Starting phenix.real_space_refine
on Wed Mar  4 05:36:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9y6t_72630/03_2026/9y6t_72630.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9y6t_72630/03_2026/9y6t_72630.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9y6t_72630/03_2026/9y6t_72630.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9y6t_72630/03_2026/9y6t_72630.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9y6t_72630/03_2026/9y6t_72630.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9y6t_72630/03_2026/9y6t_72630.map"
  }
  resolution = 2.65
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.113
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      18      5.16       5
     C    6870      2.51       5
     N    1974      2.21       5
     O    2100      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10962
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 241, 1827
          Classifications: {'peptide': 241}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 231}
    Chain: "B"
      Number of atoms: 1827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 241, 1827
          Classifications: {'peptide': 241}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 231}
    Chain: "C"
      Number of atoms: 1827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 241, 1827
          Classifications: {'peptide': 241}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 231}
    Chain: "D"
      Number of atoms: 1827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 241, 1827
          Classifications: {'peptide': 241}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 231}
    Chain: "E"
      Number of atoms: 1827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 241, 1827
          Classifications: {'peptide': 241}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 231}
    Chain: "F"
      Number of atoms: 1827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 241, 1827
          Classifications: {'peptide': 241}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 231}
  Time building chain proxies: 2.63, per 1000 atoms: 0.24
  Number of scatterers: 10962
  At special positions: 0
  Unit cell: (83.628, 86.94, 123.372, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      18     16.00
     O    2100      8.00
     N    1974      7.00
     C    6870      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: 0.79
  Conformation dependent library (CDL) restraints added in 536.6 milliseconds
  

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2652

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 9 sheets defined
      43.8% alpha, 14.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 322 through 338
      removed outlier: 3.736A  pdb=" N   ARG A 333 " --> pdb=" O   ALA A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 369
      removed outlier: 5.638A  pdb=" N   ALA A 362 " --> pdb=" O   ALA A 358 " (cutoff:3.500A)
      removed outlier: 5.562A  pdb=" N   ALA A 363 " --> pdb=" O   ARG A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 389
    Processing helix  chain 'A' and resid 428 through 432
      removed outlier: 3.541A  pdb=" N   LEU A 432 " --> pdb=" O   ALA A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 451
    Processing helix  chain 'A' and resid 454 through 459
      removed outlier: 3.903A  pdb=" N   LEU A 458 " --> pdb=" O   PRO A 455 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   SER A 459 " --> pdb=" O   ASP A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 472
    Processing helix  chain 'A' and resid 527 through 545
    Processing helix  chain 'B' and resid 322 through 338
      removed outlier: 3.777A  pdb=" N   ARG B 333 " --> pdb=" O   ALA B 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 350 through 369
      removed outlier: 5.512A  pdb=" N   ALA B 362 " --> pdb=" O   ALA B 358 " (cutoff:3.500A)
      removed outlier: 5.564A  pdb=" N   ALA B 363 " --> pdb=" O   ARG B 359 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 374 through 389
    Processing helix  chain 'B' and resid 428 through 432
    Processing helix  chain 'B' and resid 433 through 451
    Processing helix  chain 'B' and resid 455 through 459
      removed outlier: 3.800A  pdb=" N   LEU B 458 " --> pdb=" O   PRO B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 469 through 472
    Processing helix  chain 'B' and resid 527 through 545
    Processing helix  chain 'C' and resid 322 through 338
      removed outlier: 3.754A  pdb=" N   ARG C 333 " --> pdb=" O   ALA C 329 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 350 through 369
      removed outlier: 5.559A  pdb=" N   ALA C 362 " --> pdb=" O   ALA C 358 " (cutoff:3.500A)
      removed outlier: 5.566A  pdb=" N   ALA C 363 " --> pdb=" O   ARG C 359 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 374 through 389
    Processing helix  chain 'C' and resid 428 through 432
      removed outlier: 3.504A  pdb=" N   LEU C 432 " --> pdb=" O   ALA C 429 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 433 through 451
    Processing helix  chain 'C' and resid 455 through 459
      removed outlier: 3.792A  pdb=" N   LEU C 458 " --> pdb=" O   PRO C 455 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 469 through 472
    Processing helix  chain 'C' and resid 527 through 545
    Processing helix  chain 'D' and resid 322 through 338
      removed outlier: 3.738A  pdb=" N   ARG D 333 " --> pdb=" O   ALA D 329 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 350 through 369
      removed outlier: 5.611A  pdb=" N   ALA D 362 " --> pdb=" O   ALA D 358 " (cutoff:3.500A)
      removed outlier: 5.548A  pdb=" N   ALA D 363 " --> pdb=" O   ARG D 359 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 374 through 389
