Starting phenix.real_space_refine
on Thu Mar  5 05:59:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7bct_12143/03_2026/7bct_12143.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7bct_12143/03_2026/7bct_12143.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.37
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7bct_12143/03_2026/7bct_12143.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7bct_12143/03_2026/7bct_12143.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7bct_12143/03_2026/7bct_12143.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7bct_12143/03_2026/7bct_12143.cif"
  }
  resolution = 3.37
  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=   0.009
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: 5
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    6399      2.51       5
     N    1623      2.21       5
     O    1722      1.98       5
     H   10299      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 69 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: 20091
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 6697
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 442, 6697
          Classifications: {'peptide': 442}
          Link IDs: {'PTRANS': 17, 'TRANS': 424}
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 6.90, per 1000 atoms: 0.34
  Number of scatterers: 20091
  At special positions: 0
  Unit cell: (104.236, 105.248, 76.912, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      48     16.00
     O    1722      8.00
     N    1623      7.00
     C    6399      6.00
     H   10299      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.86
  Conformation dependent library (CDL) restraints added in 543.3 milliseconds
  

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2394

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 3 sheets defined
      82.3% alpha, 3.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 47 through 52
    Processing helix  chain 'A' and resid 52 through 75
    Processing helix  chain 'A' and resid 77 through 117
      Proline residue:  A  83  - end of helix
      Proline residue:  A  92  - end of helix
      removed outlier: 3.899A  pdb=" N   ILE A 103 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      removed outlier: 4.912A  pdb=" N   LEU A 105 " --> pdb=" O   ARG A 101 " (cutoff:3.500A)
      Proline residue:  A 106  - end of helix
      removed outlier: 3.649A  pdb=" N   ALA A 117 " --> pdb=" O   ILE A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 154
      removed outlier: 3.632A  pdb=" N   GLN A 154 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 163
    Processing helix  chain 'A' and resid 164 through 169
    Processing helix  chain 'A' and resid 179 through 191
    Processing helix  chain 'A' and resid 195 through 200
    Processing helix  chain 'A' and resid 230 through 248
    Processing helix  chain 'A' and resid 249 through 291
      removed outlier: 3.628A  pdb=" N   GLU A 253 " --> pdb=" O   GLY A 249 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   LEU A 254 " --> pdb=" O   PRO A 250 " (cutoff:3.500A)
      removed outlier: 4.702A  pdb=" N   LEU A 255 " --> pdb=" O   GLU A 251 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   TRP A 272 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
      Proline residue:  A 278  - end of helix
    Processing helix  chain 'A' and resid 296 through 319
      removed outlier: 6.493A  pdb=" N   LYS A 304 " --> pdb=" O   ALA A 300 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   TYR A 305 " --> pdb=" O   ARG A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 330
    Processing helix  chain 'A' and resid 332 through 339
    Processing helix  chain 'A' and resid 340 through 351
    Processing helix  chain 'A' and resid 356 through 367
    Processing helix  chain 'A' and resid 371 through 383
      Proline residue:  A 380  - end of helix
    Processing helix  chain 'A' and resid 387 through 404
    Processing helix  chain 'A' and resid 411 through 428
      removed outlier: 4.322A  pdb=" N   VAL A 426 " --> pdb=" O   THR A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 437 through 447
      removed outlier: 4.315A  pdb=" N   ILE A 441 " --> pdb=" O   LEU A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 458
      removed outlier: 3.513A  pdb=" N   ILE A 456 " --> pdb=" O   ILE A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 488
      removed outlier: 3.976A  pdb=" N   VAL A 463 " --> pdb=" O   VAL A 459 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   ARG A 465 " --> pdb=" O   TRP A 461 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   SER A 466 " --> pdb=" O   LEU A 462 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 48 through 52
    Processing helix  chain 'B' and resid 52 through 75
    Processing helix  chain 'B' and resid 77 through 117
      Proline residue:  B  83  - end of helix
      Proline residue:  B  92  - end of helix
      removed outlier: 3.898A  pdb=" N   ILE B 103 " --> pdb=" O   LEU B  99 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   LEU B 105 " --> pdb=" O   ARG B 101 " (cutoff:3.500A)
      Proline residue:  B 106  - end of helix
      removed outlier: 3.649A  pdb=" N   ALA B 117 " --> pdb=" O   ILE B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 154
      removed outlier: 3.631A  pdb=" N   GLN B 154 " --> pdb=" O   ALA B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 163
    Processing helix  chain 'B' and resid 164 through 169
