Starting phenix.real_space_refine
on Mon Jul 28 13:37:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tvf_41640/07_2025/8tvf_41640.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tvf_41640/07_2025/8tvf_41640.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tvf_41640/07_2025/8tvf_41640.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tvf_41640/07_2025/8tvf_41640.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tvf_41640/07_2025/8tvf_41640.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tvf_41640/07_2025/8tvf_41640.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.022
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      54      5.16       5
     C    6258      2.51       5
     N    1647      2.21       5
     O    2502      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10461
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3246
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 432, 3246
          Classifications: {'peptide': 432}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 15, 'TRANS': 416}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 21
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 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: 188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 188, 188
          Classifications: {'water': 188}
          Link IDs: {None: 187}
    Chain: "A"
      Number of atoms: 188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 188, 188
          Classifications: {'water': 188}
          Link IDs: {None: 187}
    Chain: "C"
      Number of atoms: 188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 188, 188
          Classifications: {'water': 188}
          Link IDs: {None: 187}
  Restraints were copied for chains:
    C, B, D, F
  Time building chain proxies: 7.16, per 1000 atoms: 0.68
  Number of scatterers: 10461
  At special positions: 0
  Unit cell: (105.042, 98.0392, 101.04, 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      54     16.00
     O    2502      8.00
     N    1647      7.00
     C    6258      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  66 " - pdb=" SG  CYS B 187 " distance=2.18
    Simple disulfide: pdb=" SG  CYS B 326 " - pdb=" SG  CYS B 335 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 350 " - pdb=" SG  CYS B 358 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 382 " - pdb=" SG  CYS B 387 " distance=2.08
    Simple disulfide: pdb=" SG  CYS B 389 " - pdb=" SG  CYS B 412 " 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 D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
    NAG-ASN
      " NAG A 601 " - " ASN A  65 "
      " NAG B 601 " - " ASN B  65 "
      " NAG C 601 " - " ASN C  65 "
      " NAG D   1 " - " ASN B 459 "
      " NAG E   1 " - " ASN A 459 "
      " NAG F   1 " - " ASN C 459 "
  Time building additional restraints: 2.69
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2418

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 15 sheets defined
      41.0% alpha, 21.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.69
  Creating SS restraints...
    Processing helix  chain 'B' and resid 24 through 30
      removed outlier: 3.844A  pdb=" N   LYS B  30 " --> pdb=" O   ASP B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 94
      Proline residue:  B  84  - end of helix
    Processing helix  chain 'B' and resid 112 through 116
    Processing helix  chain 'B' and resid 120 through 132
    Processing helix  chain 'B' and resid 132 through 141
    Processing helix  chain 'B' and resid 142 through 148
    Processing helix  chain 'B' and resid 168 through 178
      removed outlier: 3.521A  pdb=" N   GLY B 172 " --> pdb=" O   ASP B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 185
      removed outlier: 5.718A  pdb=" N   ASN B 183 " --> pdb=" O   PRO B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 186 through 209
    Processing helix  chain 'B' and resid 209 through 215
    Processing helix  chain 'B' and resid 223 through 227
    Processing helix  chain 'B' and resid 233 through 241
      removed outlier: 3.524A  pdb=" N   LEU B 237 " --> pdb=" O   ASN B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 247
    Processing helix  chain 'B' and resid 248 through 254
    Processing helix  chain 'B' and resid 323 through 326
    Processing helix  chain 'B' and resid 344 through 352
    Processing helix  chain 'B' and resid 354 through 358
    Processing helix  chain 'B' and resid 447 through 461
    Processing helix  chain 'A' and resid 24 through 30
      removed outlier: 3.844A  pdb=" N   LYS A  30 " --> pdb=" O   ASP A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 94
      Proline residue:  A  84  - end of helix
    Processing helix  chain 'A' and resid 112 through 116
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'A' and resid 132 through 141
    Processing helix  chain 'A' and resid 142 through 148
    Processing helix  chain 'A' and resid 168 through 178
      removed outlier: 3.521A  pdb=" N   GLY A 172 " --> pdb=" O   ASP A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 185
      removed outlier: 5.719A  pdb=" N   ASN A 183 " --> pdb=" O   PRO A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 209
    Processing helix  chain 'A' and resid 209 through 215
    Processing helix  chain 'A' and resid 223 through 227
    Processing helix  chain 'A' and resid 233 through 241
      removed outlier: 3.523A  pdb=" N   LEU A 237 " --> pdb=" O   ASN A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 247
    Processing helix  chain 'A' and resid 248 through 254
    Processing helix  chain 'A' and resid 323 through 326
    Processing helix  chain 'A' and resid 344 through 352
    Processing helix  chain 'A' and resid 354 through 358
    Processing helix  chain 'A' and resid 447 through 461
    Processing helix  chain 'C' and resid 24 through 30
      removed outlier: 3.845A  pdb=" N   LYS C  30 " --> pdb=" O   ASP C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 94
      Proline residue:  C  84  - end of helix
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'C' and resid 120 through 132
    Processing helix  chain 'C' and resid 132 through 141
