Starting phenix.real_space_refine
on Sat Aug 23 09:29:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8puw_17949/08_2025/8puw_17949.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8puw_17949/08_2025/8puw_17949.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8puw_17949/08_2025/8puw_17949.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8puw_17949/08_2025/8puw_17949.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8puw_17949/08_2025/8puw_17949.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8puw_17949/08_2025/8puw_17949.map"
  }
  resolution = 3.01
  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=   0.003 sd=   0.068
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      52      5.16       5
     C    7134      2.51       5
     N    1956      2.21       5
     O    2018      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11160
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1488
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 189, 1488
          Classifications: {'peptide': 189}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 8, 'TRANS': 180}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 24
          Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "B"
      Number of atoms: 4092
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 532, 4092
          Classifications: {'peptide': 532}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 52, 'TRANS': 479}
          Unresolved chain links: 1
          Chain breaks: 4
          Unresolved chain link angles: 3
          Unresolved chain link dihedrals: 4
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "E"
      Number of atoms: 4092
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 532, 4092
          Classifications: {'peptide': 532}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 52, 'TRANS': 479}
          Unresolved chain links: 1
          Chain breaks: 4
          Unresolved chain link angles: 3
          Unresolved chain link dihedrals: 4
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "D"
      Number of atoms: 1488
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 189, 1488
          Classifications: {'peptide': 189}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 8, 'TRANS': 180}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 24
          Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 17
  Time building chain proxies: 2.89, per 1000 atoms: 0.26
  Number of scatterers: 11160
  At special positions: 0
  Unit cell: (141.075, 99.275, 89.87, 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      52     16.00
     O    2018      8.00
     N    1956      7.00
     C    7134      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.39
  Conformation dependent library (CDL) restraints added in 759.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2692

