Starting phenix.real_space_refine
on Mon Jul  6 01:50:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7koq_22980/07_2026/7koq_22980_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7koq_22980/07_2026/7koq_22980.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7koq_22980/07_2026/7koq_22980.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7koq_22980/07_2026/7koq_22980.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7koq_22980/07_2026/7koq_22980_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7koq_22980/07_2026/7koq_22980_trim.cif"
  }
  resolution = 3.6
  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=   0.002
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: 7
    Type Number    sf(0)   Gaussians
     Ca      5      9.91       5
     S     110      5.16       5
     Cl      5      4.86       5
     C   10510      2.51       5
     N    2565      2.21       5
     O    2925      1.98       5
     H   15640      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 31760
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 6281
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 391, 6281
          Classifications: {'peptide': 391}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 369}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 42
          Ad-hoc single atom residues: {' CA': 1}
          Unusual residues: {'EPJ': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Restraints were copied for chains:
    B, C, D, E, G, H, I, J
  Time building chain proxies: 7.90, per 1000 atoms: 0.25
  Number of scatterers: 31760
  At special positions: 0
  Unit cell: (92.046, 93.38, 166.083, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Ca      5     19.99
     Cl      5     17.00
     S     110     16.00
     O    2925      8.00
     N    2565      7.00
     C   10510      6.00
     H   15640      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 127 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 189 " - pdb=" SG  CYS A 190 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 127 " - pdb=" SG  CYS B 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 127 " - pdb=" SG  CYS C 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 127 " - pdb=" SG  CYS D 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 127 " - pdb=" SG  CYS E 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 189 " - pdb=" SG  CYS B 190 " distance=2.05
    Simple disulfide: pdb=" SG  CYS C 189 " - pdb=" SG  CYS C 190 " distance=2.05
    Simple disulfide: pdb=" SG  CYS D 189 " - pdb=" SG  CYS D 190 " distance=2.05
    Simple disulfide: pdb=" SG  CYS E 189 " - pdb=" SG  CYS E 190 " distance=2.05

  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 F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG H   1 " - " NAG H   2 "
      " NAG I   1 " - " NAG I   2 "
      " NAG J   1 " - " NAG J   2 "
    NAG-ASN
      " NAG A 501 " - " ASN A  23 "
      " NAG A 502 " - " ASN A  67 "
      " NAG B 501 " - " ASN B  23 "
      " NAG B 502 " - " ASN B  67 "
      " NAG C 501 " - " ASN C  23 "
      " NAG C 502 " - " ASN C  67 "
      " NAG D 501 " - " ASN D  23 "
      " NAG D 502 " - " ASN D  67 "
      " NAG E 501 " - " ASN E  23 "
      " NAG E 502 " - " ASN E  67 "
      " NAG F   1 " - " ASN A 110 "
      " NAG G   1 " - " ASN B 110 "
      " NAG H   1 " - " ASN C 110 "
      " NAG I   1 " - " ASN D 110 "
      " NAG J   1 " - " ASN E 110 "
  Time building additional restraints: 3.05
  Conformation dependent library (CDL) restraints added in 880.5 milliseconds
  

