Starting phenix.real_space_refine
on Fri Aug 22 18:12:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8teq_41195/08_2025/8teq_41195.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8teq_41195/08_2025/8teq_41195.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8teq_41195/08_2025/8teq_41195.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8teq_41195/08_2025/8teq_41195.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8teq_41195/08_2025/8teq_41195.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8teq_41195/08_2025/8teq_41195.cif"
  }
  resolution = 2.84
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   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    4185      2.51       5
     N    1155      2.21       5
     O    1365      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6705
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 236
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 236
          Classifications: {'peptide': 29}
          Link IDs: {'PTRANS': 3, 'TRANS': 25}
    Chain: "B"
      Number of atoms: 211
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 211
          Classifications: {'peptide': 26}
          Link IDs: {'PTRANS': 2, 'TRANS': 23}
  Restraints were copied for chains:
    C, E, G, I, K, M, O, Q, S, U, W, Y, 0, 2, D, F, H, J, L, N, P, R,
    T, V, X, Z, 1, 3
  Time building chain proxies: 0.68, per 1000 atoms: 0.10
  Number of scatterers: 6705
  At special positions: 0
  Unit cell: (65.36, 65.36, 89.44, 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    1365      8.00
     N    1155      7.00
     C    4185      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: 0.42
  Conformation dependent library (CDL) restraints added in 246.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1530

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 6 sheets defined
      0.0% alpha, 41.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain '0' and resid 266 through 274
      removed outlier: 6.765A  pdb=" N   GLN W 266 " --> pdb=" O   GLN 0 267 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   VAL 0 269 " --> pdb=" O   GLN W 266 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   TYR W 268 " --> pdb=" O   VAL 0 269 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   GLN 0 271 " --> pdb=" O   TYR W 268 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   ILE W 270 " --> pdb=" O   GLN 0 271 " (cutoff:3.500A)
      removed outlier: 8.398A  pdb=" N   SER 0 273 " --> pdb=" O   ILE W 270 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   TYR W 272 " --> pdb=" O   SER 0 273 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   GLN S 266 " --> pdb=" O   GLN W 267 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   VAL W 269 " --> pdb=" O   GLN S 266 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   TYR S 268 " --> pdb=" O   VAL W 269 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   GLN W 271 " --> pdb=" O   TYR S 268 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   ILE S 270 " --> pdb=" O   GLN W 271 " (cutoff:3.500A)
      removed outlier: 8.398A  pdb=" N   SER W 273 " --> pdb=" O   ILE S 270 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   TYR S 272 " --> pdb=" O   SER W 273 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   GLN O 266 " --> pdb=" O   GLN S 267 " (cutoff:3.500A)
      removed outlier: 7.869A  pdb=" N   VAL S 269 " --> pdb=" O   GLN O 266 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   TYR O 268 " --> pdb=" O   VAL S 269 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   GLN S 271 " --> pdb=" O   TYR O 268 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   ILE O 270 " --> pdb=" O   GLN S 271 " (cutoff:3.500A)
      removed outlier: 8.398A  pdb=" N   SER S 273 " --> pdb=" O   ILE O 270 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   TYR O 272 " --> pdb=" O   SER S 273 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   GLN K 266 " --> pdb=" O   GLN O 267 " (cutoff:3.500A)
      removed outlier: 7.869A  pdb=" N   VAL O 269 " --> pdb=" O   GLN K 266 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   TYR K 268 " --> pdb=" O   VAL O 269 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   GLN O 271 " --> pdb=" O   TYR K 268 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   ILE K 270 " --> pdb=" O   GLN O 271 " (cutoff:3.500A)
      removed outlier: 8.399A  pdb=" N   SER O 273 " --> pdb=" O   ILE K 270 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   TYR K 272 " --> pdb=" O   SER O 273 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   GLN G 266 " --> pdb=" O   GLN K 267 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   VAL K 269 " --> pdb=" O   GLN G 266 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   TYR G 268 " --> pdb=" O   VAL K 269 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   GLN K 271 " --> pdb=" O   TYR G 268 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   ILE G 270 " --> pdb=" O   GLN K 271 " (cutoff:3.500A)
      removed outlier: 8.398A  pdb=" N   SER K 273 " --> pdb=" O   ILE G 270 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   TYR G 272 " --> pdb=" O   SER K 273 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   GLN C 266 " --> pdb=" O   GLN G 267 " (cutoff:3.500A)
      removed outlier: 7.869A  pdb=" N   VAL G 269 " --> pdb=" O   GLN C 266 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   TYR C 268 " --> pdb=" O   VAL G 269 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   GLN G 271 " --> pdb=" O   TYR C 268 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   ILE C 270 " --> pdb=" O   GLN G 271 " (cutoff:3.500A)
      removed outlier: 8.398A  pdb=" N   SER G 273 " --> pdb=" O   ILE C 270 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   TYR C 272 " --> pdb=" O   SER G 273 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   GLN A 266 " --> pdb=" O   GLN C 267 " (cutoff:3.500A)
      removed outlier: 7.869A  pdb=" N   VAL C 269 " --> pdb=" O   GLN A 266 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   TYR A 268 " --> pdb=" O   VAL C 269 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   GLN C 271 " --> pdb=" O   TYR A 268 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   ILE A 270 " --> pdb=" O   GLN C 271 " (cutoff:3.500A)
