Starting phenix.real_space_refine
on Tue Feb 11 12:39:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ter_41198/02_2025/8ter_41198.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ter_41198/02_2025/8ter_41198.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ter_41198/02_2025/8ter_41198.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ter_41198/02_2025/8ter_41198.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ter_41198/02_2025/8ter_41198.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ter_41198/02_2025/8ter_41198.cif"
  }
  resolution = 2.59
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
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: 3
    Type Number    sf(0)   Gaussians
     C    3420      2.51       5
     N     960      2.21       5
     O    1400      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5780
  Number of models: 1
  Model: ""
    Number of chains: 21
    Chain: "A"
      Number of atoms: 277
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 277
          Classifications: {'peptide': 35}
          Link IDs: {'PTRANS': 2, 'TRANS': 32}
    Chain: "A"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
    Chain: "B"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
    Chain: "C"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
    Chain: "D"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
    Chain: "E"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
    Chain: "F"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
    Chain: "G"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
    Chain: "H"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
    Chain: "I"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
    Chain: "J"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
    Chain: "K"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
    Chain: "L"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
    Chain: "M"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
    Chain: "N"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
    Chain: "O"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
    Chain: "P"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 13
          Classifications: {'water': 13}
          Link IDs: {None: 12}
    Chain: "Q"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
    Chain: "R"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 13
          Classifications: {'water': 13}
          Link IDs: {None: 12}
    Chain: "S"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 11
          Classifications: {'water': 11}
          Link IDs: {None: 10}
    Chain: "T"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 11
          Classifications: {'water': 11}
          Link IDs: {None: 10}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, T
  Time building chain proxies: 2.17, per 1000 atoms: 0.38
  Number of scatterers: 5780
  At special positions: 0
  Unit cell: (64.141, 69.531, 65.758, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O    1400      8.00
     N     960      7.00
     C    3420      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.34
  Conformation dependent library (CDL) restraints added in 623.7 milliseconds
  

