Starting phenix.real_space_refine
on Thu Feb  5 06:06:20 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9v0n_64666/02_2026/9v0n_64666.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9v0n_64666/02_2026/9v0n_64666.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9v0n_64666/02_2026/9v0n_64666.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9v0n_64666/02_2026/9v0n_64666.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9v0n_64666/02_2026/9v0n_64666.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9v0n_64666/02_2026/9v0n_64666.map"
  }
  resolution = 3.75
  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=   0.002 sd=   0.064
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      87      5.16       5
     C    9591      2.51       5
     N    2538      2.21       5
     O    3009      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15225
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 3305
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 427, 3305
          Classifications: {'peptide': 427}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 414}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "C"
      Number of atoms: 952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 952
          Classifications: {'peptide': 124}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 119}
    Chain: "B"
      Number of atoms: 818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 818
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 3305
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 427, 3305
          Classifications: {'peptide': 427}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 414}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "H"
      Number of atoms: 952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 952
          Classifications: {'peptide': 124}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 119}
    Chain: "F"
      Number of atoms: 818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 818
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 102}
    Chain: "E"
      Number of atoms: 3305
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 427, 3305
          Classifications: {'peptide': 427}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 414}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "I"
      Number of atoms: 952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 952
          Classifications: {'peptide': 124}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 119}
    Chain: "G"
      Number of atoms: 818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 818
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 102}
  Time building chain proxies: 3.33, per 1000 atoms: 0.22
  Number of scatterers: 15225
  At special positions: 0
  Unit cell: (142.48, 147.68, 116.48, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      87     16.00
     O    3009      8.00
     N    2538      7.00
     C    9591      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=30, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  37 " - pdb=" SG  CYS A 439 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  69 " - pdb=" SG  CYS A 212 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 155 " - pdb=" SG  CYS A 290 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 313 " - pdb=" SG  CYS A 343 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 322 " - pdb=" SG  CYS A 333 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 358 " - pdb=" SG  CYS A 367 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 382 " - pdb=" SG  CYS A 393 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 416 " - pdb=" SG  CYS A 422 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  37 " - pdb=" SG  CYS D 439 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  69 " - pdb=" SG  CYS D 212 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 155 " - pdb=" SG  CYS D 290 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 313 " - pdb=" SG  CYS D 343 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 322 " - pdb=" SG  CYS D 333 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 358 " - pdb=" SG  CYS D 367 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 382 " - pdb=" SG  CYS D 393 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 416 " - pdb=" SG  CYS D 422 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  22 " - pdb=" SG  CYS F  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  37 " - pdb=" SG  CYS E 439 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  69 " - pdb=" SG  CYS E 212 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 155 " - pdb=" SG  CYS E 290 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 313 " - pdb=" SG  CYS E 343 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 322 " - pdb=" SG  CYS E 333 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 358 " - pdb=" SG  CYS E 367 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 382 " - pdb=" SG  CYS E 393 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 416 " - pdb=" SG  CYS E 422 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  22 " - pdb=" SG  CYS I  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  22 " - pdb=" SG  CYS G  90 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.22
  Conformation dependent library (CDL) restraints added in 536.7 milliseconds
  

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3678

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 30 sheets defined
      22.7% alpha, 28.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 73 through 93
    Processing helix  chain 'A' and resid 94 through 96
      No H-bonds generated for 'chain 'A' and resid 94 through 96'
    Processing helix  chain 'A' and resid 148 through 160
      removed outlier: 3.547A  pdb=" N   LEU A 160 " --> pdb=" O   LYS A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 171
    Processing helix  chain 'A' and resid 194 through 203
      removed outlier: 3.601A  pdb=" N   TYR A 198 " --> pdb=" O   ASP A 194 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LEU A 203 " --> pdb=" O   ILE A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 227
      removed outlier: 4.438A  pdb=" N   VAL A 220 " --> pdb=" O   ASN A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 241
    Processing helix  chain 'A' and resid 253 through 264
    Processing helix  chain 'A' and resid 267 through 274
    Processing helix  chain 'A' and resid 277 through 282
    Processing helix  chain 'A' and resid 370 through 372
      No H-bonds generated for 'chain 'A' and resid 370 through 372'
    Processing helix  chain 'A' and resid 379 through 385
      removed outlier: 4.021A  pdb=" N   ASN A 383 " --> pdb=" O   VAL A 379 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   VAL A 384 " --> pdb=" O   ASN A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 477
    Processing helix  chain 'A' and resid 491 through 506
    Processing helix  chain 'C' and resid 28 through 32
      removed outlier: 3.698A  pdb=" N   SER C  31 " --> pdb=" O   SER C  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 85
      removed outlier: 3.763A  pdb=" N   GLU B  85 " --> pdb=" O   ALA B  82 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 73 through 93
    Processing helix  chain 'D' and resid 94 through 96
      No H-bonds generated for 'chain 'D' and resid 94 through 96'
    Processing helix  chain 'D' and resid 148 through 160
      removed outlier: 3.527A  pdb=" N   LEU D 160 " --> pdb=" O   LYS D 156 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 163 through 171
    Processing helix  chain 'D' and resid 194 through 203
      removed outlier: 3.593A  pdb=" N   TYR D 198 " --> pdb=" O   ASP D 194 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   LEU D 203 " --> pdb=" O   ILE D 199 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 216 through 227
      removed outlier: 4.438A  pdb=" N   VAL D 220 " --> pdb=" O   ASN D 216 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 227 through 241
    Processing helix  chain 'D' and resid 253 through 264
    Processing helix  chain 'D' and resid 267 through 274
      removed outlier: 3.519A  pdb=" N   LEU D 273 " --> pdb=" O   ASP D 269 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 277 through 282
      removed outlier: 3.521A  pdb=" N   ARG D 282 " --> pdb=" O   VAL D 278 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 370 through 372
      No H-bonds generated for 'chain 'D' and resid 370 through 372'
    Processing helix  chain 'D' and resid 379 through 385
      removed outlier: 4.037A  pdb=" N   ASN D 383 " --> pdb=" O   VAL D 379 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   VAL D 384 " --> pdb=" O   ASN D 380 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 473 through 477
    Processing helix  chain 'D' and resid 491 through 506
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.615A  pdb=" N   SER H  31 " --> pdb=" O   SER H  28 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 28 through 32'
    Processing helix  chain 'F' and resid 81 through 85
      removed outlier: 3.803A  pdb=" N   GLU F  85 " --> pdb=" O   ALA F  82 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 73 through 93
    Processing helix  chain 'E' and resid 94 through 96
      No H-bonds generated for 'chain 'E' and resid 94 through 96'
    Processing helix  chain 'E' and resid 148 through 160
      removed outlier: 3.585A  pdb=" N   LEU E 160 " --> pdb=" O   LYS E 156 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 163 through 171
    Processing helix  chain 'E' and resid 194 through 203
      removed outlier: 3.627A  pdb=" N   TYR E 198 " --> pdb=" O   ASP E 194 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   LEU E 203 " --> pdb=" O   ILE E 199 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 216 through 227
      removed outlier: 4.438A  pdb=" N   VAL E 220 " --> pdb=" O   ASN E 216 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 227 through 241
    Processing helix  chain 'E' and resid 253 through 264
    Processing helix  chain 'E' and resid 267 through 274
      removed outlier: 3.531A  pdb=" N   LEU E 273 " --> pdb=" O   ASP E 269 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 277 through 282
    Processing helix  chain 'E' and resid 370 through 372
      No H-bonds generated for 'chain 'E' and resid 370 through 372'
    Processing helix  chain 'E' and resid 379 through 385
      removed outlier: 4.066A  pdb=" N   ASN E 383 " --> pdb=" O   VAL E 379 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   VAL E 384 " --> pdb=" O   ASN E 380 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 474 through 478
    Processing helix  chain 'E' and resid 491 through 506
    Processing helix  chain 'I' and resid 28 through 32
      removed outlier: 3.642A  pdb=" N   SER I  31 " --> pdb=" O   SER I  28 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 81 through 85
      removed outlier: 3.805A  pdb=" N   GLU G  85 " --> pdb=" O   ALA G  82 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 308 through 309
      removed outlier: 3.946A  pdb=" N   VAL A 308 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   GLY A  43 " --> pdb=" O   CYS A 313 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   CYS A 313 " --> pdb=" O   GLY A  43 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 364 through 368
    Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 180
      removed outlier: 10.410A  pdb=" N   SER A 186 " --> pdb=" O   TRP A  52 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   THR A  54 " --> pdb=" O   SER A 186 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   LEU A 188 " --> pdb=" O   THR A  54 " (cutoff:3.500A)
      removed outlier: 7.753A  pdb=" N   GLU A  60 " --> pdb=" O   VAL A 192 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   ALA A 298 " --> pdb=" O   CYS A 290 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 333 through 336
    Processing sheet with id=AA5, first strand: chain 'A' and resid 404 through 406
    Processing sheet with id=AA6, first strand: chain 'A' and resid 422 through 425
    Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 7
    Processing sheet with id=AA8, first strand: chain 'C' and resid 58 through 59
      removed outlier: 6.471A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 4.676A  pdb=" N   SER C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   MET C  34 " --> pdb=" O   SER C  50 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 9 through 12
      removed outlier: 3.648A  pdb=" N   THR B 108 " --> pdb=" O   VAL B  10 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   GLY B  12 " --> pdb=" O   THR B 108 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   TRP B  37 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 18 through 23
    Processing sheet with id=AB2, first strand: chain 'D' and resid 308 through 309
      removed outlier: 3.928A  pdb=" N   VAL D 308 " --> pdb=" O   LEU D  48 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   GLY D  43 " --> pdb=" O   CYS D 313 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   CYS D 313 " --> pdb=" O   GLY D  43 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 364 through 368
    Processing sheet with id=AB4, first strand: chain 'D' and resid 177 through 180
      removed outlier: 10.390A  pdb=" N   SER D 186 " --> pdb=" O   TRP D  52 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   THR D  54 " --> pdb=" O   SER D 186 " (cutoff:3.500A)
      removed outlier: 4.524A  pdb=" N   LEU D 188 " --> pdb=" O   THR D  54 " (cutoff:3.500A)
      removed outlier: 7.777A  pdb=" N   GLU D  60 " --> pdb=" O   VAL D 192 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   ALA D 298 " --> pdb=" O   CYS D 290 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 333 through 336
    Processing sheet with id=AB6, first strand: chain 'D' and resid 404 through 406
    Processing sheet with id=AB7, first strand: chain 'D' and resid 430 through 431
      removed outlier: 3.540A  pdb=" N   GLY D 430 " --> pdb=" O   ASN D 426 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AB9, first strand: chain 'H' and resid 58 through 59
      removed outlier: 6.466A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 4.670A  pdb=" N   SER H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   MET H  34 " --> pdb=" O   SER H  50 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'F' and resid 9 through 12
      removed outlier: 3.581A  pdb=" N   THR F 108 " --> pdb=" O   VAL F  10 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   GLY F  12 " --> pdb=" O   THR F 108 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   TRP F  37 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'F' and resid 18 through 23
    Processing sheet with id=AC3, first strand: chain 'E' and resid 308 through 309
      removed outlier: 3.941A  pdb=" N   VAL E 308 " --> pdb=" O   LEU E  48 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   GLY E  43 " --> pdb=" O   CYS E 313 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   CYS E 313 " --> pdb=" O   GLY E  43 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'E' and resid 364 through 368
    Processing sheet with id=AC5, first strand: chain 'E' and resid 177 through 180
      removed outlier: 10.443A  pdb=" N   SER E 186 " --> pdb=" O   TRP E  52 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   THR E  54 " --> pdb=" O   SER E 186 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   LEU E 188 " --> pdb=" O   THR E  54 " (cutoff:3.500A)
      removed outlier: 7.834A  pdb=" N   GLU E  60 " --> pdb=" O   VAL E 192 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   ALA E 298 " --> pdb=" O   CYS E 290 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'E' and resid 333 through 336
    Processing sheet with id=AC7, first strand: chain 'E' and resid 404 through 406
    Processing sheet with id=AC8, first strand: chain 'E' and resid 430 through 431
      removed outlier: 3.551A  pdb=" N   GLY E 430 " --> pdb=" O   ASN E 426 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'I' and resid 3 through 7
    Processing sheet with id=AD1, first strand: chain 'I' and resid 58 through 59
      removed outlier: 6.483A  pdb=" N   TRP I  36 " --> pdb=" O   VAL I  48 " (cutoff:3.500A)
      removed outlier: 4.670A  pdb=" N   SER I  50 " --> pdb=" O   MET I  34 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   MET I  34 " --> pdb=" O   SER I  50 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'G' and resid 9 through 12
      removed outlier: 3.602A  pdb=" N   THR G 108 " --> pdb=" O   VAL G  10 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   GLY G  12 " --> pdb=" O   THR G 108 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   TRP G  37 " --> pdb=" O   LEU G  49 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'G' and resid 18 through 23