    Processing helix  chain 'D' and resid 428 through 432
      removed outlier: 3.532A  pdb=" N   LEU D 432 " --> pdb=" O   ALA D 429 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 433 through 451
    Processing helix  chain 'D' and resid 454 through 459
      removed outlier: 3.921A  pdb=" N   LEU D 458 " --> pdb=" O   PRO D 455 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   SER D 459 " --> pdb=" O   ASP D 456 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 469 through 472
    Processing helix  chain 'D' and resid 527 through 545
    Processing helix  chain 'E' and resid 322 through 338
      removed outlier: 3.770A  pdb=" N   ARG E 333 " --> pdb=" O   ALA E 329 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 350 through 369
      removed outlier: 5.513A  pdb=" N   ALA E 362 " --> pdb=" O   ALA E 358 " (cutoff:3.500A)
      removed outlier: 5.565A  pdb=" N   ALA E 363 " --> pdb=" O   ARG E 359 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 374 through 389
    Processing helix  chain 'E' and resid 428 through 432
    Processing helix  chain 'E' and resid 433 through 451
    Processing helix  chain 'E' and resid 455 through 459
      removed outlier: 3.822A  pdb=" N   LEU E 458 " --> pdb=" O   PRO E 455 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 469 through 472
    Processing helix  chain 'E' and resid 527 through 545
    Processing helix  chain 'F' and resid 322 through 338
      removed outlier: 3.750A  pdb=" N   ARG F 333 " --> pdb=" O   ALA F 329 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 350 through 369
      removed outlier: 5.586A  pdb=" N   ALA F 362 " --> pdb=" O   ALA F 358 " (cutoff:3.500A)
      removed outlier: 5.562A  pdb=" N   ALA F 363 " --> pdb=" O   ARG F 359 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 374 through 389
    Processing helix  chain 'F' and resid 428 through 432
      removed outlier: 3.507A  pdb=" N   LEU F 432 " --> pdb=" O   ALA F 429 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 433 through 451
    Processing helix  chain 'F' and resid 454 through 459
      removed outlier: 3.793A  pdb=" N   LEU F 458 " --> pdb=" O   PRO F 455 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   SER F 459 " --> pdb=" O   ASP F 456 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 469 through 472
    Processing helix  chain 'F' and resid 527 through 545
    Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 320
    Processing sheet with id=AA2, first strand: chain 'A' and resid 341 through 349
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 341 through 349
    current: chain 'A' and resid 421 through 422
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 421 through 422
    current: chain 'A' and resid 486 through 490
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 486 through 490
    current: chain 'A' and resid 507 through 522
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 507 through 522
    current: chain 'E' and resid 341 through 349
  WARNING: can't find start of bonding for strands!
    previous: chain 'E' and resid 341 through 349
    current: chain 'E' and resid 421 through 422
  WARNING: can't find start of bonding for strands!
    previous: chain 'E' and resid 421 through 422
    current: chain 'E' and resid 486 through 490
  WARNING: can't find start of bonding for strands!
    previous: chain 'E' and resid 486 through 490
    current: chain 'E' and resid 507 through 522
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 394 through 397
    Processing sheet with id=AA4, first strand: chain 'A' and resid 475 through 476
      removed outlier: 3.604A  pdb=" N   PHE A 475 " --> pdb=" O   THR B 345 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 341 through 349
    current: chain 'B' and resid 420 through 422
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 420 through 422
    current: chain 'B' and resid 486 through 490
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 486 through 490
    current: chain 'B' and resid 507 through 522
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 507 through 522
    current: chain 'D' and resid 421 through 422
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 421 through 422
    current: chain 'D' and resid 486 through 490
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 486 through 490
    current: chain 'D' and resid 507 through 522
    Processing sheet with id=AA5, first strand: chain 'B' and resid 318 through 320
    Processing sheet with id=AA6, first strand: chain 'B' and resid 475 through 476
      removed outlier: 3.597A  pdb=" N   PHE B 475 " --> pdb=" O   THR C 345 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 341 through 349
    current: chain 'C' and resid 421 through 422
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 421 through 422
    current: chain 'C' and resid 486 through 490
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 486 through 490
    current: chain 'C' and resid 507 through 522
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 507 through 522
    current: chain 'F' and resid 341 through 349
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 341 through 349
    current: chain 'F' and resid 421 through 422
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 421 through 422
    current: chain 'F' and resid 486 through 490
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 486 through 490
    current: chain 'F' and resid 507 through 522
    Processing sheet with id=AA7, first strand: chain 'D' and resid 318 through 320
    Processing sheet with id=AA8, first strand: chain 'D' and resid 394 through 397
    Processing sheet with id=AA9, first strand: chain 'E' and resid 318 through 320

    466 hydrogen bonds defined for protein.