    Processing helix  chain 'C' and resid 142 through 148
    Processing helix  chain 'C' and resid 168 through 178
      removed outlier: 3.521A  pdb=" N   GLY C 172 " --> pdb=" O   ASP C 168 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 179 through 185
      removed outlier: 5.719A  pdb=" N   ASN C 183 " --> pdb=" O   PRO C 180 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 186 through 209
    Processing helix  chain 'C' and resid 209 through 215
    Processing helix  chain 'C' and resid 223 through 227
    Processing helix  chain 'C' and resid 233 through 241
      removed outlier: 3.524A  pdb=" N   LEU C 237 " --> pdb=" O   ASN C 233 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 244 through 247
    Processing helix  chain 'C' and resid 248 through 254
    Processing helix  chain 'C' and resid 323 through 326
    Processing helix  chain 'C' and resid 344 through 352
    Processing helix  chain 'C' and resid 354 through 358
    Processing helix  chain 'C' and resid 447 through 461
    Processing sheet with id=AA1, first strand: chain 'B' and resid 327 through 328
      removed outlier: 7.811A  pdb=" N   VAL B 333 " --> pdb=" O   THR B  38 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   ASN B  40 " --> pdb=" O   VAL B 333 " (cutoff:3.500A)
      removed outlier: 7.858A  pdb=" N   CYS B 335 " --> pdb=" O   ASN B  40 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   LYS B  42 " --> pdb=" O   CYS B 335 " (cutoff:3.500A)
      removed outlier: 8.359A  pdb=" N   ILE B  33 " --> pdb=" O   LEU B 291 " (cutoff:3.500A)
      removed outlier: 8.107A  pdb=" N   LEU B 291 " --> pdb=" O   ILE B  33 " (cutoff:3.500A)
      removed outlier: 8.904A  pdb=" N   LYS B  35 " --> pdb=" O   GLN B 289 " (cutoff:3.500A)
      removed outlier: 10.187A  pdb=" N   GLN B 289 " --> pdb=" O   LYS B  35 " (cutoff:3.500A)
      removed outlier: 11.016A  pdb=" N   LEU B  37 " --> pdb=" O   VAL B 287 " (cutoff:3.500A)
      removed outlier: 10.071A  pdb=" N   VAL B 287 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 11.050A  pdb=" N   TYR B  39 " --> pdb=" O   ASN B 285 " (cutoff:3.500A)
      removed outlier: 9.655A  pdb=" N   ASN B 285 " --> pdb=" O   TYR B  39 " (cutoff:3.500A)
      removed outlier: 5.278A  pdb=" N   TYR B  41 " --> pdb=" O   VAL B 283 " (cutoff:3.500A)
      removed outlier: 5.581A  pdb=" N   PHE B 310 " --> pdb=" O   ILE B 321 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   ILE B 321 " --> pdb=" O   PHE B 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 153 through 157
      removed outlier: 7.841A  pdb=" N   THR B 163 " --> pdb=" O   THR B  49 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   LEU B  51 " --> pdb=" O   THR B 163 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   TYR B 270 " --> pdb=" O   VAL B 264 " (cutoff:3.500A)
      removed outlier: 4.721A  pdb=" N   VAL B 264 " --> pdb=" O   TYR B 270 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   ALA B 272 " --> pdb=" O   ILE B 262 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97
      removed outlier: 6.789A  pdb=" N   MET B 110 " --> pdb=" O   SER C 423 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 118 through 119
    Processing sheet with id=AA5, first strand: chain 'B' and resid 296 through 298
    Processing sheet with id=AA6, first strand: chain 'B' and resid 405 through 407
    Processing sheet with id=AA7, first strand: chain 'B' and resid 394 through 395
    Processing sheet with id=AA8, first strand: chain 'A' and resid 327 through 328
      removed outlier: 7.811A  pdb=" N   VAL A 333 " --> pdb=" O   THR A  38 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   ASN A  40 " --> pdb=" O   VAL A 333 " (cutoff:3.500A)
      removed outlier: 7.858A  pdb=" N   CYS A 335 " --> pdb=" O   ASN A  40 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   LYS A  42 " --> pdb=" O   CYS A 335 " (cutoff:3.500A)
      removed outlier: 8.358A  pdb=" N   ILE A  33 " --> pdb=" O   LEU A 291 " (cutoff:3.500A)
      removed outlier: 8.107A  pdb=" N   LEU A 291 " --> pdb=" O   ILE A  33 " (cutoff:3.500A)
      removed outlier: 8.904A  pdb=" N   LYS A  35 " --> pdb=" O   GLN A 289 " (cutoff:3.500A)
      removed outlier: 10.188A  pdb=" N   GLN A 289 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 11.016A  pdb=" N   LEU A  37 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 10.071A  pdb=" N   VAL A 287 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 11.050A  pdb=" N   TYR A  39 " --> pdb=" O   ASN A 285 " (cutoff:3.500A)
      removed outlier: 9.655A  pdb=" N   ASN A 285 " --> pdb=" O   TYR A  39 " (cutoff:3.500A)
      removed outlier: 5.278A  pdb=" N   TYR A  41 " --> pdb=" O   VAL A 283 " (cutoff:3.500A)
      removed outlier: 5.581A  pdb=" N   PHE A 310 " --> pdb=" O   ILE A 321 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   ILE A 321 " --> pdb=" O   PHE A 310 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 153 through 157
      removed outlier: 7.841A  pdb=" N   THR A 163 " --> pdb=" O   THR A  49 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   LEU A  51 " --> pdb=" O   THR A 163 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   TYR A 270 " --> pdb=" O   VAL A 264 " (cutoff:3.500A)
      removed outlier: 4.721A  pdb=" N   VAL A 264 " --> pdb=" O   TYR A 270 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   ALA A 272 " --> pdb=" O   ILE A 262 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 296 through 298
    Processing sheet with id=AB2, first strand: chain 'A' and resid 405 through 407
    Processing sheet with id=AB3, first strand: chain 'A' and resid 394 through 395
    Processing sheet with id=AB4, first strand: chain 'C' and resid 327 through 328
      removed outlier: 7.811A  pdb=" N   VAL C 333 " --> pdb=" O   THR C  38 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   ASN C  40 " --> pdb=" O   VAL C 333 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   CYS C 335 " --> pdb=" O   ASN C  40 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   LYS C  42 " --> pdb=" O   CYS C 335 " (cutoff:3.500A)
      removed outlier: 8.358A  pdb=" N   ILE C  33 " --> pdb=" O   LEU C 291 " (cutoff:3.500A)