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3730

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 20 sheets defined
      42.0% alpha, 29.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 11
      removed outlier: 3.880A  pdb=" N   LYS A   5 " --> pdb=" O   GLU A   1 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   VAL A  11 " --> pdb=" O   TYR A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 214
      removed outlier: 3.562A  pdb=" N   LEU A 214 " --> pdb=" O   TYR A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 227
    Processing helix  chain 'A' and resid 239 through 259
    Processing helix  chain 'A' and resid 268 through 296
    Processing helix  chain 'A' and resid 306 through 320
    Processing helix  chain 'A' and resid 409 through 466
    Processing helix  chain 'A' and resid 469 through 477
      removed outlier: 3.658A  pdb=" N   SER A 475 " --> pdb=" O   VAL A 471 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 11
      removed outlier: 3.702A  pdb=" N   VAL B  11 " --> pdb=" O   TYR B   7 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 214
      removed outlier: 3.562A  pdb=" N   LEU B 214 " --> pdb=" O   TYR B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 214 through 227
    Processing helix  chain 'B' and resid 239 through 259
    Processing helix  chain 'B' and resid 268 through 296
    Processing helix  chain 'B' and resid 306 through 320
    Processing helix  chain 'B' and resid 409 through 466
    Processing helix  chain 'B' and resid 469 through 477
      removed outlier: 3.658A  pdb=" N   SER B 475 " --> pdb=" O   VAL B 471 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2 through 11
      removed outlier: 3.702A  pdb=" N   VAL C  11 " --> pdb=" O   TYR C   7 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 207 through 214
      removed outlier: 3.561A  pdb=" N   LEU C 214 " --> pdb=" O   TYR C 210 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 214 through 227
    Processing helix  chain 'C' and resid 239 through 259
    Processing helix  chain 'C' and resid 268 through 296
    Processing helix  chain 'C' and resid 306 through 320
    Processing helix  chain 'C' and resid 409 through 466
    Processing helix  chain 'C' and resid 469 through 477
      removed outlier: 3.658A  pdb=" N   SER C 475 " --> pdb=" O   VAL C 471 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 2 through 11
      removed outlier: 3.702A  pdb=" N   VAL D  11 " --> pdb=" O   TYR D   7 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 207 through 214
      removed outlier: 3.562A  pdb=" N   LEU D 214 " --> pdb=" O   TYR D 210 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 214 through 227
    Processing helix  chain 'D' and resid 239 through 259
    Processing helix  chain 'D' and resid 268 through 296
    Processing helix  chain 'D' and resid 306 through 320
    Processing helix  chain 'D' and resid 409 through 466
    Processing helix  chain 'D' and resid 469 through 477
      removed outlier: 3.658A  pdb=" N   SER D 475 " --> pdb=" O   VAL D 471 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 2 through 11
      removed outlier: 3.702A  pdb=" N   VAL E  11 " --> pdb=" O   TYR E   7 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 207 through 214
      removed outlier: 3.562A  pdb=" N   LEU E 214 " --> pdb=" O   TYR E 210 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 214 through 227
    Processing helix  chain 'E' and resid 239 through 259
    Processing helix  chain 'E' and resid 268 through 296
    Processing helix  chain 'E' and resid 306 through 320
    Processing helix  chain 'E' and resid 409 through 466
    Processing helix  chain 'E' and resid 469 through 477
      removed outlier: 3.658A  pdb=" N   SER E 475 " --> pdb=" O   VAL E 471 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79
      removed outlier: 3.730A  pdb=" N   HIS A 114 " --> pdb=" O   ASN A 110 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 79
      removed outlier: 3.730A  pdb=" N   HIS A 114 " --> pdb=" O   ASN A 110 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   ASN A  52 " --> pdb=" O   ILE A  39 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   ILE A  39 " --> pdb=" O   ASN A  52 " (cutoff:3.500A)
      removed outlier: 8.860A  pdb=" N   TRP A  54 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   LEU A  37 " --> pdb=" O   TRP A  54 " (cutoff:3.500A)
      removed outlier: 7.451A  pdb=" N   GLN A  56 " --> pdb=" O   SER A  35 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   SER A  35 " --> pdb=" O   GLN A  56 " (cutoff:3.500A)
      removed outlier: 7.851A  pdb=" N   SER A  58 " --> pdb=" O   SER A  33 " (cutoff:3.500A)
      removed outlier: 8.079A  pdb=" N   SER A  33 " --> pdb=" O   SER A  58 " (cutoff:3.500A)
      removed outlier: 8.786A  pdb=" N   THR A  60 " --> pdb=" O   TYR A  31 " (cutoff:3.500A)
      removed outlier: 9.470A  pdb=" N   TYR A  31 " --> pdb=" O   THR A  60 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 91
      removed outlier: 3.741A  pdb=" N   GLY A 146 " --> pdb=" O   LEU A  90 " (cutoff:3.500A)
      removed outlier: 5.006A  pdb=" N   SER A 147 " --> pdb=" O   PRO A 195 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91
      removed outlier: 3.741A  pdb=" N   GLY A 146 " --> pdb=" O   LEU A  90 " (cutoff:3.500A)
      removed outlier: 5.006A  pdb=" N   SER A 147 " --> pdb=" O   PRO A 195 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 79
      removed outlier: 3.730A  pdb=" N   HIS B 114 " --> pdb=" O   ASN B 110 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 79
      removed outlier: 3.730A  pdb=" N   HIS B 114 " --> pdb=" O   ASN B 110 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   ASN B  52 " --> pdb=" O   ILE B  39 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   ILE B  39 " --> pdb=" O   ASN B  52 " (cutoff:3.500A)
      removed outlier: 8.860A  pdb=" N   TRP B  54 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   LEU B  37 " --> pdb=" O   TRP B  54 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   GLN B  56 " --> pdb=" O   SER B  35 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   SER B  35 " --> pdb=" O   GLN B  56 " (cutoff:3.500A)
      removed outlier: 7.851A  pdb=" N   SER B  58 " --> pdb=" O   SER B  33 " (cutoff:3.500A)
      removed outlier: 8.079A  pdb=" N   SER B  33 " --> pdb=" O   SER B  58 " (cutoff:3.500A)
      removed outlier: 8.787A  pdb=" N   THR B  60 " --> pdb=" O   TYR B  31 " (cutoff:3.500A)
      removed outlier: 9.470A  pdb=" N   TYR B  31 " --> pdb=" O   THR B  60 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 91
      removed outlier: 3.740A  pdb=" N   GLY B 146 " --> pdb=" O   LEU B  90 " (cutoff:3.500A)
      removed outlier: 5.007A  pdb=" N   SER B 147 " --> pdb=" O   PRO B 195 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 91
      removed outlier: 3.740A  pdb=" N   GLY B 146 " --> pdb=" O   LEU B  90 " (cutoff:3.500A)
      removed outlier: 5.007A  pdb=" N   SER B 147 " --> pdb=" O   PRO B 195 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 79
      removed outlier: 3.729A  pdb=" N   HIS C 114 " --> pdb=" O   ASN C 110 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79
      removed outlier: 3.729A  pdb=" N   HIS C 114 " --> pdb=" O   ASN C 110 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   ASN C  52 " --> pdb=" O   ILE C  39 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   ILE C  39 " --> pdb=" O   ASN C  52 " (cutoff:3.500A)
      removed outlier: 8.859A  pdb=" N   TRP C  54 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   LEU C  37 " --> pdb=" O   TRP C  54 " (cutoff:3.500A)
      removed outlier: 7.451A  pdb=" N   GLN C  56 " --> pdb=" O   SER C  35 " (cutoff:3.500A)
      removed outlier: 7.737A  pdb=" N   SER C  35 " --> pdb=" O   GLN C  56 " (cutoff:3.500A)
      removed outlier: 7.851A  pdb=" N   SER C  58 " --> pdb=" O   SER C  33 " (cutoff:3.500A)
      removed outlier: 8.079A  pdb=" N   SER C  33 " --> pdb=" O   SER C  58 " (cutoff:3.500A)
      removed outlier: 8.787A  pdb=" N   THR C  60 " --> pdb=" O   TYR C  31 " (cutoff:3.500A)
      removed outlier: 9.470A  pdb=" N   TYR C  31 " --> pdb=" O   THR C  60 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 89 through 91
      removed outlier: 3.740A  pdb=" N   GLY C 146 " --> pdb=" O   LEU C  90 " (cutoff:3.500A)
      removed outlier: 5.006A  pdb=" N   SER C 147 " --> pdb=" O   PRO C 195 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 89 through 91
      removed outlier: 3.740A  pdb=" N   GLY C 146 " --> pdb=" O   LEU C  90 " (cutoff:3.500A)
      removed outlier: 5.006A  pdb=" N   SER C 147 " --> pdb=" O   PRO C 195 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 79
      removed outlier: 3.729A  pdb=" N   HIS D 114 " --> pdb=" O   ASN D 110 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 79
      removed outlier: 3.729A  pdb=" N   HIS D 114 " --> pdb=" O   ASN D 110 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   ASN D  52 " --> pdb=" O   ILE D  39 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   ILE D  39 " --> pdb=" O   ASN D  52 " (cutoff:3.500A)
      removed outlier: 8.860A  pdb=" N   TRP D  54 " --> pdb=" O   LEU D  37 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   LEU D  37 " --> pdb=" O   TRP D  54 " (cutoff:3.500A)
      removed outlier: 7.451A  pdb=" N   GLN D  56 " --> pdb=" O   SER D  35 " (cutoff:3.500A)
      removed outlier: 7.737A  pdb=" N   SER D  35 " --> pdb=" O   GLN D  56 " (cutoff:3.500A)
      removed outlier: 7.851A  pdb=" N   SER D  58 " --> pdb=" O   SER D  33 " (cutoff:3.500A)
      removed outlier: 8.079A  pdb=" N   SER D  33 " --> pdb=" O   SER D  58 " (cutoff:3.500A)
      removed outlier: 8.787A  pdb=" N   THR D  60 " --> pdb=" O   TYR D  31 " (cutoff:3.500A)
      removed outlier: 9.470A  pdb=" N   TYR D  31 " --> pdb=" O   THR D  60 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 91
      removed outlier: 3.740A  pdb=" N   GLY D 146 " --> pdb=" O   LEU D  90 " (cutoff:3.500A)
      removed outlier: 5.006A  pdb=" N   SER D 147 " --> pdb=" O   PRO D 195 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 89 through 91
      removed outlier: 3.740A  pdb=" N   GLY D 146 " --> pdb=" O   LEU D  90 " (cutoff:3.500A)
      removed outlier: 5.006A  pdb=" N   SER D 147 " --> pdb=" O   PRO D 195 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 76 through 79
      removed outlier: 3.730A  pdb=" N   HIS E 114 " --> pdb=" O   ASN E 110 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 76 through 79
      removed outlier: 3.730A  pdb=" N   HIS E 114 " --> pdb=" O   ASN E 110 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   ASN E  52 " --> pdb=" O   ILE E  39 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   ILE E  39 " --> pdb=" O   ASN E  52 " (cutoff:3.500A)
      removed outlier: 8.860A  pdb=" N   TRP E  54 " --> pdb=" O   LEU E  37 " (cutoff:3.500A)
      removed outlier: 7.342A  pdb=" N   LEU E  37 " --> pdb=" O   TRP E  54 " (cutoff:3.500A)
      removed outlier: 7.451A  pdb=" N   GLN E  56 " --> pdb=" O   SER E  35 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   SER E  35 " --> pdb=" O   GLN E  56 " (cutoff:3.500A)
      removed outlier: 7.851A  pdb=" N   SER E  58 " --> pdb=" O   SER E  33 " (cutoff:3.500A)
      removed outlier: 8.079A  pdb=" N   SER E  33 " --> pdb=" O   SER E  58 " (cutoff:3.500A)
      removed outlier: 8.787A  pdb=" N   THR E  60 " --> pdb=" O   TYR E  31 " (cutoff:3.500A)
      removed outlier: 9.470A  pdb=" N   TYR E  31 " --> pdb=" O   THR E  60 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'E' and resid 89 through 91
      removed outlier: 3.741A  pdb=" N   GLY E 146 " --> pdb=" O   LEU E  90 " (cutoff:3.500A)
      removed outlier: 5.006A  pdb=" N   SER E 147 " --> pdb=" O   PRO E 195 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 89 through 91
      removed outlier: 3.741A  pdb=" N   GLY E 146 " --> pdb=" O   LEU E  90 " (cutoff:3.500A)
      removed outlier: 5.006A  pdb=" N   SER E 147 " --> pdb=" O   PRO E 195 " (cutoff:3.500A)

    950 hydrogen bonds defined for protein.
    2790 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: 7.05

