Starting phenix.real_space_refine
on Thu Jul  2 18:13:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k17_36787/07_2026/8k17_36787.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k17_36787/07_2026/8k17_36787.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k17_36787/07_2026/8k17_36787.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k17_36787/07_2026/8k17_36787.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k17_36787/07_2026/8k17_36787.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k17_36787/07_2026/8k17_36787.map"
  }
  resolution = 3.18
  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=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Fe      1      7.16       5
     S      51      5.16       5
     C    6207      2.51       5
     N    1658      2.21       5
     O    1831      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9748
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5193
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 646, 5193
          Classifications: {'peptide': 646}
          Link IDs: {'PTRANS': 33, 'TRANS': 612}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2994
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 2994
          Classifications: {'peptide': 362}
          Link IDs: {'PTRANS': 18, 'TRANS': 343}
    Chain: "C"
      Number of atoms: 1438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 185, 1438
          Classifications: {'peptide': 185}
          Link IDs: {'PTRANS': 6, 'TRANS': 178}
    Chain: "E"
      Number of atoms: 66
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 66
          Classifications: {'peptide': 10}
          Link IDs: {'PTRANS': 4, 'TRANS': 5}
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 28
          Ad-hoc single atom residues: {' FE': 1}
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 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: 1.89, per 1000 atoms: 0.19
  Number of scatterers: 9748
  At special positions: 0
  Unit cell: (93.5, 115.5, 124.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      1     26.01
     S      51     16.00
     O    1831      8.00
     N    1658      7.00
     C    6207      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  75 " - pdb=" SG  CYS A 123 " distance=2.06
    Simple disulfide: pdb=" SG  CYS A 591 " - pdb=" SG  CYS A 600 " 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 801 " - " ASN A 540 "
      " NAG A 802 " - " ASN A 316 "
      " NAG B 501 " - " ASN B  87 "
      " NAG B 502 " - " ASN B 363 "
  Time building additional restraints: 0.82
  Conformation dependent library (CDL) restraints added in 310.9 milliseconds
  

