Starting phenix.real_space_refine
on Thu Oct 22 22:04:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vh2_65053/10_2026/9vh2_65053.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vh2_65053/10_2026/9vh2_65053.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vh2_65053/10_2026/9vh2_65053.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vh2_65053/10_2026/9vh2_65053.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vh2_65053/10_2026/9vh2_65053.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vh2_65053/10_2026/9vh2_65053.cif"
  }
  resolution = 2.65
  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=  -0.001 sd=   0.080
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      16      5.16       5
     C    3927      2.51       5
     N    1014      2.21       5
     O    1262      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 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: 6219
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "B"
      Number of atoms: 1332
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 175, 1332
          Classifications: {'peptide': 175}
          Link IDs: {'PTRANS': 10, 'TRANS': 164}
    Chain: "A"
      Number of atoms: 4470
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 574, 4470
          Classifications: {'peptide': 574}
          Link IDs: {'PTRANS': 31, 'TRANS': 542}
    Chain: "C"
      Number of atoms: 151
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 151
          Classifications: {'peptide': 21}
          Link IDs: {'PTRANS': 1, 'TRANS': 19}
    Chain: "D"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          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: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      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: "H"
      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: "I"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          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
  Time building chain proxies: 1.53, per 1000 atoms: 0.25
  Number of scatterers: 6219
  At special positions: 0
  Unit cell: (72.512, 84.872, 109.592, 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      16     16.00
     O    1262      8.00
     N    1014      7.00
     C    3927      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  57 " - pdb=" SG  CYS B  64 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  53 " - pdb=" SG  CYS A  60 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  84 " - pdb=" SG  CYS A 110 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  58 " - pdb=" SG  CYS C  68 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " NAG D   3 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG H   1 " - " NAG H   2 "
      " NAG I   1 " - " NAG I   2 "
    NAG-ASN
      " NAG A 901 " - " ASN A 246 "
      " NAG A 902 " - " ASN A 293 "
      " NAG A 903 " - " ASN A 435 "
      " NAG A 904 " - " ASN A 260 "
      " NAG A 905 " - " ASN A  74 "
      " NAG A 906 " - " ASN A 389 "
      " NAG D   1 " - " ASN B 183 "
      " NAG E   1 " - " ASN B 149 "
      " NAG F   1 " - " ASN A 449 "
      " NAG G   1 " - " ASN A 573 "
      " NAG H   1 " - " ASN A 124 "
      " NAG I   1 " - " ASN A 109 "
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 329.1 milliseconds
  

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1418

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 10 sheets defined
      21.4% alpha, 13.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'B' and resid 26 through 38
    Processing helix  chain 'B' and resid 55 through 59
      removed outlier: 4.044A  pdb=" N   THR B  58 " --> pdb=" O   THR B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 91
    Processing helix  chain 'B' and resid 109 through 115
    Processing helix  chain 'B' and resid 133 through 139
    Processing helix  chain 'B' and resid 157 through 163
    Processing helix  chain 'B' and resid 183 through 188
      removed outlier: 3.669A  pdb=" N   SER B 187 " --> pdb=" O   GLY B 184 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LEU B 188 " --> pdb=" O   SER B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 195
    Processing helix  chain 'A' and resid 27 through 37
    Processing helix  chain 'A' and resid 51 through 55
    Processing helix  chain 'A' and resid 60 through 64
    Processing helix  chain 'A' and resid 130 through 134
    Processing helix  chain 'A' and resid 153 through 159
    Processing helix  chain 'A' and resid 177 through 183
      removed outlier: 3.959A  pdb=" N   ILE A 180 " --> pdb=" O   PRO A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 209
    Processing helix  chain 'A' and resid 227 through 232
      removed outlier: 4.318A  pdb=" N   PHE A 231 " --> pdb=" O   SER A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 305
    Processing helix  chain 'A' and resid 323 through 329
    Processing helix  chain 'A' and resid 395 through 401
      removed outlier: 3.543A  pdb=" N   LEU A 398 " --> pdb=" O   PRO A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 423
    Processing helix  chain 'A' and resid 465 through 471
      removed outlier: 3.818A  pdb=" N   GLY A 469 " --> pdb=" O   LYS A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 495
      removed outlier: 3.645A  pdb=" N   LEU A 492 " --> pdb=" O   PRO A 489 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU A 495 " --> pdb=" O   LEU A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 543
    Processing helix  chain 'A' and resid 561 through 567
      removed outlier: 3.583A  pdb=" N   ILE A 564 " --> pdb=" O   PRO A 561 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 39 through 40
      removed outlier: 3.547A  pdb=" N   SER B  81 " --> pdb=" O   ALA B  40 " (cutoff:3.500A)
      removed outlier: 6.061A  pdb=" N   GLY B  82 " --> pdb=" O   THR B 105 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 62 through 64
      removed outlier: 6.432A  pdb=" N   THR B  63 " --> pdb=" O   THR B  71 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   THR B  71 " --> pdb=" O   TYR B  96 " (cutoff:3.500A)
      removed outlier: 8.424A  pdb=" N   GLU B  98 " --> pdb=" O   THR B  71 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   VAL B  73 " --> pdb=" O   GLU B  98 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ARG B 146 " --> pdb=" O   LEU B 121 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ASP B 170 " --> pdb=" O   LEU B 145 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 129 through 131
      removed outlier: 5.915A  pdb=" N   GLY B 130 " --> pdb=" O   SER B 153 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 58 through 59
      removed outlier: 6.889A  pdb=" N   ILE A  68 " --> pdb=" O   ASP A  93 " (cutoff:3.500A)
      removed outlier: 7.457A  pdb=" N   LEU A  92 " --> pdb=" O   ASP A 117 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   LEU A 116 " --> pdb=" O   ASP A 142 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   LEU A 141 " --> pdb=" O   ASN A 166 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   LEU A 165 " --> pdb=" O   ARG A 190 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   LEU A 189 " --> pdb=" O   TRP A 216 " (cutoff:3.500A)