      removed outlier: 8.107A  pdb=" N   LEU C 291 " --> pdb=" O   ILE C  33 " (cutoff:3.500A)
      removed outlier: 8.904A  pdb=" N   LYS C  35 " --> pdb=" O   GLN C 289 " (cutoff:3.500A)
      removed outlier: 10.187A  pdb=" N   GLN C 289 " --> pdb=" O   LYS C  35 " (cutoff:3.500A)
      removed outlier: 11.016A  pdb=" N   LEU C  37 " --> pdb=" O   VAL C 287 " (cutoff:3.500A)
      removed outlier: 10.071A  pdb=" N   VAL C 287 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
      removed outlier: 11.050A  pdb=" N   TYR C  39 " --> pdb=" O   ASN C 285 " (cutoff:3.500A)
      removed outlier: 9.655A  pdb=" N   ASN C 285 " --> pdb=" O   TYR C  39 " (cutoff:3.500A)
      removed outlier: 5.278A  pdb=" N   TYR C  41 " --> pdb=" O   VAL C 283 " (cutoff:3.500A)
      removed outlier: 5.582A  pdb=" N   PHE C 310 " --> pdb=" O   ILE C 321 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   ILE C 321 " --> pdb=" O   PHE C 310 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 153 through 157
      removed outlier: 7.841A  pdb=" N   THR C 163 " --> pdb=" O   THR C  49 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   LEU C  51 " --> pdb=" O   THR C 163 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   TYR C 270 " --> pdb=" O   VAL C 264 " (cutoff:3.500A)
      removed outlier: 4.721A  pdb=" N   VAL C 264 " --> pdb=" O   TYR C 270 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   ALA C 272 " --> pdb=" O   ILE C 262 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 296 through 298

    496 hydrogen bonds defined for protein.
    1317 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: 3.55

  Time building geometry restraints manager: 3.14 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1954
        1.32 -     1.45: 2325
        1.45 -     1.58: 5663
        1.58 -     1.72: 3
        1.72 -     1.85: 78
  Bond restraints: 10023
  Sorted by residual:
  bond pdb=" C5  BMA D   3 "
       pdb=" O5  BMA D   3 "
    ideal  model  delta    sigma   weight residual
    1.417  1.500 -0.083 2.00e-02 2.50e+03 1.71e+01
  bond pdb=" C5  BMA E   3 "
       pdb=" O5  BMA E   3 "
    ideal  model  delta    sigma   weight residual
    1.417  1.500 -0.083 2.00e-02 2.50e+03 1.71e+01
  bond pdb=" C5  BMA F   3 "
       pdb=" O5  BMA F   3 "
    ideal  model  delta    sigma   weight residual
    1.417  1.500 -0.083 2.00e-02 2.50e+03 1.71e+01
  bond pdb=" NE  ARG C 370 "
       pdb=" CZ  ARG C 370 "
    ideal  model  delta    sigma   weight residual
    1.326  1.371 -0.045 1.10e-02 8.26e+03 1.70e+01
  bond pdb=" NE  ARG B 370 "
       pdb=" CZ  ARG B 370 "
    ideal  model  delta    sigma   weight residual
    1.326  1.371 -0.045 1.10e-02 8.26e+03 1.69e+01
  ... (remaining 10018 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 12216
        2.07 -     4.14: 1227
        4.14 -     6.20: 165
        6.20 -     8.27: 33
        8.27 -    10.34: 6
  Bond angle restraints: 13647
  Sorted by residual:
  angle pdb=" C   GLY C 441 "
        pdb=" N   PRO C 442 "
        pdb=" CA  PRO C 442 "
      ideal   model   delta    sigma   weight residual
     119.66  125.54   -5.88 7.20e-01 1.93e+00 6.68e+01
  angle pdb=" C   GLY B 441 "
        pdb=" N   PRO B 442 "
        pdb=" CA  PRO B 442 "
      ideal   model   delta    sigma   weight residual
     119.66  125.52   -5.86 7.20e-01 1.93e+00 6.62e+01
  angle pdb=" C   GLY A 441 "
        pdb=" N   PRO A 442 "
        pdb=" CA  PRO A 442 "
      ideal   model   delta    sigma   weight residual
     119.66  125.51   -5.85 7.20e-01 1.93e+00 6.60e+01
  angle pdb=" C   SER A  46 "
        pdb=" N   PRO A  47 "
        pdb=" CA  PRO A  47 "
      ideal   model   delta    sigma   weight residual
     120.31  127.85   -7.54 9.80e-01 1.04e+00 5.92e+01
  angle pdb=" C   SER C  46 "
        pdb=" N   PRO C  47 "
        pdb=" CA  PRO C  47 "
      ideal   model   delta    sigma   weight residual
     120.31  127.84   -7.53 9.80e-01 1.04e+00 5.90e+01
  ... (remaining 13642 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.32: 6062
       21.32 -    42.64: 127
       42.64 -    63.95: 42
       63.95 -    85.27: 18
       85.27 -   106.59: 18
  Dihedral angle restraints: 6267
    sinusoidal: 2508
      harmonic: 3759
  Sorted by residual:
  dihedral pdb=" CB  CYS B  66 "
           pdb=" SG  CYS B  66 "
           pdb=" SG  CYS B 187 "
           pdb=" CB  CYS B 187 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -40.03  -45.97     1      1.00e+01 1.00e-02 2.93e+01
  dihedral pdb=" O4  BMA D   3 "
           pdb=" C4  BMA D   3 "
           pdb=" C5  BMA D   3 "
           pdb=" O5  BMA D   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -71.29 -177.88  106.59     1      3.00e+01 1.11e-03 1.37e+01
  dihedral pdb=" O4  BMA F   3 "
           pdb=" C4  BMA F   3 "
           pdb=" C5  BMA F   3 "
           pdb=" O5  BMA F   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -71.29 -177.87  106.58     1      3.00e+01 1.11e-03 1.37e+01
  ... (remaining 6264 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.090: 1239
       0.090 -    0.179: 395
       0.179 -    0.269: 61
       0.269 -    0.358: 24
       0.358 -    0.448: 6
  Chirality restraints: 1725
  Sorted by residual:
  chirality pdb=" C1  NAG F   2 "
            pdb=" O4  NAG F   1 "
            pdb=" C2  NAG F   2 "
            pdb=" O5  NAG F   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.53    0.13 2.00e-02 2.50e+03 4.00e+01
  chirality pdb=" C1  BMA E   3 "
            pdb=" O4  NAG E   2 "
            pdb=" C2  BMA E   3 "
            pdb=" O5  BMA E   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.53    0.13 2.00e-02 2.50e+03 3.94e+01
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.53    0.13 2.00e-02 2.50e+03 3.92e+01
  ... (remaining 1722 not shown)

  Planarity restraints: 1734
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 459 "    0.022 2.00e-02 2.50e+03   2.36e-02 6.93e+00
        pdb=" CG  ASN A 459 "   -0.009 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 459 "   -0.005 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 459 "   -0.037 2.00e-02 2.50e+03
        pdb=" C1  NAG E   1 "    0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 459 "    0.022 2.00e-02 2.50e+03   2.35e-02 6.90e+00