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1240

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 62.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'P' and resid 266 through 273
      removed outlier: 6.824A  pdb=" N   ILE L 270 " --> pdb=" O   GLY P 269 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   GLN P 271 " --> pdb=" O   ILE L 270 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   TYR L 272 " --> pdb=" O   GLN P 271 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   SER P 273 " --> pdb=" O   TYR L 272 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   ILE H 270 " --> pdb=" O   GLY L 269 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   GLN L 271 " --> pdb=" O   ILE H 270 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   TYR H 272 " --> pdb=" O   GLN L 271 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   SER L 273 " --> pdb=" O   TYR H 272 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   ILE D 270 " --> pdb=" O   GLY H 269 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   GLN H 271 " --> pdb=" O   ILE D 270 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   TYR D 272 " --> pdb=" O   GLN H 271 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   SER H 273 " --> pdb=" O   TYR D 272 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   ILE A 270 " --> pdb=" O   GLY D 269 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   GLN D 271 " --> pdb=" O   ILE A 270 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   TYR A 272 " --> pdb=" O   GLN D 271 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   SER D 273 " --> pdb=" O   TYR A 272 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   GLN A 267 " --> pdb=" O   TYR E 268 " (cutoff:3.500A)
      removed outlier: 7.614A  pdb=" N   ILE E 270 " --> pdb=" O   GLN A 267 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   GLY A 269 " --> pdb=" O   ILE E 270 " (cutoff:3.500A)
      removed outlier: 10.474A  pdb=" N   TYR E 272 " --> pdb=" O   GLY A 269 " (cutoff:3.500A)
      removed outlier: 8.949A  pdb=" N   GLN A 271 " --> pdb=" O   TYR E 272 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   GLN E 267 " --> pdb=" O   TYR I 268 " (cutoff:3.500A)
      removed outlier: 7.614A  pdb=" N   ILE I 270 " --> pdb=" O   GLN E 267 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   GLY E 269 " --> pdb=" O   ILE I 270 " (cutoff:3.500A)
      removed outlier: 10.474A  pdb=" N   TYR I 272 " --> pdb=" O   GLY E 269 " (cutoff:3.500A)
      removed outlier: 8.949A  pdb=" N   GLN E 271 " --> pdb=" O   TYR I 272 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   GLN I 267 " --> pdb=" O   TYR M 268 " (cutoff:3.500A)
      removed outlier: 7.614A  pdb=" N   ILE M 270 " --> pdb=" O   GLN I 267 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   GLY I 269 " --> pdb=" O   ILE M 270 " (cutoff:3.500A)
      removed outlier: 10.473A  pdb=" N   TYR M 272 " --> pdb=" O   GLY I 269 " (cutoff:3.500A)
      removed outlier: 8.949A  pdb=" N   GLN I 271 " --> pdb=" O   TYR M 272 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   GLN M 267 " --> pdb=" O   TYR Q 268 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   ILE Q 270 " --> pdb=" O   GLN M 267 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   GLY M 269 " --> pdb=" O   ILE Q 270 " (cutoff:3.500A)
      removed outlier: 10.474A  pdb=" N   TYR Q 272 " --> pdb=" O   GLY M 269 " (cutoff:3.500A)
      removed outlier: 8.950A  pdb=" N   GLN M 271 " --> pdb=" O   TYR Q 272 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   GLN Q 267 " --> pdb=" O   TYR T 268 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   ILE T 270 " --> pdb=" O   GLN Q 267 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   GLY Q 269 " --> pdb=" O   ILE T 270 " (cutoff:3.500A)
      removed outlier: 10.473A  pdb=" N   TYR T 272 " --> pdb=" O   GLY Q 269 " (cutoff:3.500A)
      removed outlier: 8.949A  pdb=" N   GLN Q 271 " --> pdb=" O   TYR T 272 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'P' and resid 276 through 279
      removed outlier: 6.279A  pdb=" N   TYR L 276 " --> pdb=" O   SER P 277 " (cutoff:3.500A)
      removed outlier: 7.741A  pdb=" N   GLN P 279 " --> pdb=" O   TYR L 276 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   GLN L 278 " --> pdb=" O   GLN P 279 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   TYR H 276 " --> pdb=" O   SER L 277 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   GLN L 279 " --> pdb=" O   TYR H 276 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   GLN H 278 " --> pdb=" O   GLN L 279 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   TYR D 276 " --> pdb=" O   SER H 277 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   GLN H 279 " --> pdb=" O   TYR D 276 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   GLN D 278 " --> pdb=" O   GLN H 279 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   TYR A 276 " --> pdb=" O   SER D 277 " (cutoff:3.500A)
      removed outlier: 7.741A  pdb=" N   GLN D 279 " --> pdb=" O   TYR A 276 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   GLN A 278 " --> pdb=" O   GLN D 279 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'P' and resid 283 through 293
      removed outlier: 6.437A  pdb=" N   GLN L 284 " --> pdb=" O   LEU P 285 " (cutoff:3.500A)
      removed outlier: 7.943A  pdb=" N   GLN P 287 " --> pdb=" O   GLN L 284 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   GLN L 286 " --> pdb=" O   GLN P 287 " (cutoff:3.500A)
      removed outlier: 8.105A  pdb=" N   GLN P 289 " --> pdb=" O   GLN L 286 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   PHE L 288 " --> pdb=" O   GLN P 289 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   TYR P 291 " --> pdb=" O   PHE L 288 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   GLY L 290 " --> pdb=" O   TYR P 291 " (cutoff:3.500A)
      removed outlier: 8.056A  pdb=" N   GLN P 293 " --> pdb=" O   GLY L 290 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   GLY L 292 " --> pdb=" O   GLN P 293 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   GLN H 284 " --> pdb=" O   LEU L 285 " (cutoff:3.500A)
      removed outlier: 7.942A  pdb=" N   GLN L 287 " --> pdb=" O   GLN H 284 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   GLN H 286 " --> pdb=" O   GLN L 287 " (cutoff:3.500A)
      removed outlier: 8.104A  pdb=" N   GLN L 289 " --> pdb=" O   GLN H 286 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   PHE H 288 " --> pdb=" O   GLN L 289 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   TYR L 291 " --> pdb=" O   PHE H 288 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   GLY H 290 " --> pdb=" O   TYR L 291 " (cutoff:3.500A)
      removed outlier: 8.056A  pdb=" N   GLN L 293 " --> pdb=" O   GLY H 290 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   GLY H 292 " --> pdb=" O   GLN L 293 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   GLN D 284 " --> pdb=" O   LEU H 285 " (cutoff:3.500A)
      removed outlier: 7.942A  pdb=" N   GLN H 287 " --> pdb=" O   GLN D 284 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   GLN D 286 " --> pdb=" O   GLN H 287 " (cutoff:3.500A)
      removed outlier: 8.105A  pdb=" N   GLN H 289 " --> pdb=" O   GLN D 286 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   PHE D 288 " --> pdb=" O   GLN H 289 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   TYR H 291 " --> pdb=" O   PHE D 288 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   GLY D 290 " --> pdb=" O   TYR H 291 " (cutoff:3.500A)
      removed outlier: 8.056A  pdb=" N   GLN H 293 " --> pdb=" O   GLY D 290 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   GLY D 292 " --> pdb=" O   GLN H 293 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   GLN A 284 " --> pdb=" O   LEU D 285 " (cutoff:3.500A)
      removed outlier: 7.943A  pdb=" N   GLN D 287 " --> pdb=" O   GLN A 284 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   GLN A 286 " --> pdb=" O   GLN D 287 " (cutoff:3.500A)
      removed outlier: 8.105A  pdb=" N   GLN D 289 " --> pdb=" O   GLN A 286 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   PHE A 288 " --> pdb=" O   GLN D 289 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   TYR D 291 " --> pdb=" O   PHE A 288 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   GLY A 290 " --> pdb=" O   TYR D 291 " (cutoff:3.500A)
      removed outlier: 8.056A  pdb=" N   GLN D 293 " --> pdb=" O   GLY A 290 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   GLY A 292 " --> pdb=" O   GLN D 293 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'P' and resid 296 through 298
      removed outlier: 6.450A  pdb=" N   THR L 296 " --> pdb=" O   SER P 297 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   THR H 296 " --> pdb=" O   SER L 297 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   THR D 296 " --> pdb=" O   SER H 297 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   THR A 296 " --> pdb=" O   SER D 297 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'R' and resid 266 through 273
      removed outlier: 6.824A  pdb=" N   ILE N 270 " --> pdb=" O   GLY R 269 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   GLN R 271 " --> pdb=" O   ILE N 270 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   TYR N 272 " --> pdb=" O   GLN R 271 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   SER R 273 " --> pdb=" O   TYR N 272 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   ILE J 270 " --> pdb=" O   GLY N 269 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   GLN N 271 " --> pdb=" O   ILE J 270 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   TYR J 272 " --> pdb=" O   GLN N 271 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   SER N 273 " --> pdb=" O   TYR J 272 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   ILE F 270 " --> pdb=" O   GLY J 269 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   GLN J 271 " --> pdb=" O   ILE F 270 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   TYR F 272 " --> pdb=" O   GLN J 271 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   SER J 273 " --> pdb=" O   TYR F 272 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   ILE B 270 " --> pdb=" O   GLY F 269 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   GLN F 271 " --> pdb=" O   ILE B 270 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   TYR B 272 " --> pdb=" O   GLN F 271 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   SER F 273 " --> pdb=" O   TYR B 272 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   GLN B 267 " --> pdb=" O   TYR C 268 " (cutoff:3.500A)
      removed outlier: 7.614A  pdb=" N   ILE C 270 " --> pdb=" O   GLN B 267 " (cutoff:3.500A)
      removed outlier: 7.299A  pdb=" N   GLY B 269 " --> pdb=" O   ILE C 270 " (cutoff:3.500A)
      removed outlier: 10.473A  pdb=" N   TYR C 272 " --> pdb=" O   GLY B 269 " (cutoff:3.500A)
      removed outlier: 8.948A  pdb=" N   GLN B 271 " --> pdb=" O   TYR C 272 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   GLN C 267 " --> pdb=" O   TYR G 268 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   ILE G 270 " --> pdb=" O   GLN C 267 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   GLY C 269 " --> pdb=" O   ILE G 270 " (cutoff:3.500A)
      removed outlier: 10.474A  pdb=" N   TYR G 272 " --> pdb=" O   GLY C 269 " (cutoff:3.500A)
      removed outlier: 8.949A  pdb=" N   GLN C 271 " --> pdb=" O   TYR G 272 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   GLN G 267 " --> pdb=" O   TYR K 268 " (cutoff:3.500A)
      removed outlier: 7.614A  pdb=" N   ILE K 270 " --> pdb=" O   GLN G 267 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   GLY G 269 " --> pdb=" O   ILE K 270 " (cutoff:3.500A)
      removed outlier: 10.474A  pdb=" N   TYR K 272 " --> pdb=" O   GLY G 269 " (cutoff:3.500A)
      removed outlier: 8.950A  pdb=" N   GLN G 271 " --> pdb=" O   TYR K 272 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   GLN K 267 " --> pdb=" O   TYR O 268 " (cutoff:3.500A)
      removed outlier: 7.614A  pdb=" N   ILE O 270 " --> pdb=" O   GLN K 267 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   GLY K 269 " --> pdb=" O   ILE O 270 " (cutoff:3.500A)
      removed outlier: 10.473A  pdb=" N   TYR O 272 " --> pdb=" O   GLY K 269 " (cutoff:3.500A)
      removed outlier: 8.949A  pdb=" N   GLN K 271 " --> pdb=" O   TYR O 272 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   GLN O 267 " --> pdb=" O   TYR S 268 " (cutoff:3.500A)
      removed outlier: 7.614A  pdb=" N   ILE S 270 " --> pdb=" O   GLN O 267 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   GLY O 269 " --> pdb=" O   ILE S 270 " (cutoff:3.500A)
      removed outlier: 10.473A  pdb=" N   TYR S 272 " --> pdb=" O   GLY O 269 " (cutoff:3.500A)
      removed outlier: 8.949A  pdb=" N   GLN O 271 " --> pdb=" O   TYR S 272 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'R' and resid 276 through 279
      removed outlier: 6.279A  pdb=" N   TYR N 276 " --> pdb=" O   SER R 277 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   GLN R 279 " --> pdb=" O   TYR N 276 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   GLN N 278 " --> pdb=" O   GLN R 279 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   TYR J 276 " --> pdb=" O   SER N 277 " (cutoff:3.500A)
      removed outlier: 7.741A  pdb=" N   GLN N 279 " --> pdb=" O   TYR J 276 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   GLN J 278 " --> pdb=" O   GLN N 279 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   TYR F 276 " --> pdb=" O   SER J 277 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   GLN J 279 " --> pdb=" O   TYR F 276 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   GLN F 278 " --> pdb=" O   GLN J 279 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   TYR B 276 " --> pdb=" O   SER F 277 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   GLN F 279 " --> pdb=" O   TYR B 276 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   GLN B 278 " --> pdb=" O   GLN F 279 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'R' and resid 283 through 293
      removed outlier: 6.437A  pdb=" N   GLN N 284 " --> pdb=" O   LEU R 285 " (cutoff:3.500A)
      removed outlier: 7.942A  pdb=" N   GLN R 287 " --> pdb=" O   GLN N 284 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   GLN N 286 " --> pdb=" O   GLN R 287 " (cutoff:3.500A)
      removed outlier: 8.105A  pdb=" N   GLN R 289 " --> pdb=" O   GLN N 286 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   PHE N 288 " --> pdb=" O   GLN R 289 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   TYR R 291 " --> pdb=" O   PHE N 288 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   GLY N 290 " --> pdb=" O   TYR R 291 " (cutoff:3.500A)
      removed outlier: 8.057A  pdb=" N   GLN R 293 " --> pdb=" O   GLY N 290 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   GLY N 292 " --> pdb=" O   GLN R 293 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   GLN J 284 " --> pdb=" O   LEU N 285 " (cutoff:3.500A)
      removed outlier: 7.943A  pdb=" N   GLN N 287 " --> pdb=" O   GLN J 284 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   GLN J 286 " --> pdb=" O   GLN N 287 " (cutoff:3.500A)
      removed outlier: 8.105A  pdb=" N   GLN N 289 " --> pdb=" O   GLN J 286 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   PHE J 288 " --> pdb=" O   GLN N 289 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   TYR N 291 " --> pdb=" O   PHE J 288 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   GLY J 290 " --> pdb=" O   TYR N 291 " (cutoff:3.500A)
      removed outlier: 8.056A  pdb=" N   GLN N 293 " --> pdb=" O   GLY J 290 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   GLY J 292 " --> pdb=" O   GLN N 293 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   GLN F 284 " --> pdb=" O   LEU J 285 " (cutoff:3.500A)
      removed outlier: 7.942A  pdb=" N   GLN J 287 " --> pdb=" O   GLN F 284 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   GLN F 286 " --> pdb=" O   GLN J 287 " (cutoff:3.500A)
      removed outlier: 8.105A  pdb=" N   GLN J 289 " --> pdb=" O   GLN F 286 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   PHE F 288 " --> pdb=" O   GLN J 289 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   TYR J 291 " --> pdb=" O   PHE F 288 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   GLY F 290 " --> pdb=" O   TYR J 291 " (cutoff:3.500A)
      removed outlier: 8.056A  pdb=" N   GLN J 293 " --> pdb=" O   GLY F 290 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   GLY F 292 " --> pdb=" O   GLN J 293 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   GLN B 284 " --> pdb=" O   LEU F 285 " (cutoff:3.500A)
      removed outlier: 7.942A  pdb=" N   GLN F 287 " --> pdb=" O   GLN B 284 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   GLN B 286 " --> pdb=" O   GLN F 287 " (cutoff:3.500A)
      removed outlier: 8.105A  pdb=" N   GLN F 289 " --> pdb=" O   GLN B 286 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   PHE B 288 " --> pdb=" O   GLN F 289 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   TYR F 291 " --> pdb=" O   PHE B 288 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   GLY B 290 " --> pdb=" O   TYR F 291 " (cutoff:3.500A)
      removed outlier: 8.056A  pdb=" N   GLN F 293 " --> pdb=" O   GLY B 290 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   GLY B 292 " --> pdb=" O   GLN F 293 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'R' and resid 296 through 298
      removed outlier: 6.450A  pdb=" N   THR N 296 " --> pdb=" O   SER R 297 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   THR J 296 " --> pdb=" O   SER N 297 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   THR F 296 " --> pdb=" O   SER J 297 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   THR B 296 " --> pdb=" O   SER F 297 " (cutoff:3.500A)