      removed outlier: 8.399A  pdb=" N   SER C 273 " --> pdb=" O   ILE A 270 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   TYR A 272 " --> pdb=" O   SER C 273 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain '0' and resid 278 through 279
      removed outlier: 6.832A  pdb=" N   GLN W 278 " --> pdb=" O   GLN 0 279 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   GLN S 278 " --> pdb=" O   GLN W 279 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   GLN O 278 " --> pdb=" O   GLN S 279 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   GLN K 278 " --> pdb=" O   GLN O 279 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   GLN G 278 " --> pdb=" O   GLN K 279 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   GLN C 278 " --> pdb=" O   GLN G 279 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   GLN A 278 " --> pdb=" O   GLN C 279 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain '0' and resid 286 through 289
      removed outlier: 6.544A  pdb=" N   GLN A 287 " --> pdb=" O   PHE E 288 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   GLN E 287 " --> pdb=" O   PHE I 288 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   GLN I 287 " --> pdb=" O   PHE M 288 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   GLN M 287 " --> pdb=" O   PHE Q 288 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   GLN Q 287 " --> pdb=" O   PHE U 288 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   GLN U 287 " --> pdb=" O   PHE Y 288 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   GLN Y 287 " --> pdb=" O   PHE 2 288 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain '1' and resid 266 through 273
      removed outlier: 6.401A  pdb=" N   GLN X 267 " --> pdb=" O   TYR 1 268 " (cutoff:3.500A)
      removed outlier: 7.657A  pdb=" N   ILE 1 270 " --> pdb=" O   GLN X 267 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   VAL X 269 " --> pdb=" O   ILE 1 270 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   TYR 1 272 " --> pdb=" O   VAL X 269 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   GLN X 271 " --> pdb=" O   TYR 1 272 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   GLN T 267 " --> pdb=" O   TYR X 268 " (cutoff:3.500A)
      removed outlier: 7.657A  pdb=" N   ILE X 270 " --> pdb=" O   GLN T 267 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   VAL T 269 " --> pdb=" O   ILE X 270 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   TYR X 272 " --> pdb=" O   VAL T 269 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   GLN T 271 " --> pdb=" O   TYR X 272 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   GLN P 267 " --> pdb=" O   TYR T 268 " (cutoff:3.500A)
      removed outlier: 7.658A  pdb=" N   ILE T 270 " --> pdb=" O   GLN P 267 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   VAL P 269 " --> pdb=" O   ILE T 270 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   TYR T 272 " --> pdb=" O   VAL P 269 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   GLN P 271 " --> pdb=" O   TYR T 272 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   GLN L 267 " --> pdb=" O   TYR P 268 " (cutoff:3.500A)
      removed outlier: 7.657A  pdb=" N   ILE P 270 " --> pdb=" O   GLN L 267 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   VAL L 269 " --> pdb=" O   ILE P 270 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   TYR P 272 " --> pdb=" O   VAL L 269 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   GLN L 271 " --> pdb=" O   TYR P 272 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   GLN H 267 " --> pdb=" O   TYR L 268 " (cutoff:3.500A)
      removed outlier: 7.657A  pdb=" N   ILE L 270 " --> pdb=" O   GLN H 267 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   VAL H 269 " --> pdb=" O   ILE L 270 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   TYR L 272 " --> pdb=" O   VAL H 269 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   GLN H 271 " --> pdb=" O   TYR L 272 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   GLN D 267 " --> pdb=" O   TYR H 268 " (cutoff:3.500A)
      removed outlier: 7.657A  pdb=" N   ILE H 270 " --> pdb=" O   GLN D 267 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   VAL D 269 " --> pdb=" O   ILE H 270 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   TYR H 272 " --> pdb=" O   VAL D 269 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   GLN D 271 " --> pdb=" O   TYR H 272 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   GLN B 267 " --> pdb=" O   TYR D 268 " (cutoff:3.500A)
      removed outlier: 7.657A  pdb=" N   ILE D 270 " --> pdb=" O   GLN B 267 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   VAL B 269 " --> pdb=" O   ILE D 270 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   TYR D 272 " --> pdb=" O   VAL B 269 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   GLN B 271 " --> pdb=" O   TYR D 272 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain '1' and resid 278 through 279
      removed outlier: 6.653A  pdb=" N   GLN B 278 " --> pdb=" O   GLN F 279 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   GLN F 278 " --> pdb=" O   GLN J 279 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   GLN J 278 " --> pdb=" O   GLN N 279 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   GLN N 278 " --> pdb=" O   GLN R 279 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   GLN R 278 " --> pdb=" O   GLN V 279 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   GLN V 278 " --> pdb=" O   GLN Z 279 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   GLN Z 278 " --> pdb=" O   GLN 3 279 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain '1' and resid 286 through 289
      removed outlier: 6.508A  pdb=" N   GLN X 287 " --> pdb=" O   PHE 1 288 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   GLN T 287 " --> pdb=" O   PHE X 288 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   GLN P 287 " --> pdb=" O   PHE T 288 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   GLN L 287 " --> pdb=" O   PHE P 288 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   GLN H 287 " --> pdb=" O   PHE L 288 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   GLN D 287 " --> pdb=" O   PHE H 288 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   GLN B 287 " --> pdb=" O   PHE D 288 " (cutoff:3.500A)

    161 hydrogen bonds defined for protein.
