Starting phenix.real_space_refine
on Sat May  2 09:52:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vbv_64934/05_2026/9vbv_64934.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vbv_64934/05_2026/9vbv_64934.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vbv_64934/05_2026/9vbv_64934.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vbv_64934/05_2026/9vbv_64934.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vbv_64934/05_2026/9vbv_64934.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vbv_64934/05_2026/9vbv_64934.map"
  }
  resolution = 3.61
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      15      5.16       5
     C    2710      2.51       5
     N     666      2.21       5
     O     850      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4241
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 4037
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 521, 4023
          Classifications: {'peptide': 521}
          Link IDs: {'PTRANS': 40, 'TRANS': 480}
      Conformer: "B"
        Number of residues, atoms: 521, 4023
          Classifications: {'peptide': 521}
          Link IDs: {'PTRANS': 40, 'TRANS': 480}
          bond proxies already assigned to first conformer: 4103
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 2, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 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
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATRP A 166 " occ=0.50
      ... (26 atoms not shown)
      pdb=" CH2BTRP A 166 " occ=0.50
  Time building chain proxies: 1.45, per 1000 atoms: 0.34
  Number of scatterers: 4241
  At special positions: 0
  Unit cell: (55.61, 84.66, 97.11, 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      15     16.00
     O     850      8.00
     N     666      7.00
     C    2710      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  53 " - pdb=" SG  CYS A  62 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 395 " - pdb=" SG  CYS A 405 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 421 " - pdb=" SG  CYS A 434 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 424 " - pdb=" SG  CYS A 436 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
    BETA1-6
      " BMA E   3 " - " BMA E   4 "
    NAG-ASN
      " NAG A1001 " - " ASN A 182 "
      " NAG A1002 " - " ASN A 217 "
      " NAG A1003 " - " ASN A 456 "
      " NAG B   1 " - " ASN A 523 "
      " NAG C   1 " - " ASN A 284 "
      " NAG D   1 " - " ASN A 264 "
      " NAG E   1 " - " ASN A 298 "
      " NAG F   1 " - " ASN A 411 "
  Time building additional restraints: 0.42
  Conformation dependent library (CDL) restraints added in 258.1 milliseconds
  

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  970

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 5 sheets defined
      23.6% alpha, 12.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 27 through 40
      removed outlier: 3.518A  pdb=" N   TRP A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 88
      removed outlier: 3.553A  pdb=" N   ILE A  85 " --> pdb=" O   PRO A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 113
      removed outlier: 3.970A  pdb=" N   GLY A 111 " --> pdb=" O   PRO A 108 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU A 113 " --> pdb=" O   ILE A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 137
      removed outlier: 3.617A  pdb=" N   ILE A 134 " --> pdb=" O   PRO A 131 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   GLY A 135 " --> pdb=" O   GLU A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 161
      removed outlier: 3.659A  pdb=" N   GLY A 159 " --> pdb=" O   PRO A 156 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LEU A 161 " --> pdb=" O   ILE A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 192
    Processing helix  chain 'A' and resid 210 through 214
    Processing helix  chain 'A' and resid 235 through 241
      removed outlier: 3.514A  pdb=" N   SER A 239 " --> pdb=" O   GLU A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 265
    Processing helix  chain 'A' and resid 308 through 313
      removed outlier: 3.762A  pdb=" N   SER A 311 " --> pdb=" O   SER A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 336
      removed outlier: 4.029A  pdb=" N   PHE A 335 " --> pdb=" O   ILE A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 397
      removed outlier: 3.591A  pdb=" N   GLU A 397 " --> pdb=" O   PRO A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 406
      removed outlier: 3.959A  pdb=" N   SER A 406 " --> pdb=" O   SER A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 472
    Processing helix  chain 'A' and resid 510 through 523
    Processing helix  chain 'A' and resid 529 through 533
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 62
      removed outlier: 6.601A  pdb=" N   THR A  61 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   VAL A  68 " --> pdb=" O   ILE A  93 " (cutoff:3.500A)
      removed outlier: 8.189A  pdb=" N   ASP A  95 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   ILE A  70 " --> pdb=" O   ASP A  95 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   VAL A 223 " --> pdb=" O   ARG A 248 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   LEU A 294 " --> pdb=" O   ARG A 320 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   VAL A 367 " --> pdb=" O   ILE A 388 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 80
      removed outlier: 5.988A  pdb=" N   GLY A  79 " --> pdb=" O   SER A 103 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 176
      removed outlier: 4.408A  pdb=" N   GLY A 176 " --> pdb=" O   LYS A 204 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 304 through 305
      removed outlier: 6.125A  pdb=" N   SER A 304 " --> pdb=" O   ASN A 327 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   LEU A 326 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 478 through 488
      removed outlier: 6.306A  pdb=" N   VAL A 481 " --> pdb=" O   PHE A 502 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   PHE A 502 " --> pdb=" O   VAL A 481 " (cutoff:3.500A)
      removed outlier: 5.653A  pdb=" N   VAL A 483 " --> pdb=" O   LEU A 500 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   LEU A 500 " --> pdb=" O   VAL A 483 " (cutoff:3.500A)
      removed outlier: 5.414A  pdb=" N   ASN A 485 " --> pdb=" O   ASP A 498 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   ASP A 498 " --> pdb=" O   ASN A 485 " (cutoff:3.500A)

    90 hydrogen bonds defined for protein.