      removed outlier: 6.043A  pdb=" N   MET A 215 " --> pdb=" O   ASP A 241 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   VAL A 240 " --> pdb=" O   TYR A 265 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   LEU A 287 " --> pdb=" O   ASN A 312 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   LEU A 311 " --> pdb=" O   LYS A 336 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   PHE A 335 " --> pdb=" O   GLU A 360 " (cutoff:3.500A)
      removed outlier: 7.419A  pdb=" N   PHE A 359 " --> pdb=" O   VAL A 384 " (cutoff:3.500A)
      removed outlier: 6.055A  pdb=" N   VAL A 383 " --> pdb=" O   GLN A 408 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   VAL A 407 " --> pdb=" O   GLN A 432 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   ILE A 453 " --> pdb=" O   LYS A 478 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   PHE A 477 " --> pdb=" O   PHE A 502 " (cutoff:3.500A)
      removed outlier: 6.160A  pdb=" N   ILE A 501 " --> pdb=" O   SER A 526 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   LEU A 525 " --> pdb=" O   ASP A 550 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 76 through 77
      removed outlier: 6.125A  pdb=" N   GLY A  77 " --> pdb=" O   ALA A 100 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   PHE A  99 " --> pdb=" O   LEU A 122 " (cutoff:3.500A)
      removed outlier: 5.920A  pdb=" N   ASN A 124 " --> pdb=" O   PHE A  99 " (cutoff:3.500A)
      removed outlier: 5.788A  pdb=" N   GLY A 101 " --> pdb=" O   ASN A 124 " (cutoff:3.500A)
      removed outlier: 7.412A  pdb=" N   SER A 126 " --> pdb=" O   GLY A 101 " (cutoff:3.500A)
      removed outlier: 7.409A  pdb=" N   LEU A 123 " --> pdb=" O   GLY A 147 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   SER A 149 " --> pdb=" O   LEU A 123 " (cutoff:3.500A)
      removed outlier: 5.553A  pdb=" N   GLY A 125 " --> pdb=" O   SER A 149 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 201
      removed outlier: 5.941A  pdb=" N   ALA A 200 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 272 through 273
      removed outlier: 5.569A  pdb=" N   GLY A 273 " --> pdb=" O   THR A 295 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   LEU A 294 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392
      removed outlier: 3.988A  pdb=" N   GLY A 392 " --> pdb=" O   ASP A 413 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 439 through 440
      removed outlier: 5.693A  pdb=" N   GLY A 440 " --> pdb=" O   SER A 461 " (cutoff:3.500A)
      removed outlier: 7.471A  pdb=" N   GLU A 463 " --> pdb=" O   GLY A 440 " (cutoff:3.500A)
      removed outlier: 4.752A  pdb=" N   GLN A 483 " --> pdb=" O   ASN A 458 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   PHE A 460 " --> pdb=" O   GLN A 483 " (cutoff:3.500A)
      removed outlier: 7.142A  pdb=" N   SER A 485 " --> pdb=" O   PHE A 460 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   GLY A 462 " --> pdb=" O   SER A 485 " (cutoff:3.500A)
      removed outlier: 8.131A  pdb=" N   GLU A 487 " --> pdb=" O   GLY A 462 " (cutoff:3.500A)
      removed outlier: 5.316A  pdb=" N   ASP A 507 " --> pdb=" O   ASN A 482 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   PHE A 484 " --> pdb=" O   ASP A 507 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   THR A 509 " --> pdb=" O   PHE A 484 " (cutoff:3.500A)
      removed outlier: 6.008A  pdb=" N   GLY A 486 " --> pdb=" O   THR A 509 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 533 through 534
      removed outlier: 5.556A  pdb=" N   GLY A 534 " --> pdb=" O   SER A 557 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   PHE A 556 " --> pdb=" O   ARG A 578 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1

    95 hydrogen bonds defined for protein.
    93 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: 0.70

  Time building geometry restraints manager: 0.79 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: 1885
        1.33 -     1.45: 913
        1.45 -     1.57: 3509
        1.57 -     1.69: 0
        1.69 -     1.81: 22
  Bond restraints: 6329
  Sorted by residual:
  bond pdb=" C   PRO C  62 "
       pdb=" N   ARG C  63 "
    ideal  model  delta    sigma   weight residual
    1.333  1.281  0.051 1.42e-02 4.96e+03 1.31e+01
  bond pdb=" N   GLY C  64 "
       pdb=" CA  GLY C  64 "
    ideal  model  delta    sigma   weight residual
    1.446  1.475 -0.028 1.06e-02 8.90e+03 7.23e+00
  bond pdb=" C1  NAG A 903 "
       pdb=" O5  NAG A 903 "
    ideal  model  delta    sigma   weight residual
    1.406  1.456 -0.050 2.00e-02 2.50e+03 6.18e+00
  bond pdb=" N   SER C  65 "
       pdb=" CA  SER C  65 "
    ideal  model  delta    sigma   weight residual
    1.455  1.486 -0.031 1.27e-02 6.20e+03 6.10e+00
  bond pdb=" N   ARG C  55 "
       pdb=" CA  ARG C  55 "
    ideal  model  delta    sigma   weight residual
    1.453  1.484 -0.030 1.27e-02 6.20e+03 5.71e+00
  ... (remaining 6324 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.33: 8462
        2.33 -     4.67: 126
        4.67 -     7.00: 8
        7.00 -     9.33: 4
        9.33 -    11.67: 2
  Bond angle restraints: 8602
  Sorted by residual:
  angle pdb=" C6  NAG G   2 "
        pdb=" C5  NAG G   2 "
        pdb=" O5  NAG G   2 "
      ideal   model   delta    sigma   weight residual
     108.73  120.40  -11.67 3.00e+00 1.11e-01 1.51e+01
  angle pdb=" CA  GLY C  66 "
        pdb=" C   GLY C  66 "
        pdb=" O   GLY C  66 "
      ideal   model   delta    sigma   weight residual
     122.65  118.11    4.54 1.28e+00 6.10e-01 1.26e+01
  angle pdb=" N   ILE A 523 "
        pdb=" CA  ILE A 523 "
        pdb=" C   ILE A 523 "
      ideal   model   delta    sigma   weight residual
     112.96  109.48    3.48 1.00e+00 1.00e+00 1.21e+01
  angle pdb=" CA  GLY C  64 "
        pdb=" C   GLY C  64 "
        pdb=" O   GLY C  64 "
      ideal   model   delta    sigma   weight residual
     122.28  118.85    3.43 1.00e+00 1.00e+00 1.18e+01
  angle pdb=" C2  NAG F   1 "
        pdb=" C3  NAG F   1 "
        pdb=" C4  NAG F   1 "
      ideal   model   delta    sigma   weight residual
     110.24  100.89    9.35 3.00e+00 1.11e-01 9.72e+00
  ... (remaining 8597 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.42: 3980
       23.42 -    46.85: 65
       46.85 -    70.27: 10
       70.27 -    93.69: 2
       93.69 -   117.12: 18
  Dihedral angle restraints: 4075
    sinusoidal: 1876
      harmonic: 2199
  Sorted by residual:
  dihedral pdb=" C2  NAG A 903 "
           pdb=" C1  NAG A 903 "
           pdb=" O5  NAG A 903 "
           pdb=" C5  NAG A 903 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.96   54.16 -117.12     1      3.00e+01 1.11e-03 1.55e+01
  dihedral pdb=" C1  NAG A 903 "
           pdb=" C5  NAG A 903 "
           pdb=" O5  NAG A 903 "