    1320 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.64

  Time building geometry restraints manager: 1.15 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3787
        1.34 -     1.46: 1817
        1.46 -     1.57: 5502
        1.57 -     1.69: 0
        1.69 -     1.81: 30
  Bond restraints: 11136
  Sorted by residual:
  bond pdb=" C   LEU B 375 "
       pdb=" O   LEU B 375 "
    ideal  model  delta    sigma   weight residual
    1.244  1.234  0.010 9.80e-03 1.04e+04 1.00e+00
  bond pdb=" C   PHE C 374 "
       pdb=" N   LEU C 375 "
    ideal  model  delta    sigma   weight residual
    1.332  1.320  0.012 1.33e-02 5.65e+03 7.89e-01
  bond pdb=" C   LEU C 375 "
       pdb=" O   LEU C 375 "
    ideal  model  delta    sigma   weight residual
    1.244  1.235  0.009 9.80e-03 1.04e+04 7.74e-01
  bond pdb=" C   PHE B 374 "
       pdb=" N   LEU B 375 "
    ideal  model  delta    sigma   weight residual
    1.332  1.321  0.011 1.33e-02 5.65e+03 6.65e-01
  bond pdb=" N   GLY C 489 "
       pdb=" CA  GLY C 489 "
    ideal  model  delta    sigma   weight residual
    1.454  1.443  0.011 1.37e-02 5.33e+03 6.30e-01
  ... (remaining 11131 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.83: 13885
        0.83 -     1.67: 1039
        1.67 -     2.50: 131
        2.50 -     3.34: 21
        3.34 -     4.17: 26
  Bond angle restraints: 15102
  Sorted by residual:
  angle pdb=" C   PHE B 374 "
        pdb=" N   LEU B 375 "
        pdb=" CA  LEU B 375 "
      ideal   model   delta    sigma   weight residual
     120.09  122.48   -2.39 1.25e+00 6.40e-01 3.67e+00
  angle pdb=" N   PHE A 463 "
        pdb=" CA  PHE A 463 "
        pdb=" C   PHE A 463 "
      ideal   model   delta    sigma   weight residual
     109.23  106.42    2.81 1.55e+00 4.16e-01 3.30e+00
  angle pdb=" N   PHE E 463 "
        pdb=" CA  PHE E 463 "
        pdb=" C   PHE E 463 "
      ideal   model   delta    sigma   weight residual
     109.23  106.49    2.74 1.55e+00 4.16e-01 3.12e+00
  angle pdb=" N   PHE D 463 "
        pdb=" CA  PHE D 463 "
        pdb=" C   PHE D 463 "
      ideal   model   delta    sigma   weight residual
     109.23  106.50    2.73 1.55e+00 4.16e-01 3.11e+00
  angle pdb=" N   PHE B 463 "
        pdb=" CA  PHE B 463 "
        pdb=" C   PHE B 463 "
      ideal   model   delta    sigma   weight residual
     109.23  106.52    2.71 1.55e+00 4.16e-01 3.05e+00
  ... (remaining 15097 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.39: 5996
       17.39 -    34.78: 583
       34.78 -    52.17: 114
       52.17 -    69.56: 23
       69.56 -    86.95: 10
  Dihedral angle restraints: 6726
    sinusoidal: 2604
      harmonic: 4122
  Sorted by residual:
  dihedral pdb=" CA  ARG C 359 "
           pdb=" C   ARG C 359 "
           pdb=" N   ALA C 360 "
           pdb=" CA  ALA C 360 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.92  -16.08     0      5.00e+00 4.00e-02 1.03e+01
  dihedral pdb=" CA  ARG D 359 "
           pdb=" C   ARG D 359 "
           pdb=" N   ALA D 360 "
           pdb=" CA  ALA D 360 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.02  -15.98     0      5.00e+00 4.00e-02 1.02e+01
  dihedral pdb=" CB  GLU B 366 "
           pdb=" CG  GLU B 366 "
           pdb=" CD  GLU B 366 "
           pdb=" OE1 GLU B 366 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.95  -86.95     1      3.00e+01 1.11e-03 1.01e+01
  ... (remaining 6723 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1115
       0.030 -    0.059: 449
       0.059 -    0.089: 122
       0.089 -    0.119: 71
       0.119 -    0.148: 19
  Chirality restraints: 1776
  Sorted by residual:
  chirality pdb=" CA  VAL C 481 "
            pdb=" N   VAL C 481 "
            pdb=" C   VAL C 481 "
            pdb=" CB  VAL C 481 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.50e-01
  chirality pdb=" CA  VAL D 481 "
            pdb=" N   VAL D 481 "
            pdb=" C   VAL D 481 "
            pdb=" CB  VAL D 481 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.49e-01
  chirality pdb=" CA  VAL F 481 "
            pdb=" N   VAL F 481 "
            pdb=" C   VAL F 481 "
            pdb=" CB  VAL F 481 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.45e-01
  ... (remaining 1773 not shown)

  Planarity restraints: 1986
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 517 "   -0.035 5.00e-02 4.00e+02   5.24e-02 4.39e+00
        pdb=" N   PRO B 518 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO B 518 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 518 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU E 517 "    0.034 5.00e-02 4.00e+02   5.16e-02 4.27e+00
        pdb=" N   PRO E 518 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO E 518 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO E 518 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 517 "   -0.033 5.00e-02 4.00e+02   5.05e-02 4.09e+00
        pdb=" N   PRO C 518 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO C 518 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO C 518 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 1983 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 973
        2.74 -     3.28: 10368
        3.28 -     3.82: 19231
        3.82 -     4.36: 24438
        4.36 -     4.90: 40181
  Nonbonded interactions: 95191
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN D 393 "
            pdb=" OG1 THR D 462 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OD1 ASN A 393 "
            pdb=" OG1 THR A 462 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" OD1 ASN B 393 "
            pdb=" OG1 THR B 462 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OD1 ASN E 393 "