        pdb=" CG  ASN B 459 "   -0.009 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 459 "   -0.005 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 459 "   -0.037 2.00e-02 2.50e+03
        pdb=" C1  NAG D   1 "    0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN C 459 "    0.022 2.00e-02 2.50e+03   2.35e-02 6.88e+00
        pdb=" CG  ASN C 459 "   -0.009 2.00e-02 2.50e+03
        pdb=" OD1 ASN C 459 "   -0.005 2.00e-02 2.50e+03
        pdb=" ND2 ASN C 459 "   -0.037 2.00e-02 2.50e+03
        pdb=" C1  NAG F   1 "    0.029 2.00e-02 2.50e+03
  ... (remaining 1731 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 22
        2.60 -     3.17: 8982
        3.17 -     3.75: 15539
        3.75 -     4.32: 24469
        4.32 -     4.90: 37641
  Nonbonded interactions: 86653
  Sorted by model distance:
  nonbonded pdb=" SG  CYS A 350 "
            pdb=" SG  CYS A 358 "
     model   vdw
     2.021 3.760
  nonbonded pdb=" SG  CYS C 350 "
            pdb=" SG  CYS C 358 "
     model   vdw
     2.021 3.760
  nonbonded pdb=" SG  CYS A 389 "
            pdb=" SG  CYS A 412 "
     model   vdw
     2.028 3.760
  nonbonded pdb=" SG  CYS C 389 "
            pdb=" SG  CYS C 412 "
     model   vdw
     2.029 3.760
  nonbonded pdb=" SG  CYS A 326 "
            pdb=" SG  CYS A 335 "
     model   vdw
     2.030 3.760
  ... (remaining 86648 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'E'
  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=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:             2.500
  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:          0.430
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     28.000
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.030
  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:14.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
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      :  0.014   0.153  10040  Z= 0.769
  Angle     :  1.372  10.340  13693  Z= 0.929
  Chirality :  0.092   0.448   1725
  Planarity :  0.005   0.020   1728
  Dihedral  : 12.896 106.589   3834
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 0.75
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  1.40 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  0.84 %
    Favored  : 98.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.21), residues: 1284
  helix:  0.06 (0.22), residues: 447
  sheet:  0.29 (0.30), residues: 261
  loop :  0.05 (0.23), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.005   TRP C 303 
 HIS   0.004   0.001   HIS A 253 
 PHE   0.011   0.004   PHE C  71 
 TYR   0.030   0.006   TYR B  41 
 ARG   0.004   0.001   ARG A 258 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.06705 (    6)
  link_NAG-ASN         : angle       2.72023 (   18)
  link_BETA1-4         : bond        0.06517 (    6)
  link_BETA1-4         : angle       4.56883 (   18)
  hydrogen bonds       : bond        0.18699 (  496)
  hydrogen bonds       : angle       6.73440 ( 1317)
  SS BOND              : bond        0.07144 (    5)
  SS BOND              : angle       3.84455 (   10)
  covalent geometry    : bond        0.01404 (10023)
  covalent geometry    : angle       1.35705 (13647)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 114
  time to evaluate  : 1.184 
Fit side-chains
  outliers start: 3
  outliers final: 0
  residues processed: 116
  average time/residue: 2.2312
  time to fit residues: 272.6853
Evaluate side-chains
  62 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 1.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 108 optimal weight:    0.5980
   chunk 97 optimal weight:    0.6980
   chunk 54 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.5980
   chunk 52 optimal weight:    0.5980
   chunk 101 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9980
   chunk 117 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 260 ASN
B 320 ASN
B 454 GLN
A 260 ASN
C 260 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.080106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2682 r_free = 0.2682 target = 0.061361 restraints weight = 17996.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.2669 rms_B_bonded: 2.74
r_work: 0.2520 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.1728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10040  Z= 0.146
  Angle     :  0.621   8.968  13693  Z= 0.323
  Chirality :  0.046   0.139   1725
  Planarity :  0.004   0.038   1728
  Dihedral  : 10.034  71.376   1623
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  1.09 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  :  5.57 %
    Favored  : 93.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.22), residues: 1284
  helix:  1.29 (0.24), residues: 483
  sheet:  0.31 (0.30), residues: 267
  loop :  0.08 (0.25), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 303 
 HIS   0.002   0.001   HIS B 130 
 PHE   0.014   0.002   PHE A 230 
 TYR   0.020   0.002   TYR C 249 
 ARG   0.009   0.001   ARG A  64 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00836 (    6)
  link_NAG-ASN         : angle       1.76081 (   18)
  link_BETA1-4         : bond        0.00866 (    6)
  link_BETA1-4         : angle       4.28466 (   18)
  hydrogen bonds       : bond        0.05024 (  496)
  hydrogen bonds       : angle       4.69916 ( 1317)
  SS BOND              : bond        0.00391 (    5)
  SS BOND              : angle       1.56986 (   10)
  covalent geometry    : bond        0.00321 (10023)
  covalent geometry    : angle       0.59760 (13647)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 1.205 
Fit side-chains
REVERT: B  200 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8600 (tm-30)
REVERT: C  451 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8376 (mp)
  outliers start: 13
  outliers final: 5
  residues processed: 72
  average time/residue: 1.5800
  time to fit residues: 121.9771
Evaluate side-chains
  62 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 1.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  200 GLN
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain C residue  200 GLN
Chi-restraints excluded: chain C residue  367 TYR
