Starting phenix.real_space_refine
on Tue Feb  3 19:31:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hqn_52344/02_2026/9hqn_52344.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hqn_52344/02_2026/9hqn_52344.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hqn_52344/02_2026/9hqn_52344.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hqn_52344/02_2026/9hqn_52344.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hqn_52344/02_2026/9hqn_52344.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hqn_52344/02_2026/9hqn_52344.map"
  }
  resolution = 2.86
  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=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      28      5.16       5
     C    4135      2.51       5
     N    1039      2.21       5
     O    1187      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6389
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 2097
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 2097
          Classifications: {'peptide': 261}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 13, 'TRANS': 247}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "B"
      Number of atoms: 2124
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 2124
          Classifications: {'peptide': 264}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 13, 'TRANS': 250}
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "C"
      Number of atoms: 2097
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 2097
          Classifications: {'peptide': 261}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 13, 'TRANS': 247}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 8
          Classifications: {'water': 8}
          Link IDs: {None: 7}
    Chain: "B"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 9
          Classifications: {'water': 9}
          Link IDs: {None: 8}
    Chain: "C"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
  Time building chain proxies: 1.61, per 1000 atoms: 0.25
  Number of scatterers: 6389
  At special positions: 0
  Unit cell: (82.08, 82.08, 123.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      28     16.00
     O    1187      8.00
     N    1039      7.00
     C    4135      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 401 " - " ASN A 155 "
      " NAG B 401 " - " ASN B 155 "
      " NAG C 401 " - " ASN C 155 "
  Time building additional restraints: 0.50
  Conformation dependent library (CDL) restraints added in 337.9 milliseconds
  