    174 hydrogen bonds defined for protein.
    522 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: 1.59

  Time building geometry restraints manager: 1.55 seconds

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

  Histogram of bond lengths:
        1.22 -     1.29: 960
        1.29 -     1.35: 940
        1.35 -     1.42: 759
        1.42 -     1.48: 821
        1.48 -     1.55: 2200
  Bond restraints: 5680
  Sorted by residual:
  bond pdb=" CG  GLN J 266 "
       pdb=" CD  GLN J 266 "
    ideal  model  delta    sigma   weight residual
    1.516  1.546 -0.030 2.50e-02 1.60e+03 1.46e+00
  bond pdb=" CG  GLN S 266 "
       pdb=" CD  GLN S 266 "
    ideal  model  delta    sigma   weight residual
    1.516  1.546 -0.030 2.50e-02 1.60e+03 1.45e+00
  bond pdb=" CG  GLN Q 266 "
       pdb=" CD  GLN Q 266 "
    ideal  model  delta    sigma   weight residual
    1.516  1.546 -0.030 2.50e-02 1.60e+03 1.45e+00
  bond pdb=" CG  GLN E 266 "
       pdb=" CD  GLN E 266 "
    ideal  model  delta    sigma   weight residual
    1.516  1.546 -0.030 2.50e-02 1.60e+03 1.43e+00
  bond pdb=" CG  GLN D 266 "
       pdb=" CD  GLN D 266 "
    ideal  model  delta    sigma   weight residual
    1.516  1.546 -0.030 2.50e-02 1.60e+03 1.43e+00
  ... (remaining 5675 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.02: 6437
        1.02 -     2.03: 882
        2.03 -     3.05: 251
        3.05 -     4.06: 70
        4.06 -     5.08: 40
  Bond angle restraints: 7680
  Sorted by residual:
  angle pdb=" CA  THR D 280 "
        pdb=" CB  THR D 280 "
        pdb=" CG2 THR D 280 "
      ideal   model   delta    sigma   weight residual
     110.50  114.37   -3.87 1.70e+00 3.46e-01 5.19e+00
  angle pdb=" CA  THR K 280 "
        pdb=" CB  THR K 280 "
        pdb=" CG2 THR K 280 "
      ideal   model   delta    sigma   weight residual
     110.50  114.37   -3.87 1.70e+00 3.46e-01 5.18e+00
  angle pdb=" CA  THR G 280 "
        pdb=" CB  THR G 280 "
        pdb=" CG2 THR G 280 "
      ideal   model   delta    sigma   weight residual
     110.50  114.37   -3.87 1.70e+00 3.46e-01 5.17e+00
  angle pdb=" CA  THR J 280 "
        pdb=" CB  THR J 280 "
        pdb=" CG2 THR J 280 "
      ideal   model   delta    sigma   weight residual
     110.50  114.36   -3.86 1.70e+00 3.46e-01 5.16e+00
  angle pdb=" CA  THR E 280 "
        pdb=" CB  THR E 280 "
        pdb=" CG2 THR E 280 "
      ideal   model   delta    sigma   weight residual
     110.50  114.36   -3.86 1.70e+00 3.46e-01 5.15e+00
  ... (remaining 7675 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.32: 2660
       13.32 -    26.63: 420
       26.63 -    39.95: 160
       39.95 -    53.26: 80
       53.26 -    66.58: 40
  Dihedral angle restraints: 3360
    sinusoidal: 1360
      harmonic: 2000
  Sorted by residual:
  dihedral pdb=" CA  GLN I 266 "
           pdb=" CB  GLN I 266 "
           pdb=" CG  GLN I 266 "
           pdb=" CD  GLN I 266 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  134.27   45.73     3      1.50e+01 4.44e-03 8.22e+00
  dihedral pdb=" CA  GLN C 266 "
           pdb=" CB  GLN C 266 "
           pdb=" CG  GLN C 266 "
           pdb=" CD  GLN C 266 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  134.28   45.72     3      1.50e+01 4.44e-03 8.22e+00
  dihedral pdb=" CA  GLN Q 266 "
           pdb=" CB  GLN Q 266 "
           pdb=" CG  GLN Q 266 "
           pdb=" CD  GLN Q 266 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  134.28   45.72     3      1.50e+01 4.44e-03 8.22e+00
  ... (remaining 3357 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    0.025: 254
       0.025 -    0.047: 226
       0.047 -    0.070: 100
       0.070 -    0.093: 80
       0.093 -    0.116: 40
  Chirality restraints: 700
  Sorted by residual:
  chirality pdb=" CB  THR I 280 "
            pdb=" CA  THR I 280 "
            pdb=" OG1 THR I 280 "
            pdb=" CG2 THR I 280 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.44    0.12 2.00e-01 2.50e+01 3.35e-01
  chirality pdb=" CB  THR R 280 "
            pdb=" CA  THR R 280 "
            pdb=" OG1 THR R 280 "
            pdb=" CG2 THR R 280 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.44    0.12 2.00e-01 2.50e+01 3.32e-01
  chirality pdb=" CB  THR S 280 "
            pdb=" CA  THR S 280 "
            pdb=" OG1 THR S 280 "
            pdb=" CG2 THR S 280 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.44    0.12 2.00e-01 2.50e+01 3.32e-01
  ... (remaining 697 not shown)