    671 hydrogen bonds defined for protein.
    1761 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: 2.83

  Time building geometry restraints manager: 1.56 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4916
        1.34 -     1.46: 3504
        1.46 -     1.58: 6958
        1.58 -     1.70: 0
        1.70 -     1.82: 114
  Bond restraints: 15492
  Sorted by residual:
  bond pdb=" CB  VAL G  35 "
       pdb=" CG1 VAL G  35 "
    ideal  model  delta    sigma   weight residual
    1.521  1.473  0.048 3.30e-02 9.18e+02 2.10e+00
  bond pdb=" CG1 ILE G  29 "
       pdb=" CD1 ILE G  29 "
    ideal  model  delta    sigma   weight residual
    1.513  1.466  0.047 3.90e-02 6.57e+02 1.43e+00
  bond pdb=" N   PHE I 111 "
       pdb=" CA  PHE I 111 "
    ideal  model  delta    sigma   weight residual
    1.457  1.472 -0.015 1.29e-02 6.01e+03 1.33e+00
  bond pdb=" CB  ASN D 388 "
       pdb=" CG  ASN D 388 "
    ideal  model  delta    sigma   weight residual
    1.516  1.545 -0.029 2.50e-02 1.60e+03 1.30e+00
  bond pdb=" N   PHE H 111 "
       pdb=" CA  PHE H 111 "
    ideal  model  delta    sigma   weight residual
    1.457  1.472 -0.014 1.29e-02 6.01e+03 1.22e+00
  ... (remaining 15487 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.17: 20671
        2.17 -     4.34: 287
        4.34 -     6.50: 46
        6.50 -     8.67: 9
        8.67 -    10.84: 5
  Bond angle restraints: 21018
  Sorted by residual:
  angle pdb=" C   TYR B  33 "
        pdb=" N   ASP B  34 "
        pdb=" CA  ASP B  34 "
      ideal   model   delta    sigma   weight residual
     121.54  132.38  -10.84 1.91e+00 2.74e-01 3.22e+01
  angle pdb=" C   TYR F  33 "
        pdb=" N   ASP F  34 "
        pdb=" CA  ASP F  34 "
      ideal   model   delta    sigma   weight residual
     121.54  130.43   -8.89 1.91e+00 2.74e-01 2.17e+01
  angle pdb=" C   LEU I 108 "
        pdb=" N   ASN I 109 "
        pdb=" CA  ASN I 109 "
      ideal   model   delta    sigma   weight residual
     121.54  113.49    8.05 1.91e+00 2.74e-01 1.77e+01
  angle pdb=" C   LEU H 108 "
        pdb=" N   ASN H 109 "
        pdb=" CA  ASN H 109 "
      ideal   model   delta    sigma   weight residual
     121.54  113.53    8.01 1.91e+00 2.74e-01 1.76e+01
  angle pdb=" C   LEU C 108 "
        pdb=" N   ASN C 109 "
        pdb=" CA  ASN C 109 "
      ideal   model   delta    sigma   weight residual
     121.54  113.62    7.92 1.91e+00 2.74e-01 1.72e+01
  ... (remaining 21013 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 8307
       17.98 -    35.95: 915
       35.95 -    53.93: 137
       53.93 -    71.90: 16
       71.90 -    89.88: 18
  Dihedral angle restraints: 9393
    sinusoidal: 3660
      harmonic: 5733
  Sorted by residual:
  dihedral pdb=" CB  CYS E 155 "
           pdb=" SG  CYS E 155 "
           pdb=" SG  CYS E 290 "
           pdb=" CB  CYS E 290 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -146.92   60.92     1      1.00e+01 1.00e-02 4.93e+01
  dihedral pdb=" CB  CYS A 155 "
           pdb=" SG  CYS A 155 "
           pdb=" SG  CYS A 290 "
           pdb=" CB  CYS A 290 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -145.47   59.47     1      1.00e+01 1.00e-02 4.72e+01
  dihedral pdb=" CB  CYS D 155 "
           pdb=" SG  CYS D 155 "
           pdb=" SG  CYS D 290 "
           pdb=" CB  CYS D 290 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -144.93   58.93     1      1.00e+01 1.00e-02 4.64e+01
  ... (remaining 9390 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1818
       0.047 -    0.093: 507
       0.093 -    0.140: 114
       0.140 -    0.187: 3
       0.187 -    0.233: 3
  Chirality restraints: 2445
  Sorted by residual:
  chirality pdb=" CA  TRP I 110 "
            pdb=" N   TRP I 110 "
            pdb=" C   TRP I 110 "
            pdb=" CB  TRP I 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.36e+00
  chirality pdb=" CA  TRP H 110 "
            pdb=" N   TRP H 110 "
            pdb=" C   TRP H 110 "
            pdb=" CB  TRP H 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" CA  TRP C 110 "
            pdb=" N   TRP C 110 "
            pdb=" C   TRP C 110 "
            pdb=" CB  TRP C 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 2442 not shown)