           pdb=" C4  NAG A 903 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -64.11   51.56 -115.67     1      3.00e+01 1.11e-03 1.53e+01
  dihedral pdb=" C1  NAG A 903 "
           pdb=" C5  NAG A 903 "
           pdb=" O5  NAG A 903 "
           pdb=" C6  NAG A 903 "
      ideal   model   delta sinusoidal    sigma   weight residual
     171.16  -73.24 -115.60     1      3.00e+01 1.11e-03 1.53e+01
  ... (remaining 4072 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.339: 1051
       0.339 -    0.678: 4
       0.678 -    1.017: 0
       1.017 -    1.356: 0
       1.356 -    1.696: 1
  Chirality restraints: 1056
  Sorted by residual:
  chirality pdb=" C1  NAG H   2 "
            pdb=" O4  NAG H   1 "
            pdb=" C2  NAG H   2 "
            pdb=" O5  NAG H   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.12   -0.28 2.00e-02 2.50e+03 1.98e+02
  chirality pdb=" C1  NAG F   2 "
            pdb=" O4  NAG F   1 "
            pdb=" C2  NAG F   2 "
            pdb=" O5  NAG F   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.64    0.24 2.00e-02 2.50e+03 1.46e+02
  chirality pdb=" C1  NAG I   2 "
            pdb=" O4  NAG I   1 "
            pdb=" C2  NAG I   2 "
            pdb=" O5  NAG I   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.22   -0.18 2.00e-02 2.50e+03 7.79e+01
  ... (remaining 1053 not shown)

  Planarity restraints: 1106
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG F   1 "    0.378 2.00e-02 2.50e+03   3.22e-01 1.30e+03
        pdb=" C7  NAG F   1 "   -0.093 2.00e-02 2.50e+03
        pdb=" C8  NAG F   1 "    0.066 2.00e-02 2.50e+03
        pdb=" N2  NAG F   1 "   -0.564 2.00e-02 2.50e+03
        pdb=" O7  NAG F   1 "    0.213 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   2 "    0.346 2.00e-02 2.50e+03   2.98e-01 1.11e+03
        pdb=" C7  NAG D   2 "   -0.080 2.00e-02 2.50e+03
        pdb=" C8  NAG D   2 "    0.064 2.00e-02 2.50e+03
        pdb=" N2  NAG D   2 "   -0.526 2.00e-02 2.50e+03
        pdb=" O7  NAG D   2 "    0.196 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG E   1 "    0.323 2.00e-02 2.50e+03   2.77e-01 9.62e+02
        pdb=" C7  NAG E   1 "   -0.081 2.00e-02 2.50e+03
        pdb=" C8  NAG E   1 "    0.167 2.00e-02 2.50e+03
        pdb=" N2  NAG E   1 "   -0.489 2.00e-02 2.50e+03
        pdb=" O7  NAG E   1 "    0.080 2.00e-02 2.50e+03
  ... (remaining 1103 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 268
        2.71 -     3.26: 6773
        3.26 -     3.81: 9721
        3.81 -     4.35: 13577
        4.35 -     4.90: 21798
  Nonbonded interactions: 52137
  Sorted by model distance:
  nonbonded pdb=" O   LYS B 140 "
            pdb=" OG1 THR B 165 "
     model   vdw
     2.163 3.040
  nonbonded pdb=" NE2 GLN A 410 "
            pdb=" OE1 GLN A 432 "
     model   vdw
     2.192 3.120
  nonbonded pdb=" OD2 ASP A 456 "
            pdb=" ND2 ASN A 457 "
     model   vdw
     2.199 3.120
  nonbonded pdb=" OD2 ASP A 504 "
            pdb=" OG  SER A 528 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O   GLY A 402 "
            pdb=" OG  SER A 427 "
     model   vdw
     2.202 3.040
  ... (remaining 52132 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 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
}

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:             0.560
  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:             0.020
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.980
  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:5.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5766
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   0.051   6352  Z= 0.238
  Angle     :  0.738  12.426   8667  Z= 0.324
  Chirality :  0.076   1.696   1056
  Planarity :  0.025   0.322   1094
  Dihedral  : 12.124 117.118   2645
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  1.60 %
    Favored  : 97.96 %
  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: -3.79 (0.27), residues: 764
  helix: -3.70 (0.30), residues: 135
  sheet: -4.29 (0.34), residues: 110
  loop : -1.82 (0.25), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  51 
 TYR   0.003   0.001   TYR A 172 
 PHE   0.003   0.000   PHE A 197 
 TRP   0.003   0.000   TRP B  49 
 HIS   0.002   0.001   HIS C  69 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00411 /  0.24 ( 6329)
  covalent geometry    : angle       0.62921 /  0.30 ( 8602)
  SS BOND              : bond        0.00339 /  0.17 (    4)
  SS BOND              : angle       0.59103 /  0.38 (    8)
  hydrogen bonds       : bond        0.27198 / 18.96 (   95)
  hydrogen bonds       : angle       7.70174 /  6.16 (   93)
  link_BETA1-4         : bond        0.00543 /  0.23 (    7)
  link_BETA1-4         : angle       3.75368 /  3.03 (   21)
  link_NAG-ASN         : bond        0.01765 /  1.25 (   12)
  link_NAG-ASN         : angle       5.32776 /  4.11 (   36)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 163
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  172 SER cc_start: 0.7758 (p) cc_final: 0.7490 (m)
REVERT: A  258 LEU cc_start: 0.7032 (mt) cc_final: 0.6814 (tt)
REVERT: A  350 ILE cc_start: 0.6112 (mt) cc_final: 0.5861 (tp)
REVERT: A  360 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6564 (mt-10)
REVERT: A  376 LYS cc_start: 0.7334 (tttp) cc_final: 0.6906 (mptt)
REVERT: A  417 LYS cc_start: 0.7911 (ttmt) cc_final: 0.7399 (ttpt)
REVERT: A  552 SER cc_start: 0.7058 (p) cc_final: 0.6368 (m)
  outliers start: 3
  outliers final: 4
  residues processed: 166
  average time/residue: 0.3904
  time to fit residues: 69.0086
Evaluate side-chains
  92 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 88
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 ASN
Chi-restraints excluded: chain A residue  246 ASN
Chi-restraints excluded: chain A residue  435 ASN
Chi-restraints excluded: chain C residue   70 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74]
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0070
   overall best weight:    1.5804

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 196 ASN
A 146 ASN
A 169 GLN
A 269 ASN
A 315 ASN
A 365 GLN
A 411 ASN
** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 483 GLN
A 589 ASN
C  70 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.195670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.160120 restraints weight = 7159.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.4097 rms_B_bonded: 2.61
r_work: 0.4004 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.4004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7274
moved from start:          0.2880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   6352  Z= 0.208
  Angle     :  0.923  16.991   8667  Z= 0.399
  Chirality :  0.059   0.791   1056
  Planarity :  0.005   0.046   1094
  Dihedral  : 12.197 109.936   1211
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  :  8.60 %
    Favored  : 88.34 %
  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: -3.04 (0.29), residues: 764
  helix: -3.50 (0.35), residues: 130
  sheet: -4.03 (0.36), residues: 135