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 10 sheets defined
      42.2% alpha, 16.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 23
      removed outlier: 3.628A  pdb=" N   LEU A  15 " --> pdb=" O   ASN A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 23 through 28
    Processing helix  chain 'A' and resid 39 through 64
    Processing helix  chain 'A' and resid 67 through 86
      removed outlier: 3.643A  pdb=" N   GLN A  86 " --> pdb=" O   SER A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 116
    Processing helix  chain 'A' and resid 123 through 132
    Processing helix  chain 'A' and resid 134 through 147
      removed outlier: 4.022A  pdb=" N   VAL A 138 " --> pdb=" O   PRO A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 170
    Processing helix  chain 'A' and resid 171 through 175
      removed outlier: 3.561A  pdb=" N   LEU A 174 " --> pdb=" O   TRP A 171 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   GLY A 175 " --> pdb=" O   LYS A 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 171 through 175'
    Processing helix  chain 'B' and resid 196 through 203
      removed outlier: 3.723A  pdb=" N   LEU B 200 " --> pdb=" O   THR B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 206
      No H-bonds generated for 'chain 'B' and resid 204 through 206'
    Processing helix  chain 'B' and resid 207 through 212
    Processing helix  chain 'B' and resid 226 through 230
    Processing helix  chain 'B' and resid 242 through 259
    Processing helix  chain 'B' and resid 273 through 288
    Processing helix  chain 'B' and resid 363 through 366
      removed outlier: 4.121A  pdb=" N   LEU B 366 " --> pdb=" O   THR B 363 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 363 through 366'
    Processing helix  chain 'B' and resid 367 through 387
      removed outlier: 3.562A  pdb=" N   PHE B 371 " --> pdb=" O   ASP B 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 417
      removed outlier: 3.669A  pdb=" N   ASP B 407 " --> pdb=" O   GLY B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 444
      removed outlier: 3.889A  pdb=" N   SER B 443 " --> pdb=" O   ALA B 439 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   SER B 444 " --> pdb=" O   CYS B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 470 through 484
    Processing helix  chain 'B' and resid 538 through 544
    Processing helix  chain 'B' and resid 555 through 560
    Processing helix  chain 'B' and resid 654 through 661
      removed outlier: 3.652A  pdb=" N   PHE B 661 " --> pdb=" O   VAL B 657 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 662 through 664
      No H-bonds generated for 'chain 'B' and resid 662 through 664'
    Processing helix  chain 'B' and resid 676 through 692
      removed outlier: 3.818A  pdb=" N   TYR B 680 " --> pdb=" O   PRO B 676 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   VAL B 681 " --> pdb=" O   THR B 677 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   GLY B 683 " --> pdb=" O   ALA B 679 " (cutoff:3.500A)
      removed outlier: 4.958A  pdb=" N   LEU B 684 " --> pdb=" O   TYR B 680 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 196 through 203
      removed outlier: 3.688A  pdb=" N   LEU E 200 " --> pdb=" O   THR E 196 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 204 through 206
      No H-bonds generated for 'chain 'E' and resid 204 through 206'
    Processing helix  chain 'E' and resid 207 through 211
    Processing helix  chain 'E' and resid 226 through 230
    Processing helix  chain 'E' and resid 242 through 259
    Processing helix  chain 'E' and resid 273 through 288
    Processing helix  chain 'E' and resid 363 through 366
      removed outlier: 4.120A  pdb=" N   LEU E 366 " --> pdb=" O   THR E 363 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 363 through 366'
    Processing helix  chain 'E' and resid 367 through 387
      removed outlier: 3.563A  pdb=" N   PHE E 371 " --> pdb=" O   ASP E 367 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 403 through 417
      removed outlier: 3.601A  pdb=" N   ASP E 407 " --> pdb=" O   GLY E 403 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 429 through 444
      removed outlier: 3.891A  pdb=" N   SER E 443 " --> pdb=" O   ALA E 439 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   SER E 444 " --> pdb=" O   CYS E 440 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 470 through 484
    Processing helix  chain 'E' and resid 538 through 544
    Processing helix  chain 'E' and resid 555 through 560
    Processing helix  chain 'E' and resid 654 through 661
      removed outlier: 3.644A  pdb=" N   PHE E 661 " --> pdb=" O   VAL E 657 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 676 through 692
      removed outlier: 3.820A  pdb=" N   TYR E 680 " --> pdb=" O   PRO E 676 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   VAL E 681 " --> pdb=" O   THR E 677 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   GLY E 683 " --> pdb=" O   ALA E 679 " (cutoff:3.500A)
      removed outlier: 4.961A  pdb=" N   LEU E 684 " --> pdb=" O   TYR E 680 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 11 through 23
      removed outlier: 3.628A  pdb=" N   LEU D  15 " --> pdb=" O   ASN D  11 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 23 through 28
    Processing helix  chain 'D' and resid 39 through 64
    Processing helix  chain 'D' and resid 67 through 86
      removed outlier: 3.647A  pdb=" N   GLN D  86 " --> pdb=" O   SER D  82 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 93 through 116
    Processing helix  chain 'D' and resid 123 through 132
    Processing helix  chain 'D' and resid 134 through 147
      removed outlier: 4.053A  pdb=" N   VAL D 138 " --> pdb=" O   PRO D 134 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 151 through 170
    Processing helix  chain 'D' and resid 171 through 175
      removed outlier: 3.559A  pdb=" N   LEU D 174 " --> pdb=" O   TRP D 171 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   GLY D 175 " --> pdb=" O   LYS D 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 171 through 175'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6
    Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 349
      removed outlier: 6.912A  pdb=" N   GLU B 646 " --> pdb=" O   VAL B 638 " (cutoff:3.500A)
      removed outlier: 4.952A  pdb=" N   VAL B 638 " --> pdb=" O   GLU B 646 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   HIS B 648 " --> pdb=" O   ARG B 636 " (cutoff:3.500A)
      removed outlier: 5.495A  pdb=" N   LEU B 629 " --> pdb=" O   ARG B 552 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   ARG B 552 " --> pdb=" O   LEU B 629 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   GLY B 631 " --> pdb=" O   LEU B 550 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   ILE B 527 " --> pdb=" O   ILE B 614 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 121 through 124
      removed outlier: 6.310A  pdb=" N   VAL B 188 " --> pdb=" O   HIS B 150 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 159 through 161
    Processing sheet with id=AA5, first strand: chain 'B' and resid 351 through 358
      removed outlier: 6.719A  pdb=" N   LEU B 320 " --> pdb=" O   VAL B 354 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   MET B 356 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   VAL B 318 " --> pdb=" O   MET B 356 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   MET B 301 " --> pdb=" O   VAL B 394 " (cutoff:3.500A)
      removed outlier: 7.846A  pdb=" N   ASN B 396 " --> pdb=" O   MET B 301 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   LEU B 303 " --> pdb=" O   ASN B 396 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   LEU B 264 " --> pdb=" O   VAL B 395 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   VAL B 421 " --> pdb=" O   THR B 449 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 121 through 124
      removed outlier: 6.325A  pdb=" N   VAL E 188 " --> pdb=" O   HIS E 150 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 159 through 161
    Processing sheet with id=AA8, first strand: chain 'E' and resid 351 through 358
      removed outlier: 6.789A  pdb=" N   LEU E 320 " --> pdb=" O   VAL E 354 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   MET E 356 " --> pdb=" O   VAL E 318 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   VAL E 318 " --> pdb=" O   MET E 356 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   MET E 301 " --> pdb=" O   VAL E 394 " (cutoff:3.500A)
      removed outlier: 7.886A  pdb=" N   ASN E 396 " --> pdb=" O   MET E 301 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   LEU E 303 " --> pdb=" O   ASN E 396 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   LEU E 264 " --> pdb=" O   VAL E 395 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   VAL E 421 " --> pdb=" O   THR E 449 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 613 through 614
      removed outlier: 6.030A  pdb=" N   ILE E 527 " --> pdb=" O   ILE E 614 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   GLY E 631 " --> pdb=" O   LEU E 550 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   ARG E 552 " --> pdb=" O   LEU E 629 " (cutoff:3.500A)
      removed outlier: 5.490A  pdb=" N   LEU E 629 " --> pdb=" O   ARG E 552 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   HIS E 648 " --> pdb=" O   ARG E 636 " (cutoff:3.500A)
      removed outlier: 4.952A  pdb=" N   VAL E 638 " --> pdb=" O   GLU E 646 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   GLU E 646 " --> pdb=" O   VAL E 638 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 723 through 725

    525 hydrogen bonds defined for protein.
    1476 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.00