    483 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.92

  Time building geometry restraints manager: 0.61 seconds

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

  Histogram of bond lengths:
        1.23 -     1.29: 1155
        1.29 -     1.35: 1125
        1.35 -     1.41: 813
        1.41 -     1.48: 1047
        1.48 -     1.54: 2760
  Bond restraints: 6900
  Sorted by residual:
  bond pdb=" C   GLN F 284 "
       pdb=" N   PRO F 285 "
    ideal  model  delta    sigma   weight residual
    1.329  1.338 -0.008 1.22e-02 6.72e+03 4.72e-01
  bond pdb=" C   GLN X 284 "
       pdb=" N   PRO X 285 "
    ideal  model  delta    sigma   weight residual
    1.329  1.338 -0.008 1.22e-02 6.72e+03 4.65e-01
  bond pdb=" C   GLN V 284 "
       pdb=" N   PRO V 285 "
    ideal  model  delta    sigma   weight residual
    1.329  1.337 -0.008 1.22e-02 6.72e+03 4.26e-01
  bond pdb=" C   GLN T 284 "
       pdb=" N   PRO T 285 "
    ideal  model  delta    sigma   weight residual
    1.329  1.337 -0.008 1.22e-02 6.72e+03 4.19e-01
  bond pdb=" CB  PRO 3 285 "
       pdb=" CG  PRO 3 285 "
    ideal  model  delta    sigma   weight residual
    1.492  1.524 -0.032 5.00e-02 4.00e+02 4.11e-01
  ... (remaining 6895 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.63: 7837
        0.63 -     1.27: 1051
        1.27 -     1.90: 322
        1.90 -     2.53: 105
        2.53 -     3.16: 45
  Bond angle restraints: 9360
  Sorted by residual:
  angle pdb=" CA  PRO F 285 "
        pdb=" C   PRO F 285 "
        pdb=" N   GLN F 286 "
      ideal   model   delta    sigma   weight residual
     114.58  116.46   -1.88 1.16e+00 7.43e-01 2.62e+00
  angle pdb=" CA  PRO H 285 "
        pdb=" C   PRO H 285 "
        pdb=" N   GLN H 286 "
      ideal   model   delta    sigma   weight residual
     114.58  116.45   -1.87 1.16e+00 7.43e-01 2.59e+00
  angle pdb=" CA  PRO N 285 "
        pdb=" C   PRO N 285 "
        pdb=" N   GLN N 286 "
      ideal   model   delta    sigma   weight residual
     114.58  116.45   -1.87 1.16e+00 7.43e-01 2.59e+00
  angle pdb=" CA  PRO P 285 "
        pdb=" C   PRO P 285 "
        pdb=" N   GLN P 286 "
      ideal   model   delta    sigma   weight residual
     114.58  116.45   -1.87 1.16e+00 7.43e-01 2.59e+00
  angle pdb=" CA  PRO T 285 "
        pdb=" C   PRO T 285 "
        pdb=" N   GLN T 286 "
      ideal   model   delta    sigma   weight residual
     114.58  116.45   -1.87 1.16e+00 7.43e-01 2.59e+00
  ... (remaining 9355 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.70: 3795
       17.70 -    35.40: 165
       35.40 -    53.10: 150
       53.10 -    70.80: 30
       70.80 -    88.50: 30
  Dihedral angle restraints: 4170
    sinusoidal: 1755
      harmonic: 2415
  Sorted by residual:
  dihedral pdb=" N   GLN V 289 "
           pdb=" CA  GLN V 289 "
           pdb=" CB  GLN V 289 "
           pdb=" CG  GLN V 289 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -92.51   32.51     3      1.50e+01 4.44e-03 5.36e+00
  dihedral pdb=" N   GLN 1 289 "
           pdb=" CA  GLN 1 289 "
           pdb=" CB  GLN 1 289 "
           pdb=" CG  GLN 1 289 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -92.51   32.51     3      1.50e+01 4.44e-03 5.36e+00
  dihedral pdb=" N   GLN N 289 "
           pdb=" CA  GLN N 289 "
           pdb=" CB  GLN N 289 "
           pdb=" CG  GLN N 289 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -92.49   32.49     3      1.50e+01 4.44e-03 5.36e+00
  ... (remaining 4167 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 393
       0.024 -    0.047: 319
       0.047 -    0.071: 67
       0.071 -    0.094: 44
       0.094 -    0.118: 32
  Chirality restraints: 855
  Sorted by residual:
  chirality pdb=" CA  VAL G 269 "
            pdb=" N   VAL G 269 "
            pdb=" C   VAL G 269 "
            pdb=" CB  VAL G 269 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.45e-01
  chirality pdb=" CA  VAL C 269 "
            pdb=" N   VAL C 269 "
            pdb=" C   VAL C 269 "
            pdb=" CB  VAL C 269 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.45e-01
  chirality pdb=" CA  VAL U 269 "
            pdb=" N   VAL U 269 "
            pdb=" C   VAL U 269 "
            pdb=" CB  VAL U 269 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.42e-01
  ... (remaining 852 not shown)

  Planarity restraints: 1320
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR V 268 "    0.006 2.00e-02 2.50e+03   1.14e-02 1.30e+00
        pdb=" C   TYR V 268 "   -0.020 2.00e-02 2.50e+03
        pdb=" O   TYR V 268 "    0.007 2.00e-02 2.50e+03
        pdb=" N   VAL V 269 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR 3 268 "    0.006 2.00e-02 2.50e+03   1.13e-02 1.28e+00
        pdb=" C   TYR 3 268 "   -0.020 2.00e-02 2.50e+03
        pdb=" O   TYR 3 268 "    0.007 2.00e-02 2.50e+03
        pdb=" N   VAL 3 269 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR F 268 "    0.006 2.00e-02 2.50e+03   1.13e-02 1.28e+00
        pdb=" C   TYR F 268 "   -0.020 2.00e-02 2.50e+03
        pdb=" O   TYR F 268 "    0.007 2.00e-02 2.50e+03
        pdb=" N   VAL F 269 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1317 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1603
        2.82 -     3.34: 5072
        3.34 -     3.86: 11821
        3.86 -     4.38: 14455
        4.38 -     4.90: 23248
  Nonbonded interactions: 56199
  Sorted by model distance:
  nonbonded pdb=" O   ALA B 274 "
            pdb=" OG  SER B 277 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   ALA V 274 "
            pdb=" OG  SER V 277 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" O   ALA X 274 "
            pdb=" OG  SER X 277 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" O   ALA Z 274 "
            pdb=" OG  SER Z 277 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" O   ALA T 274 "
            pdb=" OG  SER T 277 "
     model   vdw
     2.301 3.040
  ... (remaining 56194 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
  selection = chain 'G'
  selection = chain 'I'
  selection = chain 'K'
  selection = chain 'M'
  selection = chain 'O'
  selection = chain 'Q'
  selection = chain 'S'
  selection = chain 'U'
  selection = chain 'W'
  selection = chain 'Y'
  selection = chain '0'
  selection = chain '2'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