    Processing helix  chain 'B' and resid 179 through 191
    Processing helix  chain 'B' and resid 195 through 200
    Processing helix  chain 'B' and resid 230 through 248
    Processing helix  chain 'B' and resid 249 through 291
      removed outlier: 3.629A  pdb=" N   GLU B 253 " --> pdb=" O   GLY B 249 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   LEU B 254 " --> pdb=" O   PRO B 250 " (cutoff:3.500A)
      removed outlier: 4.701A  pdb=" N   LEU B 255 " --> pdb=" O   GLU B 251 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   TRP B 272 " --> pdb=" O   VAL B 268 " (cutoff:3.500A)
      Proline residue:  B 278  - end of helix
    Processing helix  chain 'B' and resid 296 through 319
      removed outlier: 6.493A  pdb=" N   LYS B 304 " --> pdb=" O   ALA B 300 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   TYR B 305 " --> pdb=" O   ARG B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 330
    Processing helix  chain 'B' and resid 332 through 339
    Processing helix  chain 'B' and resid 340 through 351
    Processing helix  chain 'B' and resid 356 through 367
    Processing helix  chain 'B' and resid 371 through 383
      Proline residue:  B 380  - end of helix
    Processing helix  chain 'B' and resid 387 through 404
    Processing helix  chain 'B' and resid 411 through 428
      removed outlier: 4.322A  pdb=" N   VAL B 426 " --> pdb=" O   THR B 422 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 437 through 447
      removed outlier: 4.314A  pdb=" N   ILE B 441 " --> pdb=" O   LEU B 437 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 458
      removed outlier: 3.513A  pdb=" N   ILE B 456 " --> pdb=" O   ILE B 453 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 488
      removed outlier: 3.976A  pdb=" N   VAL B 463 " --> pdb=" O   VAL B 459 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   ARG B 465 " --> pdb=" O   TRP B 461 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   SER B 466 " --> pdb=" O   LEU B 462 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 48 through 52
    Processing helix  chain 'C' and resid 52 through 75
    Processing helix  chain 'C' and resid 77 through 117
      Proline residue:  C  83  - end of helix
      Proline residue:  C  92  - end of helix
      removed outlier: 3.899A  pdb=" N   ILE C 103 " --> pdb=" O   LEU C  99 " (cutoff:3.500A)
      removed outlier: 4.912A  pdb=" N   LEU C 105 " --> pdb=" O   ARG C 101 " (cutoff:3.500A)
      Proline residue:  C 106  - end of helix
      removed outlier: 3.649A  pdb=" N   ALA C 117 " --> pdb=" O   ILE C 113 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 120 through 154
      removed outlier: 3.632A  pdb=" N   GLN C 154 " --> pdb=" O   ALA C 150 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 159 through 163
    Processing helix  chain 'C' and resid 164 through 169
    Processing helix  chain 'C' and resid 179 through 191
    Processing helix  chain 'C' and resid 195 through 200
    Processing helix  chain 'C' and resid 230 through 248
    Processing helix  chain 'C' and resid 249 through 291
      removed outlier: 3.628A  pdb=" N   GLU C 253 " --> pdb=" O   GLY C 249 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   LEU C 254 " --> pdb=" O   PRO C 250 " (cutoff:3.500A)
      removed outlier: 4.702A  pdb=" N   LEU C 255 " --> pdb=" O   GLU C 251 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   TRP C 272 " --> pdb=" O   VAL C 268 " (cutoff:3.500A)
      Proline residue:  C 278  - end of helix
    Processing helix  chain 'C' and resid 296 through 319
      removed outlier: 6.493A  pdb=" N   LYS C 304 " --> pdb=" O   ALA C 300 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   TYR C 305 " --> pdb=" O   ARG C 301 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 319 through 330
    Processing helix  chain 'C' and resid 332 through 339
    Processing helix  chain 'C' and resid 340 through 351
    Processing helix  chain 'C' and resid 352 through 367
      removed outlier: 3.511A  pdb=" N   LEU C 357 " --> pdb=" O   SER C 353 " (cutoff:3.500A)
      Proline residue:  C 358  - end of helix
    Processing helix  chain 'C' and resid 371 through 383
      Proline residue:  C 380  - end of helix
    Processing helix  chain 'C' and resid 387 through 404
    Processing helix  chain 'C' and resid 411 through 428
      removed outlier: 4.321A  pdb=" N   VAL C 426 " --> pdb=" O   THR C 422 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 437 through 447
      removed outlier: 4.314A  pdb=" N   ILE C 441 " --> pdb=" O   LEU C 437 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 452 through 458
      removed outlier: 3.513A  pdb=" N   ILE C 456 " --> pdb=" O   ILE C 453 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 459 through 488
      removed outlier: 3.975A  pdb=" N   VAL C 463 " --> pdb=" O   VAL C 459 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   ARG C 465 " --> pdb=" O   TRP C 461 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   SER C 466 " --> pdb=" O   LEU C 462 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 209
      removed outlier: 3.659A  pdb=" N   SER A 205 " --> pdb=" O   GLN A 224 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 202 through 209
      removed outlier: 3.659A  pdb=" N   SER B 205 " --> pdb=" O   GLN B 224 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 202 through 209
      removed outlier: 3.658A  pdb=" N   SER C 205 " --> pdb=" O   GLN C 224 " (cutoff:3.500A)

    769 hydrogen bonds defined for protein.