  Time building geometry restraints manager: 1.74 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: 3617
        1.34 -     1.46: 1842
        1.46 -     1.57: 5923
        1.57 -     1.69: 0
        1.69 -     1.81: 84
  Bond restraints: 11466
  Sorted by residual:
  bond pdb=" N   GLY E 291 "
       pdb=" CA  GLY E 291 "
    ideal  model  delta    sigma   weight residual
    1.464  1.446  0.018 1.12e-02 7.97e+03 2.57e+00
  bond pdb=" N   GLY B 291 "
       pdb=" CA  GLY B 291 "
    ideal  model  delta    sigma   weight residual
    1.464  1.447  0.018 1.12e-02 7.97e+03 2.45e+00
  bond pdb=" CB  GLN A   3 "
       pdb=" CG  GLN A   3 "
    ideal  model  delta    sigma   weight residual
    1.520  1.561 -0.041 3.00e-02 1.11e+03 1.91e+00
  bond pdb=" CA  GLY B 291 "
       pdb=" C   GLY B 291 "
    ideal  model  delta    sigma   weight residual
    1.530  1.516  0.014 1.04e-02 9.25e+03 1.88e+00
  bond pdb=" CB  GLN D   3 "
       pdb=" CG  GLN D   3 "
    ideal  model  delta    sigma   weight residual
    1.520  1.561 -0.041 3.00e-02 1.11e+03 1.86e+00
  ... (remaining 11461 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.50: 14969
        1.50 -     3.01: 567
        3.01 -     4.51: 89
        4.51 -     6.01: 21
        6.01 -     7.51: 6
  Bond angle restraints: 15652
  Sorted by residual:
  angle pdb=" C   TYR E 530 "
        pdb=" N   ASP E 531 "
        pdb=" CA  ASP E 531 "
      ideal   model   delta    sigma   weight residual
     121.54  129.05   -7.51 1.91e+00 2.74e-01 1.55e+01
  angle pdb=" C   TYR B 530 "
        pdb=" N   ASP B 531 "
        pdb=" CA  ASP B 531 "
      ideal   model   delta    sigma   weight residual
     121.54  128.99   -7.45 1.91e+00 2.74e-01 1.52e+01
  angle pdb=" C   ILE B 359 "
        pdb=" N   ALA B 360 "
        pdb=" CA  ALA B 360 "
      ideal   model   delta    sigma   weight residual
     122.40  127.54   -5.14 1.45e+00 4.76e-01 1.26e+01
  angle pdb=" C   ILE E 359 "
        pdb=" N   ALA E 360 "
        pdb=" CA  ALA E 360 "
      ideal   model   delta    sigma   weight residual
     122.40  127.52   -5.12 1.45e+00 4.76e-01 1.25e+01
  angle pdb=" CB  GLN D   3 "
        pdb=" CG  GLN D   3 "
        pdb=" CD  GLN D   3 "
      ideal   model   delta    sigma   weight residual
     112.60  118.18   -5.58 1.70e+00 3.46e-01 1.08e+01
  ... (remaining 15647 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 6357
       17.84 -    35.68: 404
       35.68 -    53.52: 59
       53.52 -    71.36: 16
       71.36 -    89.20: 6
  Dihedral angle restraints: 6842
    sinusoidal: 2688
      harmonic: 4154
  Sorted by residual:
  dihedral pdb=" CA  TYR E 423 "
           pdb=" C   TYR E 423 "
           pdb=" N   MET E 424 "
           pdb=" CA  MET E 424 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.55  -18.45     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  TYR B 423 "
           pdb=" C   TYR B 423 "
           pdb=" N   MET B 424 "
           pdb=" CA  MET B 424 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.58  -18.42     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  MET E 286 "
           pdb=" C   MET E 286 "
           pdb=" N   THR E 287 "
           pdb=" CA  THR E 287 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.96  -17.04     0      5.00e+00 4.00e-02 1.16e+01
  ... (remaining 6839 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1303
       0.040 -    0.080: 302
       0.080 -    0.121: 125
       0.121 -    0.161: 20
       0.161 -    0.201: 4
  Chirality restraints: 1754
  Sorted by residual:
  chirality pdb=" CB  ILE E 156 "
            pdb=" CA  ILE E 156 "
            pdb=" CG1 ILE E 156 "
            pdb=" CG2 ILE E 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CB  ILE B 156 "
            pdb=" CA  ILE B 156 "
            pdb=" CG1 ILE B 156 "
            pdb=" CG2 ILE B 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.20 2.00e-01 2.50e+01 1.00e+00
  chirality pdb=" CG  LEU B 280 "
            pdb=" CB  LEU B 280 "
            pdb=" CD1 LEU B 280 "
            pdb=" CD2 LEU B 280 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.06e-01
  ... (remaining 1751 not shown)