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1512

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 9 sheets defined
      29.9% alpha, 42.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 73 through 87
      removed outlier: 3.781A  pdb=" N   LEU A  77 " --> pdb=" O   ILE A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 96
    Processing helix  chain 'A' and resid 206 through 212
      removed outlier: 3.582A  pdb=" N   PHE A 210 " --> pdb=" O   SER A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 227
      removed outlier: 3.602A  pdb=" N   SER A 225 " --> pdb=" O   GLN A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 276
    Processing helix  chain 'A' and resid 302 through 329
      removed outlier: 3.542A  pdb=" N   LEU A 317 " --> pdb=" O   ALA A 313 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 96
      removed outlier: 3.766A  pdb=" N   LEU B  77 " --> pdb=" O   ILE B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 212
      removed outlier: 3.586A  pdb=" N   PHE B 210 " --> pdb=" O   SER B 206 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 227
      removed outlier: 3.566A  pdb=" N   SER B 225 " --> pdb=" O   GLN B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 276
    Processing helix  chain 'B' and resid 302 through 331
    Processing helix  chain 'C' and resid 73 through 98
      removed outlier: 3.769A  pdb=" N   LEU C  77 " --> pdb=" O   ILE C  73 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LYS C  97 " --> pdb=" O   ARG C  93 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   HIS C  98 " --> pdb=" O   GLU C  94 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 206 through 212
      removed outlier: 3.653A  pdb=" N   PHE C 210 " --> pdb=" O   SER C 206 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 215 through 227
      removed outlier: 3.621A  pdb=" N   SER C 225 " --> pdb=" O   GLN C 221 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 272 through 276
    Processing helix  chain 'C' and resid 302 through 329
      removed outlier: 3.542A  pdb=" N   LEU C 315 " --> pdb=" O   CYS C 311 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ALA C 316 " --> pdb=" O   GLY C 312 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LEU C 317 " --> pdb=" O   ALA C 313 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   GLU C 322 " --> pdb=" O   PHE C 318 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 107
      removed outlier: 13.521A  pdb=" N   PHE A 291 " --> pdb=" O   VAL A 240 " (cutoff:3.500A)
      removed outlier: 9.521A  pdb=" N   MET A 242 " --> pdb=" O   PHE A 291 " (cutoff:3.500A)
      removed outlier: 9.554A  pdb=" N   GLN A 293 " --> pdb=" O   MET A 242 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   LEU A 244 " --> pdb=" O   GLN A 293 " (cutoff:3.500A)
      removed outlier: 8.065A  pdb=" N   VAL A 295 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   GLU A 246 " --> pdb=" O   VAL A 295 " (cutoff:3.500A)
      removed outlier: 8.556A  pdb=" N   ASP A 297 " --> pdb=" O   GLU A 246 " (cutoff:3.500A)
      removed outlier: 7.790A  pdb=" N   LYS A 248 " --> pdb=" O   ASP A 297 " (cutoff:3.500A)
      removed outlier: 6.090A  pdb=" N   PHE A 236 " --> pdb=" O   PHE A 282 " (cutoff:3.500A)
      removed outlier: 8.195A  pdb=" N   VAL A 284 " --> pdb=" O   PHE A 236 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   THR A 238 " --> pdb=" O   VAL A 284 " (cutoff:3.500A)
      removed outlier: 7.944A  pdb=" N   GLU A 286 " --> pdb=" O   THR A 238 " (cutoff:3.500A)
      removed outlier: 6.114A  pdb=" N   VAL A 240 " --> pdb=" O   GLU A 286 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   ARG A 188 " --> pdb=" O   LEU A 125 " (cutoff:3.500A)
      removed outlier: 5.571A  pdb=" N   LEU A 125 " --> pdb=" O   ARG A 188 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 107
      removed outlier: 13.521A  pdb=" N   PHE A 291 " --> pdb=" O   VAL A 240 " (cutoff:3.500A)
      removed outlier: 9.521A  pdb=" N   MET A 242 " --> pdb=" O   PHE A 291 " (cutoff:3.500A)
      removed outlier: 9.554A  pdb=" N   GLN A 293 " --> pdb=" O   MET A 242 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   LEU A 244 " --> pdb=" O   GLN A 293 " (cutoff:3.500A)
      removed outlier: 8.065A  pdb=" N   VAL A 295 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   GLU A 246 " --> pdb=" O   VAL A 295 " (cutoff:3.500A)
      removed outlier: 8.556A  pdb=" N   ASP A 297 " --> pdb=" O   GLU A 246 " (cutoff:3.500A)
      removed outlier: 7.790A  pdb=" N   LYS A 248 " --> pdb=" O   ASP A 297 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 157
      removed outlier: 4.066A  pdb=" N   ASP A 200 " --> pdb=" O   TYR A 119 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 107
      removed outlier: 7.978A  pdb=" N   PHE B 291 " --> pdb=" O   MET B 242 " (cutoff:3.500A)
      removed outlier: 5.008A  pdb=" N   LEU B 244 " --> pdb=" O   PHE B 291 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ASP B 297 " --> pdb=" O   LYS B 248 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   PHE B 236 " --> pdb=" O   PHE B 282 " (cutoff:3.500A)
      removed outlier: 8.222A  pdb=" N   VAL B 284 " --> pdb=" O   PHE B 236 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   THR B 238 " --> pdb=" O   VAL B 284 " (cutoff:3.500A)
      removed outlier: 7.994A  pdb=" N   GLU B 286 " --> pdb=" O   THR B 238 " (cutoff:3.500A)
      removed outlier: 5.965A  pdb=" N   VAL B 240 " --> pdb=" O   GLU B 286 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   ARG B 188 " --> pdb=" O   LEU B 125 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   LEU B 125 " --> pdb=" O   ARG B 188 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 107
      removed outlier: 7.978A  pdb=" N   PHE B 291 " --> pdb=" O   MET B 242 " (cutoff:3.500A)
      removed outlier: 5.008A  pdb=" N   LEU B 244 " --> pdb=" O   PHE B 291 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ASP B 297 " --> pdb=" O   LYS B 248 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 151 through 157
      removed outlier: 4.068A  pdb=" N   ASP B 200 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 107
      removed outlier: 7.845A  pdb=" N   PHE C 291 " --> pdb=" O   MET C 242 " (cutoff:3.500A)
      removed outlier: 4.900A  pdb=" N   LEU C 244 " --> pdb=" O   PHE C 291 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ASP C 297 " --> pdb=" O   LYS C 248 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   PHE C 236 " --> pdb=" O   PHE C 282 " (cutoff:3.500A)
      removed outlier: 8.135A  pdb=" N   VAL C 284 " --> pdb=" O   PHE C 236 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   THR C 238 " --> pdb=" O   VAL C 284 " (cutoff:3.500A)
      removed outlier: 7.884A  pdb=" N   GLU C 286 " --> pdb=" O   THR C 238 " (cutoff:3.500A)
      removed outlier: 6.105A  pdb=" N   VAL C 240 " --> pdb=" O   GLU C 286 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   ARG C 188 " --> pdb=" O   LEU C 125 " (cutoff:3.500A)
      removed outlier: 5.570A  pdb=" N   LEU C 125 " --> pdb=" O   ARG C 188 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 100 through 107
      removed outlier: 7.845A  pdb=" N   PHE C 291 " --> pdb=" O   MET C 242 " (cutoff:3.500A)
      removed outlier: 4.900A  pdb=" N   LEU C 244 " --> pdb=" O   PHE C 291 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ASP C 297 " --> pdb=" O   LYS C 248 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 151 through 157
      removed outlier: 4.064A  pdb=" N   ASP C 200 " --> pdb=" O   TYR C 119 " (cutoff:3.500A)