    2253 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: 4.50

  Time building geometry restraints manager: 2.60 seconds

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

  Histogram of bond lengths:
        0.83 -     1.02: 10278
        1.02 -     1.22: 24
        1.22 -     1.42: 3930
        1.42 -     1.61: 5961
        1.61 -     1.81: 75
  Bond restraints: 20268
  Sorted by residual:
  bond pdb=" N   LEU C 105 "
       pdb=" CA  LEU C 105 "
    ideal  model  delta    sigma   weight residual
    1.463  1.444  0.019 6.90e-03 2.10e+04 7.93e+00
  bond pdb=" N   LEU A 105 "
       pdb=" CA  LEU A 105 "
    ideal  model  delta    sigma   weight residual
    1.463  1.444  0.019 6.90e-03 2.10e+04 7.61e+00
  bond pdb=" N   LEU B 105 "
       pdb=" CA  LEU B 105 "
    ideal  model  delta    sigma   weight residual
    1.463  1.444  0.019 6.90e-03 2.10e+04 7.57e+00
  bond pdb=" CD  LYS A 247 "
       pdb=" HD3 LYS A 247 "
    ideal  model  delta    sigma   weight residual
    0.970  0.919  0.051 2.00e-02 2.50e+03 6.49e+00
  bond pdb=" CD  LYS C 247 "
       pdb=" HD3 LYS C 247 "
    ideal  model  delta    sigma   weight residual
    0.970  0.919  0.051 2.00e-02 2.50e+03 6.49e+00
  ... (remaining 20263 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.58: 36771
        6.58 -    13.16: 63
       13.16 -    19.74: 0
       19.74 -    26.31: 30
       26.31 -    32.89: 15
  Bond angle restraints: 36879
  Sorted by residual:
  angle pdb=" CD1 LEU A  54 "
        pdb=" CG  LEU A  54 "
        pdb=" HG  LEU A  54 "
      ideal   model   delta    sigma   weight residual
     108.00   75.11   32.89 3.00e+00 1.11e-01 1.20e+02
  angle pdb=" CD2 LEU C  54 "
        pdb=" CG  LEU C  54 "
        pdb=" HG  LEU C  54 "
      ideal   model   delta    sigma   weight residual
     108.00   75.11   32.89 3.00e+00 1.11e-01 1.20e+02
  angle pdb=" CD1 LEU B  54 "
        pdb=" CG  LEU B  54 "
        pdb=" HG  LEU B  54 "
      ideal   model   delta    sigma   weight residual
     108.00   75.12   32.88 3.00e+00 1.11e-01 1.20e+02
  angle pdb=" CD2 LEU B  54 "
        pdb=" CG  LEU B  54 "
        pdb=" HG  LEU B  54 "
      ideal   model   delta    sigma   weight residual
     108.00   75.13   32.87 3.00e+00 1.11e-01 1.20e+02
  angle pdb=" CD1 LEU C  54 "
        pdb=" CG  LEU C  54 "
        pdb=" HG  LEU C  54 "
      ideal   model   delta    sigma   weight residual
     108.00   75.13   32.87 3.00e+00 1.11e-01 1.20e+02
  ... (remaining 36874 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.12: 8234
       17.12 -    34.25: 768
       34.25 -    51.37: 257
       51.37 -    68.50: 143
       68.50 -    85.62: 27
  Dihedral angle restraints: 9429
    sinusoidal: 5151
      harmonic: 4278
  Sorted by residual:
  dihedral pdb=" CA  ASN A 190 "
           pdb=" C   ASN A 190 "
           pdb=" N   ILE A 191 "
           pdb=" CA  ILE A 191 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.75   26.25     0      5.00e+00 4.00e-02 2.76e+01
  dihedral pdb=" CA  ASN B 190 "
           pdb=" C   ASN B 190 "
           pdb=" N   ILE B 191 "
           pdb=" CA  ILE B 191 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.76   26.24     0      5.00e+00 4.00e-02 2.75e+01
  dihedral pdb=" CA  ASN C 190 "
           pdb=" C   ASN C 190 "
           pdb=" N   ILE C 191 "
           pdb=" CA  ILE C 191 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.81   26.19     0      5.00e+00 4.00e-02 2.74e+01
  ... (remaining 9426 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.363: 1680
       0.363 -    0.726: 6
       0.726 -    1.089: 0
       1.089 -    1.452: 3
       1.452 -    1.815: 9
  Chirality restraints: 1698
  Sorted by residual:
  chirality pdb=" CG  LEU B 149 "
            pdb=" CB  LEU B 149 "
            pdb=" CD1 LEU B 149 "
            pdb=" CD2 LEU B 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.77   -1.82 2.00e-01 2.50e+01 8.24e+01
  chirality pdb=" CG  LEU A 149 "
            pdb=" CB  LEU A 149 "
            pdb=" CD1 LEU A 149 "
            pdb=" CD2 LEU A 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.77   -1.81 2.00e-01 2.50e+01 8.23e+01
  chirality pdb=" CG  LEU C 149 "
            pdb=" CB  LEU C 149 "
            pdb=" CD1 LEU C 149 "
            pdb=" CD2 LEU C 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.78   -1.81 2.00e-01 2.50e+01 8.20e+01
  ... (remaining 1695 not shown)

  Planarity restraints: 2967
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 325 "    0.033 2.00e-02 2.50e+03   1.45e-02 6.31e+00
        pdb=" CG  TYR A 325 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 325 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 325 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 325 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 325 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 325 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 325 "    0.011 2.00e-02 2.50e+03
        pdb=" HD1 TYR A 325 "   -0.004 2.00e-02 2.50e+03
        pdb=" HD2 TYR A 325 "   -0.000 2.00e-02 2.50e+03
        pdb=" HE1 TYR A 325 "    0.002 2.00e-02 2.50e+03
        pdb=" HE2 TYR A 325 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 325 "    0.033 2.00e-02 2.50e+03   1.45e-02 6.28e+00