  Planarity restraints: 2012
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 115 "    0.039 5.00e-02 4.00e+02   5.98e-02 5.71e+00
        pdb=" N   PRO B 116 "   -0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO B 116 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 116 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN E 115 "    0.038 5.00e-02 4.00e+02   5.82e-02 5.43e+00
        pdb=" N   PRO E 116 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO E 116 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO E 116 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D  94 "   -0.024 2.00e-02 2.50e+03   1.52e-02 4.65e+00
        pdb=" CG  TYR D  94 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 TYR D  94 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR D  94 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR D  94 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR D  94 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR D  94 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR D  94 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 2009 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2666
        2.80 -     3.33: 10052
        3.33 -     3.85: 18567
        3.85 -     4.38: 22105
        4.38 -     4.90: 38220
  Nonbonded interactions: 91610
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 139 "
            pdb=" OG1 THR E 404 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" NE2 HIS E 174 "
            pdb=" O   ARG E 212 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" NE2 HIS B 174 "
            pdb=" O   ARG B 212 "
     model   vdw
     2.300 3.120
  nonbonded pdb=" O   GLY B 545 "
            pdb=" OH  TYR B 680 "
     model   vdw
     2.385 3.040
  nonbonded pdb=" O   GLY E 545 "
            pdb=" OH  TYR E 680 "
     model   vdw
     2.394 3.040
  ... (remaining 91605 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 'D'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'E'
}

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:             2.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.220
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  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:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
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   0.041  11466  Z= 0.185
  Angle     :  0.693   7.514  15652  Z= 0.391
  Chirality :  0.043   0.201   1754
  Planarity :  0.008   0.067   2012
  Dihedral  : 12.229  89.202   4150
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.21), residues: 1406
  helix:  1.09 (0.20), residues: 496
  sheet: -0.09 (0.37), residues: 196
  loop :  0.37 (0.22), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG E 560 
 TYR   0.034   0.002   TYR D  94 
 PHE   0.021   0.002   PHE D  22 
 TRP   0.008   0.001   TRP B 214 
 HIS   0.006   0.001   HIS B 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 (11466)
  covalent geometry    : angle       0.69345 (15652)
  hydrogen bonds       : bond        0.13705 (  525)
  hydrogen bonds       : angle       6.24437 ( 1476)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.1391
  time to fit residues: 18.9628
Evaluate side-chains
  84 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    0.4980
   chunk 130 optimal weight:    0.7980
   chunk 124 optimal weight:    0.0170
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    0.3980
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.5218

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

Flipped N/Q/H residues before XYZ refinement:
A 146 HIS
B 144 ASN
E 144 ASN
D 146 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.112833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.087057 restraints weight = 15465.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.2969 rms_B_bonded: 2.22
r_work: 0.2818 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2665 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8768
moved from start:          0.0729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11466  Z= 0.123
  Angle     :  0.504   8.560  15652  Z= 0.253
  Chirality :  0.040   0.135   1754
  Planarity :  0.006   0.043   2012
  Dihedral  :  4.143  24.195   1554
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  4.19 %
    Favored  : 95.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.68 (0.22), residues: 1406
  helix:  2.15 (0.22), residues: 506
  sheet:  0.22 (0.39), residues: 178
  loop :  0.74 (0.23), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 560 
 TYR   0.013   0.001   TYR A  94 
 PHE   0.013   0.002   PHE D 107 
 TRP   0.007   0.001   TRP E 214 
 HIS   0.007   0.001   HIS E 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (11466)
  covalent geometry    : angle       0.50388 (15652)
  hydrogen bonds       : bond        0.04346 (  525)
  hydrogen bonds       : angle       4.75204 ( 1476)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 96
  time to evaluate  : 0.301 
Fit side-chains
REVERT: B  259 LYS cc_start: 0.7435 (mtmt) cc_final: 0.6868 (ptpt)
REVERT: E  259 LYS cc_start: 0.7461 (mtmt) cc_final: 0.6890 (ptpt)
  outliers start: 4
  outliers final: 4
  residues processed: 100
  average time/residue: 0.1304
  time to fit residues: 18.2432
Evaluate side-chains
  90 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 86
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  164 ILE
Chi-restraints excluded: chain B residue  427 ASP
Chi-restraints excluded: chain E residue  164 ILE
Chi-restraints excluded: chain E residue  427 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 57 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 111 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
B 122 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.109709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.083767 restraints weight = 15743.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.2919 rms_B_bonded: 2.06
r_work: 0.2783 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2630 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8788
moved from start:          0.1140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  11466  Z= 0.173
  Angle     :  0.518   5.035  15652  Z= 0.258
  Chirality :  0.041   0.132   1754
  Planarity :  0.005   0.036   2012
  Dihedral  :  4.101  20.784   1554
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  6.53 %
    Favored  : 92.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.81 (0.22), residues: 1406
  helix:  2.44 (0.22), residues: 506
  sheet:  0.04 (0.39), residues: 178
  loop :  0.73 (0.23), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 106 
 TYR   0.014   0.002   TYR A  94 
 PHE   0.016   0.002   PHE A 107 
 TRP   0.006   0.001   TRP A 168 
 HIS   0.009   0.001   HIS E 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 (11466)
  covalent geometry    : angle       0.51835 (15652)
  hydrogen bonds       : bond        0.04414 (  525)
  hydrogen bonds       : angle       4.50262 ( 1476)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.548 
Fit side-chains
REVERT: A   94 TYR cc_start: 0.9098 (OUTLIER) cc_final: 0.8074 (m-10)
REVERT: B  259 LYS cc_start: 0.7525 (mtmt) cc_final: 0.6926 (ptpt)
REVERT: E  186 ASP cc_start: 0.8119 (t0) cc_final: 0.7682 (t0)
REVERT: E  259 LYS cc_start: 0.7532 (mtmt) cc_final: 0.6933 (ptpt)
REVERT: D   94 TYR cc_start: 0.9106 (OUTLIER) cc_final: 0.8072 (m-10)
  outliers start: 8
  outliers final: 6
  residues processed: 99
  average time/residue: 0.1171
  time to fit residues: 16.3545
Evaluate side-chains
  93 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   94 TYR
Chi-restraints excluded: chain A residue  116 GLN
Chi-restraints excluded: chain B residue  164 ILE
Chi-restraints excluded: chain B residue  427 ASP
Chi-restraints excluded: chain E residue  164 ILE
Chi-restraints excluded: chain E residue  427 ASP
Chi-restraints excluded: chain D residue   94 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 116 optimal weight:    0.0470
   chunk 70 optimal weight:    0.8980
   chunk 138 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 131 optimal weight:    1.9990
   chunk 128 optimal weight:    0.5980
   chunk 46 optimal weight:    0.6980
   chunk 54 optimal weight:    0.0370
   chunk 84 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.4156