  Time building geometry restraints manager: 4.25 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 15600
        1.04 -     1.24: 2110
        1.24 -     1.45: 5274
        1.45 -     1.65: 9051
        1.65 -     1.85: 170
  Bond restraints: 32205
  Sorted by residual:
  bond pdb=" C1  EPJ E 503 "
       pdb=" C7  EPJ E 503 "
    ideal  model  delta    sigma   weight residual
    1.505  1.732 -0.227 2.00e-02 2.50e+03 1.28e+02
  bond pdb=" C1  EPJ B 503 "
       pdb=" C7  EPJ B 503 "
    ideal  model  delta    sigma   weight residual
    1.505  1.732 -0.227 2.00e-02 2.50e+03 1.28e+02
  bond pdb=" C1  EPJ A 503 "
       pdb=" C7  EPJ A 503 "
    ideal  model  delta    sigma   weight residual
    1.505  1.731 -0.226 2.00e-02 2.50e+03 1.28e+02
  bond pdb=" C1  EPJ C 503 "
       pdb=" C7  EPJ C 503 "
    ideal  model  delta    sigma   weight residual
    1.505  1.731 -0.226 2.00e-02 2.50e+03 1.28e+02
  bond pdb=" C1  EPJ D 503 "
       pdb=" C7  EPJ D 503 "
    ideal  model  delta    sigma   weight residual
    1.505  1.731 -0.226 2.00e-02 2.50e+03 1.27e+02
  ... (remaining 32200 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     8.52: 57995
        8.52 -    17.03: 35
       17.03 -    25.55: 25
       25.55 -    34.07: 35
       34.07 -    42.58: 20
  Bond angle restraints: 58110
  Sorted by residual:
  angle pdb=" CE  LYS D   5 "
        pdb=" CD  LYS D   5 "
        pdb=" HD3 LYS D   5 "
      ideal   model   delta    sigma   weight residual
     108.00   65.42   42.58 3.00e+00 1.11e-01 2.01e+02
  angle pdb=" CE  LYS E   5 "
        pdb=" CD  LYS E   5 "
        pdb=" HD3 LYS E   5 "
      ideal   model   delta    sigma   weight residual
     108.00   65.43   42.57 3.00e+00 1.11e-01 2.01e+02
  angle pdb=" CE  LYS C   5 "
        pdb=" CD  LYS C   5 "
        pdb=" HD3 LYS C   5 "
      ideal   model   delta    sigma   weight residual
     108.00   65.43   42.57 3.00e+00 1.11e-01 2.01e+02
  angle pdb=" CE  LYS B   5 "
        pdb=" CD  LYS B   5 "
        pdb=" HD3 LYS B   5 "
      ideal   model   delta    sigma   weight residual
     108.00   65.44   42.56 3.00e+00 1.11e-01 2.01e+02
  angle pdb=" CE  LYS A   5 "
        pdb=" CD  LYS A   5 "
        pdb=" HD3 LYS A   5 "
      ideal   model   delta    sigma   weight residual
     108.00   65.45   42.55 3.00e+00 1.11e-01 2.01e+02
  ... (remaining 58105 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.17: 13685
       14.17 -    28.35: 1301
       28.35 -    42.52: 404
       42.52 -    56.69: 190
       56.69 -    70.87: 40
  Dihedral angle restraints: 15620
    sinusoidal: 8530
      harmonic: 7090
  Sorted by residual:
  dihedral pdb=" CA  CYS B 189 "
           pdb=" C   CYS B 189 "
           pdb=" N   CYS B 190 "
           pdb=" CA  CYS B 190 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.99  -25.01     0      5.00e+00 4.00e-02 2.50e+01
  dihedral pdb=" CA  CYS E 189 "
           pdb=" C   CYS E 189 "
           pdb=" N   CYS E 190 "
           pdb=" CA  CYS E 190 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.01  -24.99     0      5.00e+00 4.00e-02 2.50e+01
  dihedral pdb=" CA  CYS C 189 "
           pdb=" C   CYS C 189 "
           pdb=" N   CYS C 190 "
           pdb=" CA  CYS C 190 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.02  -24.98     0      5.00e+00 4.00e-02 2.50e+01
  ... (remaining 15617 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.278: 2580
       0.278 -    0.556: 5
       0.556 -    0.834: 5
       0.834 -    1.111: 5
       1.111 -    1.389: 5
  Chirality restraints: 2600
  Sorted by residual:
  chirality pdb=" CB  VAL C  68 "
            pdb=" CA  VAL C  68 "
            pdb=" CG1 VAL C  68 "
            pdb=" CG2 VAL C  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -1.24   -1.39 2.00e-01 2.50e+01 4.82e+01
  chirality pdb=" CB  VAL D  68 "
            pdb=" CA  VAL D  68 "
            pdb=" CG1 VAL D  68 "
            pdb=" CG2 VAL D  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -1.24   -1.39 2.00e-01 2.50e+01 4.81e+01
  chirality pdb=" CB  VAL A  68 "
            pdb=" CA  VAL A  68 "
            pdb=" CG1 VAL A  68 "
            pdb=" CG2 VAL A  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -1.24   -1.39 2.00e-01 2.50e+01 4.80e+01
  ... (remaining 2597 not shown)

  Planarity restraints: 4630
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 118 "   -0.030 5.00e-02 4.00e+02   4.55e-02 3.32e+00
        pdb=" N   PRO D 119 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO D 119 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO D 119 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 118 "   -0.030 5.00e-02 4.00e+02   4.54e-02 3.30e+00
        pdb=" N   PRO C 119 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO C 119 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO C 119 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 118 "   -0.030 5.00e-02 4.00e+02   4.53e-02 3.29e+00
        pdb=" N   PRO A 119 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 119 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 119 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 4627 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.14: 919
        2.14 -     2.76: 58646
        2.76 -     3.37: 81313
        3.37 -     3.99: 104474
        3.99 -     4.60: 168016
  Nonbonded interactions: 413368
  Sorted by model distance:
  nonbonded pdb=" O   ILE B 463 "
            pdb=" HG  SER B 466 "
     model   vdw
     1.528 2.450
  nonbonded pdb=" O   ILE D 463 "
            pdb=" HG  SER D 466 "
     model   vdw
     1.528 2.450
  nonbonded pdb=" O   ILE A 463 "
            pdb=" HG  SER A 466 "
     model   vdw
     1.528 2.450
  nonbonded pdb=" O   ILE C 463 "
            pdb=" HG  SER C 466 "
     model   vdw
     1.528 2.450
  nonbonded pdb=" O   ILE E 463 "
            pdb=" HG  SER E 466 "
     model   vdw
     1.529 2.450
  ... (remaining 413363 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.220
  Extract box with map and model:          0.580
  Check model and map are aligned:         0.100
  Set scattering table:                    0.080
  Process input model:                     31.890
  Find NCS groups from input model:        0.180
  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:             0.010
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
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   0.227  16595  Z= 0.614
  Angle     :  0.892  17.140  22660  Z= 0.434
  Chirality :  0.093   1.389   2600
  Planarity :  0.005   0.046   2775
  Dihedral  : 13.069  70.867   6330
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  3.97 %
    Favored  : 95.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  0.04 (0.19), residues: 1935
  helix:  1.74 (0.17), residues: 790
  sheet: -0.21 (0.24), residues: 445
  loop : -1.86 (0.22), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 423 
 TYR   0.012   0.002   TYR E  92 
 PHE   0.011   0.001   PHE D 134 
 TRP   0.012   0.001   TRP D 437 
 HIS   0.002   0.001   HIS D 104 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01381 /  0.61 (16565)
  covalent geometry    : angle       0.86965 /  0.43 (22580)
  SS BOND              : bond        0.01224 /  0.66 (   10)
  SS BOND              : angle       4.43007 /  2.77 (   20)
  hydrogen bonds       : bond        0.13305 /  8.87 (  850)
  hydrogen bonds       : angle       5.31647 /  3.74 ( 2790)
  link_BETA1-4         : bond        0.00070 /  0.04 (    5)
  link_BETA1-4         : angle       1.92365 /  1.18 (   15)
  link_NAG-ASN         : bond        0.00596 /  0.32 (   15)
  link_NAG-ASN         : angle       3.33439 /  2.18 (   45)

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

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

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 293
  time to evaluate  : 0.816 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7400 (ttmm)
REVERT: A   83 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7832 (mt0)
REVERT: A  160 GLN cc_start: 0.7614 (mt0) cc_final: 0.7344 (mt0)
REVERT: A  234 ASP cc_start: 0.6969 (t0) cc_final: 0.6723 (t0)
REVERT: B    5 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7383 (tttp)
REVERT: B   83 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7831 (mt0)
REVERT: B  142 LYS cc_start: 0.8205 (pttp) cc_final: 0.7982 (pttp)
REVERT: C    5 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7198 (tttp)
REVERT: C   83 GLN cc_start: 0.8265 (mm-40) cc_final: 0.7859 (mt0)
REVERT: C   93 ASN cc_start: 0.8478 (p0) cc_final: 0.8177 (p0)
REVERT: D    5 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.6987 (ttmm)
REVERT: D  293 GLN cc_start: 0.7617 (tp40) cc_final: 0.7379 (tp40)
REVERT: E    5 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.7169 (tttt)
REVERT: E  142 LYS cc_start: 0.8112 (pttp) cc_final: 0.7863 (pttp)
REVERT: E  293 GLN cc_start: 0.7486 (tp40) cc_final: 0.7232 (tp40)
REVERT: E  465 MET cc_start: 0.6602 (mmt) cc_final: 0.6258 (mmt)
  outliers start: 10
  outliers final: 0
  residues processed: 298
  average time/residue: 0.2844
  time to fit residues: 128.5381
Evaluate side-chains
  261 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 256
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LYS
Chi-restraints excluded: chain B residue    5 LYS
Chi-restraints excluded: chain C residue    5 LYS
Chi-restraints excluded: chain D residue    5 LYS
Chi-restraints excluded: chain E residue    5 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 194 optimal weight:    3.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    0.4980
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.5980
   chunk 91 optimal weight:    0.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 293 GLN
E 293 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.149305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.119347 restraints weight = 53422.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.125407 restraints weight = 21215.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.129242 restraints weight = 11471.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.131551 restraints weight = 7529.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.133003 restraints weight = 5667.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.1010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.134  16595  Z= 0.154
  Angle     :  0.660  12.962  22660  Z= 0.340
  Chirality :  0.074   1.430   2600
  Planarity :  0.005   0.055   2775
  Dihedral  :  8.638  52.118   2650
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  :  7.31 %
    Favored  : 91.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