    184 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: 0.52

  Time building geometry restraints manager: 0.51 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1320
        1.34 -     1.46: 992
        1.46 -     1.58: 2007
        1.58 -     1.70: 1
        1.70 -     1.82: 21
  Bond restraints: 4341
  Sorted by residual:
  bond pdb=" C1  BMA E   3 "
       pdb=" C2  BMA E   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.592 -0.073 2.00e-02 2.50e+03 1.34e+01
  bond pdb=" C1  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.468 -0.062 2.00e-02 2.50e+03 9.57e+00
  bond pdb=" C1  BMA E   3 "
       pdb=" O5  BMA E   3 "
    ideal  model  delta    sigma   weight residual
    1.410  1.461 -0.051 2.00e-02 2.50e+03 6.51e+00
  bond pdb=" C5  BMA E   3 "
       pdb=" O5  BMA E   3 "
    ideal  model  delta    sigma   weight residual
    1.417  1.462 -0.045 2.00e-02 2.50e+03 5.15e+00
  bond pdb=" C1  NAG E   2 "
       pdb=" O5  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.449 -0.043 2.00e-02 2.50e+03 4.64e+00
  ... (remaining 4336 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.45: 5596
        1.45 -     2.89: 265
        2.89 -     4.34: 35
        4.34 -     5.78: 17
        5.78 -     7.23: 7
  Bond angle restraints: 5920
  Sorted by residual:
  angle pdb=" CA  PRO A 418 "
        pdb=" N   PRO A 418 "
        pdb=" CD  PRO A 418 "
      ideal   model   delta    sigma   weight residual
     112.00  107.09    4.91 1.40e+00 5.10e-01 1.23e+01
  angle pdb=" C   ASN A 208 "
        pdb=" N   ILE A 209 "
        pdb=" CA  ILE A 209 "
      ideal   model   delta    sigma   weight residual
     122.60  120.33    2.27 6.80e-01 2.16e+00 1.12e+01
  angle pdb=" C   ASN A 411 "
        pdb=" CA  ASN A 411 "
        pdb=" CB  ASN A 411 "
      ideal   model   delta    sigma   weight residual
     110.45  105.34    5.11 1.73e+00 3.34e-01 8.72e+00
  angle pdb=" C   THR A  55 "
        pdb=" N   ASN A  56 "
        pdb=" CA  ASN A  56 "
      ideal   model   delta    sigma   weight residual
     121.54  127.09   -5.55 1.91e+00 2.74e-01 8.45e+00
  angle pdb=" N   THR A 433 "
        pdb=" CA  THR A 433 "
        pdb=" C   THR A 433 "
      ideal   model   delta    sigma   weight residual
     113.19  108.65    4.54 1.58e+00 4.01e-01 8.26e+00
  ... (remaining 5915 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.73: 2600
       23.73 -    47.46: 161
       47.46 -    71.19: 28
       71.19 -    94.92: 10
       94.92 -   118.65: 10
  Dihedral angle restraints: 2809
    sinusoidal: 1302
      harmonic: 1507
  Sorted by residual:
  dihedral pdb=" CB  CYS A  53 "
           pdb=" SG  CYS A  53 "
           pdb=" SG  CYS A  62 "
           pdb=" CB  CYS A  62 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  179.52  -86.52     1      1.00e+01 1.00e-02 9.02e+01
  dihedral pdb=" CA  ASN A 411 "
           pdb=" C   ASN A 411 "
           pdb=" N   THR A 412 "
           pdb=" CA  THR A 412 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  142.35   37.65     0      5.00e+00 4.00e-02 5.67e+01
  dihedral pdb=" O4  BMA E   3 "
           pdb=" C4  BMA E   3 "
           pdb=" C5  BMA E   3 "
           pdb=" O5  BMA E   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     288.71  170.06  118.65     1      3.00e+01 1.11e-03 1.58e+01
  ... (remaining 2806 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.087: 655
       0.087 -    0.174: 60
       0.174 -    0.260: 2
       0.260 -    0.347: 2
       0.347 -    0.434: 1
  Chirality restraints: 720
  Sorted by residual:
  chirality pdb=" C1  NAG B   1 "
            pdb=" ND2 ASN A 523 "
            pdb=" C2  NAG B   1 "
            pdb=" O5  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.83    0.43 2.00e-01 2.50e+01 4.71e+00
  chirality pdb=" C4  NAG B   1 "
            pdb=" C3  NAG B   1 "
            pdb=" C5  NAG B   1 "
            pdb=" O4  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.19   -0.34 2.00e-01 2.50e+01 2.88e+00
  chirality pdb=" C5  BMA E   3 "
            pdb=" C4  BMA E   3 "
            pdb=" C6  BMA E   3 "
            pdb=" O5  BMA E   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.60    0.32 2.00e-01 2.50e+01 2.62e+00
  ... (remaining 717 not shown)

  Planarity restraints: 755
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 417 "   -0.078 5.00e-02 4.00e+02   1.16e-01 2.14e+01
        pdb=" N   PRO A 418 "    0.200 5.00e-02 4.00e+02
        pdb=" CA  PRO A 418 "   -0.061 5.00e-02 4.00e+02
        pdb=" CD  PRO A 418 "   -0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 523 "   -0.031 2.00e-02 2.50e+03   2.89e-02 1.05e+01
        pdb=" CG  ASN A 523 "    0.031 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 523 "   -0.002 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 523 "    0.034 2.00e-02 2.50e+03
        pdb=" C1  NAG B   1 "   -0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 411 "    0.022 2.00e-02 2.50e+03   2.07e-02 5.35e+00
        pdb=" CG  ASN A 411 "   -0.030 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 411 "    0.005 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 411 "   -0.017 2.00e-02 2.50e+03