    357 hydrogen bonds defined for protein.
    999 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: 0.85

  Time building geometry restraints manager: 0.68 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2003
        1.34 -     1.46: 1481
        1.46 -     1.58: 2996
        1.58 -     1.69: 0
        1.69 -     1.81: 44
  Bond restraints: 6524
  Sorted by residual:
  bond pdb=" C1  NAG B 401 "
       pdb=" O5  NAG B 401 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.87e+00
  bond pdb=" C5  NAG B 401 "
       pdb=" O5  NAG B 401 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.22e+00
  bond pdb=" C3  NAG C 401 "
       pdb=" O3  NAG C 401 "
    ideal  model  delta    sigma   weight residual
    1.403  1.424 -0.021 2.00e-02 2.50e+03 1.07e+00
  bond pdb=" C5  NAG A 401 "
       pdb=" O5  NAG A 401 "
    ideal  model  delta    sigma   weight residual
    1.413  1.433 -0.020 2.00e-02 2.50e+03 1.00e+00
  bond pdb=" C3  NAG A 401 "
       pdb=" O3  NAG A 401 "
    ideal  model  delta    sigma   weight residual
    1.403  1.423 -0.020 2.00e-02 2.50e+03 9.90e-01
  ... (remaining 6519 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.31: 8529
        1.31 -     2.62: 233
        2.62 -     3.93: 70
        3.93 -     5.23: 11
        5.23 -     6.54: 5
  Bond angle restraints: 8848
  Sorted by residual:
  angle pdb=" C   LEU B  77 "
        pdb=" N   MET B  78 "
        pdb=" CA  MET B  78 "
      ideal   model   delta    sigma   weight residual
     121.14  115.08    6.06 1.75e+00 3.27e-01 1.20e+01
  angle pdb=" C   LEU C  77 "
        pdb=" N   MET C  78 "
        pdb=" CA  MET C  78 "
      ideal   model   delta    sigma   weight residual
     121.14  115.11    6.03 1.75e+00 3.27e-01 1.19e+01
  angle pdb=" C   LEU A  77 "
        pdb=" N   MET A  78 "
        pdb=" CA  MET A  78 "
      ideal   model   delta    sigma   weight residual
     121.58  115.04    6.54 1.95e+00 2.63e-01 1.13e+01
  angle pdb=" C   GLN A  87 "
        pdb=" N   THR A  88 "
        pdb=" CA  THR A  88 "
      ideal   model   delta    sigma   weight residual
     121.54  126.78   -5.24 1.91e+00 2.74e-01 7.53e+00
  angle pdb=" N   VAL C 177 "
        pdb=" CA  VAL C 177 "
        pdb=" C   VAL C 177 "
      ideal   model   delta    sigma   weight residual
     112.35  108.94    3.41 1.41e+00 5.03e-01 5.86e+00
  ... (remaining 8843 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.65: 3586
       20.65 -    41.29: 271
       41.29 -    61.94: 47
       61.94 -    82.58: 9
       82.58 -   103.23: 16
  Dihedral angle restraints: 3929
    sinusoidal: 1601
      harmonic: 2328
  Sorted by residual:
  dihedral pdb=" CA  PHE A 236 "
           pdb=" C   PHE A 236 "
           pdb=" N   ARG A 237 "
           pdb=" CA  ARG A 237 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.50   20.50     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CA  PHE B 236 "
           pdb=" C   PHE B 236 "
           pdb=" N   ARG B 237 "
           pdb=" CA  ARG B 237 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.69   20.31     0      5.00e+00 4.00e-02 1.65e+01
  dihedral pdb=" CA  PHE C 236 "
           pdb=" C   PHE C 236 "
           pdb=" N   ARG C 237 "
           pdb=" CA  ARG C 237 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.76   20.24     0      5.00e+00 4.00e-02 1.64e+01
  ... (remaining 3926 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 539
       0.027 -    0.053: 276
       0.053 -    0.080: 70
       0.080 -    0.107: 49
       0.107 -    0.133: 41
  Chirality restraints: 975
  Sorted by residual:
  chirality pdb=" CA  MET A  78 "
            pdb=" N   MET A  78 "
            pdb=" C   MET A  78 "
            pdb=" CB  MET A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.45e-01
  chirality pdb=" CA  MET C  78 "
            pdb=" N   MET C  78 "
            pdb=" C   MET C  78 "
            pdb=" CB  MET C  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.40e-01
  chirality pdb=" CA  MET B  78 "
            pdb=" N   MET B  78 "
            pdb=" C   MET B  78 "
            pdb=" CB  MET B  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.01e-01
  ... (remaining 972 not shown)