Chi-restraints excluded: chain C residue  451 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 113 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 100 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 119 optimal weight:    1.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
B 177 ASN
B 454 GLN
A 177 ASN
C 162 GLN
C 177 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.075854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2588 r_free = 0.2588 target = 0.056998 restraints weight = 18275.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.2586 rms_B_bonded: 2.76
r_work: 0.2433 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8618
moved from start:          0.2166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  10040  Z= 0.213
  Angle     :  0.599   8.359  13693  Z= 0.314
  Chirality :  0.047   0.144   1725
  Planarity :  0.004   0.036   1728
  Dihedral  :  7.434  58.583   1623
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 1.91
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  1.32 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  :  6.04 %
    Favored  : 92.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.23), residues: 1284
  helix:  1.47 (0.24), residues: 483
  sheet:  0.35 (0.29), residues: 297
  loop :  0.06 (0.26), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B 303 
 HIS   0.004   0.001   HIS B 130 
 PHE   0.012   0.002   PHE A 230 
 TYR   0.017   0.002   TYR A 249 
 ARG   0.004   0.001   ARG A  64 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00600 (    6)
  link_NAG-ASN         : angle       1.28801 (   18)
  link_BETA1-4         : bond        0.00736 (    6)
  link_BETA1-4         : angle       3.77102 (   18)
  hydrogen bonds       : bond        0.05289 (  496)
  hydrogen bonds       : angle       4.40423 ( 1317)
  SS BOND              : bond        0.00459 (    5)
  SS BOND              : angle       1.69783 (   10)
  covalent geometry    : bond        0.00523 (10023)
  covalent geometry    : angle       0.58032 (13647)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 59
  time to evaluate  : 1.971 
Fit side-chains
REVERT: B   68 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7592 (tp-100)
REVERT: B  200 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8682 (tm-30)
REVERT: A  309 ARG cc_start: 0.8813 (mtp180) cc_final: 0.8069 (ttt180)
REVERT: C  142 MET cc_start: 0.8111 (mmp) cc_final: 0.7893 (mmm)
REVERT: C  309 ARG cc_start: 0.8869 (ttp80) cc_final: 0.8522 (ttt180)
  outliers start: 13
  outliers final: 6
  residues processed: 62
  average time/residue: 1.7393
  time to fit residues: 117.9051
Evaluate side-chains
  60 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 1.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 GLN
Chi-restraints excluded: chain B residue  200 GLN
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain B residue  449 ILE
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain C residue  200 GLN
Chi-restraints excluded: chain C residue  367 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 104 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 76 optimal weight:    3.9990
   chunk 107 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
B 157 GLN
B 454 GLN
C 157 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.075609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2587 r_free = 0.2587 target = 0.056933 restraints weight = 18133.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.2588 rms_B_bonded: 2.74
r_work: 0.2436 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.2286 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8734
moved from start:          0.2463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10040  Z= 0.170
  Angle     :  0.542   7.287  13693  Z= 0.286
  Chirality :  0.045   0.144   1725
  Planarity :  0.003   0.035   1728
  Dihedral  :  5.952  52.460   1623
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 1.91
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  1.09 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  6.31 %
    Favored  : 91.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.23), residues: 1284
  helix:  1.54 (0.24), residues: 483
  sheet:  0.22 (0.30), residues: 297
  loop : -0.02 (0.26), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP A 303 
 HIS   0.003   0.001   HIS B 130 
 PHE   0.009   0.002   PHE A 277 
 TYR   0.018   0.002   TYR A 249 
 ARG   0.004   0.001   ARG C 131 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00450 (    6)
  link_NAG-ASN         : angle       1.13855 (   18)
  link_BETA1-4         : bond        0.00498 (    6)
  link_BETA1-4         : angle       3.37467 (   18)
  hydrogen bonds       : bond        0.04695 (  496)
  hydrogen bonds       : angle       4.28075 ( 1317)
  SS BOND              : bond        0.00393 (    5)
  SS BOND              : angle       1.45382 (   10)
  covalent geometry    : bond        0.00412 (10023)
  covalent geometry    : angle       0.52594 (13647)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 57
  time to evaluate  : 2.187 
Fit side-chains
REVERT: B  200 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8761 (tm-30)
REVERT: C  309 ARG cc_start: 0.9068 (ttp80) cc_final: 0.8769 (ttt180)
  outliers start: 20
  outliers final: 5
  residues processed: 67
  average time/residue: 1.9289
  time to fit residues: 139.0976
Evaluate side-chains
  57 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 1.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  200 GLN
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain C residue  200 GLN
Chi-restraints excluded: chain C residue  367 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 104 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 32 optimal weight:    0.3980
   chunk 106 optimal weight:    1.9990
   chunk 55 optimal weight:    0.2980
   chunk 39 optimal weight:    0.9980
   chunk 107 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 119 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 454 GLN
A 157 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.076873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2625 r_free = 0.2625 target = 0.058428 restraints weight = 18027.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.2617 rms_B_bonded: 2.70