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:  0.67 (0.19), residues: 1935
  helix:  2.30 (0.17), residues: 805
  sheet:  0.14 (0.24), residues: 450
  loop : -1.70 (0.23), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 205 
 TYR   0.009   0.001   TYR C 187 
 PHE   0.007   0.001   PHE B   2 
 TRP   0.010   0.001   TRP D 437 
 HIS   0.002   0.001   HIS B 114 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00359 /  0.15 (16565)
  covalent geometry    : angle       0.63146 /  0.33 (22580)
  SS BOND              : bond        0.02093 /  1.09 (   10)
  SS BOND              : angle       5.51325 /  3.04 (   20)
  hydrogen bonds       : bond        0.06405 /  4.22 (  850)
  hydrogen bonds       : angle       4.55917 /  3.23 ( 2790)
  link_BETA1-4         : bond        0.00455 /  0.23 (    5)
  link_BETA1-4         : angle       0.73638 /  0.40 (   15)
  link_NAG-ASN         : bond        0.00220 /  0.12 (   15)
  link_NAG-ASN         : angle       2.41433 /  1.51 (   45)

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

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

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 286
  time to evaluate  : 0.868 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7312 (ttmm)
REVERT: A  160 GLN cc_start: 0.7512 (mt0) cc_final: 0.7293 (mt0)
REVERT: A  234 ASP cc_start: 0.6946 (t0) cc_final: 0.6731 (t0)
REVERT: B    5 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7394 (ttmm)
REVERT: B   83 GLN cc_start: 0.8257 (mm-40) cc_final: 0.7777 (mt0)
REVERT: B  476 LYS cc_start: 0.7608 (mttt) cc_final: 0.7220 (ttmt)
REVERT: C    5 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7167 (tttp)
REVERT: C   83 GLN cc_start: 0.8309 (mm-40) cc_final: 0.7835 (mt0)
REVERT: C  184 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7624 (mt-10)
REVERT: D    5 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6934 (ttmm)
REVERT: D   13 ASN cc_start: 0.8311 (OUTLIER) cc_final: 0.8048 (m-40)
REVERT: D   83 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7701 (mt0)
REVERT: D  184 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7553 (mt-10)
REVERT: D  293 GLN cc_start: 0.7619 (tp-100) cc_final: 0.7333 (tp40)
REVERT: E    5 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.7030 (ttmt)
REVERT: E   13 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.8120 (m-40)
REVERT: E   83 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7714 (mt0)
REVERT: E  293 GLN cc_start: 0.7434 (tp-100) cc_final: 0.7160 (tp40)
REVERT: E  465 MET cc_start: 0.6347 (mmt) cc_final: 0.6045 (mmt)
  outliers start: 26
  outliers final: 16
  residues processed: 298
  average time/residue: 0.2862
  time to fit residues: 128.9644
Evaluate side-chains
  293 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 270
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LYS
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  459 CYS
Chi-restraints excluded: chain B residue    5 LYS
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  459 CYS
Chi-restraints excluded: chain C residue    5 LYS
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  149 SER
Chi-restraints excluded: chain C residue  459 CYS
Chi-restraints excluded: chain D residue    5 LYS
Chi-restraints excluded: chain D residue   13 ASN
Chi-restraints excluded: chain D residue   25 SER
Chi-restraints excluded: chain D residue  125 SER
Chi-restraints excluded: chain D residue  149 SER
Chi-restraints excluded: chain D residue  459 CYS
Chi-restraints excluded: chain E residue    5 LYS
Chi-restraints excluded: chain E residue   13 ASN
Chi-restraints excluded: chain E residue   25 SER
Chi-restraints excluded: chain E residue  125 SER
Chi-restraints excluded: chain E residue  149 SER
Chi-restraints excluded: chain E residue  184 GLU
Chi-restraints excluded: chain E residue  459 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 158 optimal weight:    2.9990
   chunk 171 optimal weight:    0.5980
   chunk 77 optimal weight:    3.9990
   chunk 144 optimal weight:    0.8980
   chunk 128 optimal weight:    0.9990
   chunk 125 optimal weight:    0.9980
   chunk 78 optimal weight:    2.9990
   chunk 99 optimal weight:    1.9990
   chunk 102 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0980
   overall best weight:    0.7182

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.148345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.118566 restraints weight = 53599.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.124604 restraints weight = 21324.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.128321 restraints weight = 11466.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.130629 restraints weight = 7534.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.131981 restraints weight = 5681.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.1328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.226  16595  Z= 0.155
  Angle     :  0.643  19.936  22660  Z= 0.329
  Chirality :  0.074   1.440   2600
  Planarity :  0.004   0.045   2775
  Dihedral  :  7.811  65.876   2650
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  :  7.48 %
    Favored  : 90.71 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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:  0.90 (0.19), residues: 1935
  helix:  2.52 (0.17), residues: 815
  sheet:  0.24 (0.24), residues: 455
  loop : -1.70 (0.23), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 423 
 TYR   0.006   0.001   TYR C 128 
 PHE   0.007   0.001   PHE A 134 
 TRP   0.008   0.001   TRP D 437 
 HIS   0.001   0.000   HIS B 104 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00388 /  0.15 (16565)
  covalent geometry    : angle       0.61780 /  0.32 (22580)
  SS BOND              : bond        0.02020 /  0.93 (   10)
  SS BOND              : angle       5.04445 /  3.26 (   20)
  hydrogen bonds       : bond        0.05966 /  3.92 (  850)
  hydrogen bonds       : angle       4.38715 /  3.11 ( 2790)
  link_BETA1-4         : bond        0.00341 /  0.16 (    5)
  link_BETA1-4         : angle       1.13746 /  0.62 (   15)
  link_NAG-ASN         : bond        0.00121 /  0.08 (   15)
  link_NAG-ASN         : angle       2.25035 /  1.40 (   45)

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

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

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 285
  time to evaluate  : 1.021 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7331 (ttmm)
REVERT: A  160 GLN cc_start: 0.7544 (mt0) cc_final: 0.7318 (mt0)
REVERT: A  234 ASP cc_start: 0.7032 (t0) cc_final: 0.6805 (t0)
REVERT: B    5 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7329 (tttp)
REVERT: B  184 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7815 (mt-10)
REVERT: B  476 LYS cc_start: 0.7420 (mttt) cc_final: 0.7086 (ttmt)
REVERT: C    5 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.7174 (tttp)
REVERT: C   83 GLN cc_start: 0.8389 (mm-40) cc_final: 0.7853 (mt0)
REVERT: C  184 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7727 (mt-10)
REVERT: C  476 LYS cc_start: 0.7634 (mttt) cc_final: 0.7372 (mttt)
REVERT: D    5 LYS cc_start: 0.7296 (OUTLIER) cc_final: 0.6999 (ttmm)
REVERT: D   13 ASN cc_start: 0.8363 (OUTLIER) cc_final: 0.8091 (m-40)
REVERT: D   83 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7782 (mt0)
REVERT: D  184 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7606 (mt-10)
REVERT: D  227 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7752 (tt)
REVERT: D  293 GLN cc_start: 0.7580 (tp-100) cc_final: 0.7323 (tp40)
REVERT: E    5 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.7033 (ttmt)
REVERT: E   13 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.8174 (m-40)
REVERT: E   83 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7715 (mt0)
REVERT: E  293 GLN cc_start: 0.7453 (tp-100) cc_final: 0.7204 (tp40)
REVERT: E  465 MET cc_start: 0.6421 (mmt) cc_final: 0.6084 (mmt)
  outliers start: 32
  outliers final: 18
  residues processed: 300
  average time/residue: 0.2777
  time to fit residues: 129.0686
Evaluate side-chains
  302 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 276
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LYS
Chi-restraints excluded: chain A residue  125 SER
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  459 CYS
Chi-restraints excluded: chain B residue    5 LYS
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  459 CYS
Chi-restraints excluded: chain B residue  465 MET
Chi-restraints excluded: chain C residue    5 LYS
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  149 SER
Chi-restraints excluded: chain C residue  459 CYS
Chi-restraints excluded: chain D residue    5 LYS
Chi-restraints excluded: chain D residue   13 ASN
Chi-restraints excluded: chain D residue   25 SER
Chi-restraints excluded: chain D residue  125 SER
Chi-restraints excluded: chain D residue  130 ASP
Chi-restraints excluded: chain D residue  149 SER
Chi-restraints excluded: chain D residue  227 LEU
Chi-restraints excluded: chain D residue  459 CYS
Chi-restraints excluded: chain E residue    5 LYS
Chi-restraints excluded: chain E residue   13 ASN
Chi-restraints excluded: chain E residue   25 SER
Chi-restraints excluded: chain E residue  125 SER
Chi-restraints excluded: chain E residue  149 SER
Chi-restraints excluded: chain E residue  459 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 122 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 183 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 175 optimal weight:    0.6980
   chunk 96 optimal weight:    2.9990
   chunk 101 optimal weight:    0.0030
   chunk 124 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 148 optimal weight:    4.9990
   chunk 184 optimal weight:    2.9990
   overall best weight:    0.8192