  Planarity restraints: 1080
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN E 289 "    0.011 2.00e-02 2.50e+03   2.27e-02 5.15e+00
        pdb=" CD  GLN E 289 "   -0.039 2.00e-02 2.50e+03
        pdb=" OE1 GLN E 289 "    0.015 2.00e-02 2.50e+03
        pdb=" NE2 GLN E 289 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN S 289 "    0.011 2.00e-02 2.50e+03   2.26e-02 5.12e+00
        pdb=" CD  GLN S 289 "   -0.039 2.00e-02 2.50e+03
        pdb=" OE1 GLN S 289 "    0.015 2.00e-02 2.50e+03
        pdb=" NE2 GLN S 289 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN K 289 "    0.011 2.00e-02 2.50e+03   2.25e-02 5.05e+00
        pdb=" CD  GLN K 289 "   -0.039 2.00e-02 2.50e+03
        pdb=" OE1 GLN K 289 "    0.015 2.00e-02 2.50e+03
        pdb=" NE2 GLN K 289 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1077 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1566
        2.81 -     3.33: 4067
        3.33 -     3.86: 11742
        3.86 -     4.38: 14891
        4.38 -     4.90: 26124
  Nonbonded interactions: 58390
  Sorted by model distance:
  nonbonded pdb=" OG  SER O 277 "
            pdb=" O   HOH O 401 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" OG  SER S 277 "
            pdb=" O   HOH S 401 "
     model   vdw
     2.351 3.040
  nonbonded pdb=" OG  SER Q 277 "
            pdb=" O   HOH Q 401 "
     model   vdw
     2.351 3.040
  nonbonded pdb=" OG  SER C 277 "
            pdb=" O   HOH C 401 "
     model   vdw
     2.351 3.040
  nonbonded pdb=" OG  SER E 277 "
            pdb=" O   HOH E 401 "
     model   vdw
     2.352 3.040
  ... (remaining 58385 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'J'
  selection = chain 'M'
  selection = chain 'L'
  selection = chain 'O'
  selection = chain 'N'
  selection = chain 'Q'
  selection = chain 'P'
  selection = chain 'S'
  selection = chain 'R'
  selection = chain 'T'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.990
  Find NCS groups from input model:        0.150
  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:11.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8843
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      :  0.007   0.034   5680  Z= 0.443
  Angle     :  0.894   5.077   7680  Z= 0.474
  Chirality :  0.048   0.116    700
  Planarity :  0.007   0.023   1080
  Dihedral  : 18.428  66.580   2120
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 17.24 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.34 (0.16), residues: 660
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.30 (0.12), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.006   0.003   PHE D 288 
 TYR   0.016   0.006   TYR R 268 

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.663 
Fit side-chains
REVERT: G  293 GLN cc_start: 0.8370 (mt0) cc_final: 0.8141 (mt0)
REVERT: J  293 GLN cc_start: 0.8356 (mt0) cc_final: 0.7953 (mt0)
REVERT: K  293 GLN cc_start: 0.8479 (mt0) cc_final: 0.8263 (mt0)
REVERT: L  293 GLN cc_start: 0.8405 (mt0) cc_final: 0.8033 (mp10)
REVERT: M  293 GLN cc_start: 0.8468 (mt0) cc_final: 0.8116 (mt0)
REVERT: N  266 GLN cc_start: 0.8810 (mt0) cc_final: 0.8487 (mt0)
REVERT: R  293 GLN cc_start: 0.8485 (mt0) cc_final: 0.8279 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.8284
  time to fit residues: 82.5658
Evaluate side-chains
  85 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    9.9990
   chunk 45 optimal weight:    0.9980
   chunk 25 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 30 optimal weight:    7.9990
   chunk 24 optimal weight:    4.9990
   chunk 47 optimal weight:    0.2980
   chunk 18 optimal weight:    0.9980
   chunk 28 optimal weight:    6.9990
   chunk 35 optimal weight:   10.0000
   chunk 54 optimal weight:    0.3980
   overall best weight:    1.3382

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

Flipped N/Q/H residues before XYZ refinement:
A 267 GLN
A 298 GLN
B 267 GLN
B 298 GLN
C 267 GLN
C 293 GLN
C 298 GLN
D 267 GLN
D 298 GLN
E 267 GLN
E 298 GLN
F 267 GLN
F 298 GLN
G 267 GLN
G 298 GLN
H 267 GLN
H 298 GLN
I 267 GLN
I 293 GLN
I 298 GLN
J 267 GLN
J 298 GLN
K 267 GLN
K 298 GLN
L 267 GLN
L 298 GLN
M 267 GLN
M 298 GLN
N 267 GLN
N 293 GLN
N 298 GLN
O 267 GLN
O 298 GLN
P 267 GLN
P 293 GLN
P 298 GLN
Q 267 GLN
Q 298 GLN
R 266 GLN
R 267 GLN
R 298 GLN
S 267 GLN
S 298 GLN
T 267 GLN
T 293 GLN
T 298 GLN

Total number of N/Q/H flips: 46

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.110533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.102980 restraints weight = 6589.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.3530 rms_B_bonded: 0.98
r_work: 0.3450 rms_B_bonded: 1.29 restraints_weight: 0.5000
r_work: 0.3365 rms_B_bonded: 2.33 restraints_weight: 0.2500
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8807
moved from start:          0.1506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   5680  Z= 0.185
  Angle     :  0.525   3.601   7680  Z= 0.260
  Chirality :  0.040   0.113    700
  Planarity :  0.004   0.023   1080
  Dihedral  :  3.147   8.574    760
  Min Nonbonded Distance : 2.691

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  7.76 %
    Allowed  : 10.17 %
    Favored  : 82.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.99 (0.15), residues: 660
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.04 (0.11), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.006   0.002   PHE E 288 
 TYR   0.007   0.001   TYR H 291 

