 /  0.21 (    6)
  link_BETA1-4         : angle       1.71140 /  1.10 (   18)
  link_NAG-ASN         : bond        0.00268 /  0.15 (   10)
  link_NAG-ASN         : angle       2.66887 /  1.60 (   30)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7470 (tp30)
REVERT: A   95 ASP cc_start: 0.8453 (t0) cc_final: 0.8011 (t0)
REVERT: B  200 CYS cc_start: 0.7521 (m) cc_final: 0.7277 (m)
REVERT: B  409 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8529 (tt)
REVERT: C  253 ILE cc_start: 0.7488 (tp) cc_final: 0.7226 (tp)
  outliers start: 18
  outliers final: 13
  residues processed: 92
  average time/residue: 0.0560
  time to fit residues: 7.9354
Evaluate side-chains
  89 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  178 SER
Chi-restraints excluded: chain B residue  242 THR
Chi-restraints excluded: chain B residue  331 THR
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  143 ASP
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  285 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks: [41, 23, 5, 51, 59, 37, 77, 50, 4, 26, 19]
   chunk 41 optimal weight:    0.0870
   chunk 23 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 77 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.9362

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 152 GLN
C 350 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.160993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.118662 restraints weight = 8183.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 3.08
r_work: 0.3075 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.1609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6892  Z= 0.137
  Angle     :  0.582   7.395   9397  Z= 0.287
  Chirality :  0.046   0.304   1084
  Planarity :  0.004   0.050   1164
  Dihedral  :  5.309  37.395   1193
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 12.01 %
    Favored  : 85.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 are not related in a simple way.
  whole: -1.48 (0.28), residues: 792
  helix: -0.47 (0.63), residues: 55
  sheet: -0.11 (0.28), residues: 345
  loop : -1.90 (0.27), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 311 
 TYR   0.014   0.001   TYR A 183 
 PHE   0.015   0.002   PHE B 339 
 TRP   0.010   0.001   TRP B 194 
 HIS   0.005   0.001   HIS C 118 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.14 ( 6867)
  covalent geometry    : angle       0.55574 /  0.28 ( 9331)
  SS BOND              : bond        0.00349 /  0.15 (    9)
  SS BOND              : angle       0.82399 /  0.74 (   18)
  hydrogen bonds       : bond        0.03189 /  2.02 (  188)
  hydrogen bonds       : angle       4.86144 /  3.48 (  579)
  link_BETA1-4         : bond        0.00381 /  0.19 (    6)
  link_BETA1-4         : angle       1.76718 /  1.12 (   18)
  link_NAG-ASN         : bond        0.00276 /  0.16 (   10)
  link_NAG-ASN         : angle       2.78774 /  1.66 (   30)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7435 (tp30)
REVERT: A   95 ASP cc_start: 0.8466 (t0) cc_final: 0.7997 (t0)
REVERT: B  200 CYS cc_start: 0.7516 (m) cc_final: 0.7241 (m)
REVERT: B  409 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8463 (tt)
  outliers start: 16
  outliers final: 14
  residues processed: 90
  average time/residue: 0.0556
  time to fit residues: 7.7175
Evaluate side-chains
  93 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  178 SER
Chi-restraints excluded: chain B residue  242 THR
Chi-restraints excluded: chain B residue  331 THR
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  143 ASP
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  285 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks: [32, 50, 57, 1, 43, 37, 63, 5, 14, 7, 15]
   chunk 32 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 63 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 7 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   overall best weight:    1.4984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 152 GLN
** C 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.158749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.116320 restraints weight = 8258.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 3.06
r_work: 0.3037 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.1673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   6892  Z= 0.201
  Angle     :  0.655   7.964   9397  Z= 0.321
  Chirality :  0.048   0.338   1084
  Planarity :  0.004   0.052   1164
  Dihedral  :  5.881  36.639   1193
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 12.42 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 are not related in a simple way.