  loop : -0.94 (0.27), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 545 
 TYR   0.034   0.003   TYR A 386 
 PHE   0.024   0.003   PHE A 148 
 TRP   0.021   0.002   TRP A 216 
 HIS   0.004   0.002   HIS A 239 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00463 /  0.21 ( 6329)
  covalent geometry    : angle       0.83212 /  0.38 ( 8602)
  SS BOND              : bond        0.00581 /  0.30 (    4)
  SS BOND              : angle       0.78519 /  0.49 (    8)
  hydrogen bonds       : bond        0.04807 /  3.33 (   95)
  hydrogen bonds       : angle       5.73618 /  4.53 (   93)
  link_BETA1-4         : bond        0.00722 /  0.41 (    7)
  link_BETA1-4         : angle       4.25170 /  3.50 (   21)
  link_NAG-ASN         : bond        0.00742 /  0.49 (   12)
  link_NAG-ASN         : angle       5.37183 /  3.73 (   36)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   68 ASN cc_start: 0.6944 (t0) cc_final: 0.6698 (t160)
REVERT: B  117 GLU cc_start: 0.6579 (mm-30) cc_final: 0.6362 (mm-30)
REVERT: A  130 ASP cc_start: 0.7636 (p0) cc_final: 0.7095 (p0)
REVERT: A  133 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7415 (mtm110)
REVERT: A  154 LYS cc_start: 0.8401 (ptpt) cc_final: 0.8022 (ptmm)
REVERT: A  258 LEU cc_start: 0.7342 (mt) cc_final: 0.7063 (tt)
REVERT: A  260 ASN cc_start: 0.5953 (m-40) cc_final: 0.5425 (m-40)
REVERT: A  350 ILE cc_start: 0.6739 (mt) cc_final: 0.6454 (tp)
REVERT: A  360 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8054 (mt-10)
REVERT: A  376 LYS cc_start: 0.7636 (tttp) cc_final: 0.7189 (ttmm)
REVERT: A  417 LYS cc_start: 0.8222 (ttmt) cc_final: 0.7706 (ttpt)
REVERT: A  448 TRP cc_start: 0.7583 (t60) cc_final: 0.7370 (t-100)
REVERT: A  463 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7377 (mp0)
REVERT: A  466 LYS cc_start: 0.7052 (ptpt) cc_final: 0.6784 (mmtt)
REVERT: A  490 LYS cc_start: 0.7026 (mtmm) cc_final: 0.6658 (tttp)
REVERT: A  511 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6800 (mp0)
  outliers start: 21
  outliers final: 7
  residues processed: 113
  average time/residue: 0.4804
  time to fit residues: 57.2678
Evaluate side-chains
  86 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  133 ARG
Chi-restraints excluded: chain A residue  155 SER
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  246 ASN
Chi-restraints excluded: chain A residue  435 ASN
Chi-restraints excluded: chain A residue  463 GLU
Chi-restraints excluded: chain A residue  473 SER
Chi-restraints excluded: chain A residue  511 GLU
Chi-restraints excluded: chain C residue   50 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [13, 57, 25, 60, 33, 61, 24, 20, 27, 72, 51]
   chunk 13 optimal weight:    2.9990
   chunk 57 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 20 optimal weight:    7.9990
   chunk 27 optimal weight:    7.9990
   chunk 72 optimal weight:    4.9990
   chunk 51 optimal weight:    0.1980
   overall best weight:    2.0388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  37 ASN
B  83 GLN
B 196 ASN
A  90 ASN
A  97 ASN
A 114 GLN
A 412 ASN
A 483 GLN
A 497 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.181700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.146231 restraints weight = 7231.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.3923 rms_B_bonded: 2.58
r_work: 0.3823 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3707 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.4244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   6352  Z= 0.233
  Angle     :  0.836  17.027   8667  Z= 0.376
  Chirality :  0.054   0.547   1056
  Planarity :  0.005   0.039   1094
  Dihedral  :  9.730 115.291   1207
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.98 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 10.20 %
    Favored  : 85.71 %
  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: -2.87 (0.29), residues: 764
  helix: -3.38 (0.38), residues: 122
  sheet: -4.05 (0.36), residues: 135
  loop : -0.82 (0.28), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 158 
 TYR   0.027   0.003   TYR A 386 
 PHE   0.021   0.002   PHE A 267 
 TRP   0.011   0.002   TRP A 423 
 HIS   0.004   0.002   HIS A 353 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00538 /  0.23 ( 6329)
  covalent geometry    : angle       0.75040 /  0.36 ( 8602)
  SS BOND              : bond        0.00706 /  0.37 (    4)
  SS BOND              : angle       1.18895 /  0.72 (    8)
  hydrogen bonds       : bond        0.04198 /  2.80 (   95)
  hydrogen bonds       : angle       5.65623 /  4.52 (   93)
  link_BETA1-4         : bond        0.00518 /  0.25 (    7)
  link_BETA1-4         : angle       3.22750 /  2.53 (   21)
  link_NAG-ASN         : bond        0.00912 /  0.58 (   12)
  link_NAG-ASN         : angle       5.23067 /  3.68 (   36)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 90
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   68 ASN cc_start: 0.6927 (t0) cc_final: 0.6689 (t0)
REVERT: B  117 GLU cc_start: 0.6896 (mm-30) cc_final: 0.6645 (mm-30)
REVERT: B  196 ASN cc_start: 0.6727 (OUTLIER) cc_final: 0.6523 (t0)
REVERT: A   75 PHE cc_start: 0.6486 (m-80) cc_final: 0.6246 (m-80)
REVERT: A  112 LYS cc_start: 0.7312 (mtpp) cc_final: 0.6997 (mttt)
REVERT: A  137 GLU cc_start: 0.7340 (pt0) cc_final: 0.7002 (pp20)
REVERT: A  154 LYS cc_start: 0.8322 (ptpt) cc_final: 0.7838 (ptmm)
REVERT: A  258 LEU cc_start: 0.7544 (mt) cc_final: 0.7079 (tt)
REVERT: A  260 ASN cc_start: 0.6660 (m-40) cc_final: 0.6247 (t0)
REVERT: A  334 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7346 (mm-30)
REVERT: A  350 ILE cc_start: 0.7232 (mt) cc_final: 0.6892 (tt)
REVERT: A  365 GLN cc_start: 0.7541 (mt0) cc_final: 0.7303 (mt0)
REVERT: A  376 LYS cc_start: 0.7964 (tttp) cc_final: 0.7429 (ttmm)
REVERT: A  417 LYS cc_start: 0.8169 (ttmt) cc_final: 0.7705 (tttp)
REVERT: A  448 TRP cc_start: 0.7564 (t60) cc_final: 0.7263 (t-100)
REVERT: A  463 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7694 (mt-10)
REVERT: A  466 LYS cc_start: 0.7418 (ptpt) cc_final: 0.7097 (mmtt)
REVERT: A  490 LYS cc_start: 0.7132 (mtmm) cc_final: 0.6680 (tttp)
  outliers start: 28
  outliers final: 14
  residues processed: 112
  average time/residue: 0.5408
  time to fit residues: 63.6880
Evaluate side-chains
  88 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  196 ASN
Chi-restraints excluded: chain A residue   58 ILE
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  155 SER
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  198 THR
Chi-restraints excluded: chain A residue  334 GLU
Chi-restraints excluded: chain A residue  406 THR
Chi-restraints excluded: chain A residue  435 ASN
Chi-restraints excluded: chain A residue  463 GLU
Chi-restraints excluded: chain A residue  473 SER
Chi-restraints excluded: chain A residue  500 SER
Chi-restraints excluded: chain A residue  519 TRP
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue   55 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [11, 37, 4, 29, 22, 55, 73, 53, 42, 15, 60]