        pdb=" C1  NAG F   1 "    0.020 2.00e-02 2.50e+03
  ... (remaining 752 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 978
        2.78 -     3.31: 3972
        3.31 -     3.84: 6808
        3.84 -     4.37: 8119
        4.37 -     4.90: 13793
  Nonbonded interactions: 33670
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 508 "
            pdb=" OG  SER A 546 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   LYS A 211 "
            pdb=" OG1 THR A 237 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" O   PRO A 108 "
            pdb=" OG  SER A 133 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" O   VAL A  68 "
            pdb=" N   ARG A  92 "
     model   vdw
     2.330 3.120
  nonbonded pdb=" NE2 GLN A 464 "
            pdb=" O   VAL A 481 "
     model   vdw
     2.332 3.120
  ... (remaining 33665 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.200
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7245
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      :  0.005   0.073   4360  Z= 0.235
  Angle     :  0.873  15.139   5973  Z= 0.397
  Chirality :  0.054   0.434    720
  Planarity :  0.006   0.116    747
  Dihedral  : 16.967 118.652   1827
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  0.00 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -2.46 (0.37), residues: 522
  helix: -1.78 (0.50), residues: 110
  sheet: -3.02 (0.50), residues: 99
  loop : -1.02 (0.35), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 447 
 TYR   0.010   0.001   TYR A 165 
 PHE   0.011   0.001   PHE A 460 
 TRP   0.004   0.001   TRP A  40 
 HIS   0.001   0.000   HIS A 410 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 ( 4341)
  covalent geometry    : angle       0.75275 ( 5920)
  SS BOND              : bond        0.00194 (    4)
  SS BOND              : angle       1.04954 (    8)
  hydrogen bonds       : bond        0.24110 (   90)
  hydrogen bonds       : angle       8.55443 (  184)
  link_BETA1-4         : bond        0.01751 (    6)
  link_BETA1-4         : angle       6.47030 (   18)
  link_BETA1-6         : bond        0.00384 (    1)
  link_BETA1-6         : angle       1.71489 (    3)
  link_NAG-ASN         : bond        0.00415 (    8)
  link_NAG-ASN         : angle       4.23810 (   24)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 0.090 
Fit side-chains
REVERT: A  371 TYR cc_start: 0.7602 (m-80) cc_final: 0.7301 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 61
  average time/residue: 0.0643
  time to fit residues: 5.0368
Evaluate side-chains
  49 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.2980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0770
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.4538

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

Flipped N/Q/H residues before XYZ refinement:
A 118 ASN
A 410 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.166697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.144631 restraints weight = 8239.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.149814 restraints weight = 3985.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.153380 restraints weight = 2405.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.155778 restraints weight = 1665.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.157462 restraints weight = 1268.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3878
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3878 r_free = 0.3878    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3878 r_free = 0.3878    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3878
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.1010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4360  Z= 0.146
  Angle     :  0.777  12.231   5973  Z= 0.350
  Chirality :  0.051   0.292    720
  Planarity :  0.006   0.086    747
  Dihedral  : 13.717 101.364    861
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  5.59 %
    Favored  : 93.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -2.73 (0.37), residues: 522
  helix: -1.85 (0.49), residues: 110
  sheet: -3.81 (0.42), residues: 109
  loop : -0.88 (0.37), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 447 
 TYR   0.011   0.001   TYR A 165 
 PHE   0.026   0.002   PHE A 414 
 TRP   0.007   0.001   TRP A  57 
 HIS   0.001   0.001   HIS A 493 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 4341)
  covalent geometry    : angle       0.70629 ( 5920)
  SS BOND              : bond        0.00144 (    4)
  SS BOND              : angle       1.59564 (    8)
  hydrogen bonds       : bond        0.04023 (   90)
  hydrogen bonds       : angle       6.53755 (  184)
  link_BETA1-4         : bond        0.00998 (    6)
  link_BETA1-4         : angle       4.69256 (   18)
  link_BETA1-6         : bond        0.00213 (    1)
  link_BETA1-6         : angle       3.85201 (    3)
  link_NAG-ASN         : bond        0.00430 (    8)
  link_NAG-ASN         : angle       2.80095 (   24)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 0.105 
Fit side-chains
REVERT: A  410 HIS cc_start: 0.5991 (OUTLIER) cc_final: 0.5634 (t-90)