  Planarity restraints: 2673
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B  33 "   -0.011 2.00e-02 2.50e+03   2.33e-02 5.42e+00
        pdb=" C   TYR B  33 "    0.040 2.00e-02 2.50e+03
        pdb=" O   TYR B  33 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ASP B  34 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET D 264 "    0.032 5.00e-02 4.00e+02   4.83e-02 3.73e+00
        pdb=" N   PRO D 265 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO D 265 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO D 265 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE H 111 "    0.017 2.00e-02 2.50e+03   1.43e-02 3.60e+00
        pdb=" CG  PHE H 111 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 PHE H 111 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE H 111 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE H 111 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE H 111 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE H 111 "    0.004 2.00e-02 2.50e+03
  ... (remaining 2670 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.85: 5210
        2.85 -     3.36: 13488
        3.36 -     3.87: 24174
        3.87 -     4.39: 27035
        4.39 -     4.90: 48421
  Nonbonded interactions: 118328
  Sorted by model distance:
  nonbonded pdb=" O   TYR B  33 "
            pdb=" OD1 ASP B  34 "
     model   vdw
     2.333 3.040
  nonbonded pdb=" OG  SER F  28 "
            pdb=" N   ILE F  29 "
     model   vdw
     2.505 3.120
  nonbonded pdb=" OG  SER B  28 "
            pdb=" N   ILE B  29 "
     model   vdw
     2.507 3.120
  nonbonded pdb=" OG  SER G  28 "
            pdb=" N   ILE G  29 "
     model   vdw
     2.510 3.120
  nonbonded pdb=" O   TYR F  33 "
            pdb=" OD1 ASP F  34 "
     model   vdw
     2.515 3.040
  ... (remaining 118323 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'D'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'H'
  selection = chain 'I'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     13.760
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
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      :  0.003   0.048  15522  Z= 0.148
  Angle     :  0.667  10.841  21078  Z= 0.359
  Chirality :  0.043   0.233   2445
  Planarity :  0.004   0.048   2673
  Dihedral  : 14.587  89.881   5625
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.96 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 13.72 %
    Favored  : 84.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -0.44 (0.20), residues: 1953
  helix:  0.63 (0.28), residues: 372
  sheet:  0.22 (0.22), residues: 636
  loop : -1.00 (0.21), residues: 945

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 429 
 TYR   0.024   0.001   TYR A 250 
 PHE   0.033   0.002   PHE H 111 
 TRP   0.018   0.001   TRP C 110 
 HIS   0.003   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (15492)
  covalent geometry    : angle       0.66637 (21018)
  SS BOND              : bond        0.00179 (   30)
  SS BOND              : angle       0.84333 (   60)
  hydrogen bonds       : bond        0.15782 (  671)
  hydrogen bonds       : angle       7.38818 ( 1761)

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

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

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 192
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 GLU cc_start: 0.7092 (tp30) cc_final: 0.6160 (mt-10)
REVERT: C  101 TYR cc_start: 0.8162 (p90) cc_final: 0.7892 (p90)
REVERT: D   92 GLU cc_start: 0.6986 (tp30) cc_final: 0.6200 (mt-10)
REVERT: D  289 MET cc_start: 0.8773 (tpp) cc_final: 0.7720 (tpp)
REVERT: D  417 TYR cc_start: 0.7868 (m-80) cc_final: 0.7164 (m-80)
REVERT: H  101 TYR cc_start: 0.8580 (p90) cc_final: 0.8083 (p90)
REVERT: E   92 GLU cc_start: 0.7132 (tp30) cc_final: 0.6300 (mt-10)
REVERT: E  250 TYR cc_start: 0.6517 (m-80) cc_final: 0.6297 (m-80)
REVERT: E  417 TYR cc_start: 0.7724 (m-80) cc_final: 0.6992 (m-80)
REVERT: I   43 LYS cc_start: 0.8769 (mmtm) cc_final: 0.8248 (mmmm)
  outliers start: 23
  outliers final: 21
  residues processed: 205
  average time/residue: 0.1135
  time to fit residues: 34.7102
Evaluate side-chains
  201 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 180
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 HIS
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  290 CYS
Chi-restraints excluded: chain A residue  319 SER
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  111 PHE
Chi-restraints excluded: chain B residue   11 SER
Chi-restraints excluded: chain D residue  171 LEU
Chi-restraints excluded: chain D residue  273 LEU
Chi-restraints excluded: chain D residue  290 CYS
Chi-restraints excluded: chain D residue  319 SER
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  102 PHE
Chi-restraints excluded: chain H residue  111 PHE
Chi-restraints excluded: chain E residue  159 HIS
Chi-restraints excluded: chain E residue  247 VAL
Chi-restraints excluded: chain E residue  290 CYS
Chi-restraints excluded: chain E residue  319 SER
Chi-restraints excluded: chain I residue   91 THR
Chi-restraints excluded: chain G residue   11 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 194 optimal weight:    1.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    0.1980
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9980
   overall best weight:    0.8386

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 388 ASN
** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 388 ASN
** E 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 388 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.159196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.131868 restraints weight = 24137.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.135531 restraints weight = 14385.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.137935 restraints weight = 10134.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.139564 restraints weight = 8017.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.140505 restraints weight = 6769.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.0789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  15522  Z= 0.142
  Angle     :  0.616  12.781  21078  Z= 0.323
  Chirality :  0.043   0.209   2445
  Planarity :  0.004   0.042   2673
  Dihedral  :  5.460  51.784   2151
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.12 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 15.55 %
    Favored  : 81.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -0.39 (0.20), residues: 1953
  helix:  0.54 (0.27), residues: 405
  sheet:  0.19 (0.21), residues: 642
  loop : -0.91 (0.22), residues: 906

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 429 
 TYR   0.017   0.001   TYR A 250 
 PHE   0.024   0.001   PHE I 111 
 TRP   0.015   0.001   TRP C 110 
 HIS   0.002   0.001   HIS E 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (15492)
  covalent geometry    : angle       0.61560 (21018)
  SS BOND              : bond        0.00156 (   30)
  SS BOND              : angle       0.78965 (   60)
  hydrogen bonds       : bond        0.03524 (  671)
  hydrogen bonds       : angle       5.64323 ( 1761)