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.149520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.119430 restraints weight = 53676.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.125384 restraints weight = 22003.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.129083 restraints weight = 12070.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.131289 restraints weight = 8035.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.132687 restraints weight = 6142.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.172  16595  Z= 0.148
  Angle     :  0.609  12.877  22660  Z= 0.312
  Chirality :  0.074   1.442   2600
  Planarity :  0.004   0.042   2775
  Dihedral  :  7.062  57.487   2650
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  :  9.01 %
    Favored  : 88.90 %
  Cbeta Deviations :  0.16 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.15 (0.19), residues: 1935
  helix:  2.73 (0.17), residues: 815
  sheet:  0.25 (0.25), residues: 465
  loop : -1.48 (0.24), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 423 
 TYR   0.011   0.001   TYR A 128 
 PHE   0.006   0.001   PHE A 134 
 TRP   0.009   0.001   TRP D 437 
 HIS   0.001   0.000   HIS A 296 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00356 /  0.15 (16565)
  covalent geometry    : angle       0.58325 /  0.30 (22580)
  SS BOND              : bond        0.01938 /  1.03 (   10)
  SS BOND              : angle       5.06168 /  3.77 (   20)
  hydrogen bonds       : bond        0.05663 /  3.72 (  850)
  hydrogen bonds       : angle       4.28331 /  3.03 ( 2790)
  link_BETA1-4         : bond        0.00264 /  0.14 (    5)
  link_BETA1-4         : angle       1.09516 /  0.62 (   15)
  link_NAG-ASN         : bond        0.00125 /  0.08 (   15)
  link_NAG-ASN         : angle       2.13608 /  1.32 (   45)

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

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

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  329 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 292
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7370 (ttmm)
REVERT: A  160 GLN cc_start: 0.7522 (mt0) cc_final: 0.7315 (mt0)
REVERT: A  234 ASP cc_start: 0.7036 (t0) cc_final: 0.6819 (t0)
REVERT: B    5 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7335 (tttp)
REVERT: B  439 PHE cc_start: 0.7722 (t80) cc_final: 0.7470 (t80)
REVERT: B  476 LYS cc_start: 0.7352 (mttt) cc_final: 0.7142 (ttmt)
REVERT: C    5 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7220 (tttp)
REVERT: C   70 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7285 (mt-10)
REVERT: C   83 GLN cc_start: 0.8456 (mm-40) cc_final: 0.8232 (mm-40)
REVERT: C  184 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7726 (mt-10)
REVERT: C  227 LEU cc_start: 0.8049 (tp) cc_final: 0.7791 (tt)
REVERT: D    5 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.6999 (ttmm)
REVERT: D   13 ASN cc_start: 0.8417 (OUTLIER) cc_final: 0.8161 (m-40)
REVERT: D  184 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7724 (mt-10)
REVERT: D  227 LEU cc_start: 0.8062 (tp) cc_final: 0.7810 (tt)
REVERT: D  293 GLN cc_start: 0.7560 (tp-100) cc_final: 0.7308 (tp40)
REVERT: D  439 PHE cc_start: 0.7781 (t80) cc_final: 0.7417 (t80)
REVERT: D  476 LYS cc_start: 0.7745 (mttt) cc_final: 0.7509 (mttt)
REVERT: E    5 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.7132 (tttp)
REVERT: E   13 ASN cc_start: 0.8507 (OUTLIER) cc_final: 0.8229 (m-40)
REVERT: E  227 LEU cc_start: 0.8040 (tp) cc_final: 0.7678 (tt)
REVERT: E  293 GLN cc_start: 0.7438 (tp-100) cc_final: 0.7203 (tp40)
REVERT: E  465 MET cc_start: 0.6408 (mmt) cc_final: 0.6075 (mmt)
  outliers start: 37
  outliers final: 20
  residues processed: 309
  average time/residue: 0.2734
  time to fit residues: 130.7040
Evaluate side-chains
  311 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 284
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LYS
Chi-restraints excluded: chain A residue  125 SER
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  459 CYS
Chi-restraints excluded: chain B residue    5 LYS
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  459 CYS
Chi-restraints excluded: chain B residue  465 MET
Chi-restraints excluded: chain C residue    5 LYS
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  149 SER
Chi-restraints excluded: chain C residue  190 CYS
Chi-restraints excluded: chain C residue  459 CYS
Chi-restraints excluded: chain C residue  464 LEU
Chi-restraints excluded: chain D residue    5 LYS
Chi-restraints excluded: chain D residue   13 ASN
Chi-restraints excluded: chain D residue   25 SER
Chi-restraints excluded: chain D residue  125 SER
Chi-restraints excluded: chain D residue  149 SER
Chi-restraints excluded: chain D residue  459 CYS
Chi-restraints excluded: chain E residue    5 LYS
Chi-restraints excluded: chain E residue   13 ASN
Chi-restraints excluded: chain E residue   25 SER
Chi-restraints excluded: chain E residue  125 SER
Chi-restraints excluded: chain E residue  149 SER
Chi-restraints excluded: chain E residue  459 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 140 optimal weight:    2.9990
   chunk 114 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 112 optimal weight:    1.9990
   chunk 159 optimal weight:    2.9990
   chunk 158 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 34 optimal weight:    5.9990
   chunk 50 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.8786

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.143583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.113288 restraints weight = 54389.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.119049 restraints weight = 22473.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.122700 restraints weight = 12457.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.124935 restraints weight = 8337.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.126266 restraints weight = 6365.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.2061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.131  16595  Z= 0.238
  Angle     :  0.667  11.845  22660  Z= 0.346
  Chirality :  0.075   1.445   2600
  Planarity :  0.004   0.043   2775
  Dihedral  :  7.457  52.067   2650
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 10.08 %
    Favored  : 87.71 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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:  0.86 (0.19), residues: 1935
  helix:  2.48 (0.17), residues: 810
  sheet:  0.12 (0.24), residues: 465
  loop : -1.60 (0.23), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 423 
 TYR   0.010   0.001   TYR C  63 
 PHE   0.012   0.001   PHE A 134 
 TRP   0.010   0.001   TRP B 437 
 HIS   0.003   0.001   HIS E 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00567 /  0.24 (16565)
  covalent geometry    : angle       0.64382 /  0.34 (22580)
  SS BOND              : bond        0.01399 /  0.90 (   10)
  SS BOND              : angle       4.91733 /  3.59 (   20)
  hydrogen bonds       : bond        0.06273 /  4.12 (  850)
  hydrogen bonds       : angle       4.60101 /  3.26 ( 2790)
  link_BETA1-4         : bond        0.00091 /  0.05 (    5)
  link_BETA1-4         : angle       1.17876 /  0.65 (   15)
  link_NAG-ASN         : bond        0.00450 /  0.24 (   15)
  link_NAG-ASN         : angle       2.23276 /  1.40 (   45)