        pdb=" CG  TYR B 325 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 325 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 325 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 325 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 325 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 325 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 325 "    0.011 2.00e-02 2.50e+03
        pdb=" HD1 TYR B 325 "   -0.004 2.00e-02 2.50e+03
        pdb=" HD2 TYR B 325 "    0.000 2.00e-02 2.50e+03
        pdb=" HE1 TYR B 325 "    0.002 2.00e-02 2.50e+03
        pdb=" HE2 TYR B 325 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 325 "    0.033 2.00e-02 2.50e+03   1.44e-02 6.18e+00
        pdb=" CG  TYR C 325 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 325 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 325 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 325 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 325 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 325 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR C 325 "    0.011 2.00e-02 2.50e+03
        pdb=" HD1 TYR C 325 "   -0.004 2.00e-02 2.50e+03
        pdb=" HD2 TYR C 325 "   -0.000 2.00e-02 2.50e+03
        pdb=" HE1 TYR C 325 "    0.002 2.00e-02 2.50e+03
        pdb=" HE2 TYR C 325 "    0.002 2.00e-02 2.50e+03
  ... (remaining 2964 not shown)

  Histogram of nonbonded interaction distances:
        1.69 -     2.27: 2755
        2.27 -     2.85: 46035
        2.85 -     3.43: 54784
        3.43 -     4.02: 71060
        4.02 -     4.60: 111631
  Nonbonded interactions: 286265
  Sorted by model distance:
  nonbonded pdb="HD21 ASN A 195 "
            pdb=" O   ALA B 200 "
     model   vdw
     1.687 2.450
  nonbonded pdb=" OG  SER B 198 "
            pdb=" HE  ARG B 202 "
     model   vdw
     1.706 2.450
  nonbonded pdb=" OG  SER A 198 "
            pdb=" HE  ARG A 202 "
     model   vdw
     1.707 2.450
  nonbonded pdb=" OG  SER C 198 "
            pdb=" HE  ARG C 202 "
     model   vdw
     1.707 2.450
  nonbonded pdb="HH12 ARG A 202 "
            pdb=" OE2 GLU B 227 "
     model   vdw
     1.718 2.450
  ... (remaining 286260 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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:             0.540
  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:             0.100
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.060
  Set scattering table:                    0.050
  Process input model:                     22.850
  Find NCS groups from input model:        0.140
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6519
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      :  0.009   0.069   9969  Z= 0.366
  Angle     :  1.151  11.386  13590  Z= 0.581
  Chirality :  0.146   1.815   1698
  Planarity :  0.007   0.060   1695
  Dihedral  : 13.354  83.516   3468
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  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 are not related in a simple way.
  whole: -0.74 (0.22), residues: 1320
  helix:  0.16 (0.15), residues: 993
  sheet: -2.88 (0.55), residues: 42
  loop : -2.09 (0.35), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 189 
 TYR   0.035   0.005   TYR A 325 
 PHE   0.029   0.004   PHE B 258 
 TRP   0.015   0.002   TRP C 130 
 HIS   0.011   0.003   HIS C 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00873 ( 9969)
  covalent geometry    : angle       1.15100 (13590)
  hydrogen bonds       : bond        0.12240 (  769)
  hydrogen bonds       : angle       5.86277 ( 2253)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 MET cc_start: 0.6343 (mmt) cc_final: 0.6142 (mmt)
REVERT: B  361 MET cc_start: 0.8102 (mtp) cc_final: 0.7884 (mtp)
REVERT: C  267 MET cc_start: 0.6703 (mmt) cc_final: 0.6469 (mmt)
REVERT: C  442 ILE cc_start: 0.3848 (mt) cc_final: 0.3457 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 188
  average time/residue: 0.1865
  time to fit residues: 52.2064
Evaluate side-chains
  152 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    0.5980
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    0.8980
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    3.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 386 ASN
A 403 GLN
B 386 ASN
B 403 GLN
B 484 ASN
C 386 ASN
C 403 GLN
C 484 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.220484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.172188 restraints weight = 25641.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.3910 rms_B_bonded: 1.83
r_work: 0.3742 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3602 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6954
moved from start:          0.1670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9969  Z= 0.154
  Angle     :  0.771  11.616  13590  Z= 0.355
  Chirality :  0.165   1.833   1698
  Planarity :  0.005   0.045   1695
  Dihedral  :  4.366  23.517   1398
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  4.18 %
    Favored  : 95.34 %
  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 are not related in a simple way.