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

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

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 195
  time to evaluate  : 0.558 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 GLU cc_start: 0.6787 (tp30) cc_final: 0.5925 (mt-10)
REVERT: A  273 LEU cc_start: 0.8749 (tt) cc_final: 0.8500 (tp)
REVERT: C   80 TYR cc_start: 0.8317 (m-80) cc_final: 0.8019 (m-80)
REVERT: C  101 TYR cc_start: 0.8181 (p90) cc_final: 0.7734 (p90)
REVERT: D   92 GLU cc_start: 0.6859 (tp30) cc_final: 0.6094 (mt-10)
REVERT: D  289 MET cc_start: 0.8070 (tpp) cc_final: 0.7312 (tpp)
REVERT: D  417 TYR cc_start: 0.7846 (m-80) cc_final: 0.7053 (m-80)
REVERT: H  101 TYR cc_start: 0.8562 (p90) cc_final: 0.8089 (p90)
REVERT: E   92 GLU cc_start: 0.7134 (tp30) cc_final: 0.5994 (mt-10)
REVERT: E  417 TYR cc_start: 0.7688 (m-80) cc_final: 0.6922 (m-80)
REVERT: I   43 LYS cc_start: 0.8750 (mmtm) cc_final: 0.8237 (mmmm)
  outliers start: 45
  outliers final: 29
  residues processed: 225
  average time/residue: 0.1119
  time to fit residues: 38.1431
Evaluate side-chains
  211 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 182
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 HIS
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain A residue  290 CYS
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  267 THR
Chi-restraints excluded: chain D residue  290 CYS
Chi-restraints excluded: chain D residue  362 SER
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  121 ILE
Chi-restraints excluded: chain F residue   11 SER
Chi-restraints excluded: chain E residue  159 HIS
Chi-restraints excluded: chain E residue  273 LEU
Chi-restraints excluded: chain E residue  288 ILE
Chi-restraints excluded: chain E residue  290 CYS
Chi-restraints excluded: chain E residue  332 ILE
Chi-restraints excluded: chain E residue  362 SER
Chi-restraints excluded: chain E residue  492 ILE
Chi-restraints excluded: chain I residue   11 LEU
Chi-restraints excluded: chain I residue  108 LEU
Chi-restraints excluded: chain I residue  111 PHE
Chi-restraints excluded: chain I residue  121 ILE
Chi-restraints excluded: chain G residue   29 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 71 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 120 optimal weight:    0.0170
   chunk 77 optimal weight:    4.9990
   chunk 142 optimal weight:    3.9990
   chunk 154 optimal weight:    1.9990
   chunk 164 optimal weight:    0.0050
   chunk 7 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.5034

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

Flipped N/Q/H residues before XYZ refinement:
** E 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 388 ASN
E 454 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.161295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.134229 restraints weight = 24209.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.137913 restraints weight = 14337.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.140353 restraints weight = 10055.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.141979 restraints weight = 7906.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.142915 restraints weight = 6665.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.1135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  15522  Z= 0.110
  Angle     :  0.578  12.930  21078  Z= 0.303
  Chirality :  0.042   0.192   2445
  Planarity :  0.003   0.035   2673
  Dihedral  :  4.941  53.862   2130
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 16.64 %
    Favored  : 80.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -0.28 (0.20), residues: 1953
  helix:  0.75 (0.28), residues: 405
  sheet:  0.41 (0.22), residues: 624
  loop : -1.00 (0.21), residues: 924

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 429 
 TYR   0.020   0.001   TYR D 250 
 PHE   0.018   0.001   PHE H 111 
 TRP   0.015   0.001   TRP H 110 
 HIS   0.003   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 (15492)
  covalent geometry    : angle       0.57765 (21018)
  SS BOND              : bond        0.00143 (   30)
  SS BOND              : angle       0.73152 (   60)
  hydrogen bonds       : bond        0.03023 (  671)
  hydrogen bonds       : angle       5.21266 ( 1761)

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

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

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 206
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.5841 (mt-10)
REVERT: C   80 TYR cc_start: 0.8310 (m-80) cc_final: 0.8004 (m-80)
REVERT: C  101 TYR cc_start: 0.8163 (p90) cc_final: 0.7777 (p90)
REVERT: D   92 GLU cc_start: 0.6587 (OUTLIER) cc_final: 0.6170 (mt-10)
REVERT: D  289 MET cc_start: 0.7971 (tpp) cc_final: 0.7326 (tpp)
REVERT: D  417 TYR cc_start: 0.7744 (m-80) cc_final: 0.6941 (m-80)
REVERT: H  101 TYR cc_start: 0.8464 (p90) cc_final: 0.7966 (p90)
REVERT: E   83 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7967 (tt)
REVERT: E   92 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.5978 (mt-10)
REVERT: E  357 THR cc_start: 0.8648 (OUTLIER) cc_final: 0.8371 (m)
REVERT: E  370 MET cc_start: 0.7642 (tmm) cc_final: 0.7347 (tmm)
REVERT: E  417 TYR cc_start: 0.7746 (m-80) cc_final: 0.7086 (m-80)
REVERT: I   43 LYS cc_start: 0.8738 (mmtm) cc_final: 0.8204 (mmmm)
  outliers start: 54
  outliers final: 28
  residues processed: 240
  average time/residue: 0.1095
  time to fit residues: 40.3249
Evaluate side-chains
  219 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 186
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 GLU
Chi-restraints excluded: chain A residue  159 HIS
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  290 CYS
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  102 PHE
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain D residue   92 GLU
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  290 CYS
Chi-restraints excluded: chain D residue  492 ILE
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  102 PHE
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain H residue  121 ILE
Chi-restraints excluded: chain F residue   11 SER
Chi-restraints excluded: chain E residue   83 LEU
Chi-restraints excluded: chain E residue   92 GLU
Chi-restraints excluded: chain E residue  159 HIS
Chi-restraints excluded: chain E residue  267 THR
Chi-restraints excluded: chain E residue  288 ILE
Chi-restraints excluded: chain E residue  290 CYS
Chi-restraints excluded: chain E residue  357 THR
Chi-restraints excluded: chain I residue   11 LEU
Chi-restraints excluded: chain I residue   91 THR
Chi-restraints excluded: chain I residue  102 PHE
Chi-restraints excluded: chain I residue  108 LEU
Chi-restraints excluded: chain I residue  111 PHE
Chi-restraints excluded: chain I residue  121 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 119 optimal weight:    0.0970
   chunk 86 optimal weight:    2.9990
   chunk 90 optimal weight:    5.9990
   chunk 187 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 80 optimal weight:    1.9990
   chunk 96 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 388 ASN
** E 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.159563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.132481 restraints weight = 24186.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.136224 restraints weight = 14292.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.138667 restraints weight = 9987.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.140305 restraints weight = 7836.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.141244 restraints weight = 6589.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.1264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  15522  Z= 0.129
  Angle     :  0.595  13.437  21078  Z= 0.309
  Chirality :  0.042   0.199   2445
  Planarity :  0.003   0.034   2673
  Dihedral  :  5.009  57.973   2130
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.12 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 17.04 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -0.22 (0.20), residues: 1953
  helix:  0.85 (0.28), residues: 405
  sheet:  0.45 (0.22), residues: 618
  loop : -0.99 (0.21), residues: 930

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 429 
 TYR   0.018   0.001   TYR A 250 
 PHE   0.019   0.001   PHE C 111 
 TRP   0.015   0.001   TRP H 110 
 HIS   0.003   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (15492)
  covalent geometry    : angle       0.59457 (21018)
  SS BOND              : bond        0.00160 (   30)
  SS BOND              : angle       0.82959 (   60)
  hydrogen bonds       : bond        0.03058 (  671)
  hydrogen bonds       : angle       5.11135 ( 1761)