-------------------------------------------------------------------------------
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 = 0.3356 r_free = 0.3356 target = 0.111790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.086678 restraints weight = 15741.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 2.09
r_work: 0.2802 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2648 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8779
moved from start:          0.1236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  11466  Z= 0.102
  Angle     :  0.458   4.594  15652  Z= 0.228
  Chirality :  0.039   0.135   1754
  Planarity :  0.005   0.037   2012
  Dihedral  :  3.869  19.972   1554
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  6.95 %
    Favored  : 92.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.05 (0.22), residues: 1406
  helix:  2.79 (0.22), residues: 506
  sheet:  0.14 (0.39), residues: 178
  loop :  0.76 (0.23), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 106 
 TYR   0.009   0.001   TYR A  94 
 PHE   0.011   0.001   PHE B 265 
 TRP   0.006   0.001   TRP E 511 
 HIS   0.005   0.001   HIS E 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 (11466)
  covalent geometry    : angle       0.45797 (15652)
  hydrogen bonds       : bond        0.03595 (  525)
  hydrogen bonds       : angle       4.33757 ( 1476)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.317 
Fit side-chains
REVERT: A   94 TYR cc_start: 0.9029 (OUTLIER) cc_final: 0.8106 (m-80)
REVERT: B  259 LYS cc_start: 0.7504 (mtmt) cc_final: 0.6894 (ptpt)
REVERT: B  280 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8832 (mp)
REVERT: E  186 ASP cc_start: 0.8108 (t0) cc_final: 0.7771 (t0)
REVERT: E  259 LYS cc_start: 0.7497 (mtmt) cc_final: 0.6884 (ptpt)
REVERT: E  280 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8832 (mp)
REVERT: D   94 TYR cc_start: 0.9046 (OUTLIER) cc_final: 0.8114 (m-80)
  outliers start: 12
  outliers final: 8
  residues processed: 102
  average time/residue: 0.1139
  time to fit residues: 16.1867
Evaluate side-chains
  100 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   94 TYR
Chi-restraints excluded: chain A residue  116 GLN
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain B residue  164 ILE
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  427 ASP
Chi-restraints excluded: chain E residue  164 ILE
Chi-restraints excluded: chain E residue  280 LEU
Chi-restraints excluded: chain E residue  427 ASP
Chi-restraints excluded: chain D residue   94 TYR
Chi-restraints excluded: chain D residue  116 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 31 optimal weight:    0.3980
   chunk 53 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   chunk 133 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 136 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0870
   overall best weight:    0.6162

-------------------------------------------------------------------------------
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 = 0.3341 r_free = 0.3341 target = 0.110745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.085422 restraints weight = 15616.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.2964 rms_B_bonded: 2.11
r_work: 0.2796 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2642 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8794
moved from start:          0.1345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11466  Z= 0.127
  Angle     :  0.471   4.860  15652  Z= 0.233
  Chirality :  0.040   0.135   1754
  Planarity :  0.005   0.035   2012
  Dihedral  :  3.851  19.303   1554
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  :  6.95 %
    Favored  : 91.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.10 (0.22), residues: 1406
  helix:  2.90 (0.22), residues: 506
  sheet:  0.09 (0.39), residues: 178
  loop :  0.75 (0.23), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 106 
 TYR   0.012   0.001   TYR A  94 
 PHE   0.013   0.001   PHE D 107 
 TRP   0.005   0.001   TRP A 168 
 HIS   0.005   0.001   HIS E 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (11466)
  covalent geometry    : angle       0.47057 (15652)
  hydrogen bonds       : bond        0.03787 (  525)
  hydrogen bonds       : angle       4.31219 ( 1476)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.517 
Fit side-chains
REVERT: A   94 TYR cc_start: 0.9090 (OUTLIER) cc_final: 0.8143 (m-10)
REVERT: B  186 ASP cc_start: 0.8071 (t0) cc_final: 0.7680 (t0)
REVERT: B  259 LYS cc_start: 0.7540 (mtmt) cc_final: 0.7110 (ptpp)
REVERT: B  280 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8843 (mp)
REVERT: E  186 ASP cc_start: 0.8108 (t0) cc_final: 0.7845 (t0)
REVERT: E  259 LYS cc_start: 0.7553 (mtmt) cc_final: 0.7124 (ptpp)
REVERT: E  280 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8842 (mp)
REVERT: D   94 TYR cc_start: 0.9099 (OUTLIER) cc_final: 0.8138 (m-80)
  outliers start: 16
  outliers final: 9
  residues processed: 104
  average time/residue: 0.0847
  time to fit residues: 13.0700
Evaluate side-chains
  103 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   94 TYR
Chi-restraints excluded: chain A residue  116 GLN
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain B residue  164 ILE
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  427 ASP
Chi-restraints excluded: chain E residue  164 ILE
Chi-restraints excluded: chain E residue  280 LEU
Chi-restraints excluded: chain E residue  356 MET
Chi-restraints excluded: chain E residue  427 ASP
Chi-restraints excluded: chain D residue   94 TYR
Chi-restraints excluded: chain D residue  116 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 88 optimal weight:    0.6980
   chunk 57 optimal weight:    0.8980
   chunk 116 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   chunk 39 optimal weight:    0.0170
   chunk 58 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 136 optimal weight:    0.9980
   chunk 121 optimal weight:    0.6980
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.6218