  outliers start: 2
  outliers final: 1
  residues processed: 56
  average time/residue: 0.0561
  time to fit residues: 4.2640
Evaluate side-chains
  48 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 46
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  410 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    0.4980
   chunk 15 optimal weight:    0.0770
   chunk 44 optimal weight:    0.5980
   chunk 5 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.5738

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.163993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.140096 restraints weight = 15067.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.147850 restraints weight = 7031.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.151954 restraints weight = 3062.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.154191 restraints weight = 1882.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.155554 restraints weight = 1385.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3855
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3855 r_free = 0.3855    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3854 r_free = 0.3854    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3854
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7260
moved from start:          0.1355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4360  Z= 0.155
  Angle     :  0.751  12.123   5973  Z= 0.342
  Chirality :  0.051   0.362    720
  Planarity :  0.005   0.073    747
  Dihedral  : 12.482 100.462    861
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  7.53 %
    Favored  : 91.40 %
  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: -2.80 (0.37), residues: 522
  helix: -1.92 (0.49), residues: 110
  sheet: -3.85 (0.42), residues: 109
  loop : -0.92 (0.37), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 447 
 TYR   0.010   0.001   TYR A 526 
 PHE   0.028   0.002   PHE A 414 
 TRP   0.004   0.001   TRP A 309 
 HIS   0.021   0.007   HIS A 410 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 4341)
  covalent geometry    : angle       0.68915 ( 5920)
  SS BOND              : bond        0.00177 (    4)
  SS BOND              : angle       1.54626 (    8)
  hydrogen bonds       : bond        0.03520 (   90)
  hydrogen bonds       : angle       6.23689 (  184)
  link_BETA1-4         : bond        0.00905 (    6)
  link_BETA1-4         : angle       4.53078 (   18)
  link_BETA1-6         : bond        0.00267 (    1)
  link_BETA1-6         : angle       3.35734 (    3)
  link_NAG-ASN         : bond        0.00395 (    8)
  link_NAG-ASN         : angle       2.38999 (   24)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.091 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 55
  average time/residue: 0.0518
  time to fit residues: 3.8173
Evaluate side-chains
  48 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ASN
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  525 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 32 optimal weight:    0.4980
   chunk 24 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0870
   chunk 38 optimal weight:    3.9990
   chunk 15 optimal weight:    0.1980
   chunk 29 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.4758

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.163668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.143092 restraints weight = 10543.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.148534 restraints weight = 4794.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.151675 restraints weight = 2638.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.154449 restraints weight = 1723.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.155036 restraints weight = 1318.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3855
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3855 r_free = 0.3855    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3855 r_free = 0.3855    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3855
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7260
moved from start:          0.1733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4360  Z= 0.137
  Angle     :  0.712  11.000   5973  Z= 0.324
  Chirality :  0.050   0.353    720
  Planarity :  0.005   0.066    747
  Dihedral  : 11.231  96.374    861
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  :  7.53 %
    Favored  : 90.97 %
  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: -2.65 (0.37), residues: 522
  helix: -1.91 (0.49), residues: 111
  sheet: -3.51 (0.45), residues: 99
  loop : -1.00 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 447 
 TYR   0.014   0.001   TYR A 371 
 PHE   0.030   0.001   PHE A 414 
 TRP   0.003   0.001   TRP A 309 
 HIS   0.003   0.001   HIS A 410 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 4341)
  covalent geometry    : angle       0.65662 ( 5920)
  SS BOND              : bond        0.00156 (    4)
  SS BOND              : angle       1.51560 (    8)
  hydrogen bonds       : bond        0.03024 (   90)
  hydrogen bonds       : angle       5.81763 (  184)