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2260

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 7 sheets defined
      57.0% alpha, 10.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 49
      removed outlier: 3.798A  pdb=" N   LEU A  38 " --> pdb=" O   THR A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 83
      removed outlier: 3.558A  pdb=" N   PHE A  83 " --> pdb=" O   CYS A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 125
      removed outlier: 3.534A  pdb=" N   ALA A 101 " --> pdb=" O   GLN A  97 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   GLY A 125 " --> pdb=" O   ARG A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 142
    Processing helix  chain 'A' and resid 143 through 156
      removed outlier: 3.792A  pdb=" N   ASN A 147 " --> pdb=" O   ARG A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 173
    Processing helix  chain 'A' and resid 176 through 189
      removed outlier: 3.514A  pdb=" N   GLN A 180 " --> pdb=" O   HIS A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 218
    Processing helix  chain 'A' and resid 220 through 223
    Processing helix  chain 'A' and resid 224 through 244
      removed outlier: 3.510A  pdb=" N   ALA A 244 " --> pdb=" O   GLU A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 286
      removed outlier: 3.654A  pdb=" N   THR A 269 " --> pdb=" O   PHE A 265 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   VAL A 283 " --> pdb=" O   LYS A 279 " (cutoff:3.500A)
      removed outlier: 4.686A  pdb=" N   THR A 284 " --> pdb=" O   GLN A 280 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLU A 285 " --> pdb=" O   ASN A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 315
      removed outlier: 3.796A  pdb=" N   PHE A 309 " --> pdb=" O   ASN A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 329
    Processing helix  chain 'A' and resid 334 through 348
      removed outlier: 3.633A  pdb=" N   ASN A 338 " --> pdb=" O   ASP A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 356
    Processing helix  chain 'A' and resid 359 through 384
    Processing helix  chain 'A' and resid 395 through 399
      removed outlier: 3.655A  pdb=" N   VAL A 398 " --> pdb=" O   PRO A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 428
    Processing helix  chain 'A' and resid 441 through 447
      removed outlier: 3.672A  pdb=" N   ARG A 447 " --> pdb=" O   SER A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 463 through 467
    Processing helix  chain 'A' and resid 479 through 493
      removed outlier: 3.661A  pdb=" N   CYS A 483 " --> pdb=" O   SER A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 528
    Processing helix  chain 'A' and resid 531 through 553
      removed outlier: 3.741A  pdb=" N   ALA A 535 " --> pdb=" O   PRO A 531 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   PHE A 553 " --> pdb=" O   MET A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 685 through 699
      removed outlier: 4.295A  pdb=" N   GLN A 689 " --> pdb=" O   ARG A 685 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 37 through 41
      removed outlier: 3.533A  pdb=" N   GLU B  40 " --> pdb=" O   PRO B  37 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   LEU B  41 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 37 through 41'
    Processing helix  chain 'B' and resid 43 through 57
    Processing helix  chain 'B' and resid 59 through 89
      removed outlier: 3.558A  pdb=" N   SER B  63 " --> pdb=" O   HIS B  59 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ASN B  87 " --> pdb=" O   PHE B  83 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   CYS B  88 " --> pdb=" O   CYS B  84 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   SER B  89 " --> pdb=" O   HIS B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 102
    Processing helix  chain 'B' and resid 103 through 124
      removed outlier: 3.625A  pdb=" N   GLN B 124 " --> pdb=" O   LYS B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 131
      removed outlier: 3.520A  pdb=" N   ARG B 130 " --> pdb=" O   PRO B 127 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   GLN B 131 " --> pdb=" O   ALA B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 144
    Processing helix  chain 'B' and resid 146 through 158
      removed outlier: 4.204A  pdb=" N   PHE B 150 " --> pdb=" O   GLU B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 175
      removed outlier: 3.932A  pdb=" N   LYS B 174 " --> pdb=" O   THR B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 191
      removed outlier: 3.933A  pdb=" N   LYS B 182 " --> pdb=" O   ASP B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 219
      removed outlier: 3.641A  pdb=" N   SER B 208 " --> pdb=" O   LYS B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 246
      Proline residue:  B 234  - end of helix
    Processing helix  chain 'B' and resid 258 through 276
      removed outlier: 3.806A  pdb=" N   ASP B 265 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   TYR B 267 " --> pdb=" O   ILE B 263 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   VAL B 268 " --> pdb=" O   ALA B 264 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   GLU B 269 " --> pdb=" O   ASP B 265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 308
    Processing helix  chain 'B' and resid 310 through 325
      Proline residue:  B 316  - end of helix
    Processing helix  chain 'B' and resid 328 through 341
      removed outlier: 3.551A  pdb=" N   HIS B 341 " --> pdb=" O   TYR B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 353
      removed outlier: 4.184A  pdb=" N   GLN B 353 " --> pdb=" O   GLU B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 355 through 379
      removed outlier: 4.025A  pdb=" N   GLU B 377 " --> pdb=" O   ASP B 373 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ASN B 378 " --> pdb=" O   PHE B 374 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 40 through 50
    Processing helix  chain 'C' and resid 143 through 152
      removed outlier: 3.508A  pdb=" N   VAL C 147 " --> pdb=" O   GLY C 143 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 458 through 461
      removed outlier: 5.798A  pdb=" N   LEU A 459 " --> pdb=" O   ASP A 475 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   ASP A 475 " --> pdb=" O   LEU A 459 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   PHE A 676 " --> pdb=" O   ASP A 611 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   SER A 613 " --> pdb=" O   LEU A 674 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   LEU A 674 " --> pdb=" O   SER A 613 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   ILE A 615 " --> pdb=" O   ILE A 672 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   ILE A 672 " --> pdb=" O   ILE A 615 " (cutoff:3.500A)
      removed outlier: 5.297A  pdb=" N   TYR A 617 " --> pdb=" O   CYS A 670 " (cutoff:3.500A)
      removed outlier: 7.922A  pdb=" N   CYS A 670 " --> pdb=" O   TYR A 617 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   THR A 677 " --> pdb=" O   PHE A 561 " (cutoff:3.500A)
      removed outlier: 5.397A  pdb=" N   PHE A 561 " --> pdb=" O   THR A 677 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 592 through 594
      removed outlier: 3.673A  pdb=" N   VAL A 601 " --> pdb=" O   ILE A 592 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 623 through 624
      removed outlier: 3.826A  pdb=" N   ARG A 666 " --> pdb=" O   ASP A 623 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 637 through 641
      removed outlier: 6.608A  pdb=" N   PHE A 629 " --> pdb=" O   THR A 638 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   GLU A 640 " --> pdb=" O   PHE A 627 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   PHE A 627 " --> pdb=" O   GLU A 640 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 284 through 285
    Processing sheet with id=AA6, first strand: chain 'B' and resid 384 through 386
      removed outlier: 3.688A  pdb=" N   VAL C  12 " --> pdb=" O   LEU C  32 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   GLY C  26 " --> pdb=" O   LEU C  18 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   ILE C  20 " --> pdb=" O   ASP C  24 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   ASP C  24 " --> pdb=" O   ILE C  20 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   VAL C 106 " --> pdb=" O   PHE C 137 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   TRP C 105 " --> pdb=" O   THR C 123 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ARG C  63 " --> pdb=" O   GLN C  71 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 384 through 386
      removed outlier: 8.062A  pdb=" N   GLY C   7 " --> pdb=" O   PHE C 179 " (cutoff:3.500A)
      removed outlier: 8.105A  pdb=" N   PHE C 179 " --> pdb=" O   GLY C   7 " (cutoff:3.500A)
      removed outlier: 9.317A  pdb=" N   LYS C   9 " --> pdb=" O   LYS C 177 " (cutoff:3.500A)
      removed outlier: 10.571A  pdb=" N   LYS C 177 " --> pdb=" O   LYS C   9 " (cutoff:3.500A)
      removed outlier: 7.066A  pdb=" N   THR C  11 " --> pdb=" O   VAL C 175 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   VAL C 175 " --> pdb=" O   THR C  11 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ASP C 169 " --> pdb=" O   ASP C  17 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   ARG C  19 " --> pdb=" O   ILE C 167 " (cutoff:3.500A)
      removed outlier: 5.552A  pdb=" N   ILE C 167 " --> pdb=" O   ARG C  19 " (cutoff:3.500A)

    524 hydrogen bonds defined for protein.
    1527 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: 1.35

