Starting phenix.real_space_refine
on Tue Mar  3 21:07:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6pqy_20456/03_2026/6pqy_20456.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6pqy_20456/03_2026/6pqy_20456.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6pqy_20456/03_2026/6pqy_20456.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6pqy_20456/03_2026/6pqy_20456.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6pqy_20456/03_2026/6pqy_20456.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6pqy_20456/03_2026/6pqy_20456.map"
  }
  resolution = 4.2
  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=   0.002
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
     P      64      5.49       5
     S      34      5.16       5
     C    5324      2.51       5
     N    1496      2.21       5
     O    1772      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 72 residue(s): 0.00s

  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: 8690
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3689
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 460, 3689
          Classifications: {'peptide': 460}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 442}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 333
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 333
          Classifications: {'DNA': 16}
          Link IDs: {'rna3p': 15}
    Chain: "C"
      Number of atoms: 323
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 323
          Classifications: {'DNA': 16}
          Link IDs: {'rna3p': 15}
    Chain: "D"
      Number of atoms: 3689
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 460, 3689
          Classifications: {'peptide': 460}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 442}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "E"
      Number of atoms: 333
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 333
          Classifications: {'DNA': 16}
          Link IDs: {'rna3p': 15}
    Chain: "F"
      Number of atoms: 323
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 323
          Classifications: {'DNA': 16}
          Link IDs: {'rna3p': 15}
  Time building chain proxies: 1.80, per 1000 atoms: 0.21
  Number of scatterers: 8690
  At special positions: 0
  Unit cell: (85.05, 122.85, 92.4, 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      34     16.00
     P      64     15.00
     O    1772      8.00
     N    1496      7.00
     C    5324      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 289.0 milliseconds
  

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1764

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 4 sheets defined
      52.6% alpha, 14.8% beta
      28 base pairs and 50 stacking pairs defined.
    Time for finding SS restraints: 1.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 37
      removed outlier: 4.031A  pdb=" N   GLY A  31 " --> pdb=" O   GLU A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 39 through 53
      removed outlier: 3.582A  pdb=" N   GLU A  53 " --> pdb=" O   THR A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 73
      removed outlier: 3.722A  pdb=" N   VAL A  65 " --> pdb=" O   SER A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 106
      removed outlier: 4.271A  pdb=" N   ILE A 105 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 175
      removed outlier: 4.030A  pdb=" N   TYR A 174 " --> pdb=" O   SER A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 201
    Processing helix  chain 'A' and resid 226 through 232
    Processing helix  chain 'A' and resid 272 through 274
      No H-bonds generated for 'chain 'A' and resid 272 through 274'
    Processing helix  chain 'A' and resid 275 through 289
      removed outlier: 3.697A  pdb=" N   VAL A 279 " --> pdb=" O   ALA A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 322
      removed outlier: 3.690A  pdb=" N   ASN A 322 " --> pdb=" O   LYS A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 344
    Processing helix  chain 'A' and resid 347 through 355
    Processing helix  chain 'A' and resid 358 through 374
      removed outlier: 3.504A  pdb=" N   ILE A 362 " --> pdb=" O   ASP A 358 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ILE A 372 " --> pdb=" O   ILE A 368 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   THR A 373 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   SER A 374 " --> pdb=" O   GLN A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 398
    Processing helix  chain 'A' and resid 404 through 412
      removed outlier: 3.571A  pdb=" N   HIS A 408 " --> pdb=" O   SER A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 421
      removed outlier: 3.512A  pdb=" N   GLU A 420 " --> pdb=" O   ASP A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 448
    Processing helix  chain 'A' and resid 454 through 470
      removed outlier: 3.892A  pdb=" N   ASN A 458 " --> pdb=" O   ARG A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 496
      removed outlier: 3.554A  pdb=" N   LEU A 495 " --> pdb=" O   GLU A 491 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 25 through 37
      removed outlier: 4.031A  pdb=" N   GLY D  31 " --> pdb=" O   GLU D  27 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 39 through 53
      removed outlier: 3.582A  pdb=" N   GLU D  53 " --> pdb=" O   THR D  49 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 61 through 73
      removed outlier: 3.721A  pdb=" N   VAL D  65 " --> pdb=" O   SER D  61 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 89 through 106
      removed outlier: 4.270A  pdb=" N   ILE D 105 " --> pdb=" O   ILE D 101 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 171 through 175
      removed outlier: 4.031A  pdb=" N   TYR D 174 " --> pdb=" O   SER D 171 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 186 through 201
    Processing helix  chain 'D' and resid 226 through 232
    Processing helix  chain 'D' and resid 272 through 274
      No H-bonds generated for 'chain 'D' and resid 272 through 274'
    Processing helix  chain 'D' and resid 275 through 289
      removed outlier: 3.698A  pdb=" N   VAL D 279 " --> pdb=" O   ALA D 275 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 302 through 322
      removed outlier: 3.690A  pdb=" N   ASN D 322 " --> pdb=" O   LYS D 318 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 337 through 344
    Processing helix  chain 'D' and resid 347 through 355
    Processing helix  chain 'D' and resid 358 through 374
      removed outlier: 3.505A  pdb=" N   ILE D 362 " --> pdb=" O   ASP D 358 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ILE D 372 " --> pdb=" O   ILE D 368 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   THR D 373 " --> pdb=" O   LEU D 369 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   SER D 374 " --> pdb=" O   GLN D 370 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 379 through 398
    Processing helix  chain 'D' and resid 404 through 412
      removed outlier: 3.572A  pdb=" N   HIS D 408 " --> pdb=" O   SER D 404 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 413 through 421
      removed outlier: 3.512A  pdb=" N   GLU D 420 " --> pdb=" O   ASP D 416 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 430 through 448
    Processing helix  chain 'D' and resid 454 through 470
      removed outlier: 3.892A  pdb=" N   ASN D 458 " --> pdb=" O   ARG D 454 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 489 through 496
      removed outlier: 3.554A  pdb=" N   LEU D 495 " --> pdb=" O   GLU D 491 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81
      removed outlier: 6.408A  pdb=" N   THR A 149 " --> pdb=" O   VAL A 178 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   PHE A 180 " --> pdb=" O   PHE A 147 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   PHE A 147 " --> pdb=" O   PHE A 180 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81
      removed outlier: 6.408A  pdb=" N   THR A 149 " --> pdb=" O   VAL A 178 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   PHE A 180 " --> pdb=" O   PHE A 147 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   PHE A 147 " --> pdb=" O   PHE A 180 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ASP A 125 " --> pdb=" O   MET A 148 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   ILE A 119 " --> pdb=" O   LEU A 154 " (cutoff:3.500A)
      removed outlier: 5.025A  pdb=" N   LEU A 156 " --> pdb=" O   ILE A 117 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   ILE A 117 " --> pdb=" O   LEU A 156 " (cutoff:3.500A)
      removed outlier: 10.174A  pdb=" N   LEU A 116 " --> pdb=" O   HIS A 216 " (cutoff:3.500A)
      removed outlier: 11.586A  pdb=" N   LEU A 218 " --> pdb=" O   LEU A 116 " (cutoff:3.500A)
      removed outlier: 10.387A  pdb=" N   LEU A 118 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
      removed outlier: 11.390A  pdb=" N   MET A 220 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
      removed outlier: 11.195A  pdb=" N   SER A 120 " --> pdb=" O   MET A 220 " (cutoff:3.500A)
      removed outlier: 8.487A  pdb=" N   MET A 222 " --> pdb=" O   SER A 120 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   TRP A 122 " --> pdb=" O   MET A 222 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 80 through 81
      removed outlier: 6.408A  pdb=" N   THR D 149 " --> pdb=" O   VAL D 178 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   PHE D 180 " --> pdb=" O   PHE D 147 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   PHE D 147 " --> pdb=" O   PHE D 180 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 80 through 81
      removed outlier: 6.408A  pdb=" N   THR D 149 " --> pdb=" O   VAL D 178 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   PHE D 180 " --> pdb=" O   PHE D 147 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   PHE D 147 " --> pdb=" O   PHE D 180 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ASP D 125 " --> pdb=" O   MET D 148 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   ILE D 119 " --> pdb=" O   LEU D 154 " (cutoff:3.500A)
      removed outlier: 5.024A  pdb=" N   LEU D 156 " --> pdb=" O   ILE D 117 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   ILE D 117 " --> pdb=" O   LEU D 156 " (cutoff:3.500A)
      removed outlier: 10.174A  pdb=" N   LEU D 116 " --> pdb=" O   HIS D 216 " (cutoff:3.500A)
      removed outlier: 11.587A  pdb=" N   LEU D 218 " --> pdb=" O   LEU D 116 " (cutoff:3.500A)
      removed outlier: 10.386A  pdb=" N   LEU D 118 " --> pdb=" O   LEU D 218 " (cutoff:3.500A)
      removed outlier: 11.390A  pdb=" N   MET D 220 " --> pdb=" O   LEU D 118 " (cutoff:3.500A)
      removed outlier: 11.194A  pdb=" N   SER D 120 " --> pdb=" O   MET D 220 " (cutoff:3.500A)
      removed outlier: 8.488A  pdb=" N   MET D 222 " --> pdb=" O   SER D 120 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   TRP D 122 " --> pdb=" O   MET D 222 " (cutoff:3.500A)