            pdb=" OG1 THR E 462 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" NH1 ARG F 357 "
            pdb=" O   LEU F 372 "
     model   vdw
     2.298 3.120
  ... (remaining 95186 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.180
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
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      :  0.004   0.039  11136  Z= 0.192
  Angle     :  0.495   4.175  15102  Z= 0.274
  Chirality :  0.040   0.148   1776
  Planarity :  0.005   0.052   1986
  Dihedral  : 14.623  86.950   4074
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.14 %
    Favored  : 89.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.80 (0.21), residues: 1434
  helix:  1.95 (0.21), residues: 564
  sheet:  0.72 (0.24), residues: 390
  loop :  0.89 (0.26), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 357 
 TYR   0.004   0.001   TYR D 521 
 PHE   0.011   0.002   PHE E 534 
 HIS   0.004   0.001   HIS F 389 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 (11136)
  covalent geometry    : angle       0.49516 (15102)
  hydrogen bonds       : bond        0.13484 (  466)
  hydrogen bonds       : angle       5.55958 ( 1320)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.366 
Fit side-chains
REVERT: C  443 ASP cc_start: 0.8155 (t70) cc_final: 0.7747 (t0)
REVERT: C  539 LYS cc_start: 0.8760 (tttt) cc_final: 0.8494 (ttmt)
REVERT: E  548 GLU cc_start: 0.7772 (mp0) cc_final: 0.7469 (mp0)
REVERT: F  443 ASP cc_start: 0.8157 (t70) cc_final: 0.7747 (t0)
REVERT: F  539 LYS cc_start: 0.8796 (tttt) cc_final: 0.8539 (ttmt)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.6865
  time to fit residues: 136.7370
Evaluate side-chains
  147 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    0.0470
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    0.0050
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    0.2980
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.8696

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

Flipped N/Q/H residues before XYZ refinement:
D 337 GLN
E 337 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.165651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.133466 restraints weight = 10087.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 1.33
r_work: 0.3245 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8780
moved from start:          0.1014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11136  Z= 0.136
  Angle     :  0.492   6.477  15102  Z= 0.265
  Chirality :  0.041   0.168   1776
  Planarity :  0.004   0.033   1986
  Dihedral  :  4.544  18.213   1572
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 14.20 %
    Favored  : 84.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.11 (0.21), residues: 1434
  helix:  2.02 (0.21), residues: 576
  sheet:  1.00 (0.26), residues: 366
  loop :  1.17 (0.26), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 357 
 TYR   0.005   0.001   TYR F 405 
 PHE   0.013   0.002   PHE B 534 
 HIS   0.004   0.001   HIS B 389 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (11136)
  covalent geometry    : angle       0.49232 (15102)
  hydrogen bonds       : bond        0.05015 (  466)
  hydrogen bonds       : angle       4.68288 ( 1320)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 159
  time to evaluate  : 0.423 
Fit side-chains
REVERT: A  443 ASP cc_start: 0.8549 (t70) cc_final: 0.8310 (t70)
REVERT: C  539 LYS cc_start: 0.8894 (tttt) cc_final: 0.8577 (ttmt)
REVERT: D  443 ASP cc_start: 0.8574 (t70) cc_final: 0.8363 (t70)
REVERT: F  366 GLU cc_start: 0.7929 (tp30) cc_final: 0.7636 (pt0)
REVERT: F  539 LYS cc_start: 0.8870 (tttt) cc_final: 0.8569 (ttmt)
  outliers start: 16
  outliers final: 4
  residues processed: 167
  average time/residue: 0.6162
  time to fit residues: 110.6179
Evaluate side-chains
  149 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 145
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain C residue  466 THR
Chi-restraints excluded: chain C residue  525 LEU
Chi-restraints excluded: chain E residue  458 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 84 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 56 optimal weight:   10.0000
   chunk 112 optimal weight:    2.9990
   chunk 104 optimal weight:   10.0000
   chunk 127 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 72 optimal weight:   10.0000
   chunk 22 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    1.8986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.163190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.130549 restraints weight = 10223.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 1.34
r_work: 0.3266 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3151 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8792
moved from start:          0.1082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  11136  Z= 0.215
  Angle     :  0.561   6.037  15102  Z= 0.296
  Chirality :  0.043   0.185   1776
  Planarity :  0.004   0.030   1986
  Dihedral  :  4.808  19.247   1572
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 3.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.07 %
    Favored  : 99.93 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 16.49 %
    Favored  : 82.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.86 (0.21), residues: 1434
  helix:  1.81 (0.21), residues: 576
  sheet:  0.77 (0.25), residues: 378
  loop :  1.15 (0.26), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 357 
 TYR   0.007   0.001   TYR F 406 
 PHE   0.013   0.002   PHE B 534 
 HIS   0.005   0.001   HIS C 389 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 (11136)
  covalent geometry    : angle       0.56077 (15102)
  hydrogen bonds       : bond        0.05543 (  466)