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

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

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  362 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 323
  time to evaluate  : 0.914 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 LYS cc_start: 0.7815 (ttpt) cc_final: 0.7511 (ttmm)
REVERT: A  234 ASP cc_start: 0.7069 (t0) cc_final: 0.6839 (t0)
REVERT: A  439 PHE cc_start: 0.8050 (t80) cc_final: 0.7772 (t80)
REVERT: B    5 LYS cc_start: 0.7796 (ttpt) cc_final: 0.7525 (ttmm)
REVERT: C    5 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7376 (tttp)
REVERT: C   70 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7265 (mt-10)
REVERT: C  184 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7704 (mt-10)
REVERT: C  227 LEU cc_start: 0.8190 (tp) cc_final: 0.7907 (tt)
REVERT: D    5 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7193 (ttmm)
REVERT: D   13 ASN cc_start: 0.8498 (OUTLIER) cc_final: 0.8253 (m-40)
REVERT: D  184 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7775 (mt-10)
REVERT: D  293 GLN cc_start: 0.7666 (tp-100) cc_final: 0.7423 (tp40)
REVERT: E    5 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7407 (tttp)
REVERT: E   13 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.8282 (m-40)
REVERT: E  293 GLN cc_start: 0.7540 (tp-100) cc_final: 0.7324 (tp40)
REVERT: E  439 PHE cc_start: 0.7971 (t80) cc_final: 0.7553 (t80)
REVERT: E  465 MET cc_start: 0.6574 (mmt) cc_final: 0.6242 (mmt)
  outliers start: 39
  outliers final: 26
  residues processed: 338
  average time/residue: 0.2706
  time to fit residues: 142.2678
Evaluate side-chains
  336 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 305
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 SER
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  459 CYS
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  459 CYS
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  465 MET
Chi-restraints excluded: chain C residue    5 LYS
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  149 SER
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  459 CYS
Chi-restraints excluded: chain C residue  464 LEU
Chi-restraints excluded: chain D residue    5 LYS
Chi-restraints excluded: chain D residue   13 ASN
Chi-restraints excluded: chain D residue   25 SER
Chi-restraints excluded: chain D residue  125 SER
Chi-restraints excluded: chain D residue  149 SER
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  459 CYS
Chi-restraints excluded: chain E residue    5 LYS
Chi-restraints excluded: chain E residue   13 ASN
Chi-restraints excluded: chain E residue   25 SER
Chi-restraints excluded: chain E residue  125 SER
Chi-restraints excluded: chain E residue  263 THR
Chi-restraints excluded: chain E residue  459 CYS
Chi-restraints excluded: chain E residue  464 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 186 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 174 optimal weight:    0.7980
   chunk 115 optimal weight:    3.9990
   chunk 152 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0070
   chunk 69 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 172 optimal weight:    0.9980
   overall best weight:    0.6800

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 106 ASN
C 106 ASN
D 106 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.144420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.114463 restraints weight = 53699.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.120283 restraints weight = 21798.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.123970 restraints weight = 11934.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.126227 restraints weight = 7910.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.127638 restraints weight = 6004.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.164  16595  Z= 0.150
  Angle     :  0.691  31.044  22660  Z= 0.347
  Chirality :  0.074   1.436   2600
  Planarity :  0.004   0.040   2775
  Dihedral  :  7.103  68.308   2642
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 11.61 %
    Favored  : 86.69 %
  Cbeta Deviations :  0.16 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.19), residues: 1935
  helix:  2.70 (0.17), residues: 810
  sheet:  0.22 (0.25), residues: 465
  loop : -1.47 (0.24), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 423 
 TYR   0.008   0.001   TYR E 128 
 PHE   0.008   0.001   PHE A 134 
 TRP   0.011   0.001   TRP B 437 
 HIS   0.001   0.000   HIS B 104 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00378 /  0.15 (16565)
  covalent geometry    : angle       0.65663 /  0.33 (22580)
  SS BOND              : bond        0.02056 /  1.02 (   10)
  SS BOND              : angle       6.76342 /  5.02 (   20)
  hydrogen bonds       : bond        0.05722 /  3.75 (  850)
  hydrogen bonds       : angle       4.32721 /  3.07 ( 2790)
  link_BETA1-4         : bond        0.00288 /  0.16 (    5)
  link_BETA1-4         : angle       1.03049 /  0.60 (   15)
  link_NAG-ASN         : bond        0.00135 /  0.08 (   15)
  link_NAG-ASN         : angle       1.87116 /  1.17 (   45)

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

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

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 296
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7450 (ttmm)
REVERT: A  230 LEU cc_start: 0.8834 (mt) cc_final: 0.8609 (mt)
REVERT: A  234 ASP cc_start: 0.7084 (t0) cc_final: 0.6856 (t0)
REVERT: B    5 LYS cc_start: 0.7767 (ttpt) cc_final: 0.7459 (ttmm)
REVERT: C    5 LYS cc_start: 0.7682 (ttpt) cc_final: 0.7314 (tttp)
REVERT: C   70 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7336 (mt-10)
REVERT: C  184 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7716 (mt-10)
REVERT: C  227 LEU cc_start: 0.8059 (tp) cc_final: 0.7792 (tt)
REVERT: D    5 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7130 (ttmm)
REVERT: D   13 ASN cc_start: 0.8477 (m110) cc_final: 0.8252 (m-40)
REVERT: D  184 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7754 (mt-10)
REVERT: D  293 GLN cc_start: 0.7590 (tp-100) cc_final: 0.7346 (tp40)
REVERT: E    5 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7221 (tttp)
REVERT: E   13 ASN cc_start: 0.8527 (m110) cc_final: 0.8272 (m-40)
REVERT: E  293 GLN cc_start: 0.7407 (tp-100) cc_final: 0.7164 (tp40)
REVERT: E  465 MET cc_start: 0.6505 (mmt) cc_final: 0.6144 (mmt)
  outliers start: 30
  outliers final: 20
  residues processed: 309
  average time/residue: 0.2682
  time to fit residues: 128.4905
Evaluate side-chains
  300 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 277
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LYS
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  190 CYS
Chi-restraints excluded: chain A residue  459 CYS
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  450 MET
Chi-restraints excluded: chain B residue  459 CYS
Chi-restraints excluded: chain B residue  465 MET
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  149 SER
Chi-restraints excluded: chain C residue  459 CYS
Chi-restraints excluded: chain C residue  464 LEU
Chi-restraints excluded: chain D residue    5 LYS
Chi-restraints excluded: chain D residue  125 SER
Chi-restraints excluded: chain D residue  149 SER
Chi-restraints excluded: chain D residue  222 SER
Chi-restraints excluded: chain D residue  459 CYS
Chi-restraints excluded: chain E residue    5 LYS
Chi-restraints excluded: chain E residue  125 SER
Chi-restraints excluded: chain E residue  459 CYS
Chi-restraints excluded: chain E residue  464 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 113 optimal weight:    3.9990
   chunk 136 optimal weight:    0.8980
   chunk 184 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 116 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 190 optimal weight:    4.9990
   chunk 133 optimal weight:    0.6980
   chunk 78 optimal weight:    1.9990
   chunk 146 optimal weight:    3.9990
   overall best weight:    1.3186

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.142740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.112689 restraints weight = 54137.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.118495 restraints weight = 22043.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.122096 restraints weight = 12067.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.124403 restraints weight = 8032.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.125872 restraints weight = 6077.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.2429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.181  16595  Z= 0.192
  Angle     :  0.715  30.403  22660  Z= 0.361
  Chirality :  0.075   1.438   2600
  Planarity :  0.004   0.039   2775
  Dihedral  :  7.217  89.060   2638
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 11.56 %
    Favored  : 86.57 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.03 (0.19), residues: 1935
  helix:  2.64 (0.17), residues: 805
  sheet:  0.22 (0.25), residues: 465
  loop : -1.52 (0.24), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 423 
 TYR   0.008   0.001   TYR D  63 
 PHE   0.008   0.001   PHE A 134 
 TRP   0.008   0.001   TRP D 437 
 HIS   0.002   0.000   HIS B 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00472 /  0.19 (16565)
  covalent geometry    : angle       0.67854 /  0.35 (22580)
  SS BOND              : bond        0.02203 /  1.06 (   10)
  SS BOND              : angle       6.97093 /  5.39 (   20)
  hydrogen bonds       : bond        0.05855 /  3.84 (  850)
  hydrogen bonds       : angle       4.38906 /  3.11 ( 2790)
  link_BETA1-4         : bond        0.00081 /  0.04 (    5)
  link_BETA1-4         : angle       1.18066 /  0.66 (   15)
  link_NAG-ASN         : bond        0.00281 /  0.15 (   15)
  link_NAG-ASN         : angle       2.05254 /  1.29 (   45)