    362 hydrogen bonds defined for protein.
    1044 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      70 hydrogen bonds
      140 hydrogen bond angles
      0 basepair planarities
      28 basepair parallelities
      50 stacking parallelities
  Total time for adding SS restraints: 1.47

  Time building geometry restraints manager: 0.82 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2151
        1.33 -     1.45: 1973
        1.45 -     1.57: 4688
        1.57 -     1.69: 124
        1.69 -     1.81: 52
  Bond restraints: 8988
  Sorted by residual:
  bond pdb=" O3'  DC F  12 "
       pdb=" P    DC F  13 "
    ideal  model  delta    sigma   weight residual
    1.607  1.647 -0.040 1.50e-02 4.44e+03 7.16e+00
  bond pdb=" O3'  DC C  12 "
       pdb=" P    DC C  13 "
    ideal  model  delta    sigma   weight residual
    1.607  1.644 -0.037 1.50e-02 4.44e+03 6.15e+00
  bond pdb=" C1'  DT B  22 "
       pdb=" N1   DT B  22 "
    ideal  model  delta    sigma   weight residual
    1.490  1.441  0.049 3.00e-02 1.11e+03 2.67e+00
  bond pdb=" C1'  DT E  22 "
       pdb=" N1   DT E  22 "
    ideal  model  delta    sigma   weight residual
    1.490  1.441  0.049 3.00e-02 1.11e+03 2.63e+00
  bond pdb=" CB  TRP D  41 "
       pdb=" CG  TRP D  41 "
    ideal  model  delta    sigma   weight residual
    1.498  1.449  0.049 3.10e-02 1.04e+03 2.47e+00
  ... (remaining 8983 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.26: 11886
        2.26 -     4.51: 471
        4.51 -     6.77: 30
        6.77 -     9.03: 8
        9.03 -    11.29: 5
  Bond angle restraints: 12400
  Sorted by residual:
  angle pdb=" C4'  DC F  12 "
        pdb=" C3'  DC F  12 "
        pdb=" O3'  DC F  12 "
      ideal   model   delta    sigma   weight residual
     110.00  121.29  -11.29 1.50e+00 4.44e-01 5.66e+01
  angle pdb=" C4'  DC C  12 "
        pdb=" C3'  DC C  12 "
        pdb=" O3'  DC C  12 "
      ideal   model   delta    sigma   weight residual
     110.00  120.69  -10.69 1.50e+00 4.44e-01 5.08e+01
  angle pdb=" O3'  DT C  15 "
        pdb=" C3'  DT C  15 "
        pdb=" C2'  DT C  15 "
      ideal   model   delta    sigma   weight residual
     111.50  120.80   -9.30 1.50e+00 4.44e-01 3.84e+01
  angle pdb=" C3'  DC F  12 "
        pdb=" C2'  DC F  12 "
        pdb=" C1'  DC F  12 "
      ideal   model   delta    sigma   weight residual
     101.60  107.16   -5.56 1.50e+00 4.44e-01 1.37e+01
  angle pdb=" C3'  DC C  12 "
        pdb=" C2'  DC C  12 "
        pdb=" C1'  DC C  12 "
      ideal   model   delta    sigma   weight residual
     101.60  106.93   -5.33 1.50e+00 4.44e-01 1.26e+01
  ... (remaining 12395 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.87: 4952
       35.87 -    71.75: 328
       71.75 -   107.62: 10
      107.62 -   143.49: 0
      143.49 -   179.36: 10
  Dihedral angle restraints: 5300
    sinusoidal: 2588
      harmonic: 2712
  Sorted by residual:
  dihedral pdb=" CA  ASP D 161 "
           pdb=" C   ASP D 161 "
           pdb=" N   THR D 162 "
           pdb=" CA  THR D 162 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.62   25.38     0      5.00e+00 4.00e-02 2.58e+01
  dihedral pdb=" CA  ASP A 161 "
           pdb=" C   ASP A 161 "
           pdb=" N   THR A 162 "
           pdb=" CA  THR A 162 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.62   25.38     0      5.00e+00 4.00e-02 2.58e+01
  dihedral pdb=" CA  SER A 453 "
           pdb=" C   SER A 453 "
           pdb=" N   ARG A 454 "
           pdb=" CA  ARG A 454 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.18   24.82     0      5.00e+00 4.00e-02 2.46e+01
  ... (remaining 5297 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1122
       0.073 -    0.146: 238
       0.146 -    0.219: 31
       0.219 -    0.292: 6
       0.292 -    0.364: 3
  Chirality restraints: 1400
  Sorted by residual:
  chirality pdb=" C3'  DC F  12 "
            pdb=" C4'  DC F  12 "
            pdb=" O3'  DC F  12 "
            pdb=" C2'  DC F  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.30   -0.36 2.00e-01 2.50e+01 3.32e+00
  chirality pdb=" C3'  DC C  12 "
            pdb=" C4'  DC C  12 "
            pdb=" O3'  DC C  12 "
            pdb=" C2'  DC C  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.30   -0.36 2.00e-01 2.50e+01 3.32e+00
  chirality pdb=" C3'  DT C  15 "
            pdb=" C4'  DT C  15 "
            pdb=" O3'  DT C  15 "
            pdb=" C2'  DT C  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.34   -0.33 2.00e-01 2.50e+01 2.64e+00
  ... (remaining 1397 not shown)