  Time building geometry restraints manager: 1.10 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2783
        1.33 -     1.45: 1797
        1.45 -     1.57: 5330
        1.57 -     1.69: 0
        1.69 -     1.82: 77
  Bond restraints: 9987
  Sorted by residual:
  bond pdb=" CB  CYS A 123 "
       pdb=" SG  CYS A 123 "
    ideal  model  delta    sigma   weight residual
    1.808  1.715  0.093 3.30e-02 9.18e+02 7.95e+00
  bond pdb=" CB  CYS A  75 "
       pdb=" SG  CYS A  75 "
    ideal  model  delta    sigma   weight residual
    1.808  1.736  0.072 3.30e-02 9.18e+02 4.72e+00
  bond pdb=" C1  NAG B 501 "
       pdb=" O5  NAG B 501 "
    ideal  model  delta    sigma   weight residual
    1.406  1.444 -0.038 2.00e-02 2.50e+03 3.52e+00
  bond pdb=" C   GLY A 254 "
       pdb=" O   GLY A 254 "
    ideal  model  delta    sigma   weight residual
    1.235  1.212  0.022 1.35e-02 5.49e+03 2.71e+00
  bond pdb=" C   TYR C  87 "
       pdb=" N   GLY C  88 "
    ideal  model  delta    sigma   weight residual
    1.331  1.307  0.023 1.46e-02 4.69e+03 2.54e+00
  ... (remaining 9982 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.97: 13461
        3.97 -     7.93: 39
        7.93 -    11.90: 3
       11.90 -    15.86: 0
       15.86 -    19.83: 1
  Bond angle restraints: 13504
  Sorted by residual:
  angle pdb=" CA  CYS A 123 "
        pdb=" CB  CYS A 123 "
        pdb=" SG  CYS A 123 "
      ideal   model   delta    sigma   weight residual
     114.40  134.23  -19.83 2.30e+00 1.89e-01 7.43e+01
  angle pdb=" C   CYS A 123 "
        pdb=" CA  CYS A 123 "
        pdb=" CB  CYS A 123 "
      ideal   model   delta    sigma   weight residual
     110.42   99.27   11.15 1.99e+00 2.53e-01 3.14e+01
  angle pdb=" C   ARG A 122 "
        pdb=" N   CYS A 123 "
        pdb=" CA  CYS A 123 "
      ideal   model   delta    sigma   weight residual
     121.54  111.78    9.76 1.91e+00 2.74e-01 2.61e+01
  angle pdb=" N   CYS A 123 "
        pdb=" CA  CYS A 123 "
        pdb=" CB  CYS A 123 "
      ideal   model   delta    sigma   weight residual
     110.49  118.35   -7.86 1.69e+00 3.50e-01 2.16e+01
  angle pdb=" C   CYS A  75 "
        pdb=" N   ARG A  76 "
        pdb=" CA  ARG A  76 "
      ideal   model   delta    sigma   weight residual
     120.28  114.96    5.32 1.34e+00 5.57e-01 1.58e+01
  ... (remaining 13499 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.28: 5134
       17.28 -    34.55: 670
       34.55 -    51.83: 196
       51.83 -    69.10: 40
       69.10 -    86.38: 13
  Dihedral angle restraints: 6053
    sinusoidal: 2530
      harmonic: 3523
  Sorted by residual:
  dihedral pdb=" CA  CYS A 123 "
           pdb=" C   CYS A 123 "
           pdb=" N   LEU A 124 "
           pdb=" CA  LEU A 124 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -139.93  -40.07     0      5.00e+00 4.00e-02 6.42e+01
  dihedral pdb=" CA  ARG A 122 "
           pdb=" C   ARG A 122 "
           pdb=" N   CYS A 123 "
           pdb=" CA  CYS A 123 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.21   25.79     0      5.00e+00 4.00e-02 2.66e+01
  dihedral pdb=" CA  LYS A 158 "
           pdb=" C   LYS A 158 "
           pdb=" N   LEU A 159 "
           pdb=" CA  LEU A 159 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.54  -21.46     0      5.00e+00 4.00e-02 1.84e+01
  ... (remaining 6050 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 1202
       0.067 -    0.133: 211
       0.133 -    0.200: 10
       0.200 -    0.267: 0
       0.267 -    0.333: 1
  Chirality restraints: 1424
  Sorted by residual:
  chirality pdb=" CA  CYS A  75 "
            pdb=" N   CYS A  75 "
            pdb=" C   CYS A  75 "
            pdb=" CB  CYS A  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.77e+00
  chirality pdb=" CA  PRO A 451 "
            pdb=" N   PRO A 451 "
            pdb=" C   PRO A 451 "
            pdb=" CB  PRO A 451 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 8.69e-01
  chirality pdb=" C1  NAG B 502 "
            pdb=" ND2 ASN B 363 "
            pdb=" C2  NAG B 502 "
            pdb=" O5  NAG B 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.24   -0.16 2.00e-01 2.50e+01 6.31e-01
  ... (remaining 1421 not shown)