   chunk 11 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0570
   chunk 55 optimal weight:    1.9990
   chunk 73 optimal weight:    0.0980
   chunk 53 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   overall best weight:    0.5498

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  83 GLN
B 196 ASN
A 114 GLN
A 482 ASN
A 483 GLN
A 497 ASN
C  69 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.186419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.150785 restraints weight = 7241.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.3979 rms_B_bonded: 2.60
r_work: 0.3878 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3760 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.4227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6352  Z= 0.119
  Angle     :  0.718  14.985   8667  Z= 0.321
  Chirality :  0.048   0.485   1056
  Planarity :  0.004   0.054   1094
  Dihedral  :  8.940 101.953   1205
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 12.39 %
    Favored  : 85.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -2.56 (0.30), residues: 764
  helix: -3.23 (0.40), residues: 117
  sheet: -3.99 (0.37), residues: 135
  loop : -0.57 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  72 
 TYR   0.022   0.002   TYR A 172 
 PHE   0.016   0.002   PHE A 148 
 TRP   0.009   0.001   TRP A 423 
 HIS   0.002   0.001   HIS A 239 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.12 ( 6329)
  covalent geometry    : angle       0.62719 /  0.30 ( 8602)
  SS BOND              : bond        0.00384 /  0.20 (    4)
  SS BOND              : angle       0.85971 /  0.51 (    8)
  hydrogen bonds       : bond        0.03400 /  2.29 (   95)
  hydrogen bonds       : angle       5.31825 /  4.35 (   93)
  link_BETA1-4         : bond        0.00452 /  0.24 (    7)
  link_BETA1-4         : angle       3.43573 /  2.88 (   21)
  link_NAG-ASN         : bond        0.00824 /  0.52 (   12)
  link_NAG-ASN         : angle       4.79125 /  3.44 (   36)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
REVERT: B   68 ASN cc_start: 0.7122 (t0) cc_final: 0.6912 (t0)
REVERT: B  110 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7117 (mp0)
REVERT: B  111 GLN cc_start: 0.7303 (mm-40) cc_final: 0.6925 (mp10)
REVERT: B  196 ASN cc_start: 0.6874 (OUTLIER) cc_final: 0.6339 (t0)
REVERT: A   75 PHE cc_start: 0.6496 (m-80) cc_final: 0.6133 (m-80)
REVERT: A  112 LYS cc_start: 0.7241 (mtpp) cc_final: 0.6952 (mttt)
REVERT: A  137 GLU cc_start: 0.7367 (pt0) cc_final: 0.7051 (pp20)
REVERT: A  154 LYS cc_start: 0.8210 (ptpt) cc_final: 0.7719 (ptmm)
REVERT: A  258 LEU cc_start: 0.7522 (mt) cc_final: 0.7094 (tt)
REVERT: A  260 ASN cc_start: 0.6479 (m-40) cc_final: 0.6054 (t0)
REVERT: A  334 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7334 (mt-10)
REVERT: A  350 ILE cc_start: 0.7105 (mt) cc_final: 0.6691 (tp)
REVERT: A  376 LYS cc_start: 0.7981 (tttp) cc_final: 0.7436 (ttmm)
REVERT: A  417 LYS cc_start: 0.8097 (ttmt) cc_final: 0.7657 (tttp)
REVERT: A  448 TRP cc_start: 0.7423 (t60) cc_final: 0.7123 (t-100)
REVERT: A  466 LYS cc_start: 0.7298 (ptpt) cc_final: 0.6926 (mmtt)
REVERT: A  490 LYS cc_start: 0.7137 (mtmm) cc_final: 0.6692 (tttp)
REVERT: A  586 GLN cc_start: 0.6670 (pm20) cc_final: 0.6368 (pt0)
REVERT: A  589 ASN cc_start: 0.4829 (m-40) cc_final: 0.4605 (m110)
  outliers start: 17
  outliers final: 7
  residues processed: 94
  average time/residue: 0.4693
  time to fit residues: 46.7437
Evaluate side-chains
  82 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  196 ASN
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  155 SER
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  334 GLU
Chi-restraints excluded: chain A residue  473 SER
Chi-restraints excluded: chain A residue  578 ARG
Chi-restraints excluded: chain C residue   50 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [72, 20, 13, 19, 37, 34, 2, 46, 42, 62, 71]
   chunk 72 optimal weight:    0.0030
   chunk 20 optimal weight:    0.6980
   chunk 13 optimal weight:    3.9990
   chunk 19 optimal weight:    0.4980
   chunk 37 optimal weight:    4.9990
   chunk 34 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0040
   chunk 46 optimal weight:    3.9990
   chunk 42 optimal weight:    0.3980
   chunk 62 optimal weight:    3.9990
   chunk 71 optimal weight:    0.3980
   overall best weight:    0.2602

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  83 GLN
A  97 ASN
A 483 GLN
A 497 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.188884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.153204 restraints weight = 7372.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.4007 rms_B_bonded: 2.67
r_work: 0.3906 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.4250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6352  Z= 0.105
  Angle     :  0.674  14.587   8667  Z= 0.303
  Chirality :  0.047   0.463   1056
  Planarity :  0.004   0.065   1094
  Dihedral  :  8.705 105.066   1203
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 13.56 %
    Favored  : 84.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -2.50 (0.31), residues: 764
  helix: -3.31 (0.39), residues: 117
  sheet: -3.88 (0.38), residues: 130
  loop : -0.56 (0.29), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B  72 
 TYR   0.033   0.003   TYR A 115 
 PHE   0.014   0.001   PHE A 267 
 TRP   0.007   0.001   TRP A 423 
 HIS   0.004   0.001   HIS B  61 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00232 /  0.10 ( 6329)
  covalent geometry    : angle       0.58608 /  0.28 ( 8602)
  SS BOND              : bond        0.00331 /  0.17 (    4)
  SS BOND              : angle       0.73531 /  0.44 (    8)
  hydrogen bonds       : bond        0.02988 /  2.01 (   95)
  hydrogen bonds       : angle       5.43822 /  4.26 (   93)
  link_BETA1-4         : bond        0.00501 /  0.26 (    7)
  link_BETA1-4         : angle       3.14036 /  2.61 (   21)
  link_NAG-ASN         : bond        0.00819 /  0.51 (   12)
  link_NAG-ASN         : angle       4.62837 /  3.31 (   36)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  110 GLU cc_start: 0.7302 (mt-10) cc_final: 0.7084 (mp0)
REVERT: B  111 GLN cc_start: 0.7157 (mm-40) cc_final: 0.6873 (mp10)
REVERT: A  112 LYS cc_start: 0.7213 (mtpp) cc_final: 0.6936 (mttt)
REVERT: A  137 GLU cc_start: 0.7323 (pt0) cc_final: 0.7019 (pp20)
REVERT: A  154 LYS cc_start: 0.8253 (ptpt) cc_final: 0.7770 (ptmm)
REVERT: A  258 LEU cc_start: 0.7410 (mt) cc_final: 0.7056 (tt)
REVERT: A  260 ASN cc_start: 0.6403 (m-40) cc_final: 0.5972 (t0)
REVERT: A  350 ILE cc_start: 0.7204 (mt) cc_final: 0.6769 (tp)
REVERT: A  376 LYS cc_start: 0.7913 (tttp) cc_final: 0.7429 (ttmm)
REVERT: A  417 LYS cc_start: 0.8017 (ttmt) cc_final: 0.7604 (tttp)
REVERT: A  448 TRP cc_start: 0.7283 (t60) cc_final: 0.6983 (t-100)
REVERT: A  466 LYS cc_start: 0.7182 (ptpt) cc_final: 0.6849 (mmtt)
REVERT: A  490 LYS cc_start: 0.7044 (mtmm) cc_final: 0.6684 (tttp)
REVERT: C   55 ARG cc_start: 0.7586 (mtm-85) cc_final: 0.7183 (mpp-170)
  outliers start: 15
  outliers final: 6