  Planarity restraints: 1348
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC C  12 "    0.041 2.00e-02 2.50e+03   2.75e-02 1.71e+01
        pdb=" N1   DC C  12 "   -0.000 2.00e-02 2.50e+03
        pdb=" C2   DC C  12 "    0.002 2.00e-02 2.50e+03
        pdb=" O2   DC C  12 "   -0.033 2.00e-02 2.50e+03
        pdb=" N3   DC C  12 "    0.000 2.00e-02 2.50e+03
        pdb=" C4   DC C  12 "    0.047 2.00e-02 2.50e+03
        pdb=" N4   DC C  12 "    0.002 2.00e-02 2.50e+03
        pdb=" C5   DC C  12 "   -0.025 2.00e-02 2.50e+03
        pdb=" C6   DC C  12 "   -0.035 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT C  15 "   -0.051 2.00e-02 2.50e+03   2.26e-02 1.28e+01
        pdb=" N1   DT C  15 "    0.024 2.00e-02 2.50e+03
        pdb=" C2   DT C  15 "    0.018 2.00e-02 2.50e+03
        pdb=" O2   DT C  15 "    0.011 2.00e-02 2.50e+03
        pdb=" N3   DT C  15 "   -0.009 2.00e-02 2.50e+03
        pdb=" C4   DT C  15 "    0.000 2.00e-02 2.50e+03
        pdb=" O4   DT C  15 "   -0.026 2.00e-02 2.50e+03
        pdb=" C5   DT C  15 "    0.013 2.00e-02 2.50e+03
        pdb=" C7   DT C  15 "   -0.005 2.00e-02 2.50e+03
        pdb=" C6   DT C  15 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA B  30 "    0.019 2.00e-02 2.50e+03   2.07e-02 1.18e+01
        pdb=" N9   DA B  30 "   -0.053 2.00e-02 2.50e+03
        pdb=" C8   DA B  30 "    0.037 2.00e-02 2.50e+03
        pdb=" N7   DA B  30 "   -0.009 2.00e-02 2.50e+03
        pdb=" C5   DA B  30 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6   DA B  30 "    0.001 2.00e-02 2.50e+03
        pdb=" N6   DA B  30 "    0.001 2.00e-02 2.50e+03
        pdb=" N1   DA B  30 "    0.005 2.00e-02 2.50e+03
        pdb=" C2   DA B  30 "    0.005 2.00e-02 2.50e+03
        pdb=" N3   DA B  30 "    0.005 2.00e-02 2.50e+03
        pdb=" C4   DA B  30 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1345 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1501
        2.76 -     3.30: 9795
        3.30 -     3.83: 15952
        3.83 -     4.37: 17791
        4.37 -     4.90: 25995
  Nonbonded interactions: 71034
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 149 "
            pdb=" OE1 GLN A 179 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OG1 THR D 149 "
            pdb=" OE1 GLN D 179 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" N   ASP D 500 "
            pdb=" OD1 ASP D 500 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" N   ASP A 500 "
            pdb=" OD1 ASP A 500 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" O   VAL D  81 "
            pdb=" NE2 GLN D 455 "
     model   vdw
     2.244 3.120
  ... (remaining 71029 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             0.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.580
  Find NCS groups from input model:        0.220
  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:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049   8988  Z= 0.361
  Angle     :  0.987  11.285  12400  Z= 0.578
  Chirality :  0.064   0.364   1400
  Planarity :  0.007   0.066   1348
  Dihedral  : 22.029 179.364   3536
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 25.03
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  :  6.83 %
    Favored  : 92.51 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  5.38 %
    Favored  : 94.13 %
  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: -4.46 (0.22), residues: 908
  helix: -2.68 (0.18), residues: 438
  sheet: -3.07 (0.55), residues: 60
  loop : -3.19 (0.26), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.044   0.008   ARG A 343 
 TYR   0.023   0.005   TYR A 174 
 PHE   0.028   0.003   PHE A 102 
 TRP   0.021   0.003   TRP D  41 
 HIS   0.015   0.003   HIS A 448 