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

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

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 203
  time to evaluate  : 0.623 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.5874 (mt-10)
REVERT: A  273 LEU cc_start: 0.8618 (tt) cc_final: 0.8321 (tp)
REVERT: A  357 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8490 (m)
REVERT: C   80 TYR cc_start: 0.8313 (m-80) cc_final: 0.7998 (m-80)
REVERT: C  101 TYR cc_start: 0.8198 (p90) cc_final: 0.7743 (p90)
REVERT: D   92 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.6140 (mt-10)
REVERT: D  289 MET cc_start: 0.7934 (tpp) cc_final: 0.7262 (tpp)
REVERT: D  357 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8378 (t)
REVERT: D  417 TYR cc_start: 0.7753 (m-80) cc_final: 0.6838 (m-80)
REVERT: H  101 TYR cc_start: 0.8509 (p90) cc_final: 0.8034 (p90)
REVERT: E   92 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.5971 (mt-10)
REVERT: E  357 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8359 (m)
REVERT: E  417 TYR cc_start: 0.7783 (m-80) cc_final: 0.7225 (m-80)
REVERT: I   43 LYS cc_start: 0.8753 (mmtm) cc_final: 0.8222 (mmmm)
REVERT: I  101 TYR cc_start: 0.8238 (p90) cc_final: 0.7643 (p90)
  outliers start: 65
  outliers final: 38
  residues processed: 244
  average time/residue: 0.1042
  time to fit residues: 39.2959
Evaluate side-chains
  236 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 192
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue   92 GLU
Chi-restraints excluded: chain A residue  159 HIS
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain A residue  290 CYS
Chi-restraints excluded: chain A residue  357 THR
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  102 PHE
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain D residue   92 GLU
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  266 ILE
Chi-restraints excluded: chain D residue  290 CYS
Chi-restraints excluded: chain D residue  357 THR
Chi-restraints excluded: chain D residue  362 SER
Chi-restraints excluded: chain D residue  492 ILE
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  102 PHE
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain H residue  121 ILE
Chi-restraints excluded: chain F residue   11 SER
Chi-restraints excluded: chain E residue   92 GLU
Chi-restraints excluded: chain E residue  159 HIS
Chi-restraints excluded: chain E residue  267 THR
Chi-restraints excluded: chain E residue  273 LEU
Chi-restraints excluded: chain E residue  288 ILE
Chi-restraints excluded: chain E residue  290 CYS
Chi-restraints excluded: chain E residue  357 THR
Chi-restraints excluded: chain E residue  362 SER
Chi-restraints excluded: chain E residue  395 ILE
Chi-restraints excluded: chain E residue  492 ILE
Chi-restraints excluded: chain I residue   11 LEU
Chi-restraints excluded: chain I residue   91 THR
Chi-restraints excluded: chain I residue  102 PHE
Chi-restraints excluded: chain I residue  108 LEU
Chi-restraints excluded: chain I residue  111 PHE
Chi-restraints excluded: chain I residue  121 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 69 optimal weight:   20.0000
   chunk 36 optimal weight:    0.5980
   chunk 66 optimal weight:    0.7980
   chunk 80 optimal weight:    0.6980
   chunk 175 optimal weight:    0.7980
   chunk 72 optimal weight:    6.9990
   chunk 88 optimal weight:    2.9990
   chunk 120 optimal weight:    9.9990
   chunk 135 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
E 227 ASN
E 388 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.158849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.131383 restraints weight = 23942.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.134983 restraints weight = 13995.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.137372 restraints weight = 9718.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.138924 restraints weight = 7561.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.139801 restraints weight = 6366.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.1415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  15522  Z= 0.130
  Angle     :  0.595  13.283  21078  Z= 0.310
  Chirality :  0.042   0.194   2445
  Planarity :  0.003   0.033   2673
  Dihedral  :  5.025  59.122   2130
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 18.35 %
    Favored  : 77.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -0.21 (0.20), residues: 1953
  helix:  0.91 (0.28), residues: 405
  sheet:  0.42 (0.22), residues: 618
  loop : -0.98 (0.21), residues: 930

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG I  76 
 TYR   0.021   0.001   TYR D 250 
 PHE   0.039   0.002   PHE H 111 
 TRP   0.014   0.001   TRP C 110 
 HIS   0.003   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (15492)
  covalent geometry    : angle       0.59405 (21018)
  SS BOND              : bond        0.00212 (   30)
  SS BOND              : angle       0.81047 (   60)
  hydrogen bonds       : bond        0.03002 (  671)
  hydrogen bonds       : angle       5.06233 ( 1761)

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

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

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 196
  time to evaluate  : 0.602 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.5898 (mt-10)
REVERT: A  273 LEU cc_start: 0.8588 (tt) cc_final: 0.8315 (tp)
REVERT: A  357 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8468 (m)
REVERT: A  417 TYR cc_start: 0.7375 (m-80) cc_final: 0.7158 (m-80)
REVERT: C   80 TYR cc_start: 0.8323 (m-80) cc_final: 0.7997 (m-80)
REVERT: C  101 TYR cc_start: 0.8218 (p90) cc_final: 0.7772 (p90)
REVERT: D   92 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.6161 (mt-10)
REVERT: D  289 MET cc_start: 0.8026 (tpp) cc_final: 0.7317 (tpp)
REVERT: D  357 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8442 (m)
REVERT: D  417 TYR cc_start: 0.7841 (m-80) cc_final: 0.6602 (m-80)
REVERT: H  101 TYR cc_start: 0.8527 (p90) cc_final: 0.8073 (p90)
REVERT: E   83 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.8013 (tt)
REVERT: E   92 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.5921 (mt-10)
REVERT: E  357 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8294 (m)
REVERT: E  370 MET cc_start: 0.7563 (tmm) cc_final: 0.7294 (ttp)
REVERT: E  417 TYR cc_start: 0.7792 (m-80) cc_final: 0.7290 (m-80)
REVERT: I   34 MET cc_start: 0.7940 (mmt) cc_final: 0.7709 (mmt)
REVERT: I   43 LYS cc_start: 0.8726 (mmtm) cc_final: 0.8194 (mmmm)
REVERT: I  101 TYR cc_start: 0.8283 (p90) cc_final: 0.7696 (p90)
  outliers start: 67
  outliers final: 44
  residues processed: 239
  average time/residue: 0.1112
  time to fit residues: 40.8309
Evaluate side-chains
  241 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 190
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue   92 GLU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain A residue  290 CYS
Chi-restraints excluded: chain A residue  357 THR
Chi-restraints excluded: chain A residue  396 MET
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  102 PHE
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   92 GLU
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  245 THR
Chi-restraints excluded: chain D residue  266 ILE
Chi-restraints excluded: chain D residue  273 LEU
Chi-restraints excluded: chain D residue  290 CYS
Chi-restraints excluded: chain D residue  319 SER
Chi-restraints excluded: chain D residue  357 THR
Chi-restraints excluded: chain D residue  492 ILE
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  102 PHE
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain H residue  121 ILE
Chi-restraints excluded: chain F residue   11 SER
Chi-restraints excluded: chain E residue   83 LEU
Chi-restraints excluded: chain E residue   92 GLU
Chi-restraints excluded: chain E residue  159 HIS
Chi-restraints excluded: chain E residue  245 THR
Chi-restraints excluded: chain E residue  251 MET
Chi-restraints excluded: chain E residue  266 ILE
Chi-restraints excluded: chain E residue  267 THR
Chi-restraints excluded: chain E residue  273 LEU
Chi-restraints excluded: chain E residue  288 ILE
Chi-restraints excluded: chain E residue  290 CYS
Chi-restraints excluded: chain E residue  332 ILE
Chi-restraints excluded: chain E residue  357 THR
Chi-restraints excluded: chain E residue  395 ILE
Chi-restraints excluded: chain E residue  492 ILE
Chi-restraints excluded: chain I residue   11 LEU
Chi-restraints excluded: chain I residue   91 THR
Chi-restraints excluded: chain I residue  102 PHE
Chi-restraints excluded: chain I residue  108 LEU
Chi-restraints excluded: chain I residue  111 PHE
Chi-restraints excluded: chain I residue  121 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 100 optimal weight:    3.9990
   chunk 7 optimal weight:    8.9990
   chunk 143 optimal weight:    8.9990
   chunk 169 optimal weight:    2.9990
   chunk 104 optimal weight:    2.9990
   chunk 133 optimal weight:    1.9990
   chunk 150 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 155 optimal weight:    0.8980
   chunk 193 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 109 ASN
E 227 ASN
I 109 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.138454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.116385 restraints weight = 23011.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.119528 restraints weight = 14239.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.121615 restraints weight = 10251.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.122990 restraints weight = 8185.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.123771 restraints weight = 7008.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.1663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.070  15522  Z= 0.279
  Angle     :  0.715  13.042  21078  Z= 0.376
  Chirality :  0.046   0.259   2445
  Planarity :  0.004   0.039   2673
  Dihedral  :  5.578  59.206   2128
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 18.12 %
    Favored  : 77.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -0.58 (0.20), residues: 1953
  helix:  0.55 (0.27), residues: 405
  sheet: -0.08 (0.21), residues: 642
  loop : -0.98 (0.21), residues: 906