  Planarity restraints: 1775
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 603 "   -0.041 5.00e-02 4.00e+02   6.26e-02 6.28e+00
        pdb=" N   PRO A 604 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO A 604 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 604 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 621 "    0.012 2.00e-02 2.50e+03   2.32e-02 5.39e+00
        pdb=" C   ASP A 621 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   ASP A 621 "    0.015 2.00e-02 2.50e+03
        pdb=" N   PHE A 622 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 604 "    0.034 5.00e-02 4.00e+02   5.10e-02 4.17e+00
        pdb=" N   PRO A 605 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 605 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 605 "    0.029 5.00e-02 4.00e+02
  ... (remaining 1772 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 43
        2.56 -     3.15: 7435
        3.15 -     3.73: 13829
        3.73 -     4.32: 19123
        4.32 -     4.90: 33240
  Nonbonded interactions: 73670
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 589 "
            pdb="FE    FE A 803 "
     model   vdw
     1.978 3.000
  nonbonded pdb=" OG1 THR A 630 "
            pdb=" O   THR A 636 "
     model   vdw
     2.085 3.040
  nonbonded pdb=" N   GLN B  27 "
            pdb=" NE2 GLN B  27 "
     model   vdw
     2.109 3.200
  nonbonded pdb=" CE1 HIS A 659 "
            pdb="FE    FE A 803 "
     model   vdw
     2.119 3.220
  nonbonded pdb=" O   ASP A 253 "
            pdb=" ND2 ASN A 256 "
     model   vdw
     2.135 3.120
  ... (remaining 73665 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             0.650
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.910
  Find NCS groups from input model:        0.030
  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:0.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.093   9993  Z= 0.329
  Angle     :  0.745  19.831  13520  Z= 0.397
  Chirality :  0.049   0.333   1424
  Planarity :  0.005   0.063   1771
  Dihedral  : 16.981  86.376   3787
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  : 17.72 %
    Favored  : 81.99 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.57 (0.24), residues: 1191
  helix:  1.72 (0.20), residues: 633
  sheet:  0.12 (0.48), residues: 105
  loop : -1.57 (0.25), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  74 
 TYR   0.021   0.002   TYR A 539 
 PHE   0.022   0.002   PHE B 324 
 TRP   0.010   0.002   TRP A  91 
 HIS   0.016   0.003   HIS B 266 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00814 /  0.33 ( 9987)
  covalent geometry    : angle       0.73681 /  0.39 (13504)
  SS BOND              : bond        0.01702 /  1.06 (    2)
  SS BOND              : angle       6.04143 /  2.58 (    4)
  hydrogen bonds       : bond        0.18309 / 12.95 (  522)
  hydrogen bonds       : angle       5.48310 /  4.05 ( 1527)
  link_NAG-ASN         : bond        0.00573 /  0.31 (    4)
  link_NAG-ASN         : angle       1.71544 /  1.15 (   12)

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 114
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.8671 (mmt) cc_final: 0.8114 (mmt)
REVERT: B  341 HIS cc_start: 0.7359 (OUTLIER) cc_final: 0.7050 (m-70)
  outliers start: 3
  outliers final: 0
  residues processed: 115
  average time/residue: 0.0850
  time to fit residues: 14.2928
Evaluate side-chains
  110 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 109
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  341 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.2980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 117 optimal weight:    4.9990
   overall best weight:    1.0586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 576 GLN
B  27 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.147455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.107408 restraints weight = 11726.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.3123 rms_B_bonded: 2.54
r_work: 0.2835 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.0958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9993  Z= 0.133
  Angle     :  0.508   6.851  13520  Z= 0.273
  Chirality :  0.040   0.179   1424
  Planarity :  0.004   0.051   1771
  Dihedral  :  4.517  42.058   1422
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 18.01 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.24), residues: 1191
  helix:  2.13 (0.21), residues: 637
  sheet:  0.61 (0.50), residues: 100
  loop : -1.34 (0.26), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 546 
 TYR   0.015   0.001   TYR A 539 
 PHE   0.013   0.001   PHE C 121 
 TRP   0.011   0.001   TRP C 105 
 HIS   0.007   0.001   HIS B 266 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.13 ( 9987)
  covalent geometry    : angle       0.50320 /  0.27 (13504)
  SS BOND              : bond        0.01008 /  0.63 (    2)
  SS BOND              : angle       2.54440 /  1.18 (    4)
  hydrogen bonds       : bond        0.06506 /  4.43 (  522)
  hydrogen bonds       : angle       3.96132 /  2.93 ( 1527)
  link_NAG-ASN         : bond        0.00468 /  0.24 (    4)
  link_NAG-ASN         : angle       1.81596 /  1.16 (   12)

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
REVERT: A  137 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7539 (mm-30)
REVERT: A  482 GLU cc_start: 0.7751 (mp0) cc_final: 0.7463 (mp0)
REVERT: B   78 ARG cc_start: 0.8087 (tpp-160) cc_final: 0.7875 (mmt180)
REVERT: C   67 ASP cc_start: 0.7009 (t0) cc_final: 0.6785 (t0)
REVERT: C  154 LYS cc_start: 0.6836 (mtpt) cc_final: 0.6508 (ptmt)
  outliers start: 14
  outliers final: 6
  residues processed: 119
  average time/residue: 0.1030
  time to fit residues: 17.3601
Evaluate side-chains
  114 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 108
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain B residue  381 ASP
Chi-restraints excluded: chain C residue   12 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 68 optimal weight:    0.8980
   chunk 83 optimal weight:   10.0000
   chunk 89 optimal weight:    0.0770
   chunk 100 optimal weight:    0.0570
   chunk 59 optimal weight:    4.9990
   chunk 99 optimal weight:    3.9990
   chunk 95 optimal weight:    9.9990
   chunk 90 optimal weight:    2.9990
   chunk 78 optimal weight:    7.9990
   chunk 81 optimal weight:    3.9990
   overall best weight:    1.0058

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.148864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.108241 restraints weight = 11773.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 2.64
r_work: 0.2846 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.1293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   9993  Z= 0.122
  Angle     :  0.490  11.628  13520  Z= 0.259
  Chirality :  0.039   0.160   1424
  Planarity :  0.004   0.049   1771
  Dihedral  :  4.033  31.564   1420
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 17.72 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  1.32 (0.24), residues: 1191
  helix:  2.34 (0.20), residues: 635
  sheet:  0.89 (0.51), residues: 94
  loop : -1.32 (0.26), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  63 
 TYR   0.014   0.001   TYR A 539 
 PHE   0.012   0.001   PHE C 121 
 TRP   0.009   0.001   TRP C 105 
 HIS   0.005   0.001   HIS B 266 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.12 ( 9987)
  covalent geometry    : angle       0.48186 /  0.26 (13504)
  SS BOND              : bond        0.00409 /  0.26 (    2)
  SS BOND              : angle       4.58730 /  2.01 (    4)
  hydrogen bonds       : bond        0.05728 /  3.90 (  522)
  hydrogen bonds       : angle       3.66762 /  2.72 ( 1527)
  link_NAG-ASN         : bond        0.00354 /  0.19 (    4)
  link_NAG-ASN         : angle       1.61507 /  1.04 (   12)