Details of bonding type rmsd
  covalent geometry    : bond        0.00747 ( 8988)
  covalent geometry    : angle       0.98663 (12400)
  hydrogen bonds       : bond        0.14250 (  418)
  hydrogen bonds       : angle       7.33435 ( 1184)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 143
  time to evaluate  : 0.321 
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  197 MET cc_start: 0.8184 (mmm) cc_final: 0.7776 (mmp)
REVERT: A  280 MET cc_start: 0.7800 (ppp) cc_final: 0.7234 (ppp)
REVERT: A  337 ASP cc_start: 0.4447 (m-30) cc_final: 0.3872 (m-30)
REVERT: D  193 GLU cc_start: 0.9063 (tp30) cc_final: 0.8540 (tp30)
REVERT: D  197 MET cc_start: 0.8507 (mmm) cc_final: 0.7847 (mmp)
REVERT: D  204 LEU cc_start: 0.8835 (pp) cc_final: 0.8560 (pt)
REVERT: D  280 MET cc_start: 0.7380 (ppp) cc_final: 0.6939 (ppp)
REVERT: D  337 ASP cc_start: 0.3946 (m-30) cc_final: 0.3736 (m-30)
  outliers start: 4
  outliers final: 1
  residues processed: 147
  average time/residue: 0.1180
  time to fit residues: 22.7039
Evaluate side-chains
  90 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 89
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    7.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 166 ASN
** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 166 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.128022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.096552 restraints weight = 30600.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.100135 restraints weight = 16105.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.102385 restraints weight = 10469.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.103853 restraints weight = 7856.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.104663 restraints weight = 6494.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.2350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8988  Z= 0.178
  Angle     :  0.672   6.429  12400  Z= 0.373
  Chirality :  0.041   0.140   1400
  Planarity :  0.005   0.058   1348
  Dihedral  : 25.232 179.932   1688
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 15.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.70 %
    Favored  : 92.30 %
  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: -2.46 (0.26), residues: 908
  helix: -0.87 (0.23), residues: 452
  sheet: -2.41 (0.57), residues: 54
  loop : -2.39 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 437 
 TYR   0.013   0.001   TYR A 174 
 PHE   0.018   0.002   PHE A 102 
 TRP   0.011   0.002   TRP D  41 
 HIS   0.007   0.002   HIS D 408 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 8988)
  covalent geometry    : angle       0.67237 (12400)
  hydrogen bonds       : bond        0.04713 (  418)
  hydrogen bonds       : angle       5.23411 ( 1184)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 ARG cc_start: 0.7437 (mmp-170) cc_final: 0.7036 (tmt170)
REVERT: A  115 GLN cc_start: 0.6720 (tp40) cc_final: 0.6071 (tp-100)
REVERT: A  176 ARG cc_start: 0.8713 (mtp85) cc_final: 0.7718 (mtp85)
REVERT: A  197 MET cc_start: 0.8104 (mmm) cc_final: 0.7695 (mmp)
REVERT: A  280 MET cc_start: 0.7926 (ppp) cc_final: 0.7507 (ppp)
REVERT: A  310 LYS cc_start: 0.6934 (tppt) cc_final: 0.6588 (tppt)
REVERT: D  106 ARG cc_start: 0.7865 (mmp-170) cc_final: 0.7432 (tmt170)
REVERT: D  146 ILE cc_start: 0.8909 (mm) cc_final: 0.8557 (mm)
REVERT: D  197 MET cc_start: 0.8460 (mmm) cc_final: 0.8157 (mmp)
REVERT: D  280 MET cc_start: 0.6990 (ppp) cc_final: 0.6643 (tpp)
REVERT: D  283 LEU cc_start: 0.7017 (pp) cc_final: 0.6808 (pp)
REVERT: D  443 ARG cc_start: 0.8872 (ttp-170) cc_final: 0.8189 (mmm160)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.1109
  time to fit residues: 21.4466
Evaluate side-chains
  104 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 71 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 29 optimal weight:    6.9990
   chunk 21 optimal weight:    5.9990
   chunk 73 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 33 optimal weight:    9.9990
   chunk 37 optimal weight:    0.3980
   chunk 76 optimal weight:    6.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 115 GLN
A 129 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.131962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.101498 restraints weight = 30329.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.105071 restraints weight = 15865.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.107369 restraints weight = 10355.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.108676 restraints weight = 7767.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.109752 restraints weight = 6479.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.3918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.3403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8988  Z= 0.134
  Angle     :  0.616   7.244  12400  Z= 0.340
  Chirality :  0.041   0.216   1400
  Planarity :  0.004   0.040   1348
  Dihedral  : 24.687 178.846   1688
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.79 %
    Favored  : 96.09 %
  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: -1.62 (0.27), residues: 908
  helix: -0.17 (0.23), residues: 458
  sheet: -1.43 (0.64), residues: 54
  loop : -2.10 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 106 
 TYR   0.013   0.001   TYR A 288 
 PHE   0.036   0.002   PHE A 102 
 TRP   0.015   0.002   TRP D 400 
 HIS   0.005   0.001   HIS D 307 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 8988)
  covalent geometry    : angle       0.61627 (12400)
  hydrogen bonds       : bond        0.03743 (  418)
  hydrogen bonds       : angle       4.56263 ( 1184)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 155
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LEU cc_start: 0.8737 (tp) cc_final: 0.8460 (tt)
REVERT: A   72 CYS cc_start: 0.9075 (m) cc_final: 0.8857 (m)
REVERT: A  115 GLN cc_start: 0.6685 (tp-100) cc_final: 0.6234 (tp-100)
REVERT: A  146 ILE cc_start: 0.9063 (mm) cc_final: 0.8799 (mm)
REVERT: A  233 GLU cc_start: 0.6725 (mp0) cc_final: 0.6394 (tm-30)
REVERT: A  280 MET cc_start: 0.7607 (ppp) cc_final: 0.7162 (ppp)
REVERT: A  310 LYS cc_start: 0.6940 (tppt) cc_final: 0.6651 (tppt)
REVERT: A  337 ASP cc_start: 0.4921 (m-30) cc_final: 0.4718 (m-30)
REVERT: A  467 ILE cc_start: 0.9414 (mt) cc_final: 0.9169 (tp)
REVERT: D  106 ARG cc_start: 0.7931 (mmp-170) cc_final: 0.7659 (tmt170)
REVERT: D  146 ILE cc_start: 0.8918 (mm) cc_final: 0.8669 (mm)
REVERT: D  197 MET cc_start: 0.8551 (mmm) cc_final: 0.8012 (mmp)
REVERT: D  283 LEU cc_start: 0.6749 (pp) cc_final: 0.6494 (pp)
REVERT: D  443 ARG cc_start: 0.8753 (ttp-170) cc_final: 0.7891 (mmm160)
  outliers start: 1
  outliers final: 0
  residues processed: 155
  average time/residue: 0.1006
  time to fit residues: 21.4424
Evaluate side-chains
  113 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 26 optimal weight:    8.9990
   chunk 4 optimal weight:    5.9990
   chunk 22 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9980
   chunk 71 optimal weight:    0.0980
   chunk 60 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   chunk 86 optimal weight:    1.9990
   chunk 90 optimal weight:    0.5980
   chunk 51 optimal weight:    0.0270
   chunk 58 optimal weight:    5.9990
   overall best weight:    0.7440