r_work: 0.2469 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2324 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8726
moved from start:          0.2627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10040  Z= 0.124
  Angle     :  0.506   6.303  13693  Z= 0.269
  Chirality :  0.044   0.154   1725
  Planarity :  0.003   0.034   1728
  Dihedral  :  5.313  40.801   1623
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  1.32 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  6.78 %
    Favored  : 91.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.23), residues: 1284
  helix:  1.66 (0.24), residues: 477
  sheet:  0.23 (0.30), residues: 297
  loop : -0.05 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP B 303 
 HIS   0.002   0.001   HIS B 130 
 PHE   0.010   0.001   PHE A 277 
 TYR   0.015   0.001   TYR C 249 
 ARG   0.004   0.001   ARG C 131 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00455 (    6)
  link_NAG-ASN         : angle       1.09983 (   18)
  link_BETA1-4         : bond        0.00495 (    6)
  link_BETA1-4         : angle       2.90140 (   18)
  hydrogen bonds       : bond        0.04146 (  496)
  hydrogen bonds       : angle       4.16216 ( 1317)
  SS BOND              : bond        0.00446 (    5)
  SS BOND              : angle       1.45884 (   10)
  covalent geometry    : bond        0.00290 (10023)
  covalent geometry    : angle       0.49308 (13647)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 61
  time to evaluate  : 1.311 
Fit side-chains
REVERT: B  200 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8826 (tm-30)
REVERT: A  309 ARG cc_start: 0.8957 (mtp180) cc_final: 0.8340 (ttt180)
REVERT: C  200 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8956 (tm-30)
REVERT: C  309 ARG cc_start: 0.9052 (ttp80) cc_final: 0.8803 (ttt180)
  outliers start: 19
  outliers final: 6
  residues processed: 72
  average time/residue: 1.5654
  time to fit residues: 120.7825
Evaluate side-chains
  59 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 1.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  200 GLN
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain C residue  200 GLN
Chi-restraints excluded: chain C residue  367 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 13 optimal weight:    0.5980
   chunk 105 optimal weight:    0.9990
   chunk 58 optimal weight:    0.5980
   chunk 100 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 29 optimal weight:    5.9990
   chunk 68 optimal weight:    5.9990
   chunk 102 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 84 optimal weight:    3.9990
   chunk 71 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.2992 r_free = 0.2992 target = 0.077140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2626 r_free = 0.2626 target = 0.058517 restraints weight = 17980.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.2621 rms_B_bonded: 2.73
r_work: 0.2471 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.2325 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8728
moved from start:          0.2763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10040  Z= 0.120
  Angle     :  0.505   6.245  13693  Z= 0.266
  Chirality :  0.044   0.211   1725
  Planarity :  0.003   0.033   1728
  Dihedral  :  4.844  26.256   1623
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  1.40 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  7.24 %
    Favored  : 90.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.23), residues: 1284
  helix:  1.73 (0.24), residues: 477
  sheet:  0.20 (0.30), residues: 297
  loop :  0.02 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP A 303 
 HIS   0.002   0.001   HIS A 130 
 PHE   0.009   0.001   PHE A 277 
 TYR   0.014   0.001   TYR C 249 
 ARG   0.004   0.000   ARG C 131 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00452 (    6)
  link_NAG-ASN         : angle       1.35236 (   18)
  link_BETA1-4         : bond        0.00478 (    6)
  link_BETA1-4         : angle       2.52977 (   18)
  hydrogen bonds       : bond        0.03935 (  496)
  hydrogen bonds       : angle       4.08370 ( 1317)
  SS BOND              : bond        0.00337 (    5)
  SS BOND              : angle       2.29555 (   10)
  covalent geometry    : bond        0.00281 (10023)
  covalent geometry    : angle       0.49078 (13647)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 56
  time to evaluate  : 1.142 
Fit side-chains
REVERT: A  309 ARG cc_start: 0.8957 (mtp180) cc_final: 0.8350 (ttt180)
REVERT: C  200 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8934 (tm-30)
REVERT: C  309 ARG cc_start: 0.9039 (ttp80) cc_final: 0.8790 (ttt180)
REVERT: C  451 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8261 (mm)
  outliers start: 19
  outliers final: 6
  residues processed: 67
  average time/residue: 1.5591
  time to fit residues: 112.5769
Evaluate side-chains
  62 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 1.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain B residue  449 ILE
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain C residue  200 GLN
Chi-restraints excluded: chain C residue  367 TYR
Chi-restraints excluded: chain C residue  451 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 120 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 121 optimal weight:    2.9990
   chunk 110 optimal weight:    0.8980
   chunk 52 optimal weight:    0.5980
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.2974 r_free = 0.2974 target = 0.076157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2600 r_free = 0.2600 target = 0.057324 restraints weight = 18434.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.2594 rms_B_bonded: 2.78
r_work: 0.2439 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8669
moved from start:          0.2857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10040  Z= 0.150
  Angle     :  0.512   6.084  13693  Z= 0.272
  Chirality :  0.044   0.168   1725
  Planarity :  0.003   0.033   1728
  Dihedral  :  4.616  22.613   1623
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  1.79 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  7.80 %