-------------------------------------------------------------------------------
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 = 0.3340 r_free = 0.3340 target = 0.110713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.085392 restraints weight = 15706.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.2948 rms_B_bonded: 2.11
r_work: 0.2780 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2627 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8796
moved from start:          0.1415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11466  Z= 0.127
  Angle     :  0.471   4.808  15652  Z= 0.234
  Chirality :  0.040   0.134   1754
  Planarity :  0.005   0.034   2012
  Dihedral  :  3.834  19.009   1554
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  7.71 %
    Favored  : 91.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.12 (0.22), residues: 1406
  helix:  2.93 (0.22), residues: 506
  sheet:  0.10 (0.39), residues: 178
  loop :  0.75 (0.23), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 106 
 TYR   0.012   0.001   TYR A  94 
 PHE   0.012   0.001   PHE D 107 
 TRP   0.005   0.001   TRP E 214 
 HIS   0.004   0.001   HIS E 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (11466)
  covalent geometry    : angle       0.47079 (15652)
  hydrogen bonds       : bond        0.03724 (  525)
  hydrogen bonds       : angle       4.28657 ( 1476)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.287 
Fit side-chains
REVERT: A   94 TYR cc_start: 0.9092 (OUTLIER) cc_final: 0.8138 (m-10)
REVERT: B  186 ASP cc_start: 0.8088 (t0) cc_final: 0.7742 (t0)
REVERT: B  259 LYS cc_start: 0.7529 (mtmt) cc_final: 0.7117 (ptpp)
REVERT: B  280 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8840 (mp)
REVERT: E  186 ASP cc_start: 0.8104 (t0) cc_final: 0.7851 (t0)
REVERT: E  259 LYS cc_start: 0.7551 (mtmt) cc_final: 0.7140 (ptpp)
REVERT: E  280 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8843 (mp)
REVERT: D   94 TYR cc_start: 0.9097 (OUTLIER) cc_final: 0.8132 (m-10)
  outliers start: 14
  outliers final: 8
  residues processed: 103
  average time/residue: 0.1130
  time to fit residues: 16.4483
Evaluate side-chains
  100 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   94 TYR
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain B residue  164 ILE
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  427 ASP
Chi-restraints excluded: chain E residue  164 ILE
Chi-restraints excluded: chain E residue  280 LEU
Chi-restraints excluded: chain E residue  356 MET
Chi-restraints excluded: chain E residue  427 ASP
Chi-restraints excluded: chain D residue   94 TYR
Chi-restraints excluded: chain D residue  116 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 103 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 36 optimal weight:    0.0870
   chunk 67 optimal weight:    0.5980
   chunk 51 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 42 optimal weight:    0.3980
   chunk 13 optimal weight:    0.9990
   chunk 60 optimal weight:    0.5980
   overall best weight:    0.4558

-------------------------------------------------------------------------------
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 = 0.3352 r_free = 0.3352 target = 0.111576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.086366 restraints weight = 15651.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 2.10
r_work: 0.2812 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2658 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8782
moved from start:          0.1484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11466  Z= 0.107
  Angle     :  0.454   4.824  15652  Z= 0.225
  Chirality :  0.039   0.135   1754
  Planarity :  0.004   0.034   2012
  Dihedral  :  3.746  18.959   1554
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  7.96 %
    Favored  : 90.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.20 (0.22), residues: 1406
  helix:  3.05 (0.22), residues: 506
  sheet:  0.13 (0.39), residues: 178
  loop :  0.76 (0.23), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 106 
 TYR   0.010   0.001   TYR A  94 
 PHE   0.010   0.001   PHE A 104 
 TRP   0.005   0.001   TRP B 511 
 HIS   0.003   0.001   HIS E 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (11466)
  covalent geometry    : angle       0.45435 (15652)
  hydrogen bonds       : bond        0.03497 (  525)
  hydrogen bonds       : angle       4.21869 ( 1476)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.331 
Fit side-chains
REVERT: A   94 TYR cc_start: 0.9064 (OUTLIER) cc_final: 0.8175 (m-80)
REVERT: B  186 ASP cc_start: 0.8096 (t0) cc_final: 0.7735 (t0)
REVERT: B  259 LYS cc_start: 0.7533 (mtmt) cc_final: 0.7139 (ptpp)
REVERT: B  280 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8836 (mp)
REVERT: E  186 ASP cc_start: 0.8084 (t0) cc_final: 0.7842 (t0)
REVERT: E  259 LYS cc_start: 0.7554 (mtmt) cc_final: 0.7163 (ptpp)
REVERT: E  280 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8838 (mp)
REVERT: D   94 TYR cc_start: 0.9066 (OUTLIER) cc_final: 0.8164 (m-80)
  outliers start: 14
  outliers final: 9
  residues processed: 103
  average time/residue: 0.1014
  time to fit residues: 15.3086
Evaluate side-chains
  103 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue   94 TYR
Chi-restraints excluded: chain A residue  116 GLN
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain B residue  164 ILE
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  427 ASP
Chi-restraints excluded: chain E residue  164 ILE
Chi-restraints excluded: chain E residue  280 LEU
Chi-restraints excluded: chain E residue  356 MET
Chi-restraints excluded: chain E residue  427 ASP
Chi-restraints excluded: chain D residue   94 TYR
Chi-restraints excluded: chain D residue  116 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 127 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 125 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 134 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   chunk 36 optimal weight:    0.3980
   overall best weight:    1.2384