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

Flipped N/Q/H residues before XYZ refinement:
A  66 GLN
D  66 GLN
D 336 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.133865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.103117 restraints weight = 31167.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.106928 restraints weight = 16289.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.109301 restraints weight = 10468.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.110880 restraints weight = 7786.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.111854 restraints weight = 6365.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.4153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8988  Z= 0.127
  Angle     :  0.589   7.042  12400  Z= 0.323
  Chirality :  0.039   0.142   1400
  Planarity :  0.004   0.039   1348
  Dihedral  : 24.533 178.002   1688
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 12.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  1.96 %
    Favored  : 97.80 %
  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 are not related in a simple way.
  whole: -1.21 (0.27), residues: 908
  helix:  0.16 (0.24), residues: 452
  sheet: -0.96 (0.72), residues: 54
  loop : -1.91 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 342 
 TYR   0.022   0.001   TYR D  73 
 PHE   0.025   0.002   PHE D 102 
 TRP   0.017   0.001   TRP D 400 
 HIS   0.004   0.001   HIS D 307 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 8988)
  covalent geometry    : angle       0.58910 (12400)
  hydrogen bonds       : bond        0.03496 (  418)
  hydrogen bonds       : angle       4.34543 ( 1184)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 142
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LEU cc_start: 0.8822 (tp) cc_final: 0.8536 (tt)
REVERT: A   36 LEU cc_start: 0.9036 (mp) cc_final: 0.8803 (mp)
REVERT: A  106 ARG cc_start: 0.6201 (tmt170) cc_final: 0.5616 (tmt170)
REVERT: A  115 GLN cc_start: 0.6446 (tp-100) cc_final: 0.6183 (tp-100)
REVERT: A  219 MET cc_start: 0.7942 (mmp) cc_final: 0.7711 (mmp)
REVERT: A  233 GLU cc_start: 0.6325 (mp0) cc_final: 0.5821 (tm-30)
REVERT: A  280 MET cc_start: 0.7301 (ppp) cc_final: 0.6798 (ppp)
REVERT: A  446 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8244 (tp30)
REVERT: A  464 MET cc_start: 0.8667 (tpp) cc_final: 0.8294 (tpp)
REVERT: A  488 TYR cc_start: 0.4767 (m-80) cc_final: 0.4005 (m-10)
REVERT: D   36 LEU cc_start: 0.8941 (mp) cc_final: 0.8737 (mp)
REVERT: D  146 ILE cc_start: 0.8883 (mm) cc_final: 0.8582 (mm)
REVERT: D  161 ASP cc_start: 0.7125 (p0) cc_final: 0.6349 (m-30)
REVERT: D  197 MET cc_start: 0.8516 (mmm) cc_final: 0.8134 (mmp)
REVERT: D  219 MET cc_start: 0.7514 (mmm) cc_final: 0.7286 (mmm)
REVERT: D  340 THR cc_start: 0.7676 (m) cc_final: 0.7287 (p)
REVERT: D  416 ASP cc_start: 0.8090 (t0) cc_final: 0.7673 (p0)
REVERT: D  443 ARG cc_start: 0.8643 (ttp-170) cc_final: 0.7805 (mmm160)
  outliers start: 2
  outliers final: 2
  residues processed: 144
  average time/residue: 0.1071
  time to fit residues: 20.4732
Evaluate side-chains
  105 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 103
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 79 optimal weight:    5.9990
   chunk 3 optimal weight:    0.3980
   chunk 19 optimal weight:    6.9990
   chunk 52 optimal weight:    4.9990
   chunk 95 optimal weight:    5.9990
   chunk 56 optimal weight:    0.6980
   chunk 47 optimal weight:    5.9990
   chunk 84 optimal weight:    5.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
D 115 GLN
D 463 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.131542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.099982 restraints weight = 30361.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.103659 restraints weight = 15777.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.105997 restraints weight = 10263.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.107552 restraints weight = 7734.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.108426 restraints weight = 6373.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.4411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8988  Z= 0.144
  Angle     :  0.596   5.836  12400  Z= 0.326
  Chirality :  0.040   0.160   1400
  Planarity :  0.004   0.041   1348
  Dihedral  : 24.468 178.350   1688
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  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: -1.12 (0.27), residues: 908
  helix:  0.16 (0.24), residues: 458
  sheet: -0.84 (0.64), residues: 64
  loop : -1.82 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 342 
 TYR   0.022   0.001   TYR A 288 
 PHE   0.025   0.002   PHE A 365 
 TRP   0.011   0.002   TRP D 400 
 HIS   0.003   0.001   HIS D 307 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8988)
  covalent geometry    : angle       0.59634 (12400)
  hydrogen bonds       : bond        0.03457 (  418)
  hydrogen bonds       : angle       4.30873 ( 1184)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LEU cc_start: 0.8830 (tp) cc_final: 0.8543 (tt)
REVERT: A   36 LEU cc_start: 0.9025 (mp) cc_final: 0.8780 (mp)
REVERT: A  106 ARG cc_start: 0.6176 (tmt170) cc_final: 0.5758 (tmt170)
REVERT: A  115 GLN cc_start: 0.6510 (tp-100) cc_final: 0.6242 (tp-100)
REVERT: A  146 ILE cc_start: 0.9091 (mm) cc_final: 0.8888 (mm)
REVERT: A  219 MET cc_start: 0.8107 (mmp) cc_final: 0.7793 (mmp)
REVERT: A  233 GLU cc_start: 0.6518 (mp0) cc_final: 0.5984 (tm-30)
REVERT: A  280 MET cc_start: 0.7284 (ppp) cc_final: 0.6767 (ppp)
REVERT: A  439 LYS cc_start: 0.8518 (tttt) cc_final: 0.8073 (ptmt)
REVERT: A  446 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8297 (tp30)
REVERT: A  464 MET cc_start: 0.8661 (tpp) cc_final: 0.8300 (tpp)
REVERT: A  488 TYR cc_start: 0.4612 (m-80) cc_final: 0.4016 (m-10)
REVERT: D  103 GLU cc_start: 0.8818 (pt0) cc_final: 0.8282 (pp20)
REVERT: D  106 ARG cc_start: 0.6319 (tmt170) cc_final: 0.5802 (tmt170)
REVERT: D  146 ILE cc_start: 0.8942 (mm) cc_final: 0.8661 (mm)
REVERT: D  161 ASP cc_start: 0.7261 (p0) cc_final: 0.6646 (m-30)
REVERT: D  197 MET cc_start: 0.8532 (mmm) cc_final: 0.8110 (mmp)
REVERT: D  219 MET cc_start: 0.7549 (mmm) cc_final: 0.7328 (mmm)
REVERT: D  233 GLU cc_start: 0.6512 (mp0) cc_final: 0.6122 (tm-30)
REVERT: D  416 ASP cc_start: 0.8094 (t0) cc_final: 0.7671 (p0)
REVERT: D  417 ILE cc_start: 0.8528 (tp) cc_final: 0.8324 (tp)
REVERT: D  439 LYS cc_start: 0.8583 (tttt) cc_final: 0.8155 (ptmt)
REVERT: D  443 ARG cc_start: 0.8659 (ttp-170) cc_final: 0.7788 (mmm160)
REVERT: D  464 MET cc_start: 0.8797 (tpp) cc_final: 0.7921 (tpp)
REVERT: D  472 LEU cc_start: 0.9244 (tp) cc_final: 0.8970 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.0980
  time to fit residues: 18.4788
Evaluate side-chains
  104 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 35 optimal weight:   10.0000
   chunk 61 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 75 optimal weight:   10.0000
   chunk 20 optimal weight:   10.0000
   chunk 18 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0470
   chunk 94 optimal weight:    5.9990
   chunk 63 optimal weight:    5.9990
   chunk 90 optimal weight:    0.9990
   overall best weight:    1.7684