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 92
  time to evaluate  : 0.667 
Fit side-chains
REVERT: C  293 GLN cc_start: 0.8531 (mt0) cc_final: 0.8324 (mt0)
REVERT: D  266 GLN cc_start: 0.8574 (mt0) cc_final: 0.8366 (mt0)
REVERT: E  293 GLN cc_start: 0.8475 (mt0) cc_final: 0.8173 (mt0)
REVERT: F  266 GLN cc_start: 0.8669 (mt0) cc_final: 0.8459 (mt0)
REVERT: J  293 GLN cc_start: 0.8480 (mt0) cc_final: 0.8073 (mt0)
REVERT: L  293 GLN cc_start: 0.8504 (mt0) cc_final: 0.8113 (mp10)
REVERT: M  293 GLN cc_start: 0.8664 (mt0) cc_final: 0.8317 (mt0)
REVERT: O  293 GLN cc_start: 0.8521 (mt0) cc_final: 0.8101 (mt0)
REVERT: R  297 SER cc_start: 0.8938 (OUTLIER) cc_final: 0.8671 (p)
  outliers start: 45
  outliers final: 23
  residues processed: 114
  average time/residue: 0.9167
  time to fit residues: 111.2512
Evaluate side-chains
  113 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 89
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain C residue  280 THR
Chi-restraints excluded: chain D residue  280 THR
Chi-restraints excluded: chain D residue  285 LEU
Chi-restraints excluded: chain E residue  280 THR
Chi-restraints excluded: chain F residue  280 THR
Chi-restraints excluded: chain G residue  280 THR
Chi-restraints excluded: chain H residue  280 THR
Chi-restraints excluded: chain I residue  280 THR
Chi-restraints excluded: chain J residue  280 THR
Chi-restraints excluded: chain K residue  280 THR
Chi-restraints excluded: chain L residue  280 THR
Chi-restraints excluded: chain M residue  280 THR
Chi-restraints excluded: chain N residue  280 THR
Chi-restraints excluded: chain O residue  280 THR
Chi-restraints excluded: chain P residue  280 THR
Chi-restraints excluded: chain Q residue  280 THR
Chi-restraints excluded: chain R residue  280 THR
Chi-restraints excluded: chain R residue  297 SER
Chi-restraints excluded: chain S residue  280 THR
Chi-restraints excluded: chain T residue  280 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 37 optimal weight:    9.9990
   chunk 44 optimal weight:   10.0000
   chunk 53 optimal weight:    7.9990
   chunk 12 optimal weight:    9.9990
   chunk 40 optimal weight:   10.0000
   chunk 0 optimal weight:    5.9990
   chunk 18 optimal weight:   10.0000
   chunk 13 optimal weight:    7.9990
   chunk 33 optimal weight:    7.9990
   chunk 32 optimal weight:    8.9990
   chunk 17 optimal weight:    9.9990
   overall best weight:    7.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 293 GLN
B 293 GLN
D 293 GLN
G 293 GLN
I 293 GLN
K 293 GLN
N 293 GLN
P 293 GLN
T 293 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.091488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.085601 restraints weight = 6609.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 0.73
r_work: 0.3139 rms_B_bonded: 1.27 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 2.26 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8894
moved from start:          0.1755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.046   5680  Z= 0.696
  Angle     :  0.751   5.132   7680  Z= 0.393
  Chirality :  0.050   0.164    700
  Planarity :  0.005   0.039   1080
  Dihedral  :  3.630   9.428    760
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  8.28 %
    Allowed  : 10.00 %
    Favored  : 81.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.98 (0.15), residues: 660
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.03 (0.12), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.014   0.005   PHE E 288 
 TYR   0.014   0.002   TYR C 291 

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 92
  time to evaluate  : 0.717 
Fit side-chains
REVERT: B  266 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8296 (mt0)
REVERT: D  266 GLN cc_start: 0.8709 (mt0) cc_final: 0.8501 (mt0)
REVERT: F  266 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8386 (mt0)
REVERT: H  266 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8533 (mt0)
REVERT: I  285 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8928 (tt)
REVERT: J  293 GLN cc_start: 0.8624 (mt0) cc_final: 0.8219 (mt0)
REVERT: L  293 GLN cc_start: 0.8622 (mt0) cc_final: 0.8286 (mt0)
REVERT: M  293 GLN cc_start: 0.8779 (mt0) cc_final: 0.8442 (mt0)
REVERT: P  285 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8833 (tt)
  outliers start: 48
  outliers final: 31
  residues processed: 109
  average time/residue: 0.8477
  time to fit residues: 98.7991
Evaluate side-chains
  127 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 91
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain B residue  266 GLN
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain C residue  280 THR
Chi-restraints excluded: chain C residue  285 LEU
Chi-restraints excluded: chain D residue  280 THR
Chi-restraints excluded: chain D residue  285 LEU
Chi-restraints excluded: chain E residue  280 THR
Chi-restraints excluded: chain E residue  285 LEU
Chi-restraints excluded: chain F residue  266 GLN
Chi-restraints excluded: chain F residue  280 THR
Chi-restraints excluded: chain G residue  280 THR
Chi-restraints excluded: chain H residue  266 GLN
Chi-restraints excluded: chain H residue  280 THR
Chi-restraints excluded: chain I residue  280 THR
Chi-restraints excluded: chain I residue  285 LEU
Chi-restraints excluded: chain J residue  280 THR
Chi-restraints excluded: chain K residue  280 THR
Chi-restraints excluded: chain L residue  280 THR
Chi-restraints excluded: chain M residue  280 THR
Chi-restraints excluded: chain N residue  280 THR
Chi-restraints excluded: chain N residue  297 SER
Chi-restraints excluded: chain O residue  280 THR
Chi-restraints excluded: chain P residue  280 THR
Chi-restraints excluded: chain P residue  285 LEU
Chi-restraints excluded: chain P residue  297 SER
Chi-restraints excluded: chain Q residue  280 THR
Chi-restraints excluded: chain Q residue  285 LEU
Chi-restraints excluded: chain R residue  280 THR
Chi-restraints excluded: chain R residue  297 SER
Chi-restraints excluded: chain S residue  280 THR
Chi-restraints excluded: chain S residue  285 LEU
Chi-restraints excluded: chain T residue  280 THR
Chi-restraints excluded: chain T residue  285 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 52 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.9780

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

Flipped N/Q/H residues before XYZ refinement:
C 293 GLN
G 293 GLN
H 293 GLN
I 293 GLN
K 293 GLN
N 293 GLN
P 293 GLN
T 279 GLN
T 293 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.110897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.103533 restraints weight = 6730.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 0.96
r_work: 0.3481 rms_B_bonded: 1.29 restraints_weight: 0.5000
r_work: 0.3400 rms_B_bonded: 2.29 restraints_weight: 0.2500
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8812
moved from start:          0.1814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   5680  Z= 0.156
  Angle     :  0.501   4.953   7680  Z= 0.245
  Chirality :  0.038   0.113    700
  Planarity :  0.004   0.025   1080
  Dihedral  :  3.158   7.901    760
  Min Nonbonded Distance : 2.685

Molprobity Statistics.
  All-atom Clashscore : 2.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  6.03 %
    Allowed  : 13.45 %
    Favored  : 80.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.93 (0.16), residues: 660
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.99 (0.12), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.004   0.001   PHE K 288 
 TYR   0.009   0.001   TYR R 276 