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 115
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
REVERT: A  106 ASP cc_start: 0.7889 (m-30) cc_final: 0.7683 (m-30)
REVERT: A  134 GLU cc_start: 0.6339 (OUTLIER) cc_final: 0.6057 (mm-30)
REVERT: A  337 MET cc_start: 0.8892 (tpp) cc_final: 0.8607 (tpt)
REVERT: A  482 GLU cc_start: 0.7820 (mp0) cc_final: 0.7516 (mp0)
REVERT: B   50 HIS cc_start: 0.7510 (m170) cc_final: 0.7260 (m170)
REVERT: B  146 GLU cc_start: 0.7616 (tt0) cc_final: 0.7408 (tt0)
REVERT: C  154 LYS cc_start: 0.6743 (mtpt) cc_final: 0.6409 (ptmt)
  outliers start: 22
  outliers final: 9
  residues processed: 132
  average time/residue: 0.0896
  time to fit residues: 16.6285
Evaluate side-chains
  125 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 115
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 GLU
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  549 MET
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  649 VAL
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue  135 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 107 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 114 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 111 optimal weight:    5.9990
   chunk 94 optimal weight:   10.0000
   chunk 41 optimal weight:    3.9990
   overall best weight:    1.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  27 GLN
B 351 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.151630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.115366 restraints weight = 11839.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 2.57
r_work: 0.2879 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2709 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.1306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   9993  Z= 0.149
  Angle     :  0.494   7.221  13520  Z= 0.265
  Chirality :  0.040   0.161   1424
  Planarity :  0.004   0.050   1771
  Dihedral  :  3.922  27.622   1420
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 18.21 %
    Favored  : 79.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.24), residues: 1191
  helix:  2.34 (0.20), residues: 637
  sheet:  0.87 (0.50), residues: 94
  loop : -1.25 (0.27), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 687 
 TYR   0.015   0.001   TYR A 539 
 PHE   0.014   0.001   PHE C 121 
 TRP   0.007   0.001   TRP C 105 
 HIS   0.006   0.001   HIS B 266 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00356 /  0.15 ( 9987)
  covalent geometry    : angle       0.48741 /  0.26 (13504)
  SS BOND              : bond        0.00342 /  0.21 (    2)
  SS BOND              : angle       4.00401 /  1.57 (    4)
  hydrogen bonds       : bond        0.06239 /  4.26 (  522)
  hydrogen bonds       : angle       3.68171 /  2.73 ( 1527)
  link_NAG-ASN         : bond        0.00360 /  0.19 (    4)
  link_NAG-ASN         : angle       1.54470 /  0.99 (   12)

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 116
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
REVERT: A  134 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.6001 (mm-30)
REVERT: A  337 MET cc_start: 0.8736 (tpp) cc_final: 0.8373 (tpt)
REVERT: A  482 GLU cc_start: 0.7922 (mp0) cc_final: 0.7580 (mp0)
REVERT: B   27 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7830 (pm20)
REVERT: B   50 HIS cc_start: 0.7310 (m170) cc_final: 0.7039 (m170)
REVERT: B  291 GLU cc_start: 0.7363 (tt0) cc_final: 0.6968 (pt0)
REVERT: C  154 LYS cc_start: 0.6708 (mtpt) cc_final: 0.6379 (ptmt)
  outliers start: 25
  outliers final: 14
  residues processed: 135
  average time/residue: 0.0936
  time to fit residues: 18.0161
Evaluate side-chains
  135 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 119
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 ARG
Chi-restraints excluded: chain A residue  123 CYS
Chi-restraints excluded: chain A residue  134 GLU
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  549 MET
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  649 VAL
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue  328 ASP
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue  135 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 74 optimal weight:    0.5980
   chunk 90 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 83 optimal weight:    6.9990
   chunk 41 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 113 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 40 optimal weight:    4.9990
   overall best weight:    1.4984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  27 GLN
B 276 GLN
B 351 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.157165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.121801 restraints weight = 11604.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 2.25
r_work: 0.3050 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2892 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.1375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   9993  Z= 0.143
  Angle     :  0.501  10.737  13520  Z= 0.264
  Chirality :  0.040   0.163   1424
  Planarity :  0.004   0.049   1771
  Dihedral  :  3.847  27.727   1420
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 18.70 %
    Favored  : 78.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.40 (0.24), residues: 1191
  helix:  2.38 (0.20), residues: 637
  sheet:  0.86 (0.50), residues: 94
  loop : -1.25 (0.27), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  30 
 TYR   0.015   0.001   TYR A 539 
 PHE   0.014   0.001   PHE C 121 
 TRP   0.008   0.001   TRP C 105 
 HIS   0.005   0.001   HIS B 266 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00340 /  0.14 ( 9987)
  covalent geometry    : angle       0.49520 /  0.26 (13504)
  SS BOND              : bond        0.00487 /  0.30 (    2)
  SS BOND              : angle       3.67601 /  1.38 (    4)
  hydrogen bonds       : bond        0.06078 /  4.15 (  522)
  hydrogen bonds       : angle       3.64361 /  2.70 ( 1527)
  link_NAG-ASN         : bond        0.00347 /  0.19 (    4)
  link_NAG-ASN         : angle       1.53828 /  0.97 (   12)