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

Flipped N/Q/H residues before XYZ refinement:
A 129 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.130195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.098776 restraints weight = 30843.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.102300 restraints weight = 16581.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.104576 restraints weight = 10959.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.105851 restraints weight = 8294.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 58)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.106896 restraints weight = 6993.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.4601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8988  Z= 0.157
  Angle     :  0.602   6.539  12400  Z= 0.330
  Chirality :  0.040   0.160   1400
  Planarity :  0.004   0.040   1348
  Dihedral  : 24.404 179.010   1688
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 14.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  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 are not related in a simple way.
  whole: -1.11 (0.28), residues: 908
  helix:  0.14 (0.24), residues: 458
  sheet: -1.00 (0.64), residues: 64
  loop : -1.74 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 343 
 TYR   0.012   0.001   TYR A 174 
 PHE   0.033   0.002   PHE A 102 
 TRP   0.011   0.002   TRP A 400 
 HIS   0.003   0.001   HIS A 408 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 8988)
  covalent geometry    : angle       0.60224 (12400)
  hydrogen bonds       : bond        0.03735 (  418)
  hydrogen bonds       : angle       4.36543 ( 1184)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LEU cc_start: 0.8865 (tp) cc_final: 0.8593 (tt)
REVERT: A   36 LEU cc_start: 0.8928 (mp) cc_final: 0.8724 (mp)
REVERT: A  115 GLN cc_start: 0.6718 (tp-100) cc_final: 0.6412 (tp-100)
REVERT: A  219 MET cc_start: 0.8198 (mmp) cc_final: 0.7882 (mmp)
REVERT: A  233 GLU cc_start: 0.6520 (mp0) cc_final: 0.5976 (tm-30)
REVERT: A  280 MET cc_start: 0.7291 (ppp) cc_final: 0.6782 (ppp)
REVERT: A  310 LYS cc_start: 0.7107 (tppt) cc_final: 0.6541 (pptt)
REVERT: A  439 LYS cc_start: 0.8586 (tttt) cc_final: 0.8127 (ptmt)
REVERT: A  446 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8348 (tp30)
REVERT: A  464 MET cc_start: 0.8758 (tpp) cc_final: 0.8173 (tpp)
REVERT: A  488 TYR cc_start: 0.4788 (m-80) cc_final: 0.4125 (m-80)
REVERT: D  103 GLU cc_start: 0.8855 (pt0) cc_final: 0.8321 (pp20)
REVERT: D  106 ARG cc_start: 0.6453 (tmt170) cc_final: 0.5797 (tmt170)
REVERT: D  146 ILE cc_start: 0.8975 (mm) cc_final: 0.8686 (mm)
REVERT: D  161 ASP cc_start: 0.7086 (p0) cc_final: 0.6502 (m-30)
REVERT: D  197 MET cc_start: 0.8553 (mmm) cc_final: 0.8159 (mmp)
REVERT: D  219 MET cc_start: 0.7629 (mmm) cc_final: 0.7383 (mmm)
REVERT: D  233 GLU cc_start: 0.6842 (mp0) cc_final: 0.6215 (tm-30)
REVERT: D  340 THR cc_start: 0.7557 (m) cc_final: 0.7293 (m)
REVERT: D  416 ASP cc_start: 0.8230 (t0) cc_final: 0.7779 (p0)
REVERT: D  417 ILE cc_start: 0.8473 (tp) cc_final: 0.8261 (tp)
REVERT: D  439 LYS cc_start: 0.8690 (tttt) cc_final: 0.8236 (ptmt)
REVERT: D  443 ARG cc_start: 0.8744 (ttp-170) cc_final: 0.7807 (mmm160)
REVERT: D  464 MET cc_start: 0.8820 (tpp) cc_final: 0.7886 (tpp)
REVERT: D  472 LEU cc_start: 0.9236 (tp) cc_final: 0.8959 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.0965
  time to fit residues: 17.7033
Evaluate side-chains
  108 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 55 optimal weight:    0.8980
   chunk 57 optimal weight:    4.9990
   chunk 18 optimal weight:    8.9990
   chunk 94 optimal weight:    5.9990
   chunk 27 optimal weight:    9.9990
   chunk 51 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 29 optimal weight:    6.9990
   chunk 93 optimal weight:    0.7980
   chunk 63 optimal weight:    7.9990
   overall best weight:    2.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 129 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 = 0.4134 r_free = 0.4134 target = 0.124428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.092677 restraints weight = 31163.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.096103 restraints weight = 16746.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.098342 restraints weight = 11036.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.099641 restraints weight = 8330.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 64)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.100687 restraints weight = 6988.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.4624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   8988  Z= 0.216
  Angle     :  0.673   7.316  12400  Z= 0.368
  Chirality :  0.042   0.147   1400
  Planarity :  0.004   0.049   1348
  Dihedral  : 24.306 179.690   1688
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 18.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  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: -1.31 (0.27), residues: 908
  helix: -0.10 (0.24), residues: 454
  sheet: -1.02 (0.65), residues: 62
  loop : -1.71 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 316 
 TYR   0.015   0.002   TYR D 488 
 PHE   0.030   0.002   PHE A 102 
 TRP   0.015   0.002   TRP D 295 
 HIS   0.007   0.001   HIS D 413 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 ( 8988)
  covalent geometry    : angle       0.67325 (12400)
  hydrogen bonds       : bond        0.04519 (  418)
  hydrogen bonds       : angle       4.78009 ( 1184)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LEU cc_start: 0.8913 (tp) cc_final: 0.8675 (tt)
REVERT: A   36 LEU cc_start: 0.8960 (mp) cc_final: 0.8742 (mp)
REVERT: A  106 ARG cc_start: 0.6334 (tmt170) cc_final: 0.5956 (tmt170)
REVERT: A  115 GLN cc_start: 0.6828 (tp-100) cc_final: 0.6482 (tp-100)
REVERT: A  219 MET cc_start: 0.8572 (mmp) cc_final: 0.8235 (mmp)
REVERT: A  220 MET cc_start: 0.8214 (ttm) cc_final: 0.7906 (tpt)
REVERT: A  233 GLU cc_start: 0.6631 (mp0) cc_final: 0.6127 (tm-30)
REVERT: A  268 PHE cc_start: 0.4575 (m-80) cc_final: 0.4343 (m-80)
REVERT: A  280 MET cc_start: 0.7397 (ppp) cc_final: 0.6841 (ppp)
REVERT: A  310 LYS cc_start: 0.7171 (tppt) cc_final: 0.6608 (pptt)
REVERT: A  439 LYS cc_start: 0.8722 (tttt) cc_final: 0.8248 (ptmt)
REVERT: A  464 MET cc_start: 0.8826 (tpp) cc_final: 0.8238 (tpp)
REVERT: D  106 ARG cc_start: 0.6493 (tmt170) cc_final: 0.5661 (tmt170)
REVERT: D  116 LEU cc_start: 0.8066 (mt) cc_final: 0.7863 (mt)
REVERT: D  146 ILE cc_start: 0.9018 (mm) cc_final: 0.8717 (mm)
REVERT: D  161 ASP cc_start: 0.7503 (p0) cc_final: 0.6880 (m-30)
REVERT: D  197 MET cc_start: 0.8635 (mmm) cc_final: 0.8219 (mmp)
REVERT: D  219 MET cc_start: 0.7678 (mmm) cc_final: 0.7419 (mmm)
REVERT: D  233 GLU cc_start: 0.6909 (mp0) cc_final: 0.6430 (tm-30)
REVERT: D  416 ASP cc_start: 0.8298 (t0) cc_final: 0.7863 (p0)
REVERT: D  439 LYS cc_start: 0.8842 (tttt) cc_final: 0.8440 (ptmt)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.1008
  time to fit residues: 17.9707
Evaluate side-chains
  112 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 62 optimal weight:    0.0570
   chunk 67 optimal weight:   10.0000
   chunk 5 optimal weight:    0.4980
   chunk 45 optimal weight:    8.9990
   chunk 31 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 81 optimal weight:   10.0000
   chunk 55 optimal weight:    2.9990
   chunk 76 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.7102