  whole:  0.37 (0.23), residues: 1320
  helix:  1.01 (0.16), residues: 993
  sheet: -2.74 (0.60), residues: 42
  loop : -1.88 (0.35), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 202 
 TYR   0.018   0.002   TYR B 485 
 PHE   0.023   0.002   PHE B 393 
 TRP   0.004   0.001   TRP B 272 
 HIS   0.004   0.001   HIS A 452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 9969)
  covalent geometry    : angle       0.77113 (13590)
  hydrogen bonds       : bond        0.04687 (  769)
  hydrogen bonds       : angle       4.85602 ( 2253)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 178
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 LEU cc_start: 0.8022 (mt) cc_final: 0.7794 (mt)
REVERT: B  134 PHE cc_start: 0.7457 (t80) cc_final: 0.7225 (t80)
REVERT: B  361 MET cc_start: 0.8406 (mtp) cc_final: 0.8017 (mtp)
REVERT: C  267 MET cc_start: 0.7566 (mmt) cc_final: 0.6758 (mmp)
REVERT: C  305 TYR cc_start: 0.8214 (t80) cc_final: 0.7800 (t80)
  outliers start: 5
  outliers final: 5
  residues processed: 182
  average time/residue: 0.1942
  time to fit residues: 52.6118
Evaluate side-chains
  159 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 154
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain B residue  484 ASN
Chi-restraints excluded: chain C residue  379 LEU
Chi-restraints excluded: chain C residue  484 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 85 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   chunk 59 optimal weight:    2.9990
   chunk 131 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 52 optimal weight:    3.9990
   chunk 125 optimal weight:    3.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 403 GLN
B 403 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.206337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.155054 restraints weight = 26348.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.3736 rms_B_bonded: 1.86
r_work: 0.3554 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3424 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7189
moved from start:          0.2850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   9969  Z= 0.210
  Angle     :  0.790  12.522  13590  Z= 0.371
  Chirality :  0.165   1.860   1698
  Planarity :  0.005   0.050   1695
  Dihedral  :  4.420  25.501   1398
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  8.07 %
    Favored  : 91.35 %
  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 are not related in a simple way.
  whole:  0.13 (0.23), residues: 1320
  helix:  0.86 (0.16), residues: 1005
  sheet: -2.75 (0.62), residues: 42
  loop : -2.18 (0.35), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 101 
 TYR   0.030   0.003   TYR C 485 
 PHE   0.028   0.002   PHE B 393 
 TRP   0.005   0.001   TRP A 275 
 HIS   0.004   0.002   HIS B 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 ( 9969)
  covalent geometry    : angle       0.78971 (13590)
  hydrogen bonds       : bond        0.05019 (  769)
  hydrogen bonds       : angle       4.89158 ( 2253)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 158
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  141 LEU cc_start: 0.7218 (tt) cc_final: 0.7010 (tt)
REVERT: B  361 MET cc_start: 0.8545 (mtp) cc_final: 0.8241 (mtp)
REVERT: B  475 ASP cc_start: 0.7066 (m-30) cc_final: 0.6844 (m-30)
REVERT: C  311 LEU cc_start: 0.7747 (mm) cc_final: 0.7519 (mm)
  outliers start: 6
  outliers final: 4
  residues processed: 161
  average time/residue: 0.2152
  time to fit residues: 49.7312
Evaluate side-chains
  148 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 144
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain C residue  356 THR
Chi-restraints excluded: chain C residue  379 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 81 optimal weight:    5.9990
   chunk 90 optimal weight:    6.9990
   chunk 96 optimal weight:    5.9990
   chunk 121 optimal weight:    0.8980
   chunk 116 optimal weight:    2.9990
   chunk 34 optimal weight:    6.9990
   chunk 102 optimal weight:    0.6980
   chunk 27 optimal weight:    6.9990
   chunk 85 optimal weight:    4.9990
   chunk 124 optimal weight:    1.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 403 GLN
A 406 GLN
A 484 ASN
C 224 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.208364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.155784 restraints weight = 26492.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.3730 rms_B_bonded: 2.02
r_work: 0.3552 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3406 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7193
moved from start:          0.3316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9969  Z= 0.156
  Angle     :  0.750  13.537  13590  Z= 0.341
  Chirality :  0.165   1.839   1698
  Planarity :  0.004   0.044   1695
  Dihedral  :  4.175  23.487   1398
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 10.11 %
    Favored  : 89.02 %
  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 are not related in a simple way.
  whole:  0.43 (0.23), residues: 1320
  helix:  1.08 (0.16), residues: 1002
  sheet: -2.76 (0.61), residues: 42
  loop : -2.07 (0.35), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 189 
 TYR   0.013   0.002   TYR A 485 
 PHE   0.021   0.001   PHE B 393 
 TRP   0.006   0.001   TRP A 275 
 HIS   0.004   0.001   HIS A 452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 9969)
  covalent geometry    : angle       0.74991 (13590)
  hydrogen bonds       : bond        0.04338 (  769)
  hydrogen bonds       : angle       4.71562 ( 2253)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 173
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  141 LEU cc_start: 0.7128 (tt) cc_final: 0.6918 (tt)
REVERT: A  352 SER cc_start: 0.8184 (t) cc_final: 0.7829 (m)
REVERT: B   53 LEU cc_start: 0.8487 (tp) cc_final: 0.8126 (tt)
REVERT: B  361 MET cc_start: 0.8596 (mtp) cc_final: 0.8260 (mtp)
REVERT: B  475 ASP cc_start: 0.7084 (m-30) cc_final: 0.6869 (m-30)
REVERT: C  297 LEU cc_start: 0.4602 (pt) cc_final: 0.4369 (tp)
  outliers start: 9
  outliers final: 7
  residues processed: 178
  average time/residue: 0.1931
  time to fit residues: 50.6413
Evaluate side-chains
  165 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 158
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  406 GLN
Chi-restraints excluded: chain A residue  484 ASN
Chi-restraints excluded: chain C residue  224 GLN
Chi-restraints excluded: chain C residue  356 THR
Chi-restraints excluded: chain C residue  379 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 90 optimal weight:    7.9990
   chunk 32 optimal weight:    0.8980
   chunk 96 optimal weight:    3.9990
   chunk 44 optimal weight:    9.9990
   chunk 108 optimal weight:    1.9990
   chunk 85 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 112 optimal weight:    3.9990
   chunk 55 optimal weight:   10.0000
   chunk 24 optimal weight:    4.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 403 GLN
A 407 GLN
B 224 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.204942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.151814 restraints weight = 26544.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3668 rms_B_bonded: 2.66
r_work: 0.3465 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7170
moved from start:          0.3819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9969  Z= 0.203
  Angle     :  0.777  10.673  13590  Z= 0.361
  Chirality :  0.167   1.922   1698
  Planarity :  0.004   0.044   1695
  Dihedral  :  4.298  24.303   1398
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 11.86 %
    Favored  : 87.17 %
  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 are not related in a simple way.