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 429 
 TYR   0.021   0.002   TYR A 250 
 PHE   0.051   0.003   PHE H 111 
 TRP   0.019   0.002   TRP H 110 
 HIS   0.004   0.001   HIS E 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00667 (15492)
  covalent geometry    : angle       0.71374 (21018)
  SS BOND              : bond        0.00273 (   30)
  SS BOND              : angle       1.09470 (   60)
  hydrogen bonds       : bond        0.04114 (  671)
  hydrogen bonds       : angle       5.56801 ( 1761)

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

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

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 189
  time to evaluate  : 0.619 
Fit side-chains
REVERT: A   92 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.5871 (mt-10)
REVERT: A  417 TYR cc_start: 0.7544 (m-80) cc_final: 0.7246 (m-80)
REVERT: C  101 TYR cc_start: 0.8340 (p90) cc_final: 0.7767 (p90)
REVERT: D   92 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6192 (mt-10)
REVERT: D  289 MET cc_start: 0.8340 (tpp) cc_final: 0.7732 (tpp)
REVERT: D  357 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8466 (m)
REVERT: D  417 TYR cc_start: 0.7904 (m-80) cc_final: 0.6952 (m-80)
REVERT: H  101 TYR cc_start: 0.8617 (p90) cc_final: 0.8174 (p90)
REVERT: E   92 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.5794 (mt-10)
REVERT: E  357 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8379 (m)
REVERT: E  417 TYR cc_start: 0.7965 (m-80) cc_final: 0.7313 (m-80)
REVERT: I   43 LYS cc_start: 0.8684 (mmtm) cc_final: 0.8152 (mmmm)
REVERT: I  101 TYR cc_start: 0.8504 (p90) cc_final: 0.8045 (p90)
REVERT: G   34 ASP cc_start: 0.8086 (m-30) cc_final: 0.7786 (m-30)
  outliers start: 73
  outliers final: 55
  residues processed: 239
  average time/residue: 0.1126
  time to fit residues: 41.3213
Evaluate side-chains
  234 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 174
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue   92 GLU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain A residue  290 CYS
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  102 PHE
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain B residue   33 TYR
Chi-restraints excluded: chain D residue   92 GLU
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  245 THR
Chi-restraints excluded: chain D residue  258 LEU
Chi-restraints excluded: chain D residue  266 ILE
Chi-restraints excluded: chain D residue  267 THR
Chi-restraints excluded: chain D residue  273 LEU
Chi-restraints excluded: chain D residue  290 CYS
Chi-restraints excluded: chain D residue  319 SER
Chi-restraints excluded: chain D residue  335 THR
Chi-restraints excluded: chain D residue  357 THR
Chi-restraints excluded: chain D residue  362 SER
Chi-restraints excluded: chain D residue  492 ILE
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  102 PHE
Chi-restraints excluded: chain H residue  121 ILE
Chi-restraints excluded: chain F residue   11 SER
Chi-restraints excluded: chain F residue   33 TYR
Chi-restraints excluded: chain E residue   92 GLU
Chi-restraints excluded: chain E residue  159 HIS
Chi-restraints excluded: chain E residue  245 THR
Chi-restraints excluded: chain E residue  251 MET
Chi-restraints excluded: chain E residue  266 ILE
Chi-restraints excluded: chain E residue  267 THR
Chi-restraints excluded: chain E residue  273 LEU
Chi-restraints excluded: chain E residue  288 ILE
Chi-restraints excluded: chain E residue  290 CYS
Chi-restraints excluded: chain E residue  305 LEU
Chi-restraints excluded: chain E residue  332 ILE
Chi-restraints excluded: chain E residue  335 THR
Chi-restraints excluded: chain E residue  357 THR
Chi-restraints excluded: chain E residue  362 SER
Chi-restraints excluded: chain E residue  395 ILE
Chi-restraints excluded: chain E residue  492 ILE
Chi-restraints excluded: chain I residue   11 LEU
Chi-restraints excluded: chain I residue   91 THR
Chi-restraints excluded: chain I residue   97 VAL
Chi-restraints excluded: chain I residue  102 PHE
Chi-restraints excluded: chain I residue  111 PHE
Chi-restraints excluded: chain I residue  121 ILE
Chi-restraints excluded: chain G residue   71 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 169 optimal weight:    0.8980
   chunk 173 optimal weight:    9.9990
   chunk 192 optimal weight:    0.9990
   chunk 107 optimal weight:    6.9990
   chunk 54 optimal weight:    0.0870
   chunk 48 optimal weight:    0.5980
   chunk 149 optimal weight:    0.6980
   chunk 137 optimal weight:    0.1980
   chunk 165 optimal weight:    5.9990
   overall best weight:    0.4558

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

Flipped N/Q/H residues before XYZ refinement:
A 454 ASN
D 454 ASN
E 227 ASN
** E 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G   6 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.158927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.131234 restraints weight = 24105.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.134850 restraints weight = 14301.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.137245 restraints weight = 10064.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.138851 restraints weight = 7913.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.139736 restraints weight = 6693.897|
|-----------------------------------------------------------------------------|
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.1596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  15522  Z= 0.113
  Angle     :  0.602  13.431  21078  Z= 0.314
  Chirality :  0.043   0.180   2445
  Planarity :  0.003   0.038   2673
  Dihedral  :  5.150  58.481   2128
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 19.67 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.20), residues: 1953
  helix:  0.87 (0.28), residues: 405
  sheet:  0.16 (0.21), residues: 609
  loop : -1.06 (0.21), residues: 939

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 429 
 TYR   0.012   0.001   TYR D 299 
 PHE   0.029   0.002   PHE H 111 
 TRP   0.016   0.001   TRP C 110 
 HIS   0.003   0.001   HIS E 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (15492)
  covalent geometry    : angle       0.60122 (21018)
  SS BOND              : bond        0.00171 (   30)
  SS BOND              : angle       0.76382 (   60)
  hydrogen bonds       : bond        0.02987 (  671)
  hydrogen bonds       : angle       5.09699 ( 1761)