  selection = chain 'H'
  selection = chain 'J'
  selection = chain 'L'
  selection = chain 'N'
  selection = chain 'P'
  selection = chain 'R'
  selection = chain 'T'
  selection = chain 'V'
  selection = chain 'X'
  selection = chain 'Z'
  selection = chain '1'
  selection = chain '3'
}

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:             4.510
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     6.230
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:5.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9001
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6900  Z= 0.128
  Angle     :  0.561   3.163   9360  Z= 0.321
  Chirality :  0.040   0.118    855
  Planarity :  0.007   0.026   1320
  Dihedral  : 17.773  88.500   2640
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.35 (0.15), residues: 765
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.31 (0.11), residues: 765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.013   0.002   TYR Y 272 
 PHE   0.006   0.002   PHE T 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6900)
  covalent geometry    : angle       0.56082 ( 9360)
  hydrogen bonds       : bond        0.21616 (  161)
  hydrogen bonds       : angle      11.02026 (  483)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.200 
Fit side-chains
REVERT: I  286 GLN cc_start: 0.9189 (mt0) cc_final: 0.8957 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.4290
  time to fit residues: 38.7240
Evaluate side-chains
  56 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 24 optimal weight:    6.9990
   chunk 48 optimal weight:    4.9990
   chunk 56 optimal weight:    0.8980
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 278 GLN
A 284 GLN
** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 271 GLN
B 289 GLN
C 278 GLN
** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 271 GLN
D 289 GLN
E 278 GLN
E 284 GLN
** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 271 GLN
F 289 GLN
G 278 GLN
G 284 GLN
** G 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 271 GLN
H 289 GLN
I 278 GLN
I 284 GLN
** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 271 GLN
J 289 GLN
K 278 GLN
K 284 GLN
** K 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 271 GLN
L 289 GLN
M 278 GLN
** M 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 271 GLN
N 289 GLN
O 278 GLN
O 284 GLN
** O 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 271 GLN
P 289 GLN
Q 278 GLN
Q 284 GLN
** Q 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 271 GLN
R 289 GLN
S 278 GLN
S 284 GLN
** S 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
T 271 GLN
T 289 GLN
U 278 GLN
U 284 GLN
** U 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 271 GLN
V 289 GLN
W 278 GLN
W 284 GLN
** W 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 271 GLN
X 289 GLN
Y 278 GLN
** Y 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z 271 GLN
Z 289 GLN
0 278 GLN
0 284 GLN
** 0 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
1 271 GLN
1 289 GLN
2 278 GLN
2 284 GLN
3 271 GLN
3 289 GLN

Total number of N/Q/H flips: 57

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.073350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.061416 restraints weight = 10222.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.2926 rms_B_bonded: 1.78
r_work: 0.2826 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.2742 rms_B_bonded: 3.04 restraints_weight: 0.2500
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9149
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.029   6900  Z= 0.299
  Angle     :  0.743   5.004   9360  Z= 0.442
  Chirality :  0.048   0.155    855
  Planarity :  0.006   0.038   1320
  Dihedral  :  5.810  15.480    885
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  7.89 %
    Favored  : 90.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.30 (0.17), residues: 765
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.50 (0.13), residues: 765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.023   0.003   TYR E 272 
 PHE   0.013   0.003   PHE P 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00716 ( 6900)
  covalent geometry    : angle       0.74341 ( 9360)
  hydrogen bonds       : bond        0.12223 (  161)
  hydrogen bonds       : angle       7.58875 (  483)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.176 
Fit side-chains
REVERT: A  289 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8708 (tt0)
REVERT: E  263 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8223 (mt0)
REVERT: I  286 GLN cc_start: 0.9275 (mt0) cc_final: 0.8972 (mt0)
REVERT: M  289 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8292 (tt0)
REVERT: O  263 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8112 (mt0)
REVERT: T  276 TYR cc_start: 0.8833 (m-80) cc_final: 0.8624 (m-80)
REVERT: 0  263 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8337 (mt0)
  outliers start: 12
  outliers final: 1
  residues processed: 73
  average time/residue: 0.3766
  time to fit residues: 29.6319
Evaluate side-chains
  70 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 GLN
Chi-restraints excluded: chain C residue  263 GLN
Chi-restraints excluded: chain E residue  263 GLN
Chi-restraints excluded: chain M residue  289 GLN
Chi-restraints excluded: chain O residue  263 GLN
Chi-restraints excluded: chain 0 residue  263 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 55 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 14 optimal weight:    0.5980
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 266 GLN
** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 0 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.078070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.066054 restraints weight = 9962.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.3011 rms_B_bonded: 1.77
r_work: 0.2914 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2830 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9076
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6900  Z= 0.148
  Angle     :  0.580   4.625   9360  Z= 0.336
  Chirality :  0.045   0.142    855
  Planarity :  0.005   0.034   1320
  Dihedral  :  5.255  16.412    885
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  8.98 %