  residues processed: 85
  average time/residue: 0.4871
  time to fit residues: 43.7079
Evaluate side-chains
  76 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 SER
Chi-restraints excluded: chain A residue  406 THR
Chi-restraints excluded: chain A residue  435 ASN
Chi-restraints excluded: chain A residue  473 SER
Chi-restraints excluded: chain A residue  578 ARG
Chi-restraints excluded: chain C residue   50 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [74, 5, 71, 54, 64, 67, 59, 31, 51, 38, 23]
   chunk 74 optimal weight:    0.0770
   chunk 5 optimal weight:    0.9990
   chunk 71 optimal weight:    0.8980
   chunk 54 optimal weight:    0.6980
   chunk 64 optimal weight:    0.7980
   chunk 67 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 23 optimal weight:    9.9990
   overall best weight:    0.6940

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  83 GLN
A 483 GLN
A 497 ASN
A 589 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.187449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.151795 restraints weight = 7272.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3992 rms_B_bonded: 2.61
r_work: 0.3894 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3776 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.4366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6352  Z= 0.120
  Angle     :  0.680  14.089   8667  Z= 0.306
  Chirality :  0.047   0.453   1056
  Planarity :  0.004   0.065   1094
  Dihedral  :  8.433  99.376   1203
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 13.85 %
    Favored  : 83.67 %
  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: -2.36 (0.31), residues: 764
  helix: -3.22 (0.41), residues: 116
  sheet: -3.85 (0.38), residues: 140
  loop : -0.35 (0.29), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B  72 
 TYR   0.025   0.002   TYR A 115 
 PHE   0.015   0.001   PHE A  75 
 TRP   0.007   0.001   TRP A 423 
 HIS   0.003   0.001   HIS B  61 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.12 ( 6329)
  covalent geometry    : angle       0.59491 /  0.29 ( 8602)
  SS BOND              : bond        0.00335 /  0.18 (    4)
  SS BOND              : angle       0.75775 /  0.44 (    8)
  hydrogen bonds       : bond        0.03070 /  2.05 (   95)
  hydrogen bonds       : angle       5.30534 /  4.17 (   93)
  link_BETA1-4         : bond        0.00490 /  0.25 (    7)
  link_BETA1-4         : angle       3.00919 /  2.49 (   21)
  link_NAG-ASN         : bond        0.00748 /  0.47 (   12)
  link_NAG-ASN         : angle       4.61091 /  3.30 (   36)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   83 GLN cc_start: 0.8314 (mt0) cc_final: 0.7995 (mt0)
REVERT: B  110 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7105 (mp0)
REVERT: B  111 GLN cc_start: 0.7090 (mm-40) cc_final: 0.6822 (mp10)
REVERT: B  196 ASN cc_start: 0.7237 (t0) cc_final: 0.6776 (t0)
REVERT: A  112 LYS cc_start: 0.7200 (mtpp) cc_final: 0.6856 (mttt)
REVERT: A  137 GLU cc_start: 0.7385 (pt0) cc_final: 0.6989 (pp20)
REVERT: A  154 LYS cc_start: 0.8225 (ptpt) cc_final: 0.7721 (ptmm)
REVERT: A  258 LEU cc_start: 0.7538 (mt) cc_final: 0.7091 (tt)
REVERT: A  260 ASN cc_start: 0.6483 (m-40) cc_final: 0.6058 (t0)
REVERT: A  350 ILE cc_start: 0.7243 (mt) cc_final: 0.6785 (tp)
REVERT: A  376 LYS cc_start: 0.7977 (tttp) cc_final: 0.7399 (ttmm)
REVERT: A  417 LYS cc_start: 0.8010 (ttmt) cc_final: 0.7582 (tttp)
REVERT: A  448 TRP cc_start: 0.7372 (t60) cc_final: 0.7123 (t-100)
REVERT: A  466 LYS cc_start: 0.7245 (ptpt) cc_final: 0.6845 (mmtt)
REVERT: A  490 LYS cc_start: 0.7044 (mtmm) cc_final: 0.6582 (tttp)
  outliers start: 17
  outliers final: 11
  residues processed: 83
  average time/residue: 0.5003
  time to fit residues: 43.8986
Evaluate side-chains
  75 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  155 SER
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  406 THR
Chi-restraints excluded: chain A residue  435 ASN
Chi-restraints excluded: chain A residue  473 SER
Chi-restraints excluded: chain A residue  500 SER
Chi-restraints excluded: chain A residue  578 ARG
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue   67 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [20, 59, 19, 71, 47, 35, 49, 30, 69, 31, 56]
   chunk 20 optimal weight:    0.9990
   chunk 59 optimal weight:    0.4980
   chunk 19 optimal weight:   10.0000
   chunk 71 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 69 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 483 GLN
A 497 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.185588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.150124 restraints weight = 7277.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3975 rms_B_bonded: 2.61
r_work: 0.3876 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3758 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.4493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6352  Z= 0.128
  Angle     :  0.676  13.849   8667  Z= 0.306
  Chirality :  0.047   0.449   1056
  Planarity :  0.004   0.052   1094
  Dihedral  :  8.375  97.704   1203
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 14.14 %
    Favored  : 83.38 %
  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: -2.42 (0.31), residues: 764
  helix: -3.19 (0.40), residues: 117
  sheet: -3.88 (0.37), residues: 146
  loop : -0.36 (0.29), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  72 
 TYR   0.022   0.002   TYR A 115 
 PHE   0.014   0.001   PHE A 267 
 TRP   0.007   0.001   TRP A 423 
 HIS   0.003   0.001   HIS B  61 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.13 ( 6329)
  covalent geometry    : angle       0.59373 /  0.29 ( 8602)
  SS BOND              : bond        0.00408 /  0.21 (    4)
  SS BOND              : angle       0.82815 /  0.48 (    8)
  hydrogen bonds       : bond        0.03190 /  2.12 (   95)
  hydrogen bonds       : angle       5.28806 /  4.17 (   93)
  link_BETA1-4         : bond        0.00488 /  0.25 (    7)
  link_BETA1-4         : angle       2.97541 /  2.46 (   21)
  link_NAG-ASN         : bond        0.00725 /  0.45 (   12)
  link_NAG-ASN         : angle       4.52206 /  3.24 (   36)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 68
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  110 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7122 (mp0)
REVERT: B  196 ASN cc_start: 0.7198 (t0) cc_final: 0.6777 (t0)
REVERT: A  137 GLU cc_start: 0.7365 (pt0) cc_final: 0.6947 (pp20)
REVERT: A  154 LYS cc_start: 0.8262 (ptpt) cc_final: 0.7770 (ptmm)
REVERT: A  258 LEU cc_start: 0.7571 (mt) cc_final: 0.7123 (tt)
REVERT: A  260 ASN cc_start: 0.6626 (m-40) cc_final: 0.6132 (t0)
REVERT: A  350 ILE cc_start: 0.7316 (mt) cc_final: 0.6854 (tp)
REVERT: A  376 LYS cc_start: 0.7972 (tttp) cc_final: 0.7421 (ttmm)
REVERT: A  417 LYS cc_start: 0.8078 (ttmt) cc_final: 0.7667 (tttp)
REVERT: A  448 TRP cc_start: 0.7373 (t60) cc_final: 0.7062 (t-100)
REVERT: A  466 LYS cc_start: 0.7302 (ptpt) cc_final: 0.6933 (mmtt)
REVERT: A  490 LYS cc_start: 0.7110 (mtmm) cc_final: 0.6630 (tttp)