  hydrogen bonds       : angle       4.68057 ( 1320)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 147
  time to evaluate  : 0.437 
Fit side-chains
REVERT: A  443 ASP cc_start: 0.8530 (t70) cc_final: 0.8319 (t70)
REVERT: C  539 LYS cc_start: 0.8845 (tttt) cc_final: 0.8561 (ttmt)
REVERT: D  443 ASP cc_start: 0.8538 (t70) cc_final: 0.8325 (t70)
REVERT: F  366 GLU cc_start: 0.7896 (tp30) cc_final: 0.7637 (pt0)
REVERT: F  539 LYS cc_start: 0.8862 (tttt) cc_final: 0.8540 (ttmt)
  outliers start: 17
  outliers final: 8
  residues processed: 157
  average time/residue: 0.6304
  time to fit residues: 106.5564
Evaluate side-chains
  156 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 148
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  525 LEU
Chi-restraints excluded: chain C residue  466 THR
Chi-restraints excluded: chain C residue  525 LEU
Chi-restraints excluded: chain D residue  525 LEU
Chi-restraints excluded: chain E residue  466 THR
Chi-restraints excluded: chain E residue  525 LEU
Chi-restraints excluded: chain F residue  525 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 110 optimal weight:    6.9990
   chunk 99 optimal weight:    0.5980
   chunk 112 optimal weight:    0.8980
   chunk 111 optimal weight:    0.9980
   chunk 100 optimal weight:    0.7980
   chunk 83 optimal weight:    6.9990
   chunk 70 optimal weight:    0.8980
   chunk 40 optimal weight:    9.9990
   chunk 74 optimal weight:    0.9990
   chunk 132 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
E 337 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.165277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.133380 restraints weight = 10214.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 1.32
r_work: 0.3247 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3128 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8780
moved from start:          0.1253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  11136  Z= 0.127
  Angle     :  0.476   5.298  15102  Z= 0.252
  Chirality :  0.040   0.189   1776
  Planarity :  0.003   0.028   1986
  Dihedral  :  4.430  17.363   1572
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 17.46 %
    Favored  : 81.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.05 (0.21), residues: 1434
  helix:  2.00 (0.22), residues: 582
  sheet:  0.71 (0.25), residues: 378
  loop :  1.33 (0.26), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 357 
 TYR   0.004   0.001   TYR F 405 
 PHE   0.013   0.002   PHE B 534 
 HIS   0.005   0.001   HIS B 389 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (11136)
  covalent geometry    : angle       0.47587 (15102)
  hydrogen bonds       : bond        0.04693 (  466)
  hydrogen bonds       : angle       4.46244 ( 1320)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 168
  time to evaluate  : 0.336 
Fit side-chains
REVERT: A  443 ASP cc_start: 0.8554 (t70) cc_final: 0.8303 (t70)
REVERT: B  502 ASP cc_start: 0.6869 (m-30) cc_final: 0.6026 (m-30)
REVERT: C  443 ASP cc_start: 0.8360 (t70) cc_final: 0.7930 (t0)
REVERT: C  539 LYS cc_start: 0.8881 (tttt) cc_final: 0.8572 (ttmt)
REVERT: D  443 ASP cc_start: 0.8580 (t70) cc_final: 0.8340 (t70)
REVERT: E  502 ASP cc_start: 0.6855 (m-30) cc_final: 0.5998 (m-30)
REVERT: F  443 ASP cc_start: 0.8380 (t70) cc_final: 0.7958 (t0)
REVERT: F  539 LYS cc_start: 0.8890 (tttt) cc_final: 0.8590 (ttmt)
  outliers start: 13
  outliers final: 8
  residues processed: 173
  average time/residue: 0.5646
  time to fit residues: 105.8376
Evaluate side-chains
  163 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 155
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  525 LEU
Chi-restraints excluded: chain C residue  525 LEU
Chi-restraints excluded: chain E residue  458 LEU
Chi-restraints excluded: chain E residue  466 THR
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  525 LEU
Chi-restraints excluded: chain F residue  525 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 82 optimal weight:    7.9990
   chunk 10 optimal weight:    3.9990
   chunk 103 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 128 optimal weight:    1.9990
   chunk 14 optimal weight:    7.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    2.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.163913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.130755 restraints weight = 9994.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 1.35
r_work: 0.3298 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3192 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8741
moved from start:          0.1188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049  11136  Z= 0.275
  Angle     :  0.618   5.659  15102  Z= 0.323
  Chirality :  0.045   0.205   1776
  Planarity :  0.004   0.030   1986
  Dihedral  :  4.974  19.918   1572
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 16.84 %
    Favored  : 80.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.70 (0.21), residues: 1434
  helix:  1.55 (0.21), residues: 582
  sheet:  0.74 (0.25), residues: 378
  loop :  1.19 (0.26), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 357 
 TYR   0.009   0.001   TYR D 405 
 PHE   0.013   0.002   PHE B 534 
 HIS   0.005   0.001   HIS C 389 

Details of bonding type rmsd
  covalent geometry    : bond        0.00651 (11136)
  covalent geometry    : angle       0.61793 (15102)
  hydrogen bonds       : bond        0.05910 (  466)
  hydrogen bonds       : angle       4.66142 ( 1320)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 153
  time to evaluate  : 0.445 
Fit side-chains
REVERT: C  443 ASP cc_start: 0.8295 (t70) cc_final: 0.7853 (t0)
REVERT: C  539 LYS cc_start: 0.8778 (tttt) cc_final: 0.8451 (ttmt)