  link_BETA1-4         : bond        0.00890 (    6)
  link_BETA1-4         : angle       4.15382 (   18)
  link_BETA1-6         : bond        0.00220 (    1)
  link_BETA1-6         : angle       2.68895 (    3)
  link_NAG-ASN         : bond        0.00407 (    8)
  link_NAG-ASN         : angle       2.30961 (   24)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.128 
Fit side-chains
REVERT: A  202 LYS cc_start: 0.7250 (mtpt) cc_final: 0.7005 (tptt)
  outliers start: 7
  outliers final: 4
  residues processed: 60
  average time/residue: 0.0470
  time to fit residues: 3.8207
Evaluate side-chains
  54 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 50
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  301 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 40 optimal weight:    0.3980
   chunk 8 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 10 optimal weight:    0.3980
   chunk 46 optimal weight:    0.0570
   chunk 12 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.5098

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.166943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.146216 restraints weight = 11982.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.152203 restraints weight = 5270.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.155094 restraints weight = 2952.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.157199 restraints weight = 1877.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.158455 restraints weight = 1574.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3830
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3830 r_free = 0.3830    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3830 r_free = 0.3830    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3830
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4360  Z= 0.142
  Angle     :  0.716  11.007   5973  Z= 0.328
  Chirality :  0.049   0.326    720
  Planarity :  0.005   0.063    747
  Dihedral  : 10.478  90.253    861
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  :  8.17 %
    Favored  : 90.11 %
  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: -2.65 (0.37), residues: 522
  helix: -1.91 (0.49), residues: 111
  sheet: -3.55 (0.45), residues: 99
  loop : -0.99 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 447 
 TYR   0.009   0.001   TYR A 445 
 PHE   0.023   0.001   PHE A 414 
 TRP   0.002   0.001   TRP A 309 
 HIS   0.001   0.000   HIS A 410 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 4341)
  covalent geometry    : angle       0.66334 ( 5920)
  SS BOND              : bond        0.00168 (    4)
  SS BOND              : angle       1.60149 (    8)
  hydrogen bonds       : bond        0.02990 (   90)
  hydrogen bonds       : angle       5.67832 (  184)
  link_BETA1-4         : bond        0.00847 (    6)
  link_BETA1-4         : angle       4.02682 (   18)
  link_BETA1-6         : bond        0.00193 (    1)
  link_BETA1-6         : angle       2.16299 (    3)
  link_NAG-ASN         : bond        0.00395 (    8)
  link_NAG-ASN         : angle       2.32399 (   24)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.092 
Fit side-chains
  outliers start: 8
  outliers final: 7
  residues processed: 55
  average time/residue: 0.0391
  time to fit residues: 3.0379
Evaluate side-chains
  52 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   64 ASN
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  531 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 31 optimal weight:    0.5980
   chunk 37 optimal weight:    0.0870
   chunk 48 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 19 optimal weight:    0.1980
   chunk 4 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.5158

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.151525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.128870 restraints weight = 13049.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.136358 restraints weight = 4883.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.140287 restraints weight = 2257.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.141729 restraints weight = 1327.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.144233 restraints weight = 1061.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3730
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3730 r_free = 0.3730    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3730 r_free = 0.3730    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3730
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7126
moved from start:          0.2200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4360  Z= 0.141
  Angle     :  0.701  11.123   5973  Z= 0.321
  Chirality :  0.049   0.321    720
  Planarity :  0.005   0.060    747
  Dihedral  :  9.688  80.604    861
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  :  9.25 %
    Favored  : 89.03 %
  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: -2.65 (0.37), residues: 522
  helix: -1.85 (0.50), residues: 111
  sheet: -3.57 (0.45), residues: 99
  loop : -1.00 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 447 