    Favored  : 89.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.05 (0.18), residues: 765
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.32 (0.14), residues: 765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.022   0.002   TYR E 272 
 PHE   0.007   0.001   PHE 0 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 6900)
  covalent geometry    : angle       0.58018 ( 9360)
  hydrogen bonds       : bond        0.09467 (  161)
  hydrogen bonds       : angle       6.84586 (  483)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.341 
Fit side-chains
REVERT: C  263 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8184 (mt0)
REVERT: I  286 GLN cc_start: 0.9234 (mt0) cc_final: 0.8990 (mt0)
REVERT: M  263 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8099 (mt0)
REVERT: M  289 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8119 (tt0)
REVERT: O  263 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8069 (mt0)
REVERT: T  276 TYR cc_start: 0.8805 (m-80) cc_final: 0.8587 (m-80)
  outliers start: 10
  outliers final: 1
  residues processed: 72
  average time/residue: 0.3497
  time to fit residues: 27.2451
Evaluate side-chains
  69 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  263 GLN
Chi-restraints excluded: chain M residue  263 GLN
Chi-restraints excluded: chain M residue  289 GLN
Chi-restraints excluded: chain O residue  263 GLN
Chi-restraints excluded: chain S residue  263 GLN
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 55 optimal weight:    0.0970
   chunk 53 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 58 optimal weight:    0.5980
   chunk 32 optimal weight:    5.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 0 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.081727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.070148 restraints weight = 9319.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.2960 rms_B_bonded: 1.72
r_work: 0.2862 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2770 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9018
moved from start:          0.2513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6900  Z= 0.111
  Angle     :  0.528   4.388   9360  Z= 0.299
  Chirality :  0.044   0.147    855
  Planarity :  0.004   0.029   1320
  Dihedral  :  4.885  16.167    885
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  9.52 %
    Favored  : 89.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.95 (0.18), residues: 765
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.24 (0.14), residues: 765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.022   0.001   TYR E 272 
 PHE   0.006   0.001   PHE W 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 6900)
  covalent geometry    : angle       0.52840 ( 9360)
  hydrogen bonds       : bond        0.07732 (  161)
  hydrogen bonds       : angle       6.38858 (  483)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A  279 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7498 (mm110)
REVERT: E  263 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8252 (mt0)
REVERT: E  279 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7897 (mm110)
REVERT: I  279 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.7928 (mp10)
REVERT: I  286 GLN cc_start: 0.9201 (mt0) cc_final: 0.8988 (mt0)
REVERT: U  284 GLN cc_start: 0.9116 (mt0) cc_final: 0.8907 (mt0)
REVERT: Z  268 TYR cc_start: 0.9225 (m-80) cc_final: 0.9009 (m-80)
  outliers start: 10
  outliers final: 1
  residues processed: 73
  average time/residue: 0.3708
  time to fit residues: 29.1821
Evaluate side-chains
  70 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  279 GLN
Chi-restraints excluded: chain E residue  263 GLN
Chi-restraints excluded: chain E residue  279 GLN
Chi-restraints excluded: chain I residue  279 GLN
Chi-restraints excluded: chain R residue  280 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 55 optimal weight:    4.9990
   chunk 56 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   chunk 49 optimal weight:    4.9990
   chunk 48 optimal weight:    0.7980
   chunk 44 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   overall best weight:    2.7186

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

Flipped N/Q/H residues before XYZ refinement:
** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 289 GLN
** S 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 289 GLN
** W 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 289 GLN
** 0 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.076002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.064671 restraints weight = 10141.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.2900 rms_B_bonded: 1.66
r_work: 0.2803 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.2720 rms_B_bonded: 2.85 restraints_weight: 0.2500
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9150
moved from start:          0.2741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.029   6900  Z= 0.286
  Angle     :  0.705   4.798   9360  Z= 0.414
  Chirality :  0.048   0.155    855
  Planarity :  0.005   0.038   1320
  Dihedral  :  5.698  16.456    885
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  :  8.98 %
    Favored  : 88.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.16 (0.18), residues: 765
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.40 (0.14), residues: 765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.024   0.002   TYR E 272 
 PHE   0.011   0.002   PHE H 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00693 ( 6900)
  covalent geometry    : angle       0.70534 ( 9360)
  hydrogen bonds       : bond        0.12068 (  161)
  hydrogen bonds       : angle       6.95374 (  483)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.187 
Fit side-chains
REVERT: A  263 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8330 (mt0)
REVERT: E  263 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8327 (mt0)
REVERT: K  263 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.7805 (mp10)
REVERT: O  263 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8103 (mt0)
REVERT: 0  263 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8436 (mt0)
  outliers start: 18
  outliers final: 5
  residues processed: 81
  average time/residue: 0.3463
  time to fit residues: 30.3061
Evaluate side-chains