  whole: -1.58 (0.28), residues: 792
  helix: -0.52 (0.63), residues: 55
  sheet: -0.23 (0.29), residues: 337
  loop : -1.88 (0.27), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 247 
 TYR   0.018   0.002   TYR A 183 
 PHE   0.021   0.002   PHE B 339 
 TRP   0.011   0.001   TRP B 194 
 HIS   0.005   0.001   HIS C 118 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00507 /  0.20 ( 6867)
  covalent geometry    : angle       0.62373 /  0.31 ( 9331)
  SS BOND              : bond        0.00451 /  0.22 (    9)
  SS BOND              : angle       1.08896 /  0.92 (   18)
  hydrogen bonds       : bond        0.03609 /  2.32 (  188)
  hydrogen bonds       : angle       5.00899 /  3.59 (  579)
  link_BETA1-4         : bond        0.00363 /  0.19 (    6)
  link_BETA1-4         : angle       2.03826 /  1.24 (   18)
  link_NAG-ASN         : bond        0.00323 /  0.21 (   10)
  link_NAG-ASN         : angle       3.18631 /  1.87 (   30)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7453 (tp30)
REVERT: A   95 ASP cc_start: 0.8531 (t0) cc_final: 0.8120 (t0)
REVERT: B  200 CYS cc_start: 0.7513 (m) cc_final: 0.7176 (m)
REVERT: B  409 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8430 (tt)
  outliers start: 17
  outliers final: 15
  residues processed: 84
  average time/residue: 0.0507
  time to fit residues: 6.7457
Evaluate side-chains
  87 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 71
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  178 SER
Chi-restraints excluded: chain B residue  242 THR
Chi-restraints excluded: chain B residue  331 THR
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  143 ASP
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  242 THR
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  285 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks: [66, 23, 17, 6, 71, 37, 74, 16, 10, 35, 73]
   chunk 66 optimal weight:    1.9990
   chunk 23 optimal weight:    8.9990
   chunk 17 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 74 optimal weight:    0.8980
   chunk 16 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 73 optimal weight:    0.0070
   overall best weight:    0.7198

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 152 GLN
C 350 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.161638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.119177 restraints weight = 8282.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 3.10
r_work: 0.3084 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.1732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6892  Z= 0.119
  Angle     :  0.577   7.157   9397  Z= 0.286
  Chirality :  0.046   0.314   1084
  Planarity :  0.004   0.049   1164
  Dihedral  :  5.399  38.398   1193
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 12.69 %
    Favored  : 85.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 are not related in a simple way.
  whole: -1.46 (0.28), residues: 792
  helix: -0.47 (0.63), residues: 55
  sheet: -0.16 (0.29), residues: 337
  loop : -1.78 (0.27), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 247 
 TYR   0.012   0.001   TYR A 183 
 PHE   0.012   0.001   PHE B 339 
 TRP   0.010   0.001   TRP B 194 
 HIS   0.004   0.001   HIS C 118 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.12 ( 6867)
  covalent geometry    : angle       0.55023 /  0.28 ( 9331)
  SS BOND              : bond        0.00337 /  0.14 (    9)
  SS BOND              : angle       0.79087 /  0.71 (   18)
  hydrogen bonds       : bond        0.03041 /  1.93 (  188)
  hydrogen bonds       : angle       4.80119 /  3.45 (  579)
  link_BETA1-4         : bond        0.00420 /  0.21 (    6)
  link_BETA1-4         : angle       1.75746 /  1.11 (   18)
  link_NAG-ASN         : bond        0.00286 /  0.15 (   10)
  link_NAG-ASN         : angle       2.82981 /  1.70 (   30)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7412 (tp30)
REVERT: A   95 ASP cc_start: 0.8446 (t0) cc_final: 0.8015 (t0)
REVERT: B  200 CYS cc_start: 0.7469 (m) cc_final: 0.7153 (m)
REVERT: B  409 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8422 (tt)
  outliers start: 17
  outliers final: 14
  residues processed: 91
  average time/residue: 0.0505
  time to fit residues: 7.3085
Evaluate side-chains
  90 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  178 SER
Chi-restraints excluded: chain B residue  331 THR
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  143 ASP
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  242 THR
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  285 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks: [69, 37, 18, 67, 44, 10, 15, 65, 70, 9, 31]
   chunk 69 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 67 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 65 optimal weight:    0.6980
   chunk 70 optimal weight:    0.3980
   chunk 9 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 152 GLN
C 350 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.161966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.119547 restraints weight = 8252.807|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 3.09
r_work: 0.3123 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.1782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6892  Z= 0.111
  Angle     :  0.579   9.053   9397  Z= 0.284
  Chirality :  0.046   0.351   1084
  Planarity :  0.004   0.049   1164
  Dihedral  :  5.296  42.458   1193
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 12.96 %
    Favored  : 85.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 are not related in a simple way.