 TYR   0.017   0.002   TYR A 165 
 PHE   0.031   0.002   PHE A 414 
 TRP   0.002   0.001   TRP A  57 
 HIS   0.001   0.000   HIS A 410 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 4341)
  covalent geometry    : angle       0.65125 ( 5920)
  SS BOND              : bond        0.00155 (    4)
  SS BOND              : angle       1.57365 (    8)
  hydrogen bonds       : bond        0.02990 (   90)
  hydrogen bonds       : angle       5.61152 (  184)
  link_BETA1-4         : bond        0.00832 (    6)
  link_BETA1-4         : angle       3.90414 (   18)
  link_BETA1-6         : bond        0.00340 (    1)
  link_BETA1-6         : angle       1.79441 (    3)
  link_NAG-ASN         : bond        0.00404 (    8)
  link_NAG-ASN         : angle       2.22875 (   24)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 49
  time to evaluate  : 0.094 
Fit side-chains
  outliers start: 8
  outliers final: 7
  residues processed: 51
  average time/residue: 0.0351
  time to fit residues: 2.5679
Evaluate side-chains
  56 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 49
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   64 ASN
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  410 HIS
Chi-restraints excluded: chain A residue  531 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 21 optimal weight:    0.2980
   chunk 51 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 13 optimal weight:    0.3980
   chunk 45 optimal weight:    0.0870
   chunk 24 optimal weight:    0.3980
   chunk 12 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.4158

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.155730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.134190 restraints weight = 11174.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.141228 restraints weight = 4694.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.144980 restraints weight = 2341.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.146214 restraints weight = 1472.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.149077 restraints weight = 1130.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3769
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3769 r_free = 0.3769    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3769 r_free = 0.3769    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3769
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7154
moved from start:          0.2328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4360  Z= 0.125
  Angle     :  0.686  11.129   5973  Z= 0.313
  Chirality :  0.049   0.307    720
  Planarity :  0.005   0.059    747
  Dihedral  :  8.900  69.132    861
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 10.32 %
    Favored  : 87.53 %
  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: -2.57 (0.38), residues: 522
  helix: -1.73 (0.51), residues: 111
  sheet: -3.52 (0.45), residues: 101
  loop : -0.95 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 447 
 TYR   0.008   0.001   TYR A 526 
 PHE   0.027   0.001   PHE A 414 
 TRP   0.002   0.001   TRP A 309 
 HIS   0.001   0.000   HIS A 410 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 4341)
  covalent geometry    : angle       0.63843 ( 5920)
  SS BOND              : bond        0.00141 (    4)
  SS BOND              : angle       1.47162 (    8)
  hydrogen bonds       : bond        0.02826 (   90)
  hydrogen bonds       : angle       5.33457 (  184)
  link_BETA1-4         : bond        0.00854 (    6)
  link_BETA1-4         : angle       3.73822 (   18)
  link_BETA1-6         : bond        0.00416 (    1)
  link_BETA1-6         : angle       1.54881 (    3)
  link_NAG-ASN         : bond        0.00346 (    8)
  link_NAG-ASN         : angle       2.22381 (   24)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
  outliers start: 10
  outliers final: 8
  residues processed: 51
  average time/residue: 0.0347
  time to fit residues: 2.5937
Evaluate side-chains
  54 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   64 ASN
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  410 HIS
Chi-restraints excluded: chain A residue  531 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0570
   chunk 25 optimal weight:    2.9990
   chunk 17 optimal weight:    0.3980
   chunk 33 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 49 optimal weight:    0.7980
   chunk 21 optimal weight:    0.3980
   chunk 50 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.4698

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.155325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.133668 restraints weight = 9653.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.139466 restraints weight = 4394.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.143670 restraints weight = 2496.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.145962 restraints weight = 1435.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.147297 restraints weight = 1145.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3761
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3761 r_free = 0.3761    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3761 r_free = 0.3761    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