  outliers start: 17
  outliers final: 12
  residues processed: 80
  average time/residue: 0.4756
  time to fit residues: 40.2236
Evaluate side-chains
  72 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  155 SER
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  406 THR
Chi-restraints excluded: chain A residue  435 ASN
Chi-restraints excluded: chain A residue  473 SER
Chi-restraints excluded: chain A residue  500 SER
Chi-restraints excluded: chain A residue  519 TRP
Chi-restraints excluded: chain A residue  578 ARG
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue   55 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [27, 4, 0, 31, 40, 36, 32, 7, 18, 5, 37]
   chunk 27 optimal weight:    0.0030
   chunk 4 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 31 optimal weight:    0.5980
   chunk 40 optimal weight:    0.5980
   chunk 36 optimal weight:    6.9990
   chunk 32 optimal weight:    0.6980
   chunk 7 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    0.5390

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  83 GLN
A 483 GLN
A 497 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.187082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.151771 restraints weight = 7328.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.3994 rms_B_bonded: 2.62
r_work: 0.3895 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3777 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.4543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6352  Z= 0.109
  Angle     :  0.661  13.166   8667  Z= 0.300
  Chirality :  0.046   0.428   1056
  Planarity :  0.004   0.051   1094
  Dihedral  :  8.279  96.536   1203
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 13.85 %
    Favored  : 83.53 %
  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: -2.33 (0.31), residues: 764
  helix: -3.23 (0.40), residues: 117
  sheet: -3.86 (0.39), residues: 140
  loop : -0.30 (0.29), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  72 
 TYR   0.019   0.002   TYR A 115 
 PHE   0.013   0.001   PHE A 267 
 TRP   0.007   0.001   TRP A 423 
 HIS   0.002   0.001   HIS B  61 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.11 ( 6329)
  covalent geometry    : angle       0.58295 /  0.28 ( 8602)
  SS BOND              : bond        0.00344 /  0.18 (    4)
  SS BOND              : angle       0.74584 /  0.44 (    8)
  hydrogen bonds       : bond        0.02954 /  1.95 (   95)
  hydrogen bonds       : angle       5.20187 /  4.12 (   93)
  link_BETA1-4         : bond        0.00490 /  0.26 (    7)
  link_BETA1-4         : angle       2.91054 /  2.41 (   21)
  link_NAG-ASN         : bond        0.00741 /  0.46 (   12)
  link_NAG-ASN         : angle       4.36210 /  3.13 (   36)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 70
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  110 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7162 (mp0)
REVERT: B  196 ASN cc_start: 0.7255 (t0) cc_final: 0.6823 (t0)
REVERT: A  137 GLU cc_start: 0.7369 (pt0) cc_final: 0.6956 (pp20)
REVERT: A  154 LYS cc_start: 0.8266 (ptpt) cc_final: 0.7758 (ptmm)
REVERT: A  258 LEU cc_start: 0.7563 (mt) cc_final: 0.7118 (tt)
REVERT: A  260 ASN cc_start: 0.6466 (m-40) cc_final: 0.6003 (t0)
REVERT: A  334 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7386 (mt-10)
REVERT: A  350 ILE cc_start: 0.7283 (mt) cc_final: 0.6876 (tp)
REVERT: A  376 LYS cc_start: 0.7953 (tttp) cc_final: 0.7420 (ttmm)
REVERT: A  417 LYS cc_start: 0.8052 (ttmt) cc_final: 0.7662 (tttp)
REVERT: A  448 TRP cc_start: 0.7351 (t60) cc_final: 0.7114 (t-100)
REVERT: A  466 LYS cc_start: 0.7260 (ptpt) cc_final: 0.6878 (mmtt)
REVERT: A  490 LYS cc_start: 0.7114 (mtmm) cc_final: 0.6642 (tttp)
  outliers start: 18
  outliers final: 9
  residues processed: 83
  average time/residue: 0.4989
  time to fit residues: 43.8498
Evaluate side-chains
  74 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  155 SER
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  334 GLU
Chi-restraints excluded: chain A residue  406 THR
Chi-restraints excluded: chain A residue  435 ASN
Chi-restraints excluded: chain A residue  473 SER
Chi-restraints excluded: chain A residue  500 SER
Chi-restraints excluded: chain C residue   50 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [21, 50, 53, 29, 10, 5, 73, 58, 67, 44, 56]
   chunk 21 optimal weight:    0.7980
   chunk 50 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 29 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 73 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 56 optimal weight:    3.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  83 GLN
A 445 ASN
A 482 ASN
A 483 GLN
A 497 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.185755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.150498 restraints weight = 7351.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.4041 rms_B_bonded: 2.62
r_work: 0.3941 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3824 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.4633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6352  Z= 0.121
  Angle     :  0.664  13.030   8667  Z= 0.301
  Chirality :  0.047   0.428   1056
  Planarity :  0.004   0.067   1094
  Dihedral  :  8.192  93.740   1203
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.72 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 13.85 %
    Favored  : 83.82 %
  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: -2.33 (0.31), residues: 764
  helix: -3.21 (0.40), residues: 117
  sheet: -3.75 (0.40), residues: 135
  loop : -0.39 (0.29), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B  72 
 TYR   0.018   0.002   TYR A 115 
 PHE   0.014   0.001   PHE A 267 
 TRP   0.006   0.001   TRP A 423 
 HIS   0.002   0.001   HIS B  61 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00279 /  0.12 ( 6329)
  covalent geometry    : angle       0.58729 /  0.28 ( 8602)
  SS BOND              : bond        0.00375 /  0.20 (    4)
  SS BOND              : angle       0.78747 /  0.46 (    8)
  hydrogen bonds       : bond        0.02932 /  1.91 (   95)
  hydrogen bonds       : angle       5.18805 /  4.10 (   93)
  link_BETA1-4         : bond        0.00484 /  0.25 (    7)
  link_BETA1-4         : angle       2.88133 /  2.39 (   21)
  link_NAG-ASN         : bond        0.00727 /  0.45 (   12)
  link_NAG-ASN         : angle       4.33812 /  3.13 (   36)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  110 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7125 (mp0)
REVERT: B  196 ASN cc_start: 0.7249 (t0) cc_final: 0.6831 (t0)
REVERT: A  137 GLU cc_start: 0.7322 (pt0) cc_final: 0.6879 (pp20)
REVERT: A  154 LYS cc_start: 0.8252 (ptpt) cc_final: 0.7742 (ptmm)
REVERT: A  258 LEU cc_start: 0.7561 (mt) cc_final: 0.7082 (tt)
REVERT: A  260 ASN cc_start: 0.6519 (m-40) cc_final: 0.6063 (t0)
REVERT: A  334 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7402 (mt-10)
REVERT: A  350 ILE cc_start: 0.7304 (mt) cc_final: 0.6879 (tp)
REVERT: A  376 LYS cc_start: 0.7964 (tttp) cc_final: 0.7412 (ttmm)