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

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

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 279
  time to evaluate  : 0.827 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7505 (ttmm)
REVERT: A  230 LEU cc_start: 0.8878 (mt) cc_final: 0.8648 (mt)
REVERT: A  234 ASP cc_start: 0.7105 (t0) cc_final: 0.6859 (t0)
REVERT: A  439 PHE cc_start: 0.7911 (t80) cc_final: 0.7628 (t80)
REVERT: B    5 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7510 (ttmm)
REVERT: C    5 LYS cc_start: 0.7766 (ttpt) cc_final: 0.7392 (tttp)
REVERT: C   70 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7352 (mt-10)
REVERT: C  227 LEU cc_start: 0.8063 (tp) cc_final: 0.7782 (tt)
REVERT: D    5 LYS cc_start: 0.7616 (ttpt) cc_final: 0.7295 (ttmm)
REVERT: D   13 ASN cc_start: 0.8466 (m110) cc_final: 0.8233 (m-40)
REVERT: D  293 GLN cc_start: 0.7622 (tp-100) cc_final: 0.7366 (tp40)
REVERT: E    5 LYS cc_start: 0.7778 (ttpt) cc_final: 0.7376 (tttp)
REVERT: E   13 ASN cc_start: 0.8572 (m110) cc_final: 0.8332 (m-40)
REVERT: E  293 GLN cc_start: 0.7437 (tp-100) cc_final: 0.7193 (tp40)
REVERT: E  439 PHE cc_start: 0.7905 (t80) cc_final: 0.7490 (t80)
REVERT: E  465 MET cc_start: 0.6622 (mmt) cc_final: 0.6234 (mmt)
  outliers start: 33
  outliers final: 26
  residues processed: 295
  average time/residue: 0.2546
  time to fit residues: 118.4139
Evaluate side-chains
  303 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 275
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LYS
Chi-restraints excluded: chain A residue  125 SER
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  190 CYS
Chi-restraints excluded: chain A residue  222 SER
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  459 CYS
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain B residue    5 LYS
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  450 MET
Chi-restraints excluded: chain B residue  459 CYS
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  465 MET
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  149 SER
Chi-restraints excluded: chain C residue  459 CYS
Chi-restraints excluded: chain C residue  464 LEU
Chi-restraints excluded: chain D residue   25 SER
Chi-restraints excluded: chain D residue  125 SER
Chi-restraints excluded: chain D residue  149 SER
Chi-restraints excluded: chain D residue  222 SER
Chi-restraints excluded: chain D residue  459 CYS
Chi-restraints excluded: chain E residue  125 SER
Chi-restraints excluded: chain E residue  459 CYS
Chi-restraints excluded: chain E residue  464 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 160 optimal weight:    2.9990
   chunk 30 optimal weight:    0.4980
   chunk 20 optimal weight:    2.9990
   chunk 186 optimal weight:    2.9990
   chunk 95 optimal weight:    0.0980
   chunk 54 optimal weight:    2.9990
   chunk 183 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 108 optimal weight:    0.8980
   chunk 188 optimal weight:    2.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 106 ASN
B 272 GLN
E 106 ASN
E 272 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.145380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.114836 restraints weight = 53994.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.120705 restraints weight = 22146.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.124423 restraints weight = 12196.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.126727 restraints weight = 8106.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.128110 restraints weight = 6152.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.2542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.222  16595  Z= 0.165
  Angle     :  0.748  29.730  22660  Z= 0.372
  Chirality :  0.074   1.426   2600
  Planarity :  0.004   0.038   2775
  Dihedral  :  6.978  91.999   2630
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 11.95 %
    Favored  : 86.18 %
  Cbeta Deviations :  0.27 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.19), residues: 1935
  helix:  2.79 (0.17), residues: 805
  sheet:  0.25 (0.24), residues: 465
  loop : -1.43 (0.24), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 423 
 TYR   0.009   0.001   TYR C 128 
 PHE   0.007   0.001   PHE C 134 
 TRP   0.010   0.001   TRP B 437 
 HIS   0.001   0.000   HIS E 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00438 /  0.16 (16565)
  covalent geometry    : angle       0.69844 /  0.35 (22580)
  SS BOND              : bond        0.02188 /  1.08 (   10)
  SS BOND              : angle       8.61036 /  6.29 (   20)
  hydrogen bonds       : bond        0.05546 /  3.64 (  850)
  hydrogen bonds       : angle       4.23195 /  3.00 ( 2790)
  link_BETA1-4         : bond        0.00325 /  0.18 (    5)
  link_BETA1-4         : angle       1.14194 /  0.66 (   15)
  link_NAG-ASN         : bond        0.00140 /  0.08 (   15)
  link_NAG-ASN         : angle       1.87403 /  1.16 (   45)

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

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

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 273
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7469 (ttmm)
REVERT: A  230 LEU cc_start: 0.8819 (mt) cc_final: 0.8560 (mt)
REVERT: A  234 ASP cc_start: 0.7093 (t0) cc_final: 0.6838 (t0)
REVERT: B    5 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7484 (ttmm)
REVERT: C    5 LYS cc_start: 0.7737 (ttpt) cc_final: 0.7335 (tttp)
REVERT: C   70 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7416 (mt-10)
REVERT: C  227 LEU cc_start: 0.7903 (tp) cc_final: 0.7632 (tt)
REVERT: D    5 LYS cc_start: 0.7583 (ttpt) cc_final: 0.7168 (ttmm)
REVERT: D   13 ASN cc_start: 0.8450 (m110) cc_final: 0.8222 (m-40)
REVERT: D  293 GLN cc_start: 0.7549 (tp-100) cc_final: 0.7290 (tp40)
REVERT: E    5 LYS cc_start: 0.7755 (ttpt) cc_final: 0.7317 (tttp)
REVERT: E   13 ASN cc_start: 0.8569 (m110) cc_final: 0.8331 (m-40)
REVERT: E  293 GLN cc_start: 0.7387 (tp-100) cc_final: 0.7132 (tp40)
REVERT: E  465 MET cc_start: 0.6576 (mmt) cc_final: 0.6160 (mmt)
  outliers start: 33
  outliers final: 26
  residues processed: 288
  average time/residue: 0.2530
  time to fit residues: 114.3527
Evaluate side-chains
  292 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 264
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LYS
Chi-restraints excluded: chain A residue  125 SER
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  190 CYS
Chi-restraints excluded: chain A residue  222 SER
Chi-restraints excluded: chain A residue  459 CYS
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain B residue    5 LYS
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  272 GLN
Chi-restraints excluded: chain B residue  450 MET
Chi-restraints excluded: chain B residue  459 CYS
Chi-restraints excluded: chain B residue  465 MET
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  149 SER
Chi-restraints excluded: chain C residue  459 CYS
Chi-restraints excluded: chain C residue  464 LEU
Chi-restraints excluded: chain D residue  125 SER
Chi-restraints excluded: chain D residue  149 SER
Chi-restraints excluded: chain D residue  222 SER
Chi-restraints excluded: chain D residue  459 CYS
Chi-restraints excluded: chain E residue   25 SER
Chi-restraints excluded: chain E residue  125 SER
Chi-restraints excluded: chain E residue  272 GLN
Chi-restraints excluded: chain E residue  459 CYS
Chi-restraints excluded: chain E residue  464 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 123 optimal weight:    1.9990
   chunk 144 optimal weight:    1.9990
   chunk 185 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9980
   chunk 97 optimal weight:    0.7980
   chunk 184 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 121 optimal weight:    0.7980
   chunk 142 optimal weight:    0.9990
   chunk 105 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9980
   overall best weight:    0.8580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.146563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.115951 restraints weight = 53755.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.121803 restraints weight = 22389.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.125442 restraints weight = 12448.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.127695 restraints weight = 8353.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.128975 restraints weight = 6382.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.2619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.237  16595  Z= 0.181
  Angle     :  0.764  29.482  22660  Z= 0.381
  Chirality :  0.074   1.429   2600
  Planarity :  0.004   0.039   2775
  Dihedral  :  6.930  93.946   2630
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 12.24 %
    Favored  : 85.89 %
  Cbeta Deviations :  0.27 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.19), residues: 1935
  helix:  2.78 (0.17), residues: 805
  sheet:  0.25 (0.24), residues: 465
  loop : -1.42 (0.24), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 423 
 TYR   0.007   0.001   TYR E 273 
 PHE   0.010   0.001   PHE B 274 
 TRP   0.008   0.001   TRP B 437 
 HIS   0.002   0.000   HIS B 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00481 /  0.18 (16565)
  covalent geometry    : angle       0.71284 /  0.36 (22580)
  SS BOND              : bond        0.02327 /  1.14 (   10)
  SS BOND              : angle       8.84132 /  6.36 (   20)
  hydrogen bonds       : bond        0.05505 /  3.60 (  850)
  hydrogen bonds       : angle       4.24145 /  3.00 ( 2790)
  link_BETA1-4         : bond        0.00201 /  0.10 (    5)
  link_BETA1-4         : angle       1.16442 /  0.66 (   15)
  link_NAG-ASN         : bond        0.00164 /  0.09 (   15)
  link_NAG-ASN         : angle       1.91598 /  1.19 (   45)