  Planarity restraints: 1132
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A  88 "    0.019 2.00e-02 2.50e+03   3.71e-02 1.38e+01
        pdb=" C   THR A  88 "   -0.064 2.00e-02 2.50e+03
        pdb=" O   THR A  88 "    0.024 2.00e-02 2.50e+03
        pdb=" N   ILE A  89 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 330 "   -0.013 2.00e-02 2.50e+03   1.44e-02 5.17e+00
        pdb=" CG  TRP B 330 "    0.039 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 330 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 330 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 330 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 330 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 330 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 330 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 330 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 330 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN C 302 "   -0.024 5.00e-02 4.00e+02   3.74e-02 2.24e+00
        pdb=" N   PRO C 303 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO C 303 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C 303 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1129 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1643
        2.81 -     3.33: 5267
        3.33 -     3.86: 10155
        3.86 -     4.38: 11987
        4.38 -     4.90: 20411
  Nonbonded interactions: 49463
  Sorted by model distance:
  nonbonded pdb=" O   PRO B 141 "
            pdb=" NE2 GLN B 186 "
     model   vdw
     2.289 3.120
  nonbonded pdb=" O   PHE A  83 "
            pdb=" NE2 GLN A  87 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" O   PRO A 141 "
            pdb=" NE2 GLN A 186 "
     model   vdw
     2.294 3.120
  nonbonded pdb=" O   PRO C 141 "
            pdb=" NE2 GLN C 186 "
     model   vdw
     2.301 3.120
  nonbonded pdb=" O   GLU B 181 "
            pdb=" O   HOH B 501 "
     model   vdw
     2.328 3.040
  ... (remaining 49458 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 69 through 329 or resid 401))
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.120
  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:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.690
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  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:8.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
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      :  0.002   0.037   6527  Z= 0.112
  Angle     :  0.569   6.543   8857  Z= 0.301
  Chirality :  0.043   0.133    975
  Planarity :  0.003   0.037   1129
  Dihedral  : 16.660 103.231   2417
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  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:  0.54 (0.29), residues: 780
  helix:  1.26 (0.37), residues: 233
  sheet:  1.11 (0.28), residues: 306
  loop : -1.57 (0.33), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 175 
 TYR   0.008   0.001   TYR B  74 
 PHE   0.022   0.001   PHE C  83 
 TRP   0.039   0.001   TRP B 330 
 HIS   0.001   0.000   HIS A  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 6524)
  covalent geometry    : angle       0.56697 ( 8848)
  hydrogen bonds       : bond        0.11129 (  325)
  hydrogen bonds       : angle       4.55397 (  999)
  link_NAG-ASN         : bond        0.00123 (    3)
  link_NAG-ASN         : angle       1.59108 (    9)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.253 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.7216
  time to fit residues: 83.8478
Evaluate side-chains
  81 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0270
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.7040

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

Flipped N/Q/H residues before XYZ refinement:
A 305 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.178352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.138250 restraints weight = 6690.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3531 rms_B_bonded: 2.33
r_work: 0.3228 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3103 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.1128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6527  Z= 0.151
  Angle     :  0.657   7.392   8857  Z= 0.334
  Chirality :  0.046   0.195    975
  Planarity :  0.004   0.030   1129
  Dihedral  : 10.028  69.999    918
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  :  7.53 %
    Favored  : 90.69 %
  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:  0.62 (0.29), residues: 780
  helix:  1.36 (0.36), residues: 235
  sheet:  0.98 (0.28), residues: 304
  loop : -1.26 (0.34), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 175 
 TYR   0.014   0.002   TYR A 132 
 PHE   0.022   0.002   PHE B 219 
 TRP   0.029   0.002   TRP B 330 
 HIS   0.001   0.001   HIS C  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 6524)
  covalent geometry    : angle       0.65427 ( 8848)
  hydrogen bonds       : bond        0.04024 (  325)
  hydrogen bonds       : angle       4.17112 (  999)
  link_NAG-ASN         : bond        0.00162 (    3)
  link_NAG-ASN         : angle       2.02012 (    9)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.172 
Fit side-chains
REVERT: A  176 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8161 (mt-10)
REVERT: B  309 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6835 (tp)
REVERT: C   93 ARG cc_start: 0.6753 (mpt180) cc_final: 0.5956 (mtp-110)
REVERT: C  176 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8194 (mt-10)
REVERT: C  306 THR cc_start: 0.8445 (m) cc_final: 0.8233 (m)
  outliers start: 12
  outliers final: 6
  residues processed: 92
  average time/residue: 0.6139
  time to fit residues: 58.9166
Evaluate side-chains
  84 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 GLU
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  206 SER
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain C residue  176 GLU
Chi-restraints excluded: chain C residue  206 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 26 optimal weight:    9.9990
   chunk 12 optimal weight:    1.9990
   chunk 38 optimal weight:    0.2980
   chunk 24 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 52 optimal weight:   10.0000
   chunk 68 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0170
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.5818