  whole:  0.27 (0.23), residues: 1320
  helix:  0.98 (0.16), residues: 1002
  sheet: -2.76 (0.67), residues: 42
  loop : -2.17 (0.34), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 488 
 TYR   0.020   0.002   TYR A 485 
 PHE   0.020   0.002   PHE B 393 
 TRP   0.007   0.001   TRP A 275 
 HIS   0.003   0.001   HIS A 452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 ( 9969)
  covalent geometry    : angle       0.77720 (13590)
  hydrogen bonds       : bond        0.04636 (  769)
  hydrogen bonds       : angle       4.78244 ( 2253)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 158
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  352 SER cc_start: 0.8272 (t) cc_final: 0.7918 (m)
REVERT: B  361 MET cc_start: 0.8620 (mtp) cc_final: 0.8339 (mtp)
REVERT: B  475 ASP cc_start: 0.6846 (m-30) cc_final: 0.6645 (m-30)
REVERT: C  297 LEU cc_start: 0.4603 (pt) cc_final: 0.4370 (tp)
  outliers start: 10
  outliers final: 6
  residues processed: 165
  average time/residue: 0.1980
  time to fit residues: 48.3146
Evaluate side-chains
  155 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 149
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain B residue  224 GLN
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain C residue  356 THR
Chi-restraints excluded: chain C residue  379 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 117 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 87 optimal weight:    5.9990
   chunk 107 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 11 optimal weight:    9.9990
   chunk 64 optimal weight:    0.5980
   chunk 112 optimal weight:    0.4980
   chunk 120 optimal weight:    0.9990
   chunk 71 optimal weight:    3.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A 224 GLN
B 407 GLN
B 484 ASN
C 224 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.206062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.161242 restraints weight = 26222.604|
|-----------------------------------------------------------------------------|
r_work (start): 0.3820 rms_B_bonded: 1.83
r_work: 0.3528 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7173
moved from start:          0.4012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9969  Z= 0.137
  Angle     :  0.734  10.819  13590  Z= 0.333
  Chirality :  0.167   2.054   1698
  Planarity :  0.004   0.042   1695
  Dihedral  :  4.088  22.259   1398
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 12.93 %
    Favored  : 86.20 %
  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 are not related in a simple way.
  whole:  0.66 (0.23), residues: 1320
  helix:  1.27 (0.16), residues: 1002
  sheet: -2.90 (0.65), residues: 42
  loop : -2.03 (0.35), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 189 
 TYR   0.014   0.002   TYR A 485 
 PHE   0.016   0.001   PHE B 393 
 TRP   0.006   0.001   TRP C 275 
 HIS   0.002   0.001   HIS A 452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 9969)
  covalent geometry    : angle       0.73390 (13590)
  hydrogen bonds       : bond        0.04140 (  769)
  hydrogen bonds       : angle       4.63767 ( 2253)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 168
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  352 SER cc_start: 0.8239 (t) cc_final: 0.7936 (m)
REVERT: A  393 PHE cc_start: 0.7664 (OUTLIER) cc_final: 0.7431 (p90)
REVERT: B  104 ILE cc_start: 0.7514 (pt) cc_final: 0.7133 (pt)
REVERT: B  361 MET cc_start: 0.8624 (mtp) cc_final: 0.8387 (mtp)
REVERT: B  377 PHE cc_start: 0.8440 (t80) cc_final: 0.7796 (t80)
REVERT: C  352 SER cc_start: 0.7709 (t) cc_final: 0.7473 (m)
REVERT: C  475 ASP cc_start: 0.7767 (m-30) cc_final: 0.7466 (m-30)
  outliers start: 9
  outliers final: 7
  residues processed: 174
  average time/residue: 0.1680
  time to fit residues: 43.7573
Evaluate side-chains
  165 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 157
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  224 GLN
Chi-restraints excluded: chain A residue  393 PHE
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain B residue  484 ASN
Chi-restraints excluded: chain C residue  224 GLN
Chi-restraints excluded: chain C residue  356 THR
Chi-restraints excluded: chain C residue  379 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 25 optimal weight:   10.0000
   chunk 46 optimal weight:    7.9990
   chunk 42 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 96 optimal weight:    0.7980
   chunk 129 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   chunk 38 optimal weight:    8.9990
   chunk 126 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
C 407 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.203582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.151233 restraints weight = 26208.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.3700 rms_B_bonded: 1.84
r_work: 0.3518 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3376 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7229
moved from start:          0.4252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9969  Z= 0.166
  Angle     :  0.751  11.463  13590  Z= 0.344
  Chirality :  0.165   1.789   1698
  Planarity :  0.004   0.041   1695
  Dihedral  :  4.145  22.557   1398
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 13.99 %
    Favored  : 84.94 %
  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 are not related in a simple way.