REVERT: F  418 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7247 (mt-10)
REVERT: F  443 ASP cc_start: 0.8274 (t70) cc_final: 0.7882 (t0)
REVERT: F  539 LYS cc_start: 0.8768 (tttt) cc_final: 0.8429 (ttmt)
  outliers start: 26
  outliers final: 15
  residues processed: 167
  average time/residue: 0.6042
  time to fit residues: 108.6484
Evaluate side-chains
  163 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 147
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  417 THR
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  525 LEU
Chi-restraints excluded: chain C residue  466 THR
Chi-restraints excluded: chain C residue  525 LEU
Chi-restraints excluded: chain D residue  466 THR
Chi-restraints excluded: chain D residue  525 LEU
Chi-restraints excluded: chain E residue  466 THR
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  525 LEU
Chi-restraints excluded: chain F residue  418 GLU
Chi-restraints excluded: chain F residue  525 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 136 optimal weight:    0.4980
   chunk 89 optimal weight:    0.7980
   chunk 112 optimal weight:    2.9990
   chunk 129 optimal weight:    4.9990
   chunk 124 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 123 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 80 optimal weight:    3.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 452 ASN
E 337 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.167117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.134357 restraints weight = 9963.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 1.35
r_work: 0.3349 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3243 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8681
moved from start:          0.1343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  11136  Z= 0.123
  Angle     :  0.482   5.627  15102  Z= 0.255
  Chirality :  0.040   0.199   1776
  Planarity :  0.003   0.027   1986
  Dihedral  :  4.467  17.602   1572
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 18.17 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.96 (0.21), residues: 1434
  helix:  1.92 (0.22), residues: 582
  sheet:  0.61 (0.24), residues: 378
  loop :  1.34 (0.26), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 357 
 TYR   0.005   0.001   TYR F 405 
 PHE   0.013   0.002   PHE B 534 
 HIS   0.006   0.001   HIS E 389 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (11136)
  covalent geometry    : angle       0.48173 (15102)
  hydrogen bonds       : bond        0.04706 (  466)
  hydrogen bonds       : angle       4.42602 ( 1320)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 158
  time to evaluate  : 0.421 
Fit side-chains
REVERT: C  443 ASP cc_start: 0.8194 (t70) cc_final: 0.7775 (t0)
REVERT: C  539 LYS cc_start: 0.8791 (tttt) cc_final: 0.8479 (ttmt)
REVERT: F  443 ASP cc_start: 0.8226 (t70) cc_final: 0.7806 (t0)
REVERT: F  539 LYS cc_start: 0.8783 (tttt) cc_final: 0.8473 (ttmt)
  outliers start: 20
  outliers final: 14
  residues processed: 170
  average time/residue: 0.5903
  time to fit residues: 108.4663
Evaluate side-chains
  166 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 152
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  525 LEU
Chi-restraints excluded: chain C residue  466 THR
Chi-restraints excluded: chain C residue  525 LEU
Chi-restraints excluded: chain D residue  466 THR
Chi-restraints excluded: chain E residue  458 LEU
Chi-restraints excluded: chain E residue  466 THR
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  525 LEU
Chi-restraints excluded: chain F residue  466 THR
Chi-restraints excluded: chain F residue  525 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 33 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 116 optimal weight:    4.9990
   chunk 109 optimal weight:    2.9990
   chunk 73 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 129 optimal weight:    5.9990
   chunk 90 optimal weight:    1.9990
   chunk 112 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 452 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.165541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.132575 restraints weight = 9951.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 1.34
r_work: 0.3320 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8715
moved from start:          0.1330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  11136  Z= 0.185
  Angle     :  0.536   5.717  15102  Z= 0.281
  Chirality :  0.042   0.214   1776
  Planarity :  0.004   0.028   1986
  Dihedral  :  4.647  18.237   1572
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 18.52 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.87 (0.21), residues: 1434
  helix:  1.80 (0.22), residues: 582
  sheet:  0.62 (0.24), residues: 378
  loop :  1.32 (0.26), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 357 
 TYR   0.007   0.001   TYR F 406 
 PHE   0.013   0.002   PHE B 534 
 HIS   0.005   0.001   HIS B 389 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 (11136)
  covalent geometry    : angle       0.53631 (15102)
  hydrogen bonds       : bond        0.05178 (  466)
  hydrogen bonds       : angle       4.48088 ( 1320)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 150
  time to evaluate  : 0.422 
Fit side-chains
REVERT: C  443 ASP cc_start: 0.8258 (t70) cc_final: 0.7827 (t0)
REVERT: F  443 ASP cc_start: 0.8234 (t70) cc_final: 0.7878 (t0)
  outliers start: 21
  outliers final: 20
  residues processed: 160
  average time/residue: 0.5819
  time to fit residues: 100.8697
Evaluate side-chains
  168 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  452 ASN
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain B residue  417 THR