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 94
  time to evaluate  : 0.699 
Fit side-chains
REVERT: E  293 GLN cc_start: 0.8494 (mt0) cc_final: 0.8162 (mt0)
REVERT: J  293 GLN cc_start: 0.8468 (mt0) cc_final: 0.8040 (mt0)
REVERT: L  293 GLN cc_start: 0.8489 (mt0) cc_final: 0.8038 (mp10)
REVERT: M  293 GLN cc_start: 0.8679 (mt0) cc_final: 0.8326 (mt0)
  outliers start: 35
  outliers final: 17
  residues processed: 109
  average time/residue: 0.9029
  time to fit residues: 104.6765
Evaluate side-chains
  108 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  280 THR
Chi-restraints excluded: chain D residue  280 THR
Chi-restraints excluded: chain E residue  280 THR
Chi-restraints excluded: chain G residue  280 THR
Chi-restraints excluded: chain H residue  280 THR
Chi-restraints excluded: chain I residue  280 THR
Chi-restraints excluded: chain J residue  280 THR
Chi-restraints excluded: chain K residue  280 THR
Chi-restraints excluded: chain L residue  280 THR
Chi-restraints excluded: chain M residue  280 THR
Chi-restraints excluded: chain N residue  280 THR
Chi-restraints excluded: chain O residue  280 THR
Chi-restraints excluded: chain P residue  280 THR
Chi-restraints excluded: chain Q residue  280 THR
Chi-restraints excluded: chain R residue  280 THR
Chi-restraints excluded: chain S residue  280 THR
Chi-restraints excluded: chain T residue  285 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 55 optimal weight:    8.9990
   chunk 43 optimal weight:    1.9990
   chunk 9 optimal weight:    9.9990
   chunk 16 optimal weight:   10.0000
   chunk 36 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   chunk 59 optimal weight:    9.9990
   chunk 51 optimal weight:    0.0570
   chunk 10 optimal weight:    2.9990
   chunk 58 optimal weight:    8.9990
   chunk 8 optimal weight:    9.9990
   overall best weight:    3.6106

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

Flipped N/Q/H residues before XYZ refinement:
B 293 GLN
C 293 GLN
D 266 GLN
D 293 GLN
F 266 GLN
F 293 GLN
G 293 GLN
H 293 GLN
I 293 GLN
K 293 GLN
N 293 GLN
P 293 GLN
R 266 GLN
S 279 GLN
T 279 GLN
T 293 GLN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.094053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.088219 restraints weight = 6465.644|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 0.73
r_work: 0.3190 rms_B_bonded: 1.19 restraints_weight: 0.5000
r_work: 0.3107 rms_B_bonded: 2.09 restraints_weight: 0.2500
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8849
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.023   5680  Z= 0.353
  Angle     :  0.593   4.405   7680  Z= 0.299
  Chirality :  0.041   0.170    700
  Planarity :  0.004   0.029   1080
  Dihedral  :  3.311   8.779    760
  Min Nonbonded Distance : 2.663

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  7.59 %
    Allowed  : 12.93 %
    Favored  : 79.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.94 (0.16), residues: 660
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.00 (0.12), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.009   0.003   PHE E 288 
 TYR   0.012   0.001   TYR R 276 

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 92
  time to evaluate  : 0.713 
Fit side-chains
REVERT: G  266 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8485 (mt0)
REVERT: H  266 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8522 (mt0)
REVERT: J  293 GLN cc_start: 0.8561 (mt0) cc_final: 0.8173 (mt0)
REVERT: L  293 GLN cc_start: 0.8573 (mt0) cc_final: 0.8235 (mt0)
REVERT: M  293 GLN cc_start: 0.8738 (mt0) cc_final: 0.8374 (mt0)
  outliers start: 44
  outliers final: 28
  residues processed: 108
  average time/residue: 0.8535
  time to fit residues: 98.5140
Evaluate side-chains
  121 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 91
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain C residue  280 THR
Chi-restraints excluded: chain D residue  280 THR
Chi-restraints excluded: chain D residue  285 LEU
Chi-restraints excluded: chain E residue  280 THR
Chi-restraints excluded: chain E residue  285 LEU
Chi-restraints excluded: chain F residue  280 THR
Chi-restraints excluded: chain G residue  266 GLN
Chi-restraints excluded: chain G residue  280 THR
Chi-restraints excluded: chain H residue  266 GLN
Chi-restraints excluded: chain H residue  280 THR
Chi-restraints excluded: chain I residue  280 THR
Chi-restraints excluded: chain J residue  280 THR
Chi-restraints excluded: chain K residue  280 THR
Chi-restraints excluded: chain L residue  280 THR
Chi-restraints excluded: chain M residue  280 THR
Chi-restraints excluded: chain N residue  280 THR
Chi-restraints excluded: chain N residue  297 SER
Chi-restraints excluded: chain O residue  280 THR
Chi-restraints excluded: chain P residue  280 THR
Chi-restraints excluded: chain Q residue  280 THR
Chi-restraints excluded: chain Q residue  285 LEU
Chi-restraints excluded: chain R residue  280 THR
Chi-restraints excluded: chain R residue  297 SER
Chi-restraints excluded: chain S residue  280 THR
Chi-restraints excluded: chain T residue  280 THR
Chi-restraints excluded: chain T residue  285 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 2 optimal weight:    9.9990
   chunk 46 optimal weight:    6.9990
   chunk 24 optimal weight:    8.9990
   chunk 50 optimal weight:   10.0000
   chunk 36 optimal weight:    1.9990
   chunk 52 optimal weight:    7.9990
   chunk 37 optimal weight:   10.0000
   chunk 35 optimal weight:    2.9990
   chunk 44 optimal weight:   10.0000
   chunk 23 optimal weight:    0.7980
   chunk 6 optimal weight:    8.9990
   overall best weight:    4.1588

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

Flipped N/Q/H residues before XYZ refinement:
C 293 GLN
D 266 GLN
D 293 GLN
G 293 GLN
H 293 GLN
I 293 GLN
K 293 GLN
N 293 GLN
R 266 GLN
S 279 GLN
T 279 GLN
T 293 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.093377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.087554 restraints weight = 6466.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 0.73
r_work: 0.3188 rms_B_bonded: 1.11 restraints_weight: 0.5000
r_work: 0.3106 rms_B_bonded: 1.98 restraints_weight: 0.2500
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8846
moved from start:          0.1853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.026   5680  Z= 0.400
  Angle     :  0.620   5.126   7680  Z= 0.312
  Chirality :  0.043   0.183    700
  Planarity :  0.004   0.030   1080
  Dihedral  :  3.400   8.955    760
  Min Nonbonded Distance : 2.659

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  7.41 %
    Allowed  : 13.79 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.92 (0.16), residues: 660
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.98 (0.12), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.009   0.003   PHE E 288 
 TYR   0.014   0.002   TYR R 276 