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

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

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 208
  time to evaluate  : 0.613 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.5827 (mt-10)
REVERT: A  250 TYR cc_start: 0.6722 (m-80) cc_final: 0.6520 (m-80)
REVERT: A  342 TYR cc_start: 0.8920 (m-80) cc_final: 0.8447 (m-80)
REVERT: A  417 TYR cc_start: 0.7435 (m-80) cc_final: 0.7120 (m-80)
REVERT: C   80 TYR cc_start: 0.8372 (m-80) cc_final: 0.8080 (m-80)
REVERT: C  101 TYR cc_start: 0.8173 (p90) cc_final: 0.7656 (p90)
REVERT: D   92 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.6189 (mt-10)
REVERT: D  289 MET cc_start: 0.8120 (tpp) cc_final: 0.7391 (tpp)
REVERT: D  357 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8362 (m)
REVERT: D  417 TYR cc_start: 0.7808 (m-80) cc_final: 0.6617 (m-80)
REVERT: H  101 TYR cc_start: 0.8444 (p90) cc_final: 0.7976 (p90)
REVERT: E   92 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.5957 (mt-10)
REVERT: E  357 THR cc_start: 0.8654 (OUTLIER) cc_final: 0.8293 (m)
REVERT: E  392 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7599 (p0)
REVERT: E  417 TYR cc_start: 0.7828 (m-80) cc_final: 0.7381 (m-80)
REVERT: I   43 LYS cc_start: 0.8703 (mmtm) cc_final: 0.8189 (mmmm)
REVERT: I  101 TYR cc_start: 0.8291 (p90) cc_final: 0.7803 (p90)
  outliers start: 62
  outliers final: 46
  residues processed: 247
  average time/residue: 0.1107
  time to fit residues: 42.3907
Evaluate side-chains
  250 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 198
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue   92 GLU
Chi-restraints excluded: chain A residue  159 HIS
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain A residue  290 CYS
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  102 PHE
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain D residue   92 GLU
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  245 THR
Chi-restraints excluded: chain D residue  273 LEU
Chi-restraints excluded: chain D residue  290 CYS
Chi-restraints excluded: chain D residue  319 SER
Chi-restraints excluded: chain D residue  357 THR
Chi-restraints excluded: chain D residue  362 SER
Chi-restraints excluded: chain D residue  492 ILE
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  102 PHE
Chi-restraints excluded: chain H residue  121 ILE
Chi-restraints excluded: chain F residue   11 SER
Chi-restraints excluded: chain E residue   92 GLU
Chi-restraints excluded: chain E residue  159 HIS
Chi-restraints excluded: chain E residue  217 ILE
Chi-restraints excluded: chain E residue  245 THR
Chi-restraints excluded: chain E residue  266 ILE
Chi-restraints excluded: chain E residue  267 THR
Chi-restraints excluded: chain E residue  288 ILE
Chi-restraints excluded: chain E residue  290 CYS
Chi-restraints excluded: chain E residue  332 ILE
Chi-restraints excluded: chain E residue  357 THR
Chi-restraints excluded: chain E residue  392 ASP
Chi-restraints excluded: chain E residue  395 ILE
Chi-restraints excluded: chain E residue  492 ILE
Chi-restraints excluded: chain I residue   91 THR
Chi-restraints excluded: chain I residue   97 VAL
Chi-restraints excluded: chain I residue  102 PHE
Chi-restraints excluded: chain I residue  108 LEU
Chi-restraints excluded: chain I residue  111 PHE
Chi-restraints excluded: chain I residue  121 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 3 optimal weight:    0.7980
   chunk 124 optimal weight:    0.2980
   chunk 32 optimal weight:    6.9990
   chunk 84 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 159 optimal weight:    5.9990
   chunk 118 optimal weight:    1.9990
   chunk 153 optimal weight:    0.3980
   chunk 175 optimal weight:    1.9990
   chunk 55 optimal weight:    9.9990
   chunk 162 optimal weight:    6.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 454 ASN
D 454 ASN
E 227 ASN
** E 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.156842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.129394 restraints weight = 24067.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.133034 restraints weight = 14249.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.135422 restraints weight = 9992.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.136806 restraints weight = 7837.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.137999 restraints weight = 6700.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.1663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15522  Z= 0.140
  Angle     :  0.616  12.957  21078  Z= 0.320
  Chirality :  0.043   0.189   2445
  Planarity :  0.003   0.037   2673
  Dihedral  :  5.105  59.541   2128
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.58 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 19.67 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -0.38 (0.20), residues: 1953
  helix:  0.95 (0.28), residues: 405
  sheet:  0.17 (0.21), residues: 609
  loop : -1.06 (0.21), residues: 939

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  76 
 TYR   0.022   0.001   TYR D 250 
 PHE   0.034   0.002   PHE H 111 
 TRP   0.014   0.001   TRP H 110 
 HIS   0.003   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (15492)
  covalent geometry    : angle       0.61480 (21018)
  SS BOND              : bond        0.00182 (   30)
  SS BOND              : angle       0.85289 (   60)
  hydrogen bonds       : bond        0.03104 (  671)
  hydrogen bonds       : angle       5.07117 ( 1761)

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

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

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 187
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.5870 (mt-10)
REVERT: A  417 TYR cc_start: 0.7459 (m-80) cc_final: 0.7088 (m-10)
REVERT: C   80 TYR cc_start: 0.8413 (m-80) cc_final: 0.8064 (m-80)
REVERT: C  101 TYR cc_start: 0.8219 (p90) cc_final: 0.7702 (p90)
REVERT: D   92 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6215 (mt-10)
REVERT: D  289 MET cc_start: 0.8082 (tpp) cc_final: 0.7353 (tpp)
REVERT: D  357 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8345 (m)
REVERT: D  417 TYR cc_start: 0.7831 (m-80) cc_final: 0.6659 (m-80)
REVERT: H  101 TYR cc_start: 0.8438 (p90) cc_final: 0.7959 (p90)
REVERT: E   92 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.5977 (mt-10)
REVERT: E  357 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8285 (m)
REVERT: E  392 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7634 (p0)
REVERT: E  417 TYR cc_start: 0.7854 (m-80) cc_final: 0.7439 (m-80)
REVERT: I   43 LYS cc_start: 0.8726 (mmtm) cc_final: 0.8169 (mmmm)
REVERT: I  101 TYR cc_start: 0.8287 (p90) cc_final: 0.7778 (p90)
  outliers start: 64
  outliers final: 56
  residues processed: 230
  average time/residue: 0.1140
  time to fit residues: 40.1532
Evaluate side-chains
  246 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 184
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue   92 GLU
Chi-restraints excluded: chain A residue  159 HIS
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain A residue  290 CYS
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  102 PHE
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain D residue   92 GLU
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  245 THR
Chi-restraints excluded: chain D residue  266 ILE
Chi-restraints excluded: chain D residue  273 LEU
Chi-restraints excluded: chain D residue  290 CYS
Chi-restraints excluded: chain D residue  319 SER
Chi-restraints excluded: chain D residue  357 THR
Chi-restraints excluded: chain D residue  362 SER
Chi-restraints excluded: chain D residue  492 ILE
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  102 PHE
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain H residue  111 PHE
Chi-restraints excluded: chain H residue  121 ILE
Chi-restraints excluded: chain F residue   11 SER
Chi-restraints excluded: chain F residue   33 TYR
Chi-restraints excluded: chain E residue   83 LEU
Chi-restraints excluded: chain E residue   92 GLU
Chi-restraints excluded: chain E residue  159 HIS
Chi-restraints excluded: chain E residue  217 ILE
Chi-restraints excluded: chain E residue  227 ASN
Chi-restraints excluded: chain E residue  245 THR
Chi-restraints excluded: chain E residue  253 THR
Chi-restraints excluded: chain E residue  266 ILE
Chi-restraints excluded: chain E residue  267 THR
Chi-restraints excluded: chain E residue  273 LEU
Chi-restraints excluded: chain E residue  288 ILE
Chi-restraints excluded: chain E residue  290 CYS
Chi-restraints excluded: chain E residue  332 ILE
Chi-restraints excluded: chain E residue  357 THR
Chi-restraints excluded: chain E residue  362 SER
Chi-restraints excluded: chain E residue  392 ASP
Chi-restraints excluded: chain E residue  395 ILE
Chi-restraints excluded: chain E residue  449 THR
Chi-restraints excluded: chain E residue  492 ILE
Chi-restraints excluded: chain I residue   91 THR
Chi-restraints excluded: chain I residue   97 VAL
Chi-restraints excluded: chain I residue  102 PHE
Chi-restraints excluded: chain I residue  108 LEU
Chi-restraints excluded: chain I residue  111 PHE
Chi-restraints excluded: chain I residue  121 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 167 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 119 optimal weight:    0.0670
   chunk 5 optimal weight:    0.8980
   chunk 108 optimal weight:    7.9990
   chunk 18 optimal weight:    0.5980
   chunk 30 optimal weight:    3.9990
   chunk 139 optimal weight:    0.0000
   chunk 194 optimal weight:    3.9990
   chunk 148 optimal weight:    0.9980
   overall best weight:    0.5122

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

Flipped N/Q/H residues before XYZ refinement:
E 227 ASN
E 388 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.159198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.131635 restraints weight = 23834.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.135264 restraints weight = 13875.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.137691 restraints weight = 9620.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.139094 restraints weight = 7459.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.140316 restraints weight = 6326.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.1721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  15522  Z= 0.115
  Angle     :  0.599  13.002  21078  Z= 0.311
  Chirality :  0.042   0.173   2445
  Planarity :  0.003   0.035   2673
  Dihedral  :  4.999  59.192   2128
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 19.90 %
    Favored  : 76.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -0.28 (0.20), residues: 1953
  helix:  1.09 (0.28), residues: 405
  sheet:  0.16 (0.21), residues: 624
  loop : -0.98 (0.21), residues: 924

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  76 
 TYR   0.016   0.001   TYR A 250 
 PHE   0.028   0.001   PHE H 111 
 TRP   0.014   0.001   TRP C 110 
 HIS   0.003   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (15492)
  covalent geometry    : angle       0.59826 (21018)
  SS BOND              : bond        0.00144 (   30)
  SS BOND              : angle       0.77354 (   60)
  hydrogen bonds       : bond        0.02853 (  671)
  hydrogen bonds       : angle       4.94566 ( 1761)