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

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

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 270
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7488 (ttmm)
REVERT: A  230 LEU cc_start: 0.8849 (mt) cc_final: 0.8583 (mt)
REVERT: A  234 ASP cc_start: 0.7093 (t0) cc_final: 0.6854 (t0)
REVERT: B    5 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7499 (ttmm)
REVERT: C    5 LYS cc_start: 0.7770 (ttpt) cc_final: 0.7378 (tttp)
REVERT: C   70 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7406 (mt-10)
REVERT: D    5 LYS cc_start: 0.7611 (ttpt) cc_final: 0.7285 (ttmm)
REVERT: D   13 ASN cc_start: 0.8472 (m110) cc_final: 0.8237 (m-40)
REVERT: D  293 GLN cc_start: 0.7578 (tp-100) cc_final: 0.7317 (tp40)
REVERT: E    5 LYS cc_start: 0.7777 (ttpt) cc_final: 0.7405 (ttmm)
REVERT: E   13 ASN cc_start: 0.8569 (m110) cc_final: 0.8327 (m-40)
REVERT: E  293 GLN cc_start: 0.7403 (tp-100) cc_final: 0.7152 (tp40)
REVERT: E  465 MET cc_start: 0.6602 (mmt) cc_final: 0.6193 (mmt)
  outliers start: 33
  outliers final: 26
  residues processed: 285
  average time/residue: 0.2567
  time to fit residues: 115.0236
Evaluate side-chains
  300 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 272
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LYS
Chi-restraints excluded: chain A residue  125 SER
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  190 CYS
Chi-restraints excluded: chain A residue  222 SER
Chi-restraints excluded: chain A residue  459 CYS
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain B residue    5 LYS
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  450 MET
Chi-restraints excluded: chain B residue  459 CYS
Chi-restraints excluded: chain B residue  465 MET
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  149 SER
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  459 CYS
Chi-restraints excluded: chain C residue  464 LEU
Chi-restraints excluded: chain C residue  465 MET
Chi-restraints excluded: chain D residue  125 SER
Chi-restraints excluded: chain D residue  149 SER
Chi-restraints excluded: chain D residue  222 SER
Chi-restraints excluded: chain D residue  459 CYS
Chi-restraints excluded: chain E residue   25 SER
Chi-restraints excluded: chain E residue  125 SER
Chi-restraints excluded: chain E residue  459 CYS
Chi-restraints excluded: chain E residue  464 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 115 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 91 optimal weight:    0.6980
   chunk 99 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   chunk 111 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   chunk 92 optimal weight:    0.7980
   chunk 120 optimal weight:    2.9990
   chunk 159 optimal weight:    2.9990
   chunk 163 optimal weight:    0.8980
   overall best weight:    0.7580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.145378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.114957 restraints weight = 54015.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.120767 restraints weight = 22384.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.124354 restraints weight = 12386.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.126534 restraints weight = 8307.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.128019 restraints weight = 6380.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.2713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.215  16595  Z= 0.172
  Angle     :  0.758  29.366  22660  Z= 0.376
  Chirality :  0.074   1.428   2600
  Planarity :  0.004   0.038   2775
  Dihedral  :  6.760  93.227   2630
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 12.63 %
    Favored  : 85.72 %
  Cbeta Deviations :  0.27 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.19), residues: 1935
  helix:  2.85 (0.17), residues: 805
  sheet:  0.24 (0.24), residues: 465
  loop : -1.38 (0.24), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 423 
 TYR   0.010   0.001   TYR E 273 
 PHE   0.006   0.001   PHE C 134 
 TRP   0.008   0.001   TRP C 437 
 HIS   0.002   0.000   HIS B 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00461 /  0.17 (16565)
  covalent geometry    : angle       0.70481 /  0.35 (22580)
  SS BOND              : bond        0.02375 /  1.18 (   10)
  SS BOND              : angle       8.96901 /  6.47 (   20)
  hydrogen bonds       : bond        0.05344 /  3.49 (  850)
  hydrogen bonds       : angle       4.16466 /  2.95 ( 2790)
  link_BETA1-4         : bond        0.00199 /  0.10 (    5)
  link_BETA1-4         : angle       1.13775 /  0.65 (   15)
  link_NAG-ASN         : bond        0.00151 /  0.09 (   15)
  link_NAG-ASN         : angle       1.87520 /  1.16 (   45)

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

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

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 278
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7482 (ttmm)
REVERT: A  230 LEU cc_start: 0.8909 (mt) cc_final: 0.8644 (mt)
REVERT: A  234 ASP cc_start: 0.7072 (t0) cc_final: 0.6851 (t0)
REVERT: B    5 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7495 (ttmm)
REVERT: C    5 LYS cc_start: 0.7735 (ttpt) cc_final: 0.7380 (tttp)
REVERT: C   70 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7316 (mt-10)
REVERT: C  163 ASP cc_start: 0.8439 (t0) cc_final: 0.8211 (t0)
REVERT: D    5 LYS cc_start: 0.7596 (ttpt) cc_final: 0.7278 (ttmm)
REVERT: D   13 ASN cc_start: 0.8461 (m110) cc_final: 0.8227 (m-40)
REVERT: D  293 GLN cc_start: 0.7553 (tp-100) cc_final: 0.7306 (tp40)
REVERT: E    5 LYS cc_start: 0.7746 (ttpt) cc_final: 0.7410 (ttmm)
REVERT: E   13 ASN cc_start: 0.8563 (m110) cc_final: 0.8318 (m-40)
REVERT: E  293 GLN cc_start: 0.7413 (tp-100) cc_final: 0.7172 (tp40)
REVERT: E  465 MET cc_start: 0.6528 (mmt) cc_final: 0.6155 (mmt)
  outliers start: 29
  outliers final: 25
  residues processed: 292
  average time/residue: 0.2430
  time to fit residues: 111.6764
Evaluate side-chains
  304 residues out of total 1765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 277
  time to evaluate  : 0.610 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LYS
Chi-restraints excluded: chain A residue  125 SER
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  190 CYS
Chi-restraints excluded: chain A residue  222 SER
Chi-restraints excluded: chain A residue  459 CYS
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain B residue    5 LYS
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  450 MET
Chi-restraints excluded: chain B residue  459 CYS
Chi-restraints excluded: chain B residue  465 MET
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  149 SER
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  459 CYS
Chi-restraints excluded: chain C residue  464 LEU
Chi-restraints excluded: chain D residue  125 SER
Chi-restraints excluded: chain D residue  149 SER
Chi-restraints excluded: chain D residue  222 SER
Chi-restraints excluded: chain D residue  459 CYS
Chi-restraints excluded: chain E residue   25 SER
Chi-restraints excluded: chain E residue  125 SER
Chi-restraints excluded: chain E residue  459 CYS
Chi-restraints excluded: chain E residue  464 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 134 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 162 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 126 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   overall best weight:    1.3588

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.142212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.112127 restraints weight = 54098.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.117871 restraints weight = 21957.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.121487 restraints weight = 12023.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.123776 restraints weight = 7995.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.125261 restraints weight = 6034.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.242  16595  Z= 0.214
  Angle     :  0.779  29.288  22660  Z= 0.390
  Chirality :  0.075   1.434   2600
  Planarity :  0.004   0.040   2775
  Dihedral  :  7.123  93.051   2630
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 12.63 %
    Favored  : 85.44 %
  Cbeta Deviations :  0.27 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.00 (0.19), residues: 1935
  helix:  2.67 (0.17), residues: 805
  sheet:  0.11 (0.24), residues: 465
  loop : -1.52 (0.24), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 423 
 TYR   0.007   0.001   TYR D 187 
 PHE   0.010   0.001   PHE A 134 
 TRP   0.007   0.001   TRP A 437 
 HIS   0.002   0.000   HIS B 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00559 /  0.21 (16565)
  covalent geometry    : angle       0.72570 /  0.37 (22580)
  SS BOND              : bond        0.02310 /  1.14 (   10)
  SS BOND              : angle       9.15551 /  6.53 (   20)
  hydrogen bonds       : bond        0.05711 /  3.75 (  850)
  hydrogen bonds       : angle       4.32699 /  3.07 ( 2790)
  link_BETA1-4         : bond        0.00048 /  0.02 (    5)
  link_BETA1-4         : angle       1.17130 /  0.66 (   15)
  link_NAG-ASN         : bond        0.00274 /  0.15 (   15)
  link_NAG-ASN         : angle       1.99071 /  1.23 (   45)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4863.33 seconds
wall clock time: 83 minutes 47.94 seconds (5027.94 seconds total)