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 119
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
REVERT: A  134 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6567 (mm-30)
REVERT: A  482 GLU cc_start: 0.7846 (mp0) cc_final: 0.7566 (mp0)
REVERT: B   50 HIS cc_start: 0.7750 (m170) cc_final: 0.7476 (m170)
REVERT: B  282 THR cc_start: 0.9390 (OUTLIER) cc_final: 0.9080 (t)
REVERT: B  291 GLU cc_start: 0.7468 (tt0) cc_final: 0.7231 (pt0)
REVERT: C  154 LYS cc_start: 0.7064 (mtpt) cc_final: 0.6798 (ptmt)
  outliers start: 26
  outliers final: 14
  residues processed: 140
  average time/residue: 0.0920
  time to fit residues: 18.3696
Evaluate side-chains
  128 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 CYS
Chi-restraints excluded: chain A residue  134 GLU
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  549 MET
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  649 VAL
Chi-restraints excluded: chain B residue  252 GLU
Chi-restraints excluded: chain B residue  282 THR
Chi-restraints excluded: chain B residue  328 ASP
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue  135 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 30 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 114 optimal weight:    0.9980
   chunk 118 optimal weight:    8.9990
   chunk 110 optimal weight:    7.9990
   chunk 2 optimal weight:    0.8980
   chunk 109 optimal weight:    0.3980
   chunk 39 optimal weight:    7.9990
   chunk 90 optimal weight:    0.7980
   chunk 63 optimal weight:    5.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  27 GLN
B 351 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.155004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.118198 restraints weight = 11672.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 2.38
r_work: 0.3089 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.055   9993  Z= 0.108
  Angle     :  0.468   8.663  13520  Z= 0.247
  Chirality :  0.039   0.174   1424
  Planarity :  0.004   0.048   1771
  Dihedral  :  3.600  26.826   1420
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 19.38 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.54 (0.24), residues: 1191
  helix:  2.51 (0.20), residues: 637
  sheet:  0.93 (0.51), residues: 93
  loop : -1.19 (0.27), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 488 
 TYR   0.013   0.001   TYR A 539 
 PHE   0.010   0.001   PHE C 121 
 TRP   0.009   0.001   TRP C 105 
 HIS   0.003   0.000   HIS B 351 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.11 ( 9987)
  covalent geometry    : angle       0.46227 /  0.25 (13504)
  SS BOND              : bond        0.00531 /  0.33 (    2)
  SS BOND              : angle       3.50542 /  1.23 (    4)
  hydrogen bonds       : bond        0.04886 /  3.31 (  522)
  hydrogen bonds       : angle       3.48098 /  2.57 ( 1527)
  link_NAG-ASN         : bond        0.00307 /  0.18 (    4)
  link_NAG-ASN         : angle       1.51626 /  0.97 (   12)

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 ASP cc_start: 0.7877 (m-30) cc_final: 0.7617 (m-30)
REVERT: A  448 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7707 (mm-30)
REVERT: A  482 GLU cc_start: 0.7739 (mp0) cc_final: 0.7525 (mp0)
REVERT: B   50 HIS cc_start: 0.7615 (m170) cc_final: 0.7326 (m170)
REVERT: C  154 LYS cc_start: 0.6980 (mtpt) cc_final: 0.6712 (ptmt)
  outliers start: 20
  outliers final: 12
  residues processed: 136
  average time/residue: 0.0894
  time to fit residues: 17.5372
Evaluate side-chains
  124 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 CYS
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  271 HIS
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  549 MET
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  649 VAL
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue  135 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 117 optimal weight:    3.9990
   chunk 90 optimal weight:    0.8980
   chunk 80 optimal weight:    0.0070
   chunk 118 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   chunk 109 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 114 optimal weight:    2.9990
   chunk 111 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.9000

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  27 GLN
B 351 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.154642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.117577 restraints weight = 11636.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 2.32
r_work: 0.2958 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2792 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9993  Z= 0.112
  Angle     :  0.465   7.832  13520  Z= 0.245
  Chirality :  0.039   0.165   1424
  Planarity :  0.004   0.047   1771
  Dihedral  :  3.526  26.526   1420
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 19.77 %
    Favored  : 78.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.61 (0.24), residues: 1191
  helix:  2.53 (0.20), residues: 640
  sheet:  1.00 (0.51), residues: 95
  loop : -1.14 (0.27), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 488 
 TYR   0.013   0.001   TYR A 539 
 PHE   0.011   0.001   PHE C 121 
 TRP   0.007   0.001   TRP C 105 
 HIS   0.004   0.001   HIS B 266 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.11 ( 9987)
  covalent geometry    : angle       0.46048 /  0.24 (13504)
  SS BOND              : bond        0.00492 /  0.31 (    2)
  SS BOND              : angle       2.87671 /  1.09 (    4)
  hydrogen bonds       : bond        0.05047 /  3.43 (  522)
  hydrogen bonds       : angle       3.44343 /  2.54 ( 1527)
  link_NAG-ASN         : bond        0.00314 /  0.18 (    4)
  link_NAG-ASN         : angle       1.47161 /  0.94 (   12)