-------------------------------------------------------------------------------
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 = 0.3306 r_free = 0.3306 target = 0.108253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.082256 restraints weight = 15751.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.2897 rms_B_bonded: 2.07
r_work: 0.2759 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2604 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8808
moved from start:          0.1565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  11466  Z= 0.214
  Angle     :  0.530   5.088  15652  Z= 0.263
  Chirality :  0.042   0.139   1754
  Planarity :  0.005   0.030   2012
  Dihedral  :  4.041  19.123   1554
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  :  8.12 %
    Favored  : 90.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.91 (0.22), residues: 1406
  helix:  2.77 (0.22), residues: 506
  sheet: -0.07 (0.38), residues: 178
  loop :  0.64 (0.23), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 106 
 TYR   0.016   0.002   TYR A  94 
 PHE   0.015   0.002   PHE D 104 
 TRP   0.008   0.001   TRP D 168 
 HIS   0.006   0.001   HIS B 484 

Details of bonding type rmsd
  covalent geometry    : bond        0.00527 (11466)
  covalent geometry    : angle       0.52989 (15652)
  hydrogen bonds       : bond        0.04449 (  525)
  hydrogen bonds       : angle       4.37909 ( 1476)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.310 
Fit side-chains
REVERT: A   94 TYR cc_start: 0.9183 (OUTLIER) cc_final: 0.8118 (m-10)
REVERT: B  186 ASP cc_start: 0.8088 (t0) cc_final: 0.7793 (t0)
REVERT: B  259 LYS cc_start: 0.7630 (mtmt) cc_final: 0.7074 (ptpt)
REVERT: B  280 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8820 (mp)
REVERT: E  186 ASP cc_start: 0.8117 (t0) cc_final: 0.7855 (t0)
REVERT: E  259 LYS cc_start: 0.7639 (mtmt) cc_final: 0.7085 (ptpt)
REVERT: E  280 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8830 (mp)
REVERT: D   94 TYR cc_start: 0.9190 (OUTLIER) cc_final: 0.8122 (m-10)
  outliers start: 16
  outliers final: 7
  residues processed: 104
  average time/residue: 0.1042
  time to fit residues: 15.0747
Evaluate side-chains
  97 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 TYR
Chi-restraints excluded: chain A residue  116 GLN
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  427 ASP
Chi-restraints excluded: chain E residue  226 THR
Chi-restraints excluded: chain E residue  280 LEU
Chi-restraints excluded: chain E residue  356 MET
Chi-restraints excluded: chain E residue  427 ASP
Chi-restraints excluded: chain D residue   94 TYR
Chi-restraints excluded: chain D residue  116 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 77 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 40 optimal weight:    0.5980
   chunk 91 optimal weight:    0.9990
   chunk 68 optimal weight:    0.1980
   chunk 65 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 28 optimal weight:    0.3980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3333 r_free = 0.3333 target = 0.110185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.084984 restraints weight = 15495.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.2942 rms_B_bonded: 2.08
r_work: 0.2773 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2618 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8802
moved from start:          0.1569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11466  Z= 0.124
  Angle     :  0.471   4.810  15652  Z= 0.234
  Chirality :  0.040   0.136   1754
  Planarity :  0.005   0.032   2012
  Dihedral  :  3.879  19.517   1554
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  8.54 %
    Favored  : 90.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.08 (0.22), residues: 1406
  helix:  2.95 (0.22), residues: 506
  sheet: -0.00 (0.39), residues: 178
  loop :  0.71 (0.23), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 106 
 TYR   0.012   0.001   TYR A  94 
 PHE   0.011   0.001   PHE A 104 
 TRP   0.006   0.001   TRP B 214 
 HIS   0.003   0.001   HIS B 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (11466)
  covalent geometry    : angle       0.47067 (15652)
  hydrogen bonds       : bond        0.03733 (  525)
  hydrogen bonds       : angle       4.28439 ( 1476)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.459 
Fit side-chains
REVERT: A   94 TYR cc_start: 0.9132 (OUTLIER) cc_final: 0.8163 (m-10)
REVERT: B  186 ASP cc_start: 0.8102 (t0) cc_final: 0.7858 (t0)
REVERT: B  259 LYS cc_start: 0.7570 (mtmt) cc_final: 0.7199 (ptpp)
REVERT: B  280 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8843 (mp)
REVERT: E  186 ASP cc_start: 0.8079 (t0) cc_final: 0.7843 (t0)
REVERT: E  259 LYS cc_start: 0.7582 (mtmt) cc_final: 0.7210 (ptpp)
REVERT: E  280 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8845 (mp)
REVERT: D   94 TYR cc_start: 0.9134 (OUTLIER) cc_final: 0.8164 (m-10)
  outliers start: 10
  outliers final: 6
  residues processed: 94
  average time/residue: 0.1190
  time to fit residues: 16.0192
Evaluate side-chains
  98 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 TYR
Chi-restraints excluded: chain A residue  116 GLN
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  427 ASP
Chi-restraints excluded: chain E residue  280 LEU
Chi-restraints excluded: chain E residue  356 MET
Chi-restraints excluded: chain E residue  427 ASP
Chi-restraints excluded: chain D residue   94 TYR
Chi-restraints excluded: chain D residue  116 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 119 optimal weight:    0.0010
   chunk 127 optimal weight:    3.9990
   chunk 131 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0770
   chunk 78 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   chunk 111 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9980
   overall best weight:    0.5144