-------------------------------------------------------------------------------
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 = 0.3905 r_free = 0.3905 target = 0.181324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.142437 restraints weight = 6582.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 2.15
r_work: 0.3211 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3088 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.1243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6527  Z= 0.132
  Angle     :  0.623   7.183   8857  Z= 0.316
  Chirality :  0.044   0.156    975
  Planarity :  0.004   0.031   1129
  Dihedral  :  7.092  44.898    918
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  :  9.75 %
    Favored  : 88.18 %
  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:  0.57 (0.29), residues: 780
  helix:  1.25 (0.35), residues: 239
  sheet:  0.93 (0.28), residues: 304
  loop : -1.25 (0.35), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 175 
 TYR   0.011   0.002   TYR A 132 
 PHE   0.038   0.002   PHE C  83 
 TRP   0.014   0.001   TRP B 330 
 HIS   0.001   0.000   HIS C  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 6524)
  covalent geometry    : angle       0.61959 ( 8848)
  hydrogen bonds       : bond        0.03627 (  325)
  hydrogen bonds       : angle       4.10267 (  999)
  link_NAG-ASN         : bond        0.00222 (    3)
  link_NAG-ASN         : angle       2.13074 (    9)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A   90 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.6967 (mmp)
REVERT: A  176 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8099 (mt-10)
REVERT: B  309 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6763 (tp)
REVERT: C  176 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8131 (mt-10)
REVERT: C  306 THR cc_start: 0.8330 (m) cc_final: 0.8125 (m)
  outliers start: 14
  outliers final: 6
  residues processed: 92
  average time/residue: 0.6416
  time to fit residues: 61.5204
Evaluate side-chains
  90 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  176 GLU
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain C residue  176 GLU
Chi-restraints excluded: chain C residue  206 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 0 optimal weight:    9.9990
   chunk 26 optimal weight:   10.0000
   chunk 43 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 58 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3893 r_free = 0.3893 target = 0.180067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.141916 restraints weight = 6583.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 2.09
r_work: 0.3165 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   6527  Z= 0.148
  Angle     :  0.647   8.057   8857  Z= 0.327
  Chirality :  0.044   0.159    975
  Planarity :  0.004   0.033   1129
  Dihedral  :  5.843  32.019    918
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 12.11 %
    Favored  : 85.23 %
  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:  0.47 (0.29), residues: 780
  helix:  1.20 (0.35), residues: 239
  sheet:  0.86 (0.28), residues: 304
  loop : -1.31 (0.34), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 175 
 TYR   0.013   0.002   TYR C 132 
 PHE   0.030   0.002   PHE C  83 
 TRP   0.009   0.001   TRP B 330 
 HIS   0.001   0.001   HIS B 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 6524)
  covalent geometry    : angle       0.64212 ( 8848)
  hydrogen bonds       : bond        0.03563 (  325)
  hydrogen bonds       : angle       4.10998 (  999)
  link_NAG-ASN         : bond        0.00243 (    3)
  link_NAG-ASN         : angle       2.44248 (    9)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7508 (mtp180)
REVERT: A  176 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8301 (mt-10)
REVERT: B  200 ASP cc_start: 0.8795 (OUTLIER) cc_final: 0.8365 (m-30)
REVERT: B  309 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6833 (tp)
REVERT: C  176 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8232 (mt-10)
REVERT: C  200 ASP cc_start: 0.8908 (m-30) cc_final: 0.8688 (m-30)
  outliers start: 18
  outliers final: 7
  residues processed: 96
  average time/residue: 0.5737
  time to fit residues: 57.3836
Evaluate side-chains
  101 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  175 ARG
Chi-restraints excluded: chain A residue  176 GLU
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain C residue  176 GLU
Chi-restraints excluded: chain C residue  206 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0970
   chunk 64 optimal weight:    0.1980
   chunk 4 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
A 208 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.180337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.141246 restraints weight = 6644.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 2.25
r_work: 0.3184 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3058 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.1516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6527  Z= 0.123