-------------------------------------------------------------------------------
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 = 0.4267 r_free = 0.4267 target = 0.132932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.102289 restraints weight = 30437.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.105767 restraints weight = 16332.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.108005 restraints weight = 10792.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.109336 restraints weight = 8147.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.110347 restraints weight = 6809.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.3932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.5164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8988  Z= 0.128
  Angle     :  0.591   6.653  12400  Z= 0.325
  Chirality :  0.040   0.145   1400
  Planarity :  0.004   0.041   1348
  Dihedral  : 24.302 179.695   1688
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  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: -1.01 (0.28), residues: 908
  helix:  0.06 (0.24), residues: 464
  sheet: -0.71 (0.66), residues: 64
  loop : -1.52 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 443 
 TYR   0.028   0.001   TYR D  73 
 PHE   0.029   0.001   PHE A 102 
 TRP   0.013   0.001   TRP D 295 
 HIS   0.002   0.001   HIS D 307 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 8988)
  covalent geometry    : angle       0.59115 (12400)
  hydrogen bonds       : bond        0.03562 (  418)
  hydrogen bonds       : angle       4.32386 ( 1184)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LEU cc_start: 0.8750 (tp) cc_final: 0.8545 (tt)
REVERT: A   36 LEU cc_start: 0.8920 (mp) cc_final: 0.8702 (mp)
REVERT: A  102 PHE cc_start: 0.8741 (m-80) cc_final: 0.8260 (m-80)
REVERT: A  176 ARG cc_start: 0.8636 (mtp85) cc_final: 0.7745 (mtp85)
REVERT: A  219 MET cc_start: 0.8649 (mmp) cc_final: 0.8234 (mmp)
REVERT: A  233 GLU cc_start: 0.6534 (mp0) cc_final: 0.6125 (tm-30)
REVERT: A  280 MET cc_start: 0.7310 (ppp) cc_final: 0.6865 (ppp)
REVERT: A  310 LYS cc_start: 0.7121 (tppt) cc_final: 0.6588 (pptt)
REVERT: A  439 LYS cc_start: 0.8581 (tttt) cc_final: 0.8133 (ptmt)
REVERT: A  464 MET cc_start: 0.8766 (tpp) cc_final: 0.8116 (tpp)
REVERT: D   71 GLN cc_start: 0.9085 (mm110) cc_final: 0.8817 (tm-30)
REVERT: D  106 ARG cc_start: 0.6307 (tmt170) cc_final: 0.5558 (tmt170)
REVERT: D  116 LEU cc_start: 0.7977 (mt) cc_final: 0.7765 (mt)
REVERT: D  146 ILE cc_start: 0.8958 (mm) cc_final: 0.8660 (mm)
REVERT: D  161 ASP cc_start: 0.7257 (p0) cc_final: 0.6759 (m-30)
REVERT: D  176 ARG cc_start: 0.8735 (mtp85) cc_final: 0.7888 (mtp85)
REVERT: D  197 MET cc_start: 0.8588 (mmm) cc_final: 0.8200 (mmp)
REVERT: D  219 MET cc_start: 0.7751 (mmm) cc_final: 0.7470 (mmm)
REVERT: D  233 GLU cc_start: 0.6529 (mp0) cc_final: 0.6006 (tm-30)
REVERT: D  402 TYR cc_start: 0.6581 (m-80) cc_final: 0.6300 (m-10)
REVERT: D  416 ASP cc_start: 0.8223 (t0) cc_final: 0.7801 (p0)
REVERT: D  439 LYS cc_start: 0.8741 (tttt) cc_final: 0.8318 (ptmt)
REVERT: D  472 LEU cc_start: 0.9149 (tp) cc_final: 0.8880 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.1091
  time to fit residues: 20.1352
Evaluate side-chains
  105 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 15 optimal weight:    0.0570
   chunk 86 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 48 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 70 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    0.9704

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

Flipped N/Q/H residues before XYZ refinement:
A 408 HIS
D 285 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.130431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.099622 restraints weight = 29944.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.103162 restraints weight = 16023.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.105501 restraints weight = 10569.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.107006 restraints weight = 7955.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.107844 restraints weight = 6582.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.5468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8988  Z= 0.129
  Angle     :  0.592   6.900  12400  Z= 0.322
  Chirality :  0.039   0.161   1400
  Planarity :  0.004   0.040   1348
  Dihedral  : 24.222 177.972   1688
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 13.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.92 (0.28), residues: 908
  helix:  0.14 (0.24), residues: 464
  sheet: -0.70 (0.62), residues: 62
  loop : -1.48 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 443 
 TYR   0.026   0.001   TYR D  73 
 PHE   0.032   0.002   PHE D 102 
 TRP   0.011   0.001   TRP D 295 
 HIS   0.004   0.001   HIS A 408 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 8988)
  covalent geometry    : angle       0.59199 (12400)
  hydrogen bonds       : bond        0.03425 (  418)
  hydrogen bonds       : angle       4.23509 ( 1184)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 LEU cc_start: 0.8888 (mp) cc_final: 0.8650 (mp)
REVERT: A  102 PHE cc_start: 0.8825 (m-80) cc_final: 0.8363 (m-80)
REVERT: A  176 ARG cc_start: 0.8729 (mtp85) cc_final: 0.7766 (mtp85)
REVERT: A  219 MET cc_start: 0.8489 (mmp) cc_final: 0.8089 (mmp)
REVERT: A  280 MET cc_start: 0.7281 (ppp) cc_final: 0.6767 (ppp)
REVERT: A  310 LYS cc_start: 0.7120 (tppt) cc_final: 0.6545 (pptt)
REVERT: A  439 LYS cc_start: 0.8569 (tttt) cc_final: 0.8124 (ptmt)
REVERT: A  464 MET cc_start: 0.8769 (tpp) cc_final: 0.8244 (tpp)
REVERT: D   71 GLN cc_start: 0.9068 (mm110) cc_final: 0.8855 (tm-30)
REVERT: D  102 PHE cc_start: 0.8687 (m-80) cc_final: 0.8127 (m-80)
REVERT: D  106 ARG cc_start: 0.6276 (tmt170) cc_final: 0.6034 (tmt170)
REVERT: D  146 ILE cc_start: 0.9021 (mm) cc_final: 0.8749 (mm)
REVERT: D  161 ASP cc_start: 0.7487 (p0) cc_final: 0.7037 (m-30)
REVERT: D  176 ARG cc_start: 0.8789 (mtp85) cc_final: 0.7878 (mtp85)
REVERT: D  197 MET cc_start: 0.8551 (mmm) cc_final: 0.8148 (mmp)
REVERT: D  219 MET cc_start: 0.7792 (mmm) cc_final: 0.7527 (mmm)
REVERT: D  233 GLU cc_start: 0.6440 (mp0) cc_final: 0.5946 (tm-30)
REVERT: D  402 TYR cc_start: 0.6610 (m-80) cc_final: 0.6344 (m-10)
REVERT: D  416 ASP cc_start: 0.8186 (t0) cc_final: 0.7790 (p0)
REVERT: D  417 ILE cc_start: 0.8418 (tp) cc_final: 0.8208 (tp)
REVERT: D  439 LYS cc_start: 0.8721 (tttt) cc_final: 0.8292 (ptmt)
REVERT: D  464 MET cc_start: 0.9239 (ttm) cc_final: 0.8533 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.1083
  time to fit residues: 18.7740
Evaluate side-chains
  103 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 95 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 3 optimal weight:    0.8980
   chunk 73 optimal weight:    9.9990
   chunk 31 optimal weight:    7.9990
   chunk 52 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0770
   chunk 71 optimal weight:    3.9990
   chunk 24 optimal weight:   10.0000
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.1740