    Favored  : 90.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.24), residues: 1284
  helix:  1.71 (0.24), residues: 477
  sheet:  0.14 (0.30), residues: 297
  loop :  0.06 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B 303 
 HIS   0.002   0.001   HIS A 130 
 PHE   0.009   0.002   PHE C 234 
 TYR   0.014   0.001   TYR C 249 
 ARG   0.003   0.000   ARG B 131 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00390 (    6)
  link_NAG-ASN         : angle       1.35769 (   18)
  link_BETA1-4         : bond        0.00443 (    6)
  link_BETA1-4         : angle       2.25255 (   18)
  hydrogen bonds       : bond        0.04254 (  496)
  hydrogen bonds       : angle       4.12066 ( 1317)
  SS BOND              : bond        0.00259 (    5)
  SS BOND              : angle       1.63761 (   10)
  covalent geometry    : bond        0.00364 (10023)
  covalent geometry    : angle       0.50202 (13647)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 57
  time to evaluate  : 1.154 
Fit side-chains
REVERT: A  309 ARG cc_start: 0.8795 (mtp180) cc_final: 0.8161 (ttt180)
REVERT: C  200 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8828 (tm-30)
REVERT: C  309 ARG cc_start: 0.8882 (ttp80) cc_final: 0.8585 (ttt180)
REVERT: C  451 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8299 (mm)
  outliers start: 14
  outliers final: 6
  residues processed: 64
  average time/residue: 1.3593
  time to fit residues: 94.5031
Evaluate side-chains
  60 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 1.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain C residue  200 GLN
Chi-restraints excluded: chain C residue  367 TYR
Chi-restraints excluded: chain C residue  451 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 109 optimal weight:    0.1980
   chunk 66 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 90 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 92 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.2982 r_free = 0.2982 target = 0.076678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2604 r_free = 0.2604 target = 0.057648 restraints weight = 18023.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.2606 rms_B_bonded: 2.77
r_work: 0.2456 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8661
moved from start:          0.2944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10040  Z= 0.134
  Angle     :  0.502   6.621  13693  Z= 0.265
  Chirality :  0.044   0.152   1725
  Planarity :  0.003   0.032   1728
  Dihedral  :  4.482  20.248   1623
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  1.40 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  8.36 %
    Favored  : 90.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.24), residues: 1284
  helix:  1.70 (0.24), residues: 483
  sheet:  0.26 (0.31), residues: 282
  loop : -0.04 (0.27), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP A 303 
 HIS   0.002   0.001   HIS A 130 
 PHE   0.008   0.001   PHE A 277 
 TYR   0.014   0.001   TYR A 249 
 ARG   0.003   0.000   ARG A  64 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00433 (    6)
  link_NAG-ASN         : angle       1.20963 (   18)
  link_BETA1-4         : bond        0.00404 (    6)
  link_BETA1-4         : angle       2.17149 (   18)
  hydrogen bonds       : bond        0.04001 (  496)
  hydrogen bonds       : angle       4.07804 ( 1317)
  SS BOND              : bond        0.00264 (    5)
  SS BOND              : angle       1.42836 (   10)
  covalent geometry    : bond        0.00323 (10023)
  covalent geometry    : angle       0.49323 (13647)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 1.132 
Fit side-chains
REVERT: A   79 LYS cc_start: 0.8886 (ttmm) cc_final: 0.8614 (ttmm)
REVERT: A  309 ARG cc_start: 0.8789 (mtp180) cc_final: 0.8164 (ttt180)
REVERT: C  200 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8841 (tm-30)
REVERT: C  309 ARG cc_start: 0.8861 (ttp80) cc_final: 0.8559 (ttt180)
REVERT: C  451 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8263 (mm)
  outliers start: 14
  outliers final: 9
  residues processed: 63
  average time/residue: 1.5961
  time to fit residues: 109.3481
Evaluate side-chains
  64 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 2.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain B residue  449 ILE
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  200 GLN
Chi-restraints excluded: chain C residue  367 TYR
Chi-restraints excluded: chain C residue  451 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 100 optimal weight:    2.9990
   chunk 115 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   chunk 102 optimal weight:    0.9980
   chunk 29 optimal weight:    5.9990
   chunk 97 optimal weight:    0.9980
   chunk 47 optimal weight:    0.4980
   chunk 16 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   overall best weight:    1.6984

-------------------------------------------------------------------------------
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 = 0.2953 r_free = 0.2953 target = 0.074926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2574 r_free = 0.2574 target = 0.056072 restraints weight = 18497.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.2571 rms_B_bonded: 2.77
r_work: 0.2415 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8685
moved from start:          0.2944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066  10040  Z= 0.221
  Angle     :  0.565  10.165  13693  Z= 0.298
  Chirality :  0.046   0.146   1725
  Planarity :  0.003   0.032   1728
  Dihedral  :  4.596  20.782   1623
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 2.92
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  1.79 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  8.36 %
    Favored  : 90.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.24), residues: 1284
  helix:  1.61 (0.24), residues: 483
  sheet:  0.04 (0.30), residues: 297
  loop :  0.01 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP C 303 
 HIS   0.002   0.001   HIS C 130 
 PHE   0.011   0.002   PHE B 234 
 TYR   0.015   0.002   TYR A 249 
 ARG   0.003   0.000   ARG A 388 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00388 (    6)