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

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

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3906 Ramachandran restraints generated.
    1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 200
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.5818 (mt-10)
REVERT: A  342 TYR cc_start: 0.8893 (m-80) cc_final: 0.8448 (m-80)
REVERT: A  417 TYR cc_start: 0.7443 (m-80) cc_final: 0.7094 (m-10)
REVERT: C   80 TYR cc_start: 0.8353 (m-80) cc_final: 0.8023 (m-80)
REVERT: C  101 TYR cc_start: 0.8181 (p90) cc_final: 0.7704 (p90)
REVERT: D   92 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6019 (mt-10)
REVERT: D  289 MET cc_start: 0.7979 (tpp) cc_final: 0.7375 (tpp)
REVERT: D  357 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8293 (m)
REVERT: D  417 TYR cc_start: 0.7844 (m-80) cc_final: 0.6558 (m-80)
REVERT: H  101 TYR cc_start: 0.8395 (p90) cc_final: 0.7926 (p90)
REVERT: E   92 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6017 (mt-10)
REVERT: E  357 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8231 (m)
REVERT: E  392 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7616 (p0)
REVERT: E  417 TYR cc_start: 0.7881 (m-80) cc_final: 0.7512 (m-80)
REVERT: I   43 LYS cc_start: 0.8730 (mmtm) cc_final: 0.8160 (mmmm)
REVERT: I  101 TYR cc_start: 0.8237 (p90) cc_final: 0.7723 (p90)
  outliers start: 67
  outliers final: 53
  residues processed: 244
  average time/residue: 0.1140
  time to fit residues: 42.7032
Evaluate side-chains
  247 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 188
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue   92 GLU
Chi-restraints excluded: chain A residue  159 HIS
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain A residue  290 CYS
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  102 PHE
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  121 ILE
Chi-restraints excluded: chain B residue   33 TYR
Chi-restraints excluded: chain D residue   92 GLU
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  245 THR
Chi-restraints excluded: chain D residue  266 ILE
Chi-restraints excluded: chain D residue  273 LEU
Chi-restraints excluded: chain D residue  290 CYS
Chi-restraints excluded: chain D residue  319 SER
Chi-restraints excluded: chain D residue  357 THR
Chi-restraints excluded: chain D residue  362 SER
Chi-restraints excluded: chain D residue  449 THR
Chi-restraints excluded: chain D residue  492 ILE
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  102 PHE
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain H residue  111 PHE
Chi-restraints excluded: chain H residue  121 ILE
Chi-restraints excluded: chain F residue   11 SER
Chi-restraints excluded: chain F residue   33 TYR
Chi-restraints excluded: chain E residue   92 GLU
Chi-restraints excluded: chain E residue  159 HIS
Chi-restraints excluded: chain E residue  227 ASN
Chi-restraints excluded: chain E residue  245 THR
Chi-restraints excluded: chain E residue  253 THR
Chi-restraints excluded: chain E residue  266 ILE
Chi-restraints excluded: chain E residue  267 THR
Chi-restraints excluded: chain E residue  273 LEU
Chi-restraints excluded: chain E residue  288 ILE
Chi-restraints excluded: chain E residue  290 CYS
Chi-restraints excluded: chain E residue  305 LEU
Chi-restraints excluded: chain E residue  332 ILE
Chi-restraints excluded: chain E residue  357 THR
Chi-restraints excluded: chain E residue  392 ASP
Chi-restraints excluded: chain E residue  395 ILE
Chi-restraints excluded: chain E residue  492 ILE
Chi-restraints excluded: chain I residue   91 THR
Chi-restraints excluded: chain I residue   97 VAL
Chi-restraints excluded: chain I residue  102 PHE
Chi-restraints excluded: chain I residue  108 LEU
Chi-restraints excluded: chain I residue  111 PHE
Chi-restraints excluded: chain I residue  121 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run
    self.rsr_result = rsr_wrappers.run_real_space_refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__
    self._refined = macro_cycle_real_space.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs
    ro = mmtbx.refinement.real_space.individual_sites.easy(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__
    self.weight = mmtbx.refinement.real_space.weight.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine
    real_space_result = refinery(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine
    self.refined = maptbx.real_space_refinement_simple.lbfgs(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__
    O.minimizer = scitbx.lbfgs.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients
    gr_e = O.geometry_restraints_manager.energies_sites(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites
    pair_proxies = self.pair_proxies(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 50.128 > 50:
  distance: 18 - 109:  22.233
  distance: 29 - 92:   9.684
  distance: 32 - 89:  13.363
  distance: 64 - 69:  13.979
  distance: 69 - 70:  20.370
  distance: 70 - 71:  17.178
  distance: 70 - 73:  28.277
  distance: 71 - 72:  15.182
  distance: 71 - 75:  12.512
  distance: 73 - 74:  17.611
  distance: 74 - 238:  11.961
  distance: 75 - 76:   3.220
  distance: 75 - 226:  14.961
  distance: 76 - 77:  16.693
  distance: 76 - 79:  20.397
  distance: 77 - 78:   5.221
  distance: 77 - 89:   7.030
  distance: 78 - 223:   8.863
  distance: 79 - 80:   9.575
  distance: 80 - 81:   8.764
  distance: 81 - 83:   3.308
  distance: 82 - 84:   3.510
  distance: 82 - 85:   6.567
  distance: 83 - 84:   8.917
  distance: 84 - 86:   4.323
  distance: 85 - 87:   9.546
  distance: 86 - 88:   7.249
  distance: 87 - 88:   4.612
  distance: 89 - 90:   3.214
  distance: 90 - 91:   8.661
  distance: 90 - 93:   7.228
  distance: 91 - 92:  15.942
  distance: 91 - 98:   7.987
  distance: 93 - 94:  12.316
  distance: 94 - 95:   6.445
  distance: 95 - 96:   6.803
  distance: 96 - 97:   8.863
  distance: 98 - 99:   6.795
  distance: 98 - 208:   9.845
  distance: 99 - 100:  12.040
  distance: 99 - 102:  12.650
  distance: 100 - 101:   9.746
  distance: 100 - 106:  12.756
  distance: 101 - 205:  12.149
  distance: 102 - 103:   9.451
  distance: 103 - 104:   6.229
  distance: 103 - 105:  20.703
  distance: 106 - 107:  17.249
  distance: 107 - 108:  21.470
  distance: 107 - 110:  25.226
  distance: 108 - 109:  27.789
  distance: 108 - 116:   9.900
  distance: 110 - 111:  28.899
  distance: 111 - 112:  27.304
  distance: 111 - 113:  16.540
  distance: 112 - 114:  11.681
  distance: 113 - 115:  12.955
  distance: 114 - 115:  14.803
  distance: 116 - 117:  17.786
  distance: 117 - 118:  19.836
  distance: 117 - 120:  30.814
  distance: 118 - 119:  23.014
  distance: 118 - 123:  38.937
  distance: 120 - 121:   9.263
  distance: 120 - 122:  24.291
  distance: 123 - 124:  34.093
  distance: 124 - 125:  16.454
  distance: 124 - 127:  23.376
  distance: 125 - 126:  14.843
  distance: 125 - 129:  27.270
  distance: 127 - 128:  20.168
  distance: 129 - 130:  24.456
  distance: 129 - 135:  24.178
  distance: 130 - 131:  25.354
  distance: 130 - 133:  40.636
  distance: 131 - 132:  24.573
  distance: 131 - 136:  17.584
  distance: 133 - 134:  36.820
  distance: 134 - 135:  22.056
  distance: 136 - 137:  13.227
  distance: 137 - 138:  12.759
  distance: 137 - 140:  24.394
  distance: 138 - 139:  23.897
  distance: 138 - 144:  19.175
  distance: 140 - 141:  31.984
  distance: 141 - 142:  24.212
  distance: 141 - 143:  21.343
  distance: 144 - 145:   9.476
  distance: 145 - 146:  10.457
  distance: 145 - 148:  16.803
  distance: 146 - 147:  15.805
  distance: 146 - 150:   8.296
  distance: 148 - 149:   9.906
  distance: 149 - 167:  14.987