-------------------------------------------------------------------------------
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 = 0.4226 r_free = 0.4226 target = 0.130341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.099454 restraints weight = 29805.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.103005 restraints weight = 15959.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.105397 restraints weight = 10541.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.106876 restraints weight = 7934.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.107756 restraints weight = 6575.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.5618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8988  Z= 0.133
  Angle     :  0.589   8.184  12400  Z= 0.319
  Chirality :  0.040   0.201   1400
  Planarity :  0.004   0.040   1348
  Dihedral  : 24.177 178.672   1688
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  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: -0.89 (0.28), residues: 908
  helix:  0.14 (0.24), residues: 466
  sheet: -0.74 (0.60), residues: 62
  loop : -1.42 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 443 
 TYR   0.027   0.001   TYR D  73 
 PHE   0.029   0.002   PHE D 102 
 TRP   0.010   0.001   TRP D 295 
 HIS   0.003   0.001   HIS D 408 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 8988)
  covalent geometry    : angle       0.58920 (12400)
  hydrogen bonds       : bond        0.03345 (  418)
  hydrogen bonds       : angle       4.18953 ( 1184)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 PHE cc_start: 0.8830 (m-80) cc_final: 0.8393 (m-80)
REVERT: A  176 ARG cc_start: 0.8724 (mtp85) cc_final: 0.7720 (mtp85)
REVERT: A  219 MET cc_start: 0.8592 (mmp) cc_final: 0.8203 (mmp)
REVERT: A  280 MET cc_start: 0.7047 (ppp) cc_final: 0.6773 (tpt)
REVERT: A  310 LYS cc_start: 0.7197 (tppt) cc_final: 0.6588 (pptt)
REVERT: A  426 ILE cc_start: 0.7404 (mm) cc_final: 0.7080 (tp)
REVERT: A  439 LYS cc_start: 0.8569 (tttt) cc_final: 0.8093 (ptmt)
REVERT: A  464 MET cc_start: 0.8791 (tpp) cc_final: 0.8272 (tpp)
REVERT: D  102 PHE cc_start: 0.8705 (m-80) cc_final: 0.8204 (m-80)
REVERT: D  106 ARG cc_start: 0.6206 (tmt170) cc_final: 0.5746 (tmt170)
REVERT: D  161 ASP cc_start: 0.7479 (p0) cc_final: 0.7026 (m-30)
REVERT: D  176 ARG cc_start: 0.8785 (mtp85) cc_final: 0.7831 (mtp85)
REVERT: D  197 MET cc_start: 0.8524 (mmm) cc_final: 0.8137 (mmp)
REVERT: D  233 GLU cc_start: 0.6509 (mp0) cc_final: 0.5989 (tm-30)
REVERT: D  289 ARG cc_start: 0.6108 (mtt-85) cc_final: 0.5784 (mtt180)
REVERT: D  402 TYR cc_start: 0.6818 (m-80) cc_final: 0.6535 (m-10)
REVERT: D  416 ASP cc_start: 0.8176 (t0) cc_final: 0.7791 (p0)
REVERT: D  417 ILE cc_start: 0.8425 (tp) cc_final: 0.8216 (tp)
REVERT: D  439 LYS cc_start: 0.8744 (tttt) cc_final: 0.8322 (ptmt)
REVERT: D  464 MET cc_start: 0.9275 (ttm) cc_final: 0.8531 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.1056
  time to fit residues: 18.3388
Evaluate side-chains
  104 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 40 optimal weight:    8.9990
   chunk 92 optimal weight:    6.9990
   chunk 61 optimal weight:    7.9990
   chunk 66 optimal weight:    0.0040
   chunk 80 optimal weight:   10.0000
   chunk 89 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0070
   chunk 13 optimal weight:    6.9990
   chunk 91 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   overall best weight:    1.5814

-------------------------------------------------------------------------------
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 = 0.4205 r_free = 0.4205 target = 0.129500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.097895 restraints weight = 30195.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.101525 restraints weight = 16067.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.103871 restraints weight = 10529.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.105383 restraints weight = 7912.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.106280 restraints weight = 6538.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.5682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8988  Z= 0.148
  Angle     :  0.610   8.502  12400  Z= 0.330
  Chirality :  0.040   0.157   1400
  Planarity :  0.004   0.046   1348
  Dihedral  : 24.135 178.955   1688
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 14.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  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: -0.89 (0.28), residues: 908
  helix:  0.13 (0.24), residues: 468
  sheet: -0.71 (0.60), residues: 62
  loop : -1.42 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 443 
 TYR   0.026   0.001   TYR D  73 
 PHE   0.032   0.002   PHE D 102 
 TRP   0.011   0.002   TRP D 295 
 HIS   0.003   0.001   HIS D 408 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 8988)
  covalent geometry    : angle       0.60954 (12400)
  hydrogen bonds       : bond        0.03548 (  418)
  hydrogen bonds       : angle       4.24739 ( 1184)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1703.02 seconds
wall clock time: 30 minutes 4.98 seconds (1804.98 seconds total)