r_final: 0.3761
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7190
moved from start:          0.2560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4360  Z= 0.131
  Angle     :  0.697  10.843   5973  Z= 0.317
  Chirality :  0.048   0.271    720
  Planarity :  0.005   0.058    747
  Dihedral  :  8.112  57.241    861
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 10.97 %
    Favored  : 87.10 %
  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: -2.66 (0.38), residues: 522
  helix: -1.72 (0.51), residues: 111
  sheet: -3.67 (0.44), residues: 106
  loop : -0.94 (0.37), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 447 
 TYR   0.011   0.001   TYR A 165 
 PHE   0.027   0.001   PHE A 414 
 TRP   0.002   0.000   TRP A  47 
 HIS   0.001   0.000   HIS A 410 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 4341)
  covalent geometry    : angle       0.65222 ( 5920)
  SS BOND              : bond        0.00143 (    4)
  SS BOND              : angle       1.54595 (    8)
  hydrogen bonds       : bond        0.02901 (   90)
  hydrogen bonds       : angle       5.37100 (  184)
  link_BETA1-4         : bond        0.00800 (    6)
  link_BETA1-4         : angle       3.64388 (   18)
  link_BETA1-6         : bond        0.00490 (    1)
  link_BETA1-6         : angle       1.42375 (    3)
  link_NAG-ASN         : bond        0.00428 (    8)
  link_NAG-ASN         : angle       2.25774 (   24)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.090 
Fit side-chains
REVERT: A   56 ASN cc_start: 0.8480 (p0) cc_final: 0.8243 (t0)
  outliers start: 9
  outliers final: 8
  residues processed: 48
  average time/residue: 0.0308
  time to fit residues: 2.1436
Evaluate side-chains
  52 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   64 ASN
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  410 HIS
Chi-restraints excluded: chain A residue  531 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 51 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0980
   chunk 34 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.5580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.154584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.131647 restraints weight = 13460.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.138896 restraints weight = 5308.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.143700 restraints weight = 2497.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.144820 restraints weight = 1516.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.147464 restraints weight = 1176.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3760
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3760 r_free = 0.3760    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3760 r_free = 0.3760    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3760
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
moved from start:          0.2629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4360  Z= 0.142
  Angle     :  0.699  10.701   5973  Z= 0.320
  Chirality :  0.049   0.308    720
  Planarity :  0.005   0.058    747
  Dihedral  :  7.353  45.443    861
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 11.61 %
    Favored  : 86.67 %
  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: -2.71 (0.38), residues: 522
  helix: -1.76 (0.51), residues: 111
  sheet: -3.70 (0.44), residues: 106
  loop : -0.98 (0.37), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 447 
 TYR   0.010   0.001   TYR A 165 
 PHE   0.025   0.001   PHE A 414 
 TRP   0.002   0.001   TRP A  47 
 HIS   0.001   0.001   HIS A 410 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 4341)
  covalent geometry    : angle       0.65516 ( 5920)
  SS BOND              : bond        0.00163 (    4)
  SS BOND              : angle       1.48766 (    8)
  hydrogen bonds       : bond        0.02995 (   90)
  hydrogen bonds       : angle       5.28921 (  184)
  link_BETA1-4         : bond        0.00861 (    6)
  link_BETA1-4         : angle       3.63026 (   18)
  link_BETA1-6         : bond        0.00584 (    1)
  link_BETA1-6         : angle       1.34572 (    3)
  link_NAG-ASN         : bond        0.00564 (    8)
  link_NAG-ASN         : angle       2.23441 (   24)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.089 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 ASN cc_start: 0.8448 (p0) cc_final: 0.8243 (t0)
  outliers start: 8
  outliers final: 8
  residues processed: 49
  average time/residue: 0.0308
  time to fit residues: 2.1803
Evaluate side-chains
  52 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   64 ASN
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  410 HIS
Chi-restraints excluded: chain A residue  531 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 36 optimal weight:    0.3980
   chunk 11 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 20 optimal weight:    0.1980