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  525 LEU
Chi-restraints excluded: chain C residue  466 THR
Chi-restraints excluded: chain C residue  502 ASP
Chi-restraints excluded: chain C residue  525 LEU
Chi-restraints excluded: chain D residue  466 THR
Chi-restraints excluded: chain D residue  525 LEU
Chi-restraints excluded: chain E residue  458 LEU
Chi-restraints excluded: chain E residue  466 THR
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  525 LEU
Chi-restraints excluded: chain F residue  466 THR
Chi-restraints excluded: chain F residue  502 ASP
Chi-restraints excluded: chain F residue  525 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 110 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9990
   chunk 82 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9990
   chunk 132 optimal weight:    2.9990
   chunk 137 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 70 optimal weight:    0.7980
   chunk 118 optimal weight:    0.6980
   chunk 77 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 452 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.166917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.134208 restraints weight = 9935.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 1.33
r_work: 0.3341 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3238 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.1408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  11136  Z= 0.132
  Angle     :  0.491   5.601  15102  Z= 0.259
  Chirality :  0.041   0.200   1776
  Planarity :  0.003   0.026   1986
  Dihedral  :  4.436  17.229   1572
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 18.43 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.04 (0.21), residues: 1434
  helix:  1.95 (0.22), residues: 582
  sheet:  0.74 (0.25), residues: 366
  loop :  1.35 (0.26), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 512 
 TYR   0.005   0.001   TYR F 405 
 PHE   0.013   0.002   PHE B 534 
 HIS   0.006   0.001   HIS E 389 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (11136)
  covalent geometry    : angle       0.49127 (15102)
  hydrogen bonds       : bond        0.04772 (  466)
  hydrogen bonds       : angle       4.40788 ( 1320)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 156
  time to evaluate  : 0.451 
Fit side-chains
REVERT: B  502 ASP cc_start: 0.6737 (m-30) cc_final: 0.5972 (m-30)
REVERT: C  443 ASP cc_start: 0.8217 (t70) cc_final: 0.7780 (t0)
REVERT: C  539 LYS cc_start: 0.8666 (ttmt) cc_final: 0.8457 (ttmt)
REVERT: E  502 ASP cc_start: 0.6744 (m-30) cc_final: 0.5971 (m-30)
REVERT: F  443 ASP cc_start: 0.8250 (t70) cc_final: 0.7826 (t0)
REVERT: F  539 LYS cc_start: 0.8668 (ttmt) cc_final: 0.8466 (ttmt)
  outliers start: 20
  outliers final: 16
  residues processed: 165
  average time/residue: 0.5842
  time to fit residues: 104.3261
Evaluate side-chains
  172 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 156
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain B residue  417 THR
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  525 LEU
Chi-restraints excluded: chain C residue  466 THR
Chi-restraints excluded: chain C residue  502 ASP
Chi-restraints excluded: chain C residue  525 LEU
Chi-restraints excluded: chain D residue  466 THR
Chi-restraints excluded: chain D residue  525 LEU
Chi-restraints excluded: chain E residue  466 THR
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  525 LEU
Chi-restraints excluded: chain F residue  466 THR
Chi-restraints excluded: chain F residue  502 ASP
Chi-restraints excluded: chain F residue  525 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 90 optimal weight:    0.8980
   chunk 24 optimal weight:   10.0000
   chunk 85 optimal weight:    2.9990
   chunk 93 optimal weight:    5.9990
   chunk 67 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 116 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 68 optimal weight:    0.7980
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
B 452 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.165369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.132319 restraints weight = 9934.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 1.34
r_work: 0.3317 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3211 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8717
moved from start:          0.1380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  11136  Z= 0.200
  Angle     :  0.552   5.798  15102  Z= 0.289
  Chirality :  0.043   0.234   1776
  Planarity :  0.004   0.028   1986
  Dihedral  :  4.679  18.510   1572
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 19.14 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.85 (0.21), residues: 1434
  helix:  1.76 (0.22), residues: 582
  sheet:  0.63 (0.24), residues: 378
  loop :  1.32 (0.26), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 357 
 TYR   0.007   0.001   TYR D 405 
 PHE   0.013   0.002   PHE B 534 
 HIS   0.005   0.001   HIS B 389 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 (11136)
  covalent geometry    : angle       0.55250 (15102)
  hydrogen bonds       : bond        0.05293 (  466)
  hydrogen bonds       : angle       4.49717 ( 1320)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 151
  time to evaluate  : 0.531 
Fit side-chains
REVERT: C  443 ASP cc_start: 0.8288 (t70) cc_final: 0.7848 (t0)
REVERT: C  539 LYS cc_start: 0.8693 (ttmt) cc_final: 0.8444 (ttmt)
REVERT: F  443 ASP cc_start: 0.8256 (t70) cc_final: 0.7899 (t0)
REVERT: F  539 LYS cc_start: 0.8697 (ttmt) cc_final: 0.8456 (ttmt)
  outliers start: 20
  outliers final: 18
  residues processed: 163
  average time/residue: 0.6039
  time to fit residues: 106.2713
Evaluate side-chains
  166 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 148