  Angle     :  0.608   8.148   8857  Z= 0.309
  Chirality :  0.043   0.172    975
  Planarity :  0.003   0.032   1129
  Dihedral  :  5.297  25.373    918
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 13.88 %
    Favored  : 83.90 %
  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:  0.50 (0.29), residues: 780
  helix:  1.25 (0.35), residues: 239
  sheet:  0.88 (0.28), residues: 304
  loop : -1.32 (0.34), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 175 
 TYR   0.010   0.001   TYR A 132 
 PHE   0.025   0.002   PHE A 219 
 TRP   0.007   0.001   TRP B 330 
 HIS   0.001   0.000   HIS C  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6524)
  covalent geometry    : angle       0.60220 ( 8848)
  hydrogen bonds       : bond        0.03268 (  325)
  hydrogen bonds       : angle       4.03459 (  999)
  link_NAG-ASN         : bond        0.00152 (    3)
  link_NAG-ASN         : angle       2.58406 (    9)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.7911 (pmm) cc_final: 0.7629 (ppp)
REVERT: A   90 MET cc_start: 0.7284 (OUTLIER) cc_final: 0.6549 (mmp)
REVERT: A  176 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8285 (mt-10)
REVERT: B   87 GLN cc_start: 0.6491 (tm-30) cc_final: 0.6105 (mt0)
REVERT: B  200 ASP cc_start: 0.8782 (OUTLIER) cc_final: 0.8343 (m-30)
REVERT: B  309 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6764 (tp)
REVERT: B  331 MET cc_start: 0.6510 (tpp) cc_final: 0.5889 (tpt)
REVERT: C   78 MET cc_start: 0.8064 (pmm) cc_final: 0.7848 (ppp)
REVERT: C  176 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8238 (mt-10)
REVERT: C  200 ASP cc_start: 0.8923 (m-30) cc_final: 0.8690 (m-30)
  outliers start: 15
  outliers final: 5
  residues processed: 100
  average time/residue: 0.5551
  time to fit residues: 57.8754
Evaluate side-chains
  97 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain A residue  176 GLU
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain C residue  176 GLU
Chi-restraints excluded: chain C residue  206 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 69 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 208 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.178972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.139637 restraints weight = 6634.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 2.27
r_work: 0.3167 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3041 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.1665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6527  Z= 0.150
  Angle     :  0.633   8.381   8857  Z= 0.325
  Chirality :  0.044   0.174    975
  Planarity :  0.004   0.033   1129
  Dihedral  :  5.164  24.664    918
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 14.92 %
    Favored  : 82.72 %
  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:  0.42 (0.29), residues: 780
  helix:  1.19 (0.35), residues: 239
  sheet:  0.85 (0.28), residues: 304
  loop : -1.40 (0.34), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 175 
 TYR   0.013   0.002   TYR C 132 
 PHE   0.038   0.002   PHE C  83 
 TRP   0.007   0.001   TRP C 304 
 HIS   0.002   0.001   HIS C  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 6524)
  covalent geometry    : angle       0.62839 ( 8848)
  hydrogen bonds       : bond        0.03465 (  325)
  hydrogen bonds       : angle       4.08039 (  999)
  link_NAG-ASN         : bond        0.00114 (    3)
  link_NAG-ASN         : angle       2.38349 (    9)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.7906 (pmm) cc_final: 0.7674 (pmm)
REVERT: A   90 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6443 (mmp)
REVERT: A  176 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8363 (mt-10)
REVERT: B   94 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7420 (tp30)
REVERT: B  200 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8343 (m-30)
REVERT: B  248 LYS cc_start: 0.7069 (mptt) cc_final: 0.6866 (mptt)
REVERT: B  309 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6747 (tp)
REVERT: C   78 MET cc_start: 0.8065 (pmm) cc_final: 0.7843 (ppp)
REVERT: C   94 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7375 (tp30)
REVERT: C  176 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8264 (mt-10)
REVERT: C  200 ASP cc_start: 0.8892 (m-30) cc_final: 0.8664 (m-30)
REVERT: C  248 LYS cc_start: 0.7120 (mptt) cc_final: 0.6781 (mptt)
  outliers start: 16
  outliers final: 8
  residues processed: 90
  average time/residue: 0.6181
  time to fit residues: 57.9481
Evaluate side-chains
  95 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  176 GLU
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain C residue  176 GLU
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  206 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 58 optimal weight:    0.0040
   chunk 57 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0370
   chunk 66 optimal weight:    0.0000
   chunk 59 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0470
   overall best weight:    0.1572