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 92
  time to evaluate  : 0.839 
Fit side-chains
REVERT: B  266 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8288 (mt0)
REVERT: G  266 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8481 (mt0)
REVERT: H  266 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8522 (mt0)
REVERT: J  293 GLN cc_start: 0.8550 (mt0) cc_final: 0.8142 (mt0)
REVERT: L  293 GLN cc_start: 0.8569 (mt0) cc_final: 0.8210 (mt0)
  outliers start: 43
  outliers final: 29
  residues processed: 107
  average time/residue: 0.8510
  time to fit residues: 97.1659
Evaluate side-chains
  121 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 89
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain B residue  266 GLN
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain C residue  280 THR
Chi-restraints excluded: chain C residue  285 LEU
Chi-restraints excluded: chain D residue  280 THR
Chi-restraints excluded: chain D residue  285 LEU
Chi-restraints excluded: chain E residue  280 THR
Chi-restraints excluded: chain E residue  285 LEU
Chi-restraints excluded: chain F residue  280 THR
Chi-restraints excluded: chain G residue  266 GLN
Chi-restraints excluded: chain G residue  280 THR
Chi-restraints excluded: chain H residue  266 GLN
Chi-restraints excluded: chain H residue  280 THR
Chi-restraints excluded: chain I residue  280 THR
Chi-restraints excluded: chain J residue  280 THR
Chi-restraints excluded: chain K residue  280 THR
Chi-restraints excluded: chain L residue  280 THR
Chi-restraints excluded: chain M residue  280 THR
Chi-restraints excluded: chain N residue  280 THR
Chi-restraints excluded: chain N residue  297 SER
Chi-restraints excluded: chain O residue  280 THR
Chi-restraints excluded: chain P residue  280 THR
Chi-restraints excluded: chain Q residue  280 THR
Chi-restraints excluded: chain Q residue  285 LEU
Chi-restraints excluded: chain R residue  280 THR
Chi-restraints excluded: chain R residue  297 SER
Chi-restraints excluded: chain S residue  280 THR
Chi-restraints excluded: chain T residue  280 THR
Chi-restraints excluded: chain T residue  285 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 17 optimal weight:    8.9990
   chunk 1 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 40 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 44 optimal weight:    9.9990
   chunk 8 optimal weight:    9.9990
   chunk 55 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9980
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
C 293 GLN
D 266 GLN
D 293 GLN
G 293 GLN
H 293 GLN
I 293 GLN
K 293 GLN
M 293 GLN
N 293 GLN
P 293 GLN
R 266 GLN
T 279 GLN
T 293 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.096166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.089757 restraints weight = 6419.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 0.81
r_work: 0.3214 rms_B_bonded: 1.29 restraints_weight: 0.5000
r_work: 0.3127 rms_B_bonded: 2.27 restraints_weight: 0.2500
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8826
moved from start:          0.1901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   5680  Z= 0.209
  Angle     :  0.531   5.112   7680  Z= 0.258
  Chirality :  0.039   0.132    700
  Planarity :  0.004   0.026   1080
  Dihedral  :  3.149   8.484    760
  Min Nonbonded Distance : 2.675

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  7.07 %
    Allowed  : 14.48 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.94 (0.16), residues: 660
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.99 (0.12), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.005   0.002   PHE E 288 
 TYR   0.011   0.001   TYR R 276 

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 92
  time to evaluate  : 0.535 
Fit side-chains
REVERT: H  266 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8518 (mt0)
REVERT: J  293 GLN cc_start: 0.8563 (mt0) cc_final: 0.8160 (mt0)
REVERT: L  293 GLN cc_start: 0.8548 (mt0) cc_final: 0.8077 (mt0)
REVERT: R  297 SER cc_start: 0.8941 (m) cc_final: 0.8663 (p)
  outliers start: 41
  outliers final: 22
  residues processed: 107
  average time/residue: 0.8619
  time to fit residues: 98.3782
Evaluate side-chains
  114 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 91
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain C residue  280 THR
Chi-restraints excluded: chain C residue  285 LEU
Chi-restraints excluded: chain D residue  280 THR
Chi-restraints excluded: chain D residue  285 LEU
Chi-restraints excluded: chain E residue  280 THR
Chi-restraints excluded: chain F residue  280 THR
Chi-restraints excluded: chain G residue  280 THR
Chi-restraints excluded: chain H residue  266 GLN
Chi-restraints excluded: chain H residue  280 THR
Chi-restraints excluded: chain I residue  280 THR
Chi-restraints excluded: chain J residue  280 THR
Chi-restraints excluded: chain K residue  280 THR
Chi-restraints excluded: chain L residue  280 THR
Chi-restraints excluded: chain M residue  280 THR
Chi-restraints excluded: chain N residue  280 THR
Chi-restraints excluded: chain O residue  280 THR
Chi-restraints excluded: chain P residue  280 THR
Chi-restraints excluded: chain Q residue  280 THR
Chi-restraints excluded: chain R residue  280 THR
Chi-restraints excluded: chain S residue  280 THR
Chi-restraints excluded: chain T residue  280 THR
Chi-restraints excluded: chain T residue  285 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 40 optimal weight:    9.9990
   chunk 37 optimal weight:    5.9990
   chunk 5 optimal weight:   10.0000
   chunk 15 optimal weight:    6.9990
   chunk 18 optimal weight:    9.9990
   chunk 58 optimal weight:    2.9990
   chunk 7 optimal weight:    8.9990
   chunk 14 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
C 293 GLN
D 266 GLN
D 293 GLN
G 293 GLN
H 293 GLN
I 293 GLN
K 293 GLN
M 293 GLN
N 293 GLN
R 266 GLN
S 279 GLN
T 279 GLN
T 293 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.094099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.088114 restraints weight = 6393.045|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 0.76
r_work: 0.3182 rms_B_bonded: 1.26 restraints_weight: 0.5000
r_work: 0.3096 rms_B_bonded: 2.24 restraints_weight: 0.2500
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8850
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.023   5680  Z= 0.338
  Angle     :  0.594   5.120   7680  Z= 0.294
  Chirality :  0.042   0.190    700
  Planarity :  0.004   0.027   1080
  Dihedral  :  3.294   8.858    760
  Min Nonbonded Distance : 2.664

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  6.72 %
    Allowed  : 15.00 %
    Favored  : 78.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.94 (0.16), residues: 660
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.00 (0.12), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.008   0.003   PHE G 288 
 TYR   0.015   0.001   TYR R 276 

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 91
  time to evaluate  : 0.711 
Fit side-chains
REVERT: H  266 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8542 (mt0)
REVERT: J  293 GLN cc_start: 0.8572 (mt0) cc_final: 0.8172 (mt0)
REVERT: L  293 GLN cc_start: 0.8570 (mt0) cc_final: 0.8102 (mt0)
  outliers start: 39
  outliers final: 28
  residues processed: 103
  average time/residue: 0.8504
  time to fit residues: 93.6188
Evaluate side-chains
  119 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 90
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain C residue  280 THR
Chi-restraints excluded: chain C residue  285 LEU
Chi-restraints excluded: chain D residue  280 THR
Chi-restraints excluded: chain D residue  285 LEU
Chi-restraints excluded: chain E residue  280 THR
Chi-restraints excluded: chain E residue  285 LEU
Chi-restraints excluded: chain F residue  280 THR
Chi-restraints excluded: chain G residue  280 THR
Chi-restraints excluded: chain H residue  266 GLN
Chi-restraints excluded: chain H residue  280 THR
Chi-restraints excluded: chain I residue  280 THR
Chi-restraints excluded: chain J residue  280 THR
Chi-restraints excluded: chain K residue  280 THR
Chi-restraints excluded: chain L residue  280 THR
Chi-restraints excluded: chain M residue  280 THR
Chi-restraints excluded: chain N residue  280 THR
Chi-restraints excluded: chain N residue  297 SER
Chi-restraints excluded: chain O residue  280 THR
Chi-restraints excluded: chain P residue  280 THR
Chi-restraints excluded: chain P residue  297 SER
Chi-restraints excluded: chain Q residue  280 THR
Chi-restraints excluded: chain Q residue  285 LEU
Chi-restraints excluded: chain R residue  280 THR
Chi-restraints excluded: chain R residue  297 SER
Chi-restraints excluded: chain S residue  280 THR
Chi-restraints excluded: chain T residue  280 THR
Chi-restraints excluded: chain T residue  285 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 47 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 49 optimal weight:    6.9990
   chunk 8 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 40 optimal weight:    6.9990
   chunk 15 optimal weight:    4.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
C 293 GLN
D 266 GLN
D 293 GLN
G 293 GLN
H 293 GLN
K 293 GLN
M 293 GLN
N 293 GLN
R 266 GLN
S 279 GLN
T 279 GLN
T 293 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.095268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.088969 restraints weight = 6440.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 0.80
r_work: 0.3194 rms_B_bonded: 1.29 restraints_weight: 0.5000
r_work: 0.3108 rms_B_bonded: 2.26 restraints_weight: 0.2500
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8836
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.020   5680  Z= 0.255
  Angle     :  0.558   5.397   7680  Z= 0.273
  Chirality :  0.040   0.162    700
  Planarity :  0.004   0.025   1080
  Dihedral  :  3.198   8.672    760
  Min Nonbonded Distance : 2.672