  link_NAG-ASN         : angle       1.26163 (   18)
  link_BETA1-4         : bond        0.00428 (    6)
  link_BETA1-4         : angle       2.16934 (   18)
  hydrogen bonds       : bond        0.04833 (  496)
  hydrogen bonds       : angle       4.27121 ( 1317)
  SS BOND              : bond        0.00335 (    5)
  SS BOND              : angle       1.18356 (   10)
  covalent geometry    : bond        0.00547 (10023)
  covalent geometry    : angle       0.55760 (13647)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 56
  time to evaluate  : 1.108 
Fit side-chains
REVERT: A   79 LYS cc_start: 0.8897 (ttmm) cc_final: 0.8658 (ttmm)
REVERT: A  309 ARG cc_start: 0.8819 (mtp180) cc_final: 0.8170 (ttt180)
REVERT: C  309 ARG cc_start: 0.8915 (ttp80) cc_final: 0.8627 (ttt180)
REVERT: C  451 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8302 (mm)
  outliers start: 16
  outliers final: 7
  residues processed: 66
  average time/residue: 1.2941
  time to fit residues: 92.7620
Evaluate side-chains
  61 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 1.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  367 TYR
Chi-restraints excluded: chain C residue  451 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 57 optimal weight:    0.6980
   chunk 65 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 83 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0570
   chunk 123 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.6698

-------------------------------------------------------------------------------
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 = 0.2993 r_free = 0.2993 target = 0.077122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2624 r_free = 0.2624 target = 0.058343 restraints weight = 18073.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.2625 rms_B_bonded: 2.76
r_work: 0.2473 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
moved from start:          0.3058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10040  Z= 0.118
  Angle     :  0.501   6.697  13693  Z= 0.266
  Chirality :  0.044   0.157   1725
  Planarity :  0.003   0.032   1728
  Dihedral  :  4.460  20.132   1623
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  1.17 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  9.29 %
    Favored  : 89.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.24), residues: 1284
  helix:  1.70 (0.24), residues: 483
  sheet:  0.22 (0.31), residues: 282
  loop : -0.06 (0.27), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP C 303 
 HIS   0.002   0.001   HIS A 130 
 PHE   0.009   0.001   PHE B 277 
 TYR   0.013   0.001   TYR A 249 
 ARG   0.004   0.000   ARG B 131 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00470 (    6)
  link_NAG-ASN         : angle       1.15476 (   18)
  link_BETA1-4         : bond        0.00429 (    6)
  link_BETA1-4         : angle       2.07438 (   18)
  hydrogen bonds       : bond        0.03842 (  496)
  hydrogen bonds       : angle       4.12174 ( 1317)
  SS BOND              : bond        0.00197 (    5)
  SS BOND              : angle       1.09587 (   10)
  covalent geometry    : bond        0.00280 (10023)
  covalent geometry    : angle       0.49328 (13647)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 1.218 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.8897 (ttmm) cc_final: 0.8643 (ttmm)
REVERT: A  274 GLU cc_start: 0.8966 (tt0) cc_final: 0.8712 (tt0)
REVERT: A  309 ARG cc_start: 0.8786 (mtp180) cc_final: 0.8170 (ttt180)
REVERT: C  309 ARG cc_start: 0.8887 (ttp80) cc_final: 0.8677 (ttt180)
REVERT: C  451 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8310 (mm)
  outliers start: 11
  outliers final: 8
  residues processed: 64
  average time/residue: 1.3242
  time to fit residues: 92.3426
Evaluate side-chains
  61 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 1.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  367 TYR
Chi-restraints excluded: chain C residue  451 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 76 optimal weight:    0.0060
   chunk 38 optimal weight:    2.9990
   chunk 125 optimal weight:    1.9990
   chunk 88 optimal weight:    0.0570
   chunk 22 optimal weight:    3.9990
   chunk 108 optimal weight:    3.9990
   chunk 122 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.7116

-------------------------------------------------------------------------------
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 = 0.2993 r_free = 0.2993 target = 0.077093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2624 r_free = 0.2624 target = 0.058310 restraints weight = 18023.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.2616 rms_B_bonded: 2.75
r_work: 0.2465 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8658
moved from start:          0.3098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10040  Z= 0.121
  Angle     :  0.502   7.118  13693  Z= 0.266
  Chirality :  0.044   0.152   1725
  Planarity :  0.003   0.032   1728
  Dihedral  :  4.382  19.523   1623
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  1.64 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  9.56 %
    Favored  : 89.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.24), residues: 1284
  helix:  1.76 (0.24), residues: 483
  sheet:  0.21 (0.31), residues: 282
  loop : -0.02 (0.28), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B 303 
 HIS   0.002   0.001   HIS A 130 
 PHE   0.008   0.001   PHE A 277 
 TYR   0.014   0.001   TYR A 249 
 ARG   0.003   0.000   ARG A  64 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00466 (    6)
  link_NAG-ASN         : angle       1.17980 (   18)
  link_BETA1-4         : bond        0.00390 (    6)
  link_BETA1-4         : angle       2.04201 (   18)
  hydrogen bonds       : bond        0.03850 (  496)
  hydrogen bonds       : angle       4.10045 ( 1317)
  SS BOND              : bond        0.00221 (    5)
  SS BOND              : angle       0.98584 (   10)
  covalent geometry    : bond        0.00287 (10023)
  covalent geometry    : angle       0.49498 (13647)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5900.86 seconds
wall clock time: 104 minutes 46.36 seconds (6286.36 seconds total)