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

Flipped N/Q/H residues before XYZ refinement:
A 208 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.181852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.142369 restraints weight = 6649.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3620 rms_B_bonded: 2.13
r_work: 0.3331 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3207 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.1579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6527  Z= 0.091
  Angle     :  0.555   8.305   8857  Z= 0.283
  Chirality :  0.042   0.185    975
  Planarity :  0.003   0.028   1129
  Dihedral  :  4.622  21.145    918
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 16.40 %
    Favored  : 81.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.29), residues: 780
  helix:  1.34 (0.35), residues: 239
  sheet:  0.89 (0.27), residues: 310
  loop : -1.21 (0.36), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 175 
 TYR   0.009   0.001   TYR A  74 
 PHE   0.035   0.001   PHE C  83 
 TRP   0.005   0.001   TRP B 330 
 HIS   0.001   0.000   HIS A 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00203 ( 6524)
  covalent geometry    : angle       0.55041 ( 8848)
  hydrogen bonds       : bond        0.02838 (  325)
  hydrogen bonds       : angle       3.93636 (  999)
  link_NAG-ASN         : bond        0.00072 (    3)
  link_NAG-ASN         : angle       2.33567 (    9)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: B  200 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8331 (m-30)
REVERT: B  309 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6689 (tp)
REVERT: C   78 MET cc_start: 0.8047 (pmm) cc_final: 0.7809 (ppp)
REVERT: C  176 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8301 (mt-10)
  outliers start: 13
  outliers final: 4
  residues processed: 103
  average time/residue: 0.5802
  time to fit residues: 62.3641
Evaluate side-chains
  92 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain C residue  176 GLU
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  206 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 40 optimal weight:    0.1980
   chunk 70 optimal weight:    0.9980
   chunk 36 optimal weight:    0.1980
   chunk 58 optimal weight:    0.4980
   chunk 21 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9990
   chunk 14 optimal weight:    0.3980
   overall best weight:    0.3780

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

Flipped N/Q/H residues before XYZ refinement:
A 208 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.179977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.140270 restraints weight = 6677.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3657 rms_B_bonded: 2.15
r_work: 0.3358 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3230 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.1681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6527  Z= 0.109
  Angle     :  0.595   8.509   8857  Z= 0.305
  Chirality :  0.043   0.202    975
  Planarity :  0.003   0.028   1129
  Dihedral  :  4.587  21.610    918
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 17.28 %
    Favored  : 80.65 %
  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:  0.64 (0.29), residues: 780
  helix:  1.34 (0.35), residues: 239
  sheet:  0.92 (0.27), residues: 310
  loop : -1.21 (0.35), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 175 
 TYR   0.008   0.001   TYR A  74 
 PHE   0.032   0.002   PHE C  83 
 TRP   0.005   0.001   TRP C 304 
 HIS   0.001   0.000   HIS C  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 6524)
  covalent geometry    : angle       0.59123 ( 8848)
  hydrogen bonds       : bond        0.03021 (  325)
  hydrogen bonds       : angle       3.93202 (  999)
  link_NAG-ASN         : bond        0.00098 (    3)
  link_NAG-ASN         : angle       2.07063 (    9)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   94 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7437 (tp30)
REVERT: B  200 ASP cc_start: 0.8815 (OUTLIER) cc_final: 0.8366 (m-30)
REVERT: B  309 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6638 (tp)
REVERT: C   94 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7431 (tp30)
REVERT: C  176 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8320 (mt-10)
  outliers start: 14
  outliers final: 7
  residues processed: 92
  average time/residue: 0.6870
  time to fit residues: 65.6805
Evaluate side-chains
  92 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain C residue  176 GLU
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  206 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 59 optimal weight:    0.0020
   chunk 19 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 76 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 26 optimal weight:   10.0000
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.8592