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain B residue  417 THR
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  525 LEU
Chi-restraints excluded: chain C residue  466 THR
Chi-restraints excluded: chain C residue  502 ASP
Chi-restraints excluded: chain C residue  525 LEU
Chi-restraints excluded: chain D residue  466 THR
Chi-restraints excluded: chain D residue  525 LEU
Chi-restraints excluded: chain E residue  411 LEU
Chi-restraints excluded: chain E residue  466 THR
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  525 LEU
Chi-restraints excluded: chain F residue  466 THR
Chi-restraints excluded: chain F residue  502 ASP
Chi-restraints excluded: chain F residue  525 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 104 optimal weight:    0.6980
   chunk 70 optimal weight:    0.5980
   chunk 94 optimal weight:    0.8980
   chunk 113 optimal weight:    0.6980
   chunk 40 optimal weight:   10.0000
   chunk 5 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 118 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 452 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.167766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.135094 restraints weight = 9995.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 1.34
r_work: 0.3346 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3242 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8684
moved from start:          0.1495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  11136  Z= 0.123
  Angle     :  0.485   5.706  15102  Z= 0.256
  Chirality :  0.041   0.237   1776
  Planarity :  0.003   0.026   1986
  Dihedral  :  4.339  16.919   1572
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 19.49 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.11 (0.21), residues: 1434
  helix:  1.99 (0.22), residues: 582
  sheet:  0.76 (0.25), residues: 366
  loop :  1.43 (0.26), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 357 
 TYR   0.006   0.001   TYR F 405 
 PHE   0.013   0.002   PHE B 534 
 HIS   0.005   0.001   HIS E 389 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (11136)
  covalent geometry    : angle       0.48536 (15102)
  hydrogen bonds       : bond        0.04653 (  466)
  hydrogen bonds       : angle       4.37625 ( 1320)

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

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

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2868 Ramachandran restraints generated.
    1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 159
  time to evaluate  : 0.433 
Fit side-chains
REVERT: B  502 ASP cc_start: 0.6707 (m-30) cc_final: 0.5946 (m-30)
REVERT: C  443 ASP cc_start: 0.8214 (t70) cc_final: 0.7790 (t0)
REVERT: C  539 LYS cc_start: 0.8679 (ttmt) cc_final: 0.8456 (ttmt)
REVERT: E  502 ASP cc_start: 0.6699 (m-30) cc_final: 0.5944 (m-30)
REVERT: F  443 ASP cc_start: 0.8222 (t70) cc_final: 0.7899 (t0)
REVERT: F  539 LYS cc_start: 0.8667 (ttmt) cc_final: 0.8452 (ttmt)
  outliers start: 16
  outliers final: 15
  residues processed: 168
  average time/residue: 0.5657
  time to fit residues: 102.9486
Evaluate side-chains
  170 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 155
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  466 THR
Chi-restraints excluded: chain B residue  417 THR
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  525 LEU
Chi-restraints excluded: chain C residue  466 THR
Chi-restraints excluded: chain C residue  502 ASP
Chi-restraints excluded: chain C residue  525 LEU
Chi-restraints excluded: chain D residue  466 THR
Chi-restraints excluded: chain E residue  466 THR
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  525 LEU
Chi-restraints excluded: chain F residue  466 THR
Chi-restraints excluded: chain F residue  502 ASP
Chi-restraints excluded: chain F residue  525 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 124 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 74 optimal weight:    0.7980
   chunk 122 optimal weight:    0.9990
   chunk 118 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 8 optimal weight:    7.9990
   chunk 59 optimal weight:    1.9990
   chunk 107 optimal weight:    0.6980
   chunk 104 optimal weight:    6.9990
   overall best weight:    1.0384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.163821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.130515 restraints weight = 10039.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 1.36
r_work: 0.3336 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3231 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8695
moved from start:          0.1525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  11136  Z= 0.143
  Angle     :  0.501   5.906  15102  Z= 0.263
  Chirality :  0.041   0.229   1776
  Planarity :  0.003   0.027   1986
  Dihedral  :  4.389  16.384   1572
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.07 %
    Favored  : 99.93 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 19.66 %
    Favored  : 78.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.11 (0.21), residues: 1434
  helix:  1.97 (0.22), residues: 582
  sheet:  0.77 (0.25), residues: 366
  loop :  1.44 (0.26), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 357 
 TYR   0.006   0.001   TYR F 405 
 PHE   0.013   0.002   PHE B 534 
 HIS   0.005   0.001   HIS E 389 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (11136)
  covalent geometry    : angle       0.50108 (15102)
  hydrogen bonds       : bond        0.04811 (  466)
  hydrogen bonds       : angle       4.38715 ( 1320)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3970.84 seconds
wall clock time: 68 minutes 28.94 seconds (4108.94 seconds total)