   chunk 47 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.5580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.153343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.130458 restraints weight = 13296.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.137329 restraints weight = 4966.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.140449 restraints weight = 2334.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.142922 restraints weight = 1682.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.145806 restraints weight = 1182.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3742
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3742 r_free = 0.3742    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3742 r_free = 0.3742    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3742
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7196
moved from start:          0.2795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4360  Z= 0.143
  Angle     :  0.705  10.567   5973  Z= 0.322
  Chirality :  0.049   0.260    720
  Planarity :  0.005   0.057    747
  Dihedral  :  6.432  37.427    861
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 11.83 %
    Favored  : 86.45 %
  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: -2.69 (0.38), residues: 522
  helix: -1.71 (0.51), residues: 111
  sheet: -3.67 (0.44), residues: 106
  loop : -1.00 (0.37), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 447 
 TYR   0.012   0.002   TYR A 371 
 PHE   0.025   0.001   PHE A 414 
 TRP   0.002   0.001   TRP A  47 
 HIS   0.001   0.000   HIS A 410 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 4341)
  covalent geometry    : angle       0.66380 ( 5920)
  SS BOND              : bond        0.00148 (    4)
  SS BOND              : angle       1.59774 (    8)
  hydrogen bonds       : bond        0.02953 (   90)
  hydrogen bonds       : angle       5.31204 (  184)
  link_BETA1-4         : bond        0.00845 (    6)
  link_BETA1-4         : angle       3.45494 (   18)
  link_BETA1-6         : bond        0.00707 (    1)
  link_BETA1-6         : angle       1.26444 (    3)
  link_NAG-ASN         : bond        0.00509 (    8)
  link_NAG-ASN         : angle       2.24279 (   24)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.088 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 ASN cc_start: 0.8463 (p0) cc_final: 0.8237 (t0)
REVERT: A  526 TYR cc_start: 0.7285 (t80) cc_final: 0.7074 (t80)
  outliers start: 8
  outliers final: 7
  residues processed: 48
  average time/residue: 0.0304
  time to fit residues: 2.1249
Evaluate side-chains
  51 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   64 ASN
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  531 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 44 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 27 optimal weight:    0.7980
   chunk 24 optimal weight:    0.4980
   chunk 46 optimal weight:    0.0870
   chunk 30 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.4958

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.151012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.130298 restraints weight = 8618.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.135046 restraints weight = 4165.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.138510 restraints weight = 2481.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.140940 restraints weight = 1687.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.142583 restraints weight = 1252.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3753
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3753 r_free = 0.3753    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3753 r_free = 0.3753    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3753
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.2871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4360  Z= 0.133
  Angle     :  0.687  10.583   5973  Z= 0.316
  Chirality :  0.048   0.260    720
  Planarity :  0.005   0.056    747
  Dihedral  :  5.796  38.011    861
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 12.26 %
    Favored  : 86.24 %
  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: -2.69 (0.38), residues: 522
  helix: -1.73 (0.51), residues: 111
  sheet: -3.64 (0.44), residues: 106
  loop : -0.99 (0.37), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 447 
 TYR   0.011   0.001   TYR A 165 
 PHE   0.025   0.001   PHE A 414 
 TRP   0.003   0.001   TRP A  47 
 HIS   0.001   0.001   HIS A 410 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 4341)
  covalent geometry    : angle       0.64818 ( 5920)
  SS BOND              : bond        0.00154 (    4)
  SS BOND              : angle       1.45310 (    8)
  hydrogen bonds       : bond        0.02897 (   90)
  hydrogen bonds       : angle       5.25519 (  184)
  link_BETA1-4         : bond        0.00875 (    6)
  link_BETA1-4         : angle       3.30990 (   18)
  link_BETA1-6         : bond        0.00722 (    1)
  link_BETA1-6         : angle       1.33369 (    3)
  link_NAG-ASN         : bond        0.00436 (    8)
  link_NAG-ASN         : angle       2.18312 (   24)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 894.29 seconds
wall clock time: 16 minutes 4.09 seconds (964.09 seconds total)