  80 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 GLN
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain E residue  263 GLN
Chi-restraints excluded: chain K residue  263 GLN
Chi-restraints excluded: chain O residue  263 GLN
Chi-restraints excluded: chain O residue  280 THR
Chi-restraints excluded: chain Q residue  269 VAL
Chi-restraints excluded: chain R residue  280 THR
Chi-restraints excluded: chain 0 residue  263 GLN
Chi-restraints excluded: chain 1 residue  280 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 38 optimal weight:    0.3980
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 0 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.078039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.066081 restraints weight = 10074.197|
|-----------------------------------------------------------------------------|
r_work (start): 0.2959 rms_B_bonded: 1.77
r_work: 0.2862 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.2778 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9065
moved from start:          0.2727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6900  Z= 0.137
  Angle     :  0.567   4.444   9360  Z= 0.326
  Chirality :  0.045   0.146    855
  Planarity :  0.005   0.035   1320
  Dihedral  :  5.200  16.738    885
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  :  9.66 %
    Favored  : 87.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.02 (0.18), residues: 765
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.29 (0.14), residues: 765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.022   0.002   TYR E 272 
 PHE   0.006   0.001   PHE 3 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6900)
  covalent geometry    : angle       0.56661 ( 9360)
  hydrogen bonds       : bond        0.09066 (  161)
  hydrogen bonds       : angle       6.50255 (  483)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A  263 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8325 (mt0)
REVERT: E  263 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8285 (mt0)
REVERT: I  286 GLN cc_start: 0.9216 (mt0) cc_final: 0.8946 (mt0)
REVERT: O  263 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8097 (mt0)
REVERT: Z  268 TYR cc_start: 0.9241 (m-80) cc_final: 0.9010 (m-80)
REVERT: 0  263 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8469 (mt0)
  outliers start: 18
  outliers final: 4
  residues processed: 85
  average time/residue: 0.3733
  time to fit residues: 33.9577
Evaluate side-chains
  80 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 GLN
Chi-restraints excluded: chain E residue  263 GLN
Chi-restraints excluded: chain O residue  263 GLN
Chi-restraints excluded: chain O residue  269 VAL
Chi-restraints excluded: chain Q residue  269 VAL
Chi-restraints excluded: chain R residue  280 THR
Chi-restraints excluded: chain 0 residue  263 GLN
Chi-restraints excluded: chain 1 residue  280 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 55 optimal weight:    0.0670
   chunk 29 optimal weight:    6.9990
   chunk 50 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 53 optimal weight:    5.9990
   chunk 56 optimal weight:    0.8980
   chunk 25 optimal weight:    7.9990
   chunk 42 optimal weight:    0.9990
   chunk 13 optimal weight:    6.9990
   overall best weight:    2.5924

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 0 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.072773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.061073 restraints weight = 10167.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.2867 rms_B_bonded: 1.72
r_work: 0.2767 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.2684 rms_B_bonded: 2.95 restraints_weight: 0.2500
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9151
moved from start:          0.2856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.029   6900  Z= 0.273
  Angle     :  0.693   4.738   9360  Z= 0.406
  Chirality :  0.048   0.154    855
  Planarity :  0.005   0.040   1320
  Dihedral  :  5.707  16.622    885
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 2.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  :  8.71 %
    Favored  : 88.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.21 (0.18), residues: 765
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.44 (0.14), residues: 765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.024   0.002   TYR E 272 
 PHE   0.010   0.002   PHE 3 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00659 ( 6900)
  covalent geometry    : angle       0.69315 ( 9360)
  hydrogen bonds       : bond        0.11942 (  161)
  hydrogen bonds       : angle       6.91314 (  483)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 70
  time to evaluate  : 0.455 
Fit side-chains
REVERT: A  263 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8323 (mt0)
REVERT: A  279 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.7521 (mp10)
REVERT: C  263 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8281 (mt0)
REVERT: E  263 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8329 (mt0)
REVERT: I  289 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8392 (tt0)
REVERT: K  263 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.7794 (mp10)
REVERT: O  263 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8116 (mt0)
REVERT: 0  263 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8472 (mt0)
REVERT: 0  279 GLN cc_start: 0.9298 (OUTLIER) cc_final: 0.7660 (mp10)
  outliers start: 24
  outliers final: 10
  residues processed: 84
  average time/residue: 0.3749
  time to fit residues: 34.0013
Evaluate side-chains
  88 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 69
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 GLN
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  279 GLN
Chi-restraints excluded: chain C residue  263 GLN
Chi-restraints excluded: chain E residue  263 GLN
Chi-restraints excluded: chain E residue  269 VAL
Chi-restraints excluded: chain I residue  273 SER
Chi-restraints excluded: chain I residue  289 GLN
Chi-restraints excluded: chain K residue  263 GLN
Chi-restraints excluded: chain O residue  263 GLN
Chi-restraints excluded: chain O residue  269 VAL
Chi-restraints excluded: chain O residue  280 THR
Chi-restraints excluded: chain Q residue  269 VAL