  whole:  0.62 (0.23), residues: 1320
  helix:  1.24 (0.16), residues: 1002
  sheet: -2.87 (0.68), residues: 42
  loop : -2.07 (0.35), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 189 
 TYR   0.025   0.002   TYR B 485 
 PHE   0.016   0.001   PHE B 393 
 TRP   0.007   0.001   TRP C 275 
 HIS   0.002   0.001   HIS A 452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 9969)
  covalent geometry    : angle       0.75063 (13590)
  hydrogen bonds       : bond        0.04288 (  769)
  hydrogen bonds       : angle       4.66802 ( 2253)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 162
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  352 SER cc_start: 0.8149 (t) cc_final: 0.7843 (m)
REVERT: A  393 PHE cc_start: 0.7649 (OUTLIER) cc_final: 0.7436 (p90)
REVERT: B  104 ILE cc_start: 0.7506 (pt) cc_final: 0.7148 (pt)
REVERT: B  224 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7243 (pp30)
REVERT: B  361 MET cc_start: 0.8668 (mtp) cc_final: 0.8424 (mtp)
REVERT: C   81 LEU cc_start: 0.5942 (OUTLIER) cc_final: 0.5583 (mp)
  outliers start: 11
  outliers final: 8
  residues processed: 168
  average time/residue: 0.1929
  time to fit residues: 47.8455
Evaluate side-chains
  167 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 156
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  393 PHE
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain B residue  224 GLN
Chi-restraints excluded: chain B residue  340 ILE
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue  311 LEU
Chi-restraints excluded: chain C residue  356 THR
Chi-restraints excluded: chain C residue  379 LEU
Chi-restraints excluded: chain C residue  437 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 61 optimal weight:    8.9990
   chunk 76 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
A 386 ASN
A 484 ASN
C 224 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.201752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.153522 restraints weight = 26195.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3735 rms_B_bonded: 2.08
r_work: 0.3485 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3348 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7299
moved from start:          0.4709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9969  Z= 0.168
  Angle     :  0.750  12.940  13590  Z= 0.345
  Chirality :  0.163   1.755   1698
  Planarity :  0.004   0.042   1695
  Dihedral  :  4.137  22.659   1398
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 13.99 %
    Favored  : 84.55 %
  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 are not related in a simple way.
  whole:  0.66 (0.23), residues: 1320
  helix:  1.26 (0.16), residues: 1005
  sheet: -2.66 (0.70), residues: 42
  loop : -2.10 (0.35), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 465 
 TYR   0.013   0.002   TYR C 485 
 PHE   0.011   0.001   PHE B 393 
 TRP   0.008   0.001   TRP A 275 
 HIS   0.004   0.001   HIS C 452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 9969)
  covalent geometry    : angle       0.75032 (13590)
  hydrogen bonds       : bond        0.04302 (  769)
  hydrogen bonds       : angle       4.67386 ( 2253)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 173
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8014 (tt)
REVERT: A  352 SER cc_start: 0.8197 (t) cc_final: 0.7911 (m)
REVERT: A  484 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.7816 (m110)
REVERT: B  104 ILE cc_start: 0.7533 (pt) cc_final: 0.7159 (pt)
REVERT: B  134 PHE cc_start: 0.8020 (t80) cc_final: 0.7790 (t80)
REVERT: C  352 SER cc_start: 0.7704 (t) cc_final: 0.7442 (m)
  outliers start: 15
  outliers final: 9
  residues processed: 181
  average time/residue: 0.1930
  time to fit residues: 52.0869
Evaluate side-chains
  173 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 162
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  393 PHE
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  484 ASN
Chi-restraints excluded: chain B residue  340 ILE
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain C residue  356 THR
Chi-restraints excluded: chain C residue  379 LEU
Chi-restraints excluded: chain C residue  393 PHE
Chi-restraints excluded: chain C residue  437 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   chunk 128 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 121 optimal weight:    2.9990
   chunk 100 optimal weight:    9.9990
   chunk 18 optimal weight:    2.9990
   chunk 125 optimal weight:    5.9990
   chunk 130 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 386 ASN
B 367 ASN
** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.205635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.153083 restraints weight = 25917.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 1.88
r_work: 0.3480 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3341 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7249
moved from start:          0.4885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9969  Z= 0.148
  Angle     :  0.741  11.792  13590  Z= 0.338
  Chirality :  0.163   1.756   1698
  Planarity :  0.004   0.041   1695
  Dihedral  :  4.061  22.102   1398
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 14.19 %
    Favored  : 84.26 %
  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 are not related in a simple way.