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  6.21 %
    Allowed  : 15.69 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.93 (0.16), residues: 660
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.99 (0.12), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.006   0.002   PHE E 288 
 TYR   0.013   0.001   TYR R 276 

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 94
  time to evaluate  : 0.694 
Fit side-chains
REVERT: H  266 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8522 (mt0)
REVERT: J  293 GLN cc_start: 0.8558 (mt0) cc_final: 0.8147 (mt0)
REVERT: L  293 GLN cc_start: 0.8553 (mt0) cc_final: 0.8079 (mt0)
  outliers start: 36
  outliers final: 26
  residues processed: 103
  average time/residue: 0.9432
  time to fit residues: 103.3715
Evaluate side-chains
  118 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 91
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain C residue  280 THR
Chi-restraints excluded: chain C residue  285 LEU
Chi-restraints excluded: chain D residue  280 THR
Chi-restraints excluded: chain D residue  285 LEU
Chi-restraints excluded: chain E residue  280 THR
Chi-restraints excluded: chain E residue  285 LEU
Chi-restraints excluded: chain F residue  280 THR
Chi-restraints excluded: chain G residue  280 THR
Chi-restraints excluded: chain H residue  266 GLN
Chi-restraints excluded: chain H residue  280 THR
Chi-restraints excluded: chain I residue  280 THR
Chi-restraints excluded: chain J residue  280 THR
Chi-restraints excluded: chain K residue  280 THR
Chi-restraints excluded: chain L residue  280 THR
Chi-restraints excluded: chain M residue  280 THR
Chi-restraints excluded: chain N residue  280 THR
Chi-restraints excluded: chain N residue  297 SER
Chi-restraints excluded: chain O residue  280 THR
Chi-restraints excluded: chain P residue  280 THR
Chi-restraints excluded: chain P residue  297 SER
Chi-restraints excluded: chain Q residue  280 THR
Chi-restraints excluded: chain Q residue  285 LEU
Chi-restraints excluded: chain R residue  280 THR
Chi-restraints excluded: chain S residue  280 THR
Chi-restraints excluded: chain T residue  280 THR
Chi-restraints excluded: chain T residue  285 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 1 optimal weight:    7.9990
   chunk 59 optimal weight:   10.0000
   chunk 2 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 43 optimal weight:    8.9990
   chunk 6 optimal weight:    8.9990
   chunk 51 optimal weight:    0.7980
   chunk 42 optimal weight:    5.9990
   chunk 32 optimal weight:   10.0000
   chunk 34 optimal weight:   10.0000
   overall best weight:    3.5588

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

Flipped N/Q/H residues before XYZ refinement:
C 293 GLN
D 266 GLN
D 293 GLN
G 293 GLN
H 293 GLN
K 293 GLN
M 293 GLN
N 293 GLN
P 293 GLN
R 266 GLN
S 279 GLN
T 279 GLN
T 293 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.093832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.087771 restraints weight = 6558.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 0.76
r_work: 0.3182 rms_B_bonded: 1.29 restraints_weight: 0.5000
r_work: 0.3096 rms_B_bonded: 2.28 restraints_weight: 0.2500
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8855
moved from start:          0.1924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.023   5680  Z= 0.350
  Angle     :  0.601   5.376   7680  Z= 0.298
  Chirality :  0.043   0.165    700
  Planarity :  0.004   0.027   1080
  Dihedral  :  3.316   8.892    760
  Min Nonbonded Distance : 2.664

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  6.03 %
    Allowed  : 16.03 %
    Favored  : 77.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.94 (0.16), residues: 660
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.99 (0.12), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.008   0.003   PHE E 288 
 TYR   0.014   0.001   TYR R 276 

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

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

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1320 Ramachandran restraints generated.
    660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 91
  time to evaluate  : 0.730 
Fit side-chains
REVERT: H  266 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8542 (mt0)
REVERT: J  293 GLN cc_start: 0.8574 (mt0) cc_final: 0.8182 (mt0)
REVERT: L  293 GLN cc_start: 0.8570 (mt0) cc_final: 0.8217 (mt0)
  outliers start: 35
  outliers final: 28
  residues processed: 99
  average time/residue: 0.9043
  time to fit residues: 95.2516
Evaluate side-chains
  119 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 90
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain C residue  280 THR
Chi-restraints excluded: chain C residue  285 LEU
Chi-restraints excluded: chain D residue  280 THR
Chi-restraints excluded: chain D residue  285 LEU
Chi-restraints excluded: chain E residue  280 THR
Chi-restraints excluded: chain E residue  285 LEU
Chi-restraints excluded: chain F residue  280 THR
Chi-restraints excluded: chain G residue  280 THR
Chi-restraints excluded: chain H residue  266 GLN
Chi-restraints excluded: chain H residue  280 THR
Chi-restraints excluded: chain I residue  280 THR
Chi-restraints excluded: chain J residue  280 THR
Chi-restraints excluded: chain K residue  280 THR
Chi-restraints excluded: chain L residue  280 THR
Chi-restraints excluded: chain M residue  280 THR
Chi-restraints excluded: chain N residue  280 THR
Chi-restraints excluded: chain N residue  297 SER
Chi-restraints excluded: chain O residue  280 THR
Chi-restraints excluded: chain P residue  280 THR
Chi-restraints excluded: chain P residue  297 SER
Chi-restraints excluded: chain Q residue  280 THR
Chi-restraints excluded: chain Q residue  285 LEU
Chi-restraints excluded: chain R residue  280 THR
Chi-restraints excluded: chain R residue  297 SER
Chi-restraints excluded: chain S residue  280 THR
Chi-restraints excluded: chain S residue  285 LEU
Chi-restraints excluded: chain T residue  280 THR
Chi-restraints excluded: chain T residue  285 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 40 optimal weight:    7.9990
   chunk 11 optimal weight:    6.9990
   chunk 54 optimal weight:    7.9990
   chunk 4 optimal weight:    6.9990
   chunk 41 optimal weight:    6.9990
   chunk 45 optimal weight:    0.1980
   chunk 58 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
C 293 GLN
D 266 GLN
D 293 GLN
G 293 GLN
H 293 GLN
K 293 GLN
M 293 GLN
N 293 GLN
R 266 GLN
S 279 GLN
T 279 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.097000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.090588 restraints weight = 6418.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 0.82
r_work: 0.3227 rms_B_bonded: 1.29 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 2.25 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8813
moved from start:          0.1949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   5680  Z= 0.175
  Angle     :  0.523   5.824   7680  Z= 0.249
  Chirality :  0.039   0.127    700
  Planarity :  0.003   0.025   1080
  Dihedral  :  3.080   8.364    760
  Min Nonbonded Distance : 2.678

Molprobity Statistics.
  All-atom Clashscore : 2.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 16.72 %
    Favored  : 77.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.92 (0.16), residues: 660
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.98 (0.12), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.005   0.001   PHE G 288 
 TYR   0.010   0.001   TYR R 276 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3677.90 seconds
wall clock time: 66 minutes 2.92 seconds (3962.92 seconds total)