Chi-restraints excluded: chain R residue  280 THR
Chi-restraints excluded: chain U residue  269 VAL
Chi-restraints excluded: chain 0 residue  263 GLN
Chi-restraints excluded: chain 0 residue  279 GLN
Chi-restraints excluded: chain 1 residue  280 THR
Chi-restraints excluded: chain 2 residue  269 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 289 GLN
** M 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 289 GLN
** Q 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 289 GLN
** U 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
W 289 GLN
0 289 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.080081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.068655 restraints weight = 9903.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 1.66
r_work: 0.2872 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.2790 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9094
moved from start:          0.2859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   6900  Z= 0.151
  Angle     :  0.582   4.498   9360  Z= 0.336
  Chirality :  0.045   0.147    855
  Planarity :  0.005   0.037   1320
  Dihedral  :  5.302  16.976    885
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  :  9.39 %
    Favored  : 87.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.05 (0.18), residues: 765
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.32 (0.14), residues: 765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.022   0.002   TYR E 272 
 PHE   0.007   0.001   PHE W 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 6900)
  covalent geometry    : angle       0.58234 ( 9360)
  hydrogen bonds       : bond        0.09537 (  161)
  hydrogen bonds       : angle       6.56282 (  483)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 75
  time to evaluate  : 0.170 
Fit side-chains
REVERT: A  263 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8358 (mt0)
REVERT: A  279 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7264 (mp10)
REVERT: C  263 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8259 (mt0)
REVERT: E  263 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8337 (mt0)
REVERT: E  279 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.7505 (mp10)
REVERT: I  286 GLN cc_start: 0.9210 (mt0) cc_final: 0.8948 (mt0)
REVERT: I  289 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8228 (tt0)
REVERT: K  263 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.7799 (mp10)
REVERT: O  263 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8112 (mt0)
REVERT: Z  268 TYR cc_start: 0.9210 (m-80) cc_final: 0.8970 (m-80)
REVERT: 0  263 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8456 (mt0)
  outliers start: 23
  outliers final: 8
  residues processed: 90
  average time/residue: 0.3634
  time to fit residues: 35.2635
Evaluate side-chains
  90 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 73
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 GLN
Chi-restraints excluded: chain A residue  279 GLN
Chi-restraints excluded: chain C residue  263 GLN
Chi-restraints excluded: chain C residue  269 VAL
Chi-restraints excluded: chain E residue  263 GLN
Chi-restraints excluded: chain E residue  269 VAL
Chi-restraints excluded: chain E residue  279 GLN
Chi-restraints excluded: chain I residue  289 GLN
Chi-restraints excluded: chain K residue  263 GLN
Chi-restraints excluded: chain O residue  263 GLN
Chi-restraints excluded: chain O residue  269 VAL
Chi-restraints excluded: chain Q residue  269 VAL
Chi-restraints excluded: chain R residue  280 THR
Chi-restraints excluded: chain U residue  269 VAL
Chi-restraints excluded: chain 0 residue  263 GLN
Chi-restraints excluded: chain 1 residue  280 THR
Chi-restraints excluded: chain 2 residue  269 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 57 optimal weight:    0.9980
   chunk 35 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 37 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 47 optimal weight:    6.9990
   chunk 54 optimal weight:    0.6980
   chunk 43 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   overall best weight:    1.4582

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.078520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.067090 restraints weight = 10000.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.2951 rms_B_bonded: 1.66
r_work: 0.2856 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.2774 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9113
moved from start:          0.2860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   6900  Z= 0.176
  Angle     :  0.608   4.547   9360  Z= 0.352
  Chirality :  0.045   0.151    855
  Planarity :  0.005   0.037   1320
  Dihedral  :  5.381  16.877    885
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  :  8.98 %
    Favored  : 87.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.10 (0.18), residues: 765
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.35 (0.14), residues: 765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.023   0.002   TYR I 272 
 PHE   0.008   0.002   PHE 3 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 6900)
  covalent geometry    : angle       0.60779 ( 9360)
  hydrogen bonds       : bond        0.10233 (  161)
  hydrogen bonds       : angle       6.67077 (  483)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 74
  time to evaluate  : 0.209 
Fit side-chains
REVERT: A  263 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8331 (mt0)
REVERT: A  279 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.7361 (mp10)
REVERT: C  263 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8270 (mt0)
REVERT: E  263 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8367 (mt0)
REVERT: I  289 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8257 (tt0)
REVERT: K  263 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.7815 (mp10)
REVERT: M  263 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8350 (mt0)
REVERT: M  289 GLN cc_start: 0.9349 (OUTLIER) cc_final: 0.8299 (tm-30)
REVERT: O  263 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8128 (mt0)
REVERT: Q  263 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.7859 (mt0)
REVERT: Z  268 TYR cc_start: 0.9223 (m-80) cc_final: 0.8937 (m-80)
REVERT: 0  263 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8450 (mt0)