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

Flipped N/Q/H residues before XYZ refinement:
B 309 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.110647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.085487 restraints weight = 15557.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.2950 rms_B_bonded: 2.09
r_work: 0.2782 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2627 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8795
moved from start:          0.1617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11466  Z= 0.114
  Angle     :  0.463   4.857  15652  Z= 0.230
  Chirality :  0.039   0.144   1754
  Planarity :  0.004   0.032   2012
  Dihedral  :  3.797  19.651   1554
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  :  8.63 %
    Favored  : 90.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.13 (0.22), residues: 1406
  helix:  3.03 (0.22), residues: 506
  sheet: -0.04 (0.39), residues: 178
  loop :  0.73 (0.23), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 106 
 TYR   0.011   0.001   TYR A  94 
 PHE   0.011   0.001   PHE A 104 
 TRP   0.007   0.001   TRP E 214 
 HIS   0.003   0.001   HIS B 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (11466)
  covalent geometry    : angle       0.46288 (15652)
  hydrogen bonds       : bond        0.03596 (  525)
  hydrogen bonds       : angle       4.23663 ( 1476)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.381 
Fit side-chains
REVERT: A   94 TYR cc_start: 0.9092 (OUTLIER) cc_final: 0.8216 (m-10)
REVERT: B  259 LYS cc_start: 0.7551 (mtmt) cc_final: 0.6984 (ptpt)
REVERT: B  280 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8840 (mp)
REVERT: E  186 ASP cc_start: 0.8068 (t0) cc_final: 0.7843 (t0)
REVERT: E  259 LYS cc_start: 0.7577 (mtmt) cc_final: 0.7010 (ptpt)
REVERT: E  280 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8845 (mp)
REVERT: D   94 TYR cc_start: 0.9106 (OUTLIER) cc_final: 0.8219 (m-10)
  outliers start: 11
  outliers final: 7
  residues processed: 96
  average time/residue: 0.1072
  time to fit residues: 14.5575
Evaluate side-chains
  98 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 TYR
Chi-restraints excluded: chain A residue  116 GLN
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  427 ASP
Chi-restraints excluded: chain E residue  226 THR
Chi-restraints excluded: chain E residue  280 LEU
Chi-restraints excluded: chain E residue  356 MET
Chi-restraints excluded: chain E residue  427 ASP
Chi-restraints excluded: chain D residue   94 TYR
Chi-restraints excluded: chain D residue  116 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 97 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 135 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 117 optimal weight:    0.5980
   chunk 89 optimal weight:    4.9990
   chunk 92 optimal weight:    2.9990
   chunk 102 optimal weight:    0.4980
   chunk 130 optimal weight:    1.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3330 r_free = 0.3330 target = 0.109884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.084702 restraints weight = 15700.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.2936 rms_B_bonded: 2.08
r_work: 0.2767 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2611 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8808
moved from start:          0.1634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11466  Z= 0.138
  Angle     :  0.478   4.957  15652  Z= 0.238
  Chirality :  0.040   0.149   1754
  Planarity :  0.005   0.032   2012
  Dihedral  :  3.831  19.595   1554
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  :  8.71 %
    Favored  : 90.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.09 (0.22), residues: 1406
  helix:  2.98 (0.22), residues: 506
  sheet: -0.05 (0.39), residues: 178
  loop :  0.71 (0.23), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 106 
 TYR   0.013   0.001   TYR A  94 
 PHE   0.013   0.001   PHE A 104 
 TRP   0.006   0.001   TRP E 214 
 HIS   0.004   0.001   HIS B 484 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (11466)
  covalent geometry    : angle       0.47795 (15652)
  hydrogen bonds       : bond        0.03793 (  525)
  hydrogen bonds       : angle       4.25025 ( 1476)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2532.02 seconds
wall clock time: 44 minutes 7.82 seconds (2647.82 seconds total)