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.412 
Fit side-chains
REVERT: A   78 GLN cc_start: 0.8035 (tt0) cc_final: 0.7804 (tt0)
REVERT: A  106 ASP cc_start: 0.8150 (m-30) cc_final: 0.7881 (m-30)
REVERT: A  448 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7691 (mm-30)
REVERT: A  482 GLU cc_start: 0.7955 (mp0) cc_final: 0.7628 (mp0)
REVERT: B   50 HIS cc_start: 0.7522 (m170) cc_final: 0.7218 (m170)
REVERT: B  282 THR cc_start: 0.9304 (OUTLIER) cc_final: 0.8987 (t)
REVERT: C  154 LYS cc_start: 0.6961 (mtpt) cc_final: 0.6682 (ptmt)
  outliers start: 18
  outliers final: 11
  residues processed: 128
  average time/residue: 0.0949
  time to fit residues: 17.5935
Evaluate side-chains
  123 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  549 MET
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  649 VAL
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  282 THR
Chi-restraints excluded: chain B residue  328 ASP
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue  135 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 101 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 66 optimal weight:    0.8980
   chunk 109 optimal weight:    2.9990
   chunk 79 optimal weight:    4.9990
   chunk 114 optimal weight:    0.7980
   chunk 42 optimal weight:    7.9990
   chunk 112 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 423 ASN
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 351 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.157830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.122076 restraints weight = 11591.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 2.26
r_work: 0.2945 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2780 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.1797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9993  Z= 0.113
  Angle     :  0.477   8.414  13520  Z= 0.250
  Chirality :  0.039   0.192   1424
  Planarity :  0.004   0.047   1771
  Dihedral  :  3.470  23.632   1420
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 19.28 %
    Favored  : 78.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.65 (0.24), residues: 1191
  helix:  2.60 (0.20), residues: 637
  sheet:  0.89 (0.51), residues: 96
  loop : -1.14 (0.27), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 488 
 TYR   0.014   0.001   TYR A 539 
 PHE   0.011   0.001   PHE C 121 
 TRP   0.008   0.001   TRP C 105 
 HIS   0.004   0.001   HIS B 266 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.11 ( 9987)
  covalent geometry    : angle       0.47105 /  0.25 (13504)
  SS BOND              : bond        0.00138 /  0.08 (    2)
  SS BOND              : angle       3.52675 /  1.29 (    4)
  hydrogen bonds       : bond        0.05066 /  3.45 (  522)
  hydrogen bonds       : angle       3.42972 /  2.54 ( 1527)
  link_NAG-ASN         : bond        0.00305 /  0.17 (    4)
  link_NAG-ASN         : angle       1.46247 /  0.93 (   12)

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.384 
Fit side-chains
REVERT: A   78 GLN cc_start: 0.7808 (tt0) cc_final: 0.7538 (tt0)
REVERT: A  106 ASP cc_start: 0.7988 (m-30) cc_final: 0.7696 (m-30)
REVERT: A  259 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7546 (pm20)
REVERT: A  448 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7516 (mm-30)
REVERT: A  482 GLU cc_start: 0.7931 (mp0) cc_final: 0.7639 (mp0)
REVERT: B   50 HIS cc_start: 0.7282 (m170) cc_final: 0.6971 (m170)
REVERT: B  282 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8870 (t)
REVERT: C  154 LYS cc_start: 0.6900 (mtpt) cc_final: 0.6579 (ptmt)
  outliers start: 19
  outliers final: 12
  residues processed: 128
  average time/residue: 0.0930
  time to fit residues: 17.0672
Evaluate side-chains
  123 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  271 HIS
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  549 MET
Chi-restraints excluded: chain A residue  566 LEU
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  649 VAL
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  282 THR
Chi-restraints excluded: chain B residue  328 ASP
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue  135 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 109 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9980
   chunk 117 optimal weight:    1.9990
   chunk 100 optimal weight:    3.9990
   chunk 99 optimal weight:    3.9990
   chunk 113 optimal weight:    3.9990
   chunk 98 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9980
   chunk 92 optimal weight:    6.9990
   chunk 94 optimal weight:    1.9990
   overall best weight:    1.5986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 341 HIS
B 351 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.147374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.107927 restraints weight = 11707.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 2.70
r_work: 0.2858 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.1596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9993  Z= 0.144
  Angle     :  0.505   8.683  13520  Z= 0.267
  Chirality :  0.041   0.216   1424
  Planarity :  0.004   0.048   1771
  Dihedral  :  3.599  20.751   1420
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 19.28 %
    Favored  : 79.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.56 (0.24), residues: 1191
  helix:  2.52 (0.20), residues: 638
  sheet:  0.80 (0.50), residues: 97
  loop : -1.18 (0.27), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 687 
 TYR   0.014   0.001   TYR A 539 
 PHE   0.015   0.001   PHE C 121 
 TRP   0.005   0.001   TRP C 105 
 HIS   0.005   0.001   HIS B 266 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00343 /  0.14 ( 9987)
  covalent geometry    : angle       0.49932 /  0.26 (13504)
  SS BOND              : bond        0.00185 /  0.11 (    2)
  SS BOND              : angle       3.62631 /  1.31 (    4)
  hydrogen bonds       : bond        0.06144 /  4.20 (  522)
  hydrogen bonds       : angle       3.56244 /  2.63 ( 1527)
  link_NAG-ASN         : bond        0.00317 /  0.18 (    4)
  link_NAG-ASN         : angle       1.49339 /  0.93 (   12)