  outliers start: 23
  outliers final: 9
  residues processed: 87
  average time/residue: 0.3389
  time to fit residues: 31.8424
Evaluate side-chains
  92 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 72
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 GLN
Chi-restraints excluded: chain A residue  279 GLN
Chi-restraints excluded: chain C residue  263 GLN
Chi-restraints excluded: chain C residue  269 VAL
Chi-restraints excluded: chain E residue  263 GLN
Chi-restraints excluded: chain E residue  269 VAL
Chi-restraints excluded: chain I residue  289 GLN
Chi-restraints excluded: chain K residue  263 GLN
Chi-restraints excluded: chain K residue  269 VAL
Chi-restraints excluded: chain M residue  263 GLN
Chi-restraints excluded: chain M residue  289 GLN
Chi-restraints excluded: chain O residue  263 GLN
Chi-restraints excluded: chain O residue  269 VAL
Chi-restraints excluded: chain Q residue  263 GLN
Chi-restraints excluded: chain Q residue  269 VAL
Chi-restraints excluded: chain R residue  280 THR
Chi-restraints excluded: chain U residue  269 VAL
Chi-restraints excluded: chain 0 residue  263 GLN
Chi-restraints excluded: chain 1 residue  280 THR
Chi-restraints excluded: chain 2 residue  269 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 43 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 10 optimal weight:    4.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.078266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.066361 restraints weight = 9996.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3028 rms_B_bonded: 1.74
r_work: 0.2936 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.2854 rms_B_bonded: 3.03 restraints_weight: 0.2500
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9076
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   6900  Z= 0.132
  Angle     :  0.558   4.515   9360  Z= 0.320
  Chirality :  0.044   0.149    855
  Planarity :  0.005   0.034   1320
  Dihedral  :  5.143  16.940    885
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  :  9.12 %
    Favored  : 87.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.99 (0.19), residues: 765
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.27 (0.14), residues: 765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.023   0.002   TYR I 272 
 PHE   0.006   0.001   PHE W 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 6900)
  covalent geometry    : angle       0.55836 ( 9360)
  hydrogen bonds       : bond        0.08866 (  161)
  hydrogen bonds       : angle       6.45364 (  483)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 75
  time to evaluate  : 0.214 
Fit side-chains
REVERT: A  263 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8374 (mt0)
REVERT: A  279 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7397 (mp10)
REVERT: E  263 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8372 (mt0)
REVERT: E  279 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.7281 (mp10)
REVERT: I  286 GLN cc_start: 0.9188 (mt0) cc_final: 0.8938 (mt0)
REVERT: I  289 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8168 (tt0)
REVERT: K  263 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.7808 (mp10)
REVERT: M  263 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8342 (mt0)
REVERT: M  289 GLN cc_start: 0.9342 (OUTLIER) cc_final: 0.8356 (tm-30)
REVERT: O  263 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.7761 (mt0)
REVERT: Q  263 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.7918 (mt0)
REVERT: Q  279 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.7985 (mp10)
REVERT: 0  263 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8419 (mt0)
  outliers start: 22
  outliers final: 9
  residues processed: 88
  average time/residue: 0.3535
  time to fit residues: 33.4245
Evaluate side-chains
  92 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 71
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 GLN
Chi-restraints excluded: chain A residue  279 GLN
Chi-restraints excluded: chain C residue  269 VAL
Chi-restraints excluded: chain E residue  263 GLN
Chi-restraints excluded: chain E residue  269 VAL
Chi-restraints excluded: chain E residue  279 GLN
Chi-restraints excluded: chain I residue  289 GLN
Chi-restraints excluded: chain K residue  263 GLN
Chi-restraints excluded: chain K residue  269 VAL
Chi-restraints excluded: chain M residue  263 GLN
Chi-restraints excluded: chain M residue  289 GLN
Chi-restraints excluded: chain O residue  263 GLN
Chi-restraints excluded: chain O residue  269 VAL
Chi-restraints excluded: chain Q residue  263 GLN
Chi-restraints excluded: chain Q residue  269 VAL
Chi-restraints excluded: chain Q residue  279 GLN
Chi-restraints excluded: chain R residue  280 THR
Chi-restraints excluded: chain U residue  269 VAL
Chi-restraints excluded: chain 0 residue  263 GLN
Chi-restraints excluded: chain 1 residue  280 THR
Chi-restraints excluded: chain 2 residue  269 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 284 GLN
** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.075900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.064183 restraints weight = 10055.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.2943 rms_B_bonded: 1.68
r_work: 0.2847 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.2766 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9107
moved from start:          0.2864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.020   6900  Z= 0.170
  Angle     :  0.601   4.677   9360  Z= 0.348
  Chirality :  0.045   0.148    855
  Planarity :  0.005   0.036   1320
  Dihedral  :  5.328  17.057    885
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  :  9.12 %
    Favored  : 87.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.06 (0.19), residues: 765
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.32 (0.14), residues: 765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.023   0.002   TYR E 272 
 PHE   0.008   0.002   PHE 3 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 6900)
  covalent geometry    : angle       0.60074 ( 9360)
  hydrogen bonds       : bond        0.09989 (  161)
  hydrogen bonds       : angle       6.61313 (  483)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1708.92 seconds
wall clock time: 30 minutes 1.84 seconds (1801.84 seconds total)