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

Flipped N/Q/H residues before XYZ refinement:
A 208 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.177159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.137707 restraints weight = 6722.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 2.33
r_work: 0.3061 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2914 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.1810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6527  Z= 0.163
  Angle     :  0.675  10.590   8857  Z= 0.344
  Chirality :  0.044   0.204    975
  Planarity :  0.004   0.032   1129
  Dihedral  :  4.770  24.140    918
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 17.58 %
    Favored  : 80.65 %
  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:  0.47 (0.29), residues: 780
  helix:  1.24 (0.35), residues: 239
  sheet:  0.80 (0.27), residues: 310
  loop : -1.34 (0.35), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 172 
 TYR   0.014   0.002   TYR C 132 
 PHE   0.029   0.002   PHE C  83 
 TRP   0.006   0.001   TRP C 304 
 HIS   0.002   0.001   HIS B 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 6524)
  covalent geometry    : angle       0.67211 ( 8848)
  hydrogen bonds       : bond        0.03505 (  325)
  hydrogen bonds       : angle       4.10814 (  999)
  link_NAG-ASN         : bond        0.00063 (    3)
  link_NAG-ASN         : angle       2.03318 (    9)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   94 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7356 (tp30)
REVERT: B  200 ASP cc_start: 0.8869 (OUTLIER) cc_final: 0.8395 (m-30)
REVERT: B  309 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.6470 (tp)
REVERT: C   94 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7308 (tp30)
REVERT: C  176 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8269 (mt-10)
  outliers start: 12
  outliers final: 6
  residues processed: 88
  average time/residue: 0.5953
  time to fit residues: 54.7193
Evaluate side-chains
  91 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain C residue  176 GLU
Chi-restraints excluded: chain C residue  206 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0980
   chunk 56 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 208 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.177180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.136436 restraints weight = 6624.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 2.21
r_work: 0.3165 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.1823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6527  Z= 0.145
  Angle     :  0.662  10.454   8857  Z= 0.337
  Chirality :  0.044   0.220    975
  Planarity :  0.004   0.034   1129
  Dihedral  :  4.732  24.347    918
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 18.17 %
    Favored  : 80.35 %
  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:  0.42 (0.29), residues: 780
  helix:  1.24 (0.35), residues: 237
  sheet:  0.77 (0.27), residues: 310
  loop : -1.37 (0.34), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 175 
 TYR   0.012   0.002   TYR C 132 
 PHE   0.028   0.002   PHE B 219 
 TRP   0.006   0.001   TRP B 304 
 HIS   0.001   0.001   HIS C  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 6524)
  covalent geometry    : angle       0.65908 ( 8848)
  hydrogen bonds       : bond        0.03407 (  325)
  hydrogen bonds       : angle       4.11586 (  999)
  link_NAG-ASN         : bond        0.00064 (    3)
  link_NAG-ASN         : angle       1.98575 (    9)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   94 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7452 (tp30)
REVERT: B  200 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8417 (m-30)
REVERT: B  309 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6699 (tp)
REVERT: C  176 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8360 (mt-10)
  outliers start: 10
  outliers final: 5
  residues processed: 87
  average time/residue: 0.5664
  time to fit residues: 51.5141
Evaluate side-chains
  90 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  309 LEU
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain C residue  176 GLU
Chi-restraints excluded: chain C residue  206 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 64 optimal weight:    0.0770
   chunk 35 optimal weight:    0.7980
   chunk 40 optimal weight:    0.0170
   chunk 7 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 12 optimal weight:    0.1980
   chunk 73 optimal weight:    0.5980
   chunk 49 optimal weight:    3.9990
   overall best weight:    0.3176

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

Flipped N/Q/H residues before XYZ refinement:
A 208 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.179991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.139476 restraints weight = 6634.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.3532 rms_B_bonded: 2.13
r_work: 0.3258 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3131 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.1767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6527  Z= 0.106
  Angle     :  0.622   9.922   8857  Z= 0.316
  Chirality :  0.043   0.225    975
  Planarity :  0.003   0.030   1129
  Dihedral  :  4.470  22.286    918
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 18.02 %
    Favored  : 80.06 %
  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:  0.55 (0.29), residues: 780
  helix:  1.29 (0.35), residues: 237
  sheet:  0.87 (0.27), residues: 310
  loop : -1.29 (0.35), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 175 
 TYR   0.010   0.001   TYR A  74 
 PHE   0.029   0.002   PHE B 219 
 TRP   0.005   0.001   TRP B 304 
 HIS   0.001   0.000   HIS C  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 6524)
  covalent geometry    : angle       0.61954 ( 8848)
  hydrogen bonds       : bond        0.03041 (  325)
  hydrogen bonds       : angle       4.00718 (  999)
  link_NAG-ASN         : bond        0.00063 (    3)
  link_NAG-ASN         : angle       1.89306 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2515.87 seconds
wall clock time: 43 minutes 27.11 seconds (2607.11 seconds total)