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A  106 ASP cc_start: 0.7938 (m-30) cc_final: 0.7656 (m-30)
REVERT: A  259 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7546 (pm20)
REVERT: A  482 GLU cc_start: 0.7812 (mp0) cc_final: 0.7538 (mp0)
REVERT: B   50 HIS cc_start: 0.7512 (m170) cc_final: 0.7218 (m170)
REVERT: B  282 THR cc_start: 0.9305 (OUTLIER) cc_final: 0.9013 (t)
REVERT: C  154 LYS cc_start: 0.7014 (mtpt) cc_final: 0.6726 (ptmt)
  outliers start: 17
  outliers final: 13
  residues processed: 132
  average time/residue: 0.0919
  time to fit residues: 17.6373
Evaluate side-chains
  130 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  549 MET
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  649 VAL
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  282 THR
Chi-restraints excluded: chain B residue  328 ASP
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   64 VAL
Chi-restraints excluded: chain C residue  135 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 117 optimal weight:    0.0040
   chunk 5 optimal weight:    0.2980
   chunk 116 optimal weight:    3.9990
   chunk 50 optimal weight:    0.6980
   chunk 106 optimal weight:    0.9980
   chunk 98 optimal weight:    0.8980
   chunk 6 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9990
   chunk 114 optimal weight:    0.9990
   chunk 15 optimal weight:    9.9990
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.5792

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  27 GLN
B 351 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.156064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.119106 restraints weight = 11509.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 2.39
r_work: 0.3084 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.1945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9993  Z= 0.102
  Angle     :  0.466   7.734  13520  Z= 0.244
  Chirality :  0.039   0.187   1424
  Planarity :  0.004   0.047   1771
  Dihedral  :  3.398  21.109   1420
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 19.47 %
    Favored  : 79.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.66 (0.25), residues: 1191
  helix:  2.56 (0.20), residues: 643
  sheet:  0.86 (0.51), residues: 96
  loop : -1.08 (0.27), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 488 
 TYR   0.011   0.001   TYR A 539 
 PHE   0.009   0.001   PHE C 121 
 TRP   0.009   0.001   TRP C 105 
 HIS   0.003   0.000   HIS B 351 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00221 /  0.10 ( 9987)
  covalent geometry    : angle       0.46008 /  0.24 (13504)
  SS BOND              : bond        0.00181 /  0.11 (    2)
  SS BOND              : angle       3.42092 /  1.28 (    4)
  hydrogen bonds       : bond        0.04566 /  3.09 (  522)
  hydrogen bonds       : angle       3.38536 /  2.50 ( 1527)
  link_NAG-ASN         : bond        0.00278 /  0.16 (    4)
  link_NAG-ASN         : angle       1.50562 /  0.96 (   12)

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

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

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2382 Ramachandran restraints generated.
    1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.360 
Fit side-chains
REVERT: A  106 ASP cc_start: 0.7868 (m-30) cc_final: 0.7594 (m-30)
REVERT: A  259 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7448 (pm20)
REVERT: A  448 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7770 (mm-30)
REVERT: A  475 ASP cc_start: 0.7873 (m-30) cc_final: 0.7626 (m-30)
REVERT: A  482 GLU cc_start: 0.7720 (mp0) cc_final: 0.7489 (mp0)
REVERT: A  669 ARG cc_start: 0.7763 (tmm-80) cc_final: 0.6663 (ttt-90)
REVERT: B   50 HIS cc_start: 0.7573 (m170) cc_final: 0.7273 (m170)
REVERT: B  282 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.9074 (t)
REVERT: C  154 LYS cc_start: 0.7053 (mtpt) cc_final: 0.6771 (ptmt)
  outliers start: 14
  outliers final: 11
  residues processed: 125
  average time/residue: 0.0897
  time to fit residues: 16.1855
Evaluate side-chains
  122 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  549 MET
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain A residue  649 VAL
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue  282 THR
Chi-restraints excluded: chain B residue  328 ASP
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue  135 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 101 optimal weight:    4.9990
   chunk 36 optimal weight:    0.1980
   chunk 117 optimal weight:    0.0040
   chunk 85 optimal weight:    1.9990
   chunk 89 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 118 optimal weight:    0.4980
   chunk 5 optimal weight:    0.8980
   chunk 12 optimal weight:    5.9990
   chunk 107 optimal weight:    0.9990
   overall best weight:    0.5194

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  27 GLN
B 341 HIS
B 351 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.151455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.112286 restraints weight = 11723.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 2.70
r_work: 0.3063 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.1976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.185   9993  Z= 0.213
  Angle     :  0.858  59.199  13520  Z= 0.495
  Chirality :  0.039   0.190   1424
  Planarity :  0.004   0.047   1771
  Dihedral  :  3.395  21.091   1420
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 19.57 %
    Favored  : 78.77 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.67 (0.25), residues: 1191
  helix:  2.57 (0.20), residues: 643
  sheet:  0.86 (0.51), residues: 96
  loop : -1.08 (0.27), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 488 
 TYR   0.011   0.001   TYR A 539 
 PHE   0.009   0.001   PHE C 121 
 TRP   0.008   0.001   TRP C 105 
 HIS   0.004   0.001   HIS B 341 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00464 /  0.21 ( 9987)
  covalent geometry    : angle       0.85532 /  0.49 (13504)
  SS BOND              : bond        0.00080 /  0.05 (    2)
  SS BOND              : angle       3.35187 /  1.26 (    4)
  hydrogen bonds       : bond        0.04557 /  3.09 (  522)
  hydrogen bonds       : angle       3.38452 /  2.50 ( 1527)
  link_NAG-ASN         : bond        0.00273 /  0.16 (    4)
  link_NAG-ASN         : angle       1.50845 /  0.96 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2230.80 seconds
wall clock time: 38 minutes 50.55 seconds (2330.55 seconds total)