REVERT: A  417 LYS cc_start: 0.8069 (ttmt) cc_final: 0.7652 (tttp)
REVERT: A  448 TRP cc_start: 0.7349 (t60) cc_final: 0.7005 (t-100)
REVERT: A  466 LYS cc_start: 0.7305 (ptpt) cc_final: 0.6918 (mmtt)
REVERT: A  490 LYS cc_start: 0.7091 (mtmm) cc_final: 0.6629 (tttp)
REVERT: A  586 GLN cc_start: 0.6906 (pm20) cc_final: 0.6631 (pm20)
  outliers start: 16
  outliers final: 9
  residues processed: 77
  average time/residue: 0.5151
  time to fit residues: 41.8153
Evaluate side-chains
  71 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  155 SER
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  334 GLU
Chi-restraints excluded: chain A residue  406 THR
Chi-restraints excluded: chain A residue  435 ASN
Chi-restraints excluded: chain A residue  473 SER
Chi-restraints excluded: chain A residue  500 SER
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue   67 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [67, 19, 56, 5, 51, 13, 6, 38, 69, 12, 18]
   chunk 67 optimal weight:    1.9990
   chunk 19 optimal weight:    6.9990
   chunk 56 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 13 optimal weight:    0.3980
   chunk 6 optimal weight:    0.8980
   chunk 38 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 18 optimal weight:    7.9990
   overall best weight:    0.8384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  83 GLN
B 196 ASN
A 483 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.184922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.149807 restraints weight = 7310.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.4046 rms_B_bonded: 2.60
r_work: 0.3947 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3830 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.4779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6352  Z= 0.127
  Angle     :  0.674  12.731   8667  Z= 0.306
  Chirality :  0.046   0.423   1056
  Planarity :  0.004   0.067   1094
  Dihedral  :  8.116  90.640   1203
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 14.87 %
    Favored  : 83.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.47 (0.31), residues: 764
  helix: -3.32 (0.38), residues: 124
  sheet: -3.78 (0.40), residues: 137
  loop : -0.45 (0.29), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  72 
 TYR   0.019   0.002   TYR A 115 
 PHE   0.014   0.001   PHE A 267 
 TRP   0.006   0.001   TRP A 423 
 HIS   0.002   0.001   HIS A 239 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.13 ( 6329)
  covalent geometry    : angle       0.59978 /  0.29 ( 8602)
  SS BOND              : bond        0.00301 /  0.16 (    4)
  SS BOND              : angle       0.90839 /  0.53 (    8)
  hydrogen bonds       : bond        0.02917 /  1.89 (   95)
  hydrogen bonds       : angle       5.24743 /  4.16 (   93)
  link_BETA1-4         : bond        0.00510 /  0.26 (    7)
  link_BETA1-4         : angle       2.80415 /  2.32 (   21)
  link_NAG-ASN         : bond        0.00703 /  0.43 (   12)
  link_NAG-ASN         : angle       4.30114 /  3.10 (   36)

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

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

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1528 Ramachandran restraints generated.
    764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  110 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7154 (mp0)
REVERT: B  196 ASN cc_start: 0.7257 (OUTLIER) cc_final: 0.6937 (t0)
REVERT: A  137 GLU cc_start: 0.7213 (pt0) cc_final: 0.6787 (pp20)
REVERT: A  154 LYS cc_start: 0.8256 (ptpt) cc_final: 0.7741 (ptmm)
REVERT: A  258 LEU cc_start: 0.7588 (mt) cc_final: 0.7079 (tt)
REVERT: A  260 ASN cc_start: 0.6596 (m-40) cc_final: 0.6161 (t0)
REVERT: A  334 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7403 (mt-10)
REVERT: A  350 ILE cc_start: 0.7321 (mt) cc_final: 0.6897 (tp)
REVERT: A  376 LYS cc_start: 0.7950 (tttp) cc_final: 0.7403 (ttmm)
REVERT: A  417 LYS cc_start: 0.8145 (ttmt) cc_final: 0.7730 (tttp)
REVERT: A  448 TRP cc_start: 0.7355 (t60) cc_final: 0.7109 (t-100)
REVERT: A  466 LYS cc_start: 0.7314 (ptpt) cc_final: 0.7010 (mmtt)
REVERT: A  490 LYS cc_start: 0.7107 (mtmm) cc_final: 0.6642 (tttp)
REVERT: A  586 GLN cc_start: 0.6804 (pm20) cc_final: 0.6577 (pm20)
  outliers start: 14
  outliers final: 9
  residues processed: 73
  average time/residue: 0.5039
  time to fit residues: 39.0081
Evaluate side-chains
  73 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  196 ASN
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  155 SER
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  334 GLU
Chi-restraints excluded: chain A residue  406 THR
Chi-restraints excluded: chain A residue  435 ASN
Chi-restraints excluded: chain A residue  473 SER
Chi-restraints excluded: chain A residue  500 SER
Chi-restraints excluded: chain C residue   50 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks: [4, 41, 51, 34, 48, 20, 0, 38, 19, 5, 71]
   chunk 4 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   chunk 20 optimal weight:    8.9990
   chunk 0 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 19 optimal weight:    8.9990
   chunk 5 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  83 GLN
A 445 ASN
A 483 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.184707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.149535 restraints weight = 7289.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3966 rms_B_bonded: 2.62
r_work: 0.3867 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3750 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.4761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.146   6352  Z= 0.210
  Angle     :  1.141  59.199   8667  Z= 0.649
  Chirality :  0.047   0.425   1056
  Planarity :  0.005   0.068   1094
  Dihedral  :  8.136  90.638   1203
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 15.01 %
    Favored  : 83.09 %
  Cbeta Deviations :  0.14 %
  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: -2.48 (0.31), residues: 764
  helix: -3.32 (0.38), residues: 124
  sheet: -3.78 (0.40), residues: 137
  loop : -0.46 (0.29), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B  72 
 TYR   0.016   0.002   TYR A 115 
 PHE   0.014   0.001   PHE A 267 
 TRP   0.007   0.001   TRP A 423 
 HIS   0.002   0.001   HIS B  61 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00423 /  0.21 ( 6329)
  covalent geometry    : angle       1.10221 /  0.64 ( 8602)
  SS BOND              : bond        0.00530 /  0.28 (    4)
  SS BOND              : angle       0.83732 /  0.49 (    8)
  hydrogen bonds       : bond        0.02937 /  1.90 (   95)
  hydrogen bonds       : angle       5.25237 /  4.16 (   93)
  link_BETA1-4         : bond        0.00467 /  0.25 (    7)
  link_BETA1-4         : angle       2.81915 /  2.32 (   21)
  link_NAG-ASN         : bond        0.00691 /  0.42 (   12)
  link_NAG-ASN         : angle       4.30189 /  3.10 (   36)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2502.35 seconds
wall clock time: 43 minutes 15.20 seconds (2595.20 seconds total)