  whole: -1.40 (0.28), residues: 792
  helix: -0.46 (0.63), residues: 55
  sheet: -0.10 (0.29), residues: 336
  loop : -1.75 (0.27), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 161 
 TYR   0.011   0.001   TYR A 183 
 PHE   0.012   0.001   PHE B 339 
 TRP   0.009   0.001   TRP B 194 
 HIS   0.004   0.001   HIS C 118 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.11 ( 6867)
  covalent geometry    : angle       0.54312 /  0.28 ( 9331)
  SS BOND              : bond        0.00333 /  0.14 (    9)
  SS BOND              : angle       0.75635 /  0.69 (   18)
  hydrogen bonds       : bond        0.02954 /  1.88 (  188)
  hydrogen bonds       : angle       4.72891 /  3.40 (  579)
  link_BETA1-4         : bond        0.00451 /  0.23 (    6)
  link_BETA1-4         : angle       1.67436 /  1.07 (   18)
  link_NAG-ASN         : bond        0.00243 /  0.11 (   10)
  link_NAG-ASN         : angle       3.36119 /  1.92 (   30)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7406 (tp30)
REVERT: A   95 ASP cc_start: 0.8445 (t0) cc_final: 0.8039 (t0)
REVERT: B  200 CYS cc_start: 0.7462 (m) cc_final: 0.7155 (m)
REVERT: B  409 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8444 (tt)
  outliers start: 15
  outliers final: 13
  residues processed: 86
  average time/residue: 0.0430
  time to fit residues: 5.8627
Evaluate side-chains
  88 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  178 SER
Chi-restraints excluded: chain B residue  331 THR
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  143 ASP
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  285 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks: [19, 29, 44, 62, 31, 68, 45, 74, 25, 30, 47]
   chunk 19 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 152 GLN
C 350 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.161496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.119067 restraints weight = 8210.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 3.08
r_work: 0.3082 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.1818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6892  Z= 0.127
  Angle     :  0.586   8.700   9397  Z= 0.288
  Chirality :  0.046   0.251   1084
  Planarity :  0.004   0.049   1164
  Dihedral  :  5.388  46.113   1193
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 12.82 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 are not related in a simple way.
  whole: -1.39 (0.28), residues: 792
  helix: -0.40 (0.63), residues: 55
  sheet: -0.10 (0.29), residues: 336
  loop : -1.75 (0.27), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 247 
 TYR   0.013   0.001   TYR A 183 
 PHE   0.013   0.002   PHE B 339 
 TRP   0.008   0.001   TRP B 194 
 HIS   0.004   0.001   HIS C 118 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.13 ( 6867)
  covalent geometry    : angle       0.55338 /  0.28 ( 9331)
  SS BOND              : bond        0.00346 /  0.14 (    9)
  SS BOND              : angle       0.83037 /  0.75 (   18)
  hydrogen bonds       : bond        0.03041 /  1.94 (  188)
  hydrogen bonds       : angle       4.72760 /  3.40 (  579)
  link_BETA1-4         : bond        0.00416 /  0.21 (    6)
  link_BETA1-4         : angle       1.71382 /  1.08 (   18)
  link_NAG-ASN         : bond        0.00297 /  0.18 (   10)
  link_NAG-ASN         : angle       3.19065 /  1.85 (   30)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1528.22 seconds
wall clock time: 26 minutes 55.80 seconds (1615.80 seconds total)