  whole:  0.80 (0.23), residues: 1320
  helix:  1.36 (0.16), residues: 1005
  sheet: -2.55 (0.67), residues: 42
  loop : -2.03 (0.36), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 101 
 TYR   0.016   0.002   TYR A 485 
 PHE   0.010   0.001   PHE B 258 
 TRP   0.006   0.001   TRP C 275 
 HIS   0.002   0.001   HIS A 452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 9969)
  covalent geometry    : angle       0.74116 (13590)
  hydrogen bonds       : bond        0.04130 (  769)
  hydrogen bonds       : angle       4.65269 ( 2253)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 175
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8008 (tt)
REVERT: A  224 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7129 (pp30)
REVERT: A  352 SER cc_start: 0.8119 (t) cc_final: 0.7854 (m)
REVERT: B  104 ILE cc_start: 0.7470 (pt) cc_final: 0.7084 (pt)
REVERT: B  224 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7520 (pt0)
REVERT: B  331 LYS cc_start: 0.7475 (ttpt) cc_final: 0.7210 (mttp)
REVERT: C  352 SER cc_start: 0.7584 (t) cc_final: 0.7341 (m)
REVERT: C  464 ASP cc_start: 0.6791 (t0) cc_final: 0.6497 (t0)
  outliers start: 16
  outliers final: 13
  residues processed: 182
  average time/residue: 0.1848
  time to fit residues: 49.8305
Evaluate side-chains
  185 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 169
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  224 GLN
Chi-restraints excluded: chain A residue  386 ASN
Chi-restraints excluded: chain A residue  393 PHE
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  485 TYR
Chi-restraints excluded: chain B residue  224 GLN
Chi-restraints excluded: chain B residue  340 ILE
Chi-restraints excluded: chain B residue  393 PHE
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain C residue  356 THR
Chi-restraints excluded: chain C residue  379 LEU
Chi-restraints excluded: chain C residue  393 PHE
Chi-restraints excluded: chain C residue  437 LEU
Chi-restraints excluded: chain C residue  442 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 82 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   chunk 110 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 55 optimal weight:    5.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** C 484 ASN ** 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 = 0.4215 r_free = 0.4215 target = 0.203321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.155188 restraints weight = 26039.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.3739 rms_B_bonded: 1.78
r_work: 0.3466 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
moved from start:          0.4956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.126   9969  Z= 0.171
  Angle     :  0.976  59.198  13590  Z= 0.523
  Chirality :  0.164   1.766   1698
  Planarity :  0.004   0.041   1695
  Dihedral  :  4.083  22.019   1398
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 15.06 %
    Favored  : 83.48 %
  Cbeta Deviations :  0.08 %
  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 are not related in a simple way.
  whole:  0.81 (0.23), residues: 1320
  helix:  1.36 (0.16), residues: 1005
  sheet: -2.55 (0.67), residues: 42
  loop : -2.03 (0.36), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  85 
 TYR   0.018   0.002   TYR A 485 
 PHE   0.010   0.001   PHE B 258 
 TRP   0.006   0.001   TRP C 275 
 HIS   0.002   0.001   HIS A 452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 9969)
  covalent geometry    : angle       0.97581 (13590)
  hydrogen bonds       : bond        0.04117 (  769)
  hydrogen bonds       : angle       4.65798 ( 2253)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 170
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7971 (tt)
REVERT: A  224 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7133 (pp30)
REVERT: A  352 SER cc_start: 0.8246 (t) cc_final: 0.7996 (m)
REVERT: B  104 ILE cc_start: 0.7483 (pt) cc_final: 0.7092 (pt)
REVERT: B  224 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7446 (pt0)
REVERT: C  352 SER cc_start: 0.7720 (t) cc_final: 0.7485 (m)
  outliers start: 15
  outliers final: 12
  residues processed: 177
  average time/residue: 0.1940
  time to fit residues: 51.2550
Evaluate side-chains
  183 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 168
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  224 GLN
Chi-restraints excluded: chain A residue  393 PHE
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  485 TYR
Chi-restraints excluded: chain B residue  224 GLN
Chi-restraints excluded: chain B residue  340 ILE
Chi-restraints excluded: chain B residue  393 PHE
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain C residue  356 THR
Chi-restraints excluded: chain C residue  379 LEU
Chi-restraints excluded: chain C residue  393 PHE
Chi-restraints excluded: chain C residue  437 LEU
Chi-restraints excluded: chain C residue  442 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 26 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9980
   chunk 97 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 40 optimal weight:    6.9990
   chunk 103 optimal weight:    0.1980
   chunk 68 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 83 optimal weight:    0.4980
   chunk 116 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 484 ASN
** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.204145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.156806 restraints weight = 26089.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3753 rms_B_bonded: 2.05
r_work: 0.3490 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3355 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7310
moved from start:          0.4975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.126   9969  Z= 0.171
  Angle     :  0.976  59.198  13590  Z= 0.523
  Chirality :  0.164   1.766   1698
  Planarity :  0.004   0.041   1695
  Dihedral  :  4.083  22.019   1398
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 14.97 %
    Favored  : 83.48 %
  Cbeta Deviations :  0.08 %
  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 are not related in a simple way.
  whole:  0.81 (0.23), residues: 1320
  helix:  1.36 (0.16), residues: 1005
  sheet: -2.55 (0.67), residues: 42
  loop : -2.03 (0.36), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  85 
 TYR   0.018   0.002   TYR A 485 
 PHE   0.010   0.001   PHE B 258 
 TRP   0.006   0.001   TRP C 275 
 HIS   0.002   0.001   HIS A 452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 9969)
  covalent geometry    : angle       0.97581 (13590)
  hydrogen bonds       : bond        0.04117 (  769)
  hydrogen bonds       : angle       4.65798 ( 2253)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5918.62 seconds
wall clock time: 100 minutes 46.93 seconds (6046.93 seconds total)