Starting phenix.real_space_refine
on Thu Feb  5 02:12:38 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ia5_52779/02_2026/9ia5_52779.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ia5_52779/02_2026/9ia5_52779.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ia5_52779/02_2026/9ia5_52779.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ia5_52779/02_2026/9ia5_52779.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ia5_52779/02_2026/9ia5_52779.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ia5_52779/02_2026/9ia5_52779.cif"
  }
  resolution = 2.63
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      29      5.16       5
     C    4529      2.51       5
     N    1246      2.21       5
     O    1399      1.98       5
     H    6858      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14061
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 11461
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 727, 11461
          Classifications: {'peptide': 727}
          Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 697}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 2432
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 153, 2432
          Classifications: {'peptide': 153}
          Link IDs: {'PTRANS': 8, 'TRANS': 144}
    Chain: "D"
      Number of atoms: 168
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 168
          Classifications: {'peptide': 11}
          Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 7}
  Time building chain proxies: 2.61, per 1000 atoms: 0.19
  Number of scatterers: 14061
  At special positions: 0
  Unit cell: (95.761, 79.679, 114.767, 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      29     16.00
     O    1399      8.00
     N    1246      7.00
     C    4529      6.00
     H    6858      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  31 " - pdb=" SG  CYS A 724 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 173 " - pdb=" SG  CYS A 725 " distance=2.00

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.30
  Conformation dependent library (CDL) restraints added in 463.4 milliseconds
  

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1670

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 3 sheets defined
      13.9% alpha, 42.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 34
      removed outlier: 3.955A  pdb=" N   GLY A  34 " --> pdb=" O   GLN A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 302
      removed outlier: 3.519A  pdb=" N   GLU A 301 " --> pdb=" O   VAL A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 463 through 470
      removed outlier: 3.671A  pdb=" N   ARG A 469 " --> pdb=" O   TRP A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 542
    Processing helix  chain 'A' and resid 631 through 633
      No H-bonds generated for 'chain 'A' and resid 631 through 633'
    Processing helix  chain 'A' and resid 660 through 668
    Processing helix  chain 'A' and resid 669 through 674
    Processing helix  chain 'A' and resid 675 through 680
      removed outlier: 4.699A  pdb=" N   ASN A 680 " --> pdb=" O   GLU A 676 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 768 through 773
    Processing helix  chain 'B' and resid 30 through 33
    Processing helix  chain 'B' and resid 45 through 58
    Processing helix  chain 'B' and resid 132 through 158
      removed outlier: 3.670A  pdb=" N   ASP B 149 " --> pdb=" O   LYS B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 171
      removed outlier: 3.545A  pdb=" N   ILE B 162 " --> pdb=" O   LYS B 158 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 55
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 81 through 83
    current: chain 'A' and resid 103 through 113
      removed outlier: 7.057A  pdb=" N   VAL A 104 " --> pdb=" O   ASN A 127 " (cutoff:3.500A)
      removed outlier: 5.719A  pdb=" N   ASN A 127 " --> pdb=" O   VAL A 104 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   ALA A 106 " --> pdb=" O   TRP A 125 " (cutoff:3.500A)
      removed outlier: 5.184A  pdb=" N   TRP A 125 " --> pdb=" O   ALA A 106 " (cutoff:3.500A)
      removed outlier: 7.498A  pdb=" N   GLY A 108 " --> pdb=" O   LYS A 123 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   LYS A 123 " --> pdb=" O   GLY A 108 " (cutoff:3.500A)
      removed outlier: 8.313A  pdb=" N   GLU A 137 " --> pdb=" O   PRO A 122 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   GLY A 124 " --> pdb=" O   VAL A 135 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   VAL A 135 " --> pdb=" O   GLY A 124 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   ALA A 126 " --> pdb=" O   THR A 133 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   THR A 133 " --> pdb=" O   ALA A 126 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   ASP A 152 " --> pdb=" O   GLU A 137 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ASP A 139 " --> pdb=" O   LYS A 150 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   LYS A 150 " --> pdb=" O   ASP A 139 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   GLN A 141 " --> pdb=" O   ARG A 148 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   ARG A 148 " --> pdb=" O   GLN A 141 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LEU A 153 " --> pdb=" O   ASP A 166 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 162 through 166
    current: chain 'A' and resid 180 through 183
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 180 through 183
    current: chain 'A' and resid 195 through 205
      removed outlier: 6.811A  pdb=" N   ARG A 202 " --> pdb=" O   TYR A 212 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   TYR A 212 " --> pdb=" O   ARG A 202 " (cutoff:3.500A)
      removed outlier: 7.531A  pdb=" N   LYS A 204 " --> pdb=" O   ILE A 210 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   ILE A 210 " --> pdb=" O   LYS A 204 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 227 through 228
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 227 through 228
    current: chain 'A' and resid 240 through 244
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 240 through 244
    current: chain 'A' and resid 255 through 264
      removed outlier: 3.557A  pdb=" N   MET A 264 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ASN A 269 " --> pdb=" O   MET A 264 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   THR A 356 " --> pdb=" O   THR A 332 " (cutoff:3.500A)
      removed outlier: 9.275A  pdb=" N   VAL A 334 " --> pdb=" O   TYR A 354 " (cutoff:3.500A)
      removed outlier: 11.061A  pdb=" N   TYR A 354 " --> pdb=" O   VAL A 334 " (cutoff:3.500A)
      removed outlier: 7.936A  pdb=" N   LYS A 375 " --> pdb=" O   GLU A 391 " (cutoff:3.500A)
      removed outlier: 5.393A  pdb=" N   GLU A 391 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 8.043A  pdb=" N   PHE A 377 " --> pdb=" O   SER A 389 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   SER A 389 " --> pdb=" O   PHE A 377 " (cutoff:3.500A)
      removed outlier: 5.468A  pdb=" N   ALA A 390 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   VAL A 418 " --> pdb=" O   ALA A 390 " (cutoff:3.500A)
      removed outlier: 5.691A  pdb=" N   PHE A 406 " --> pdb=" O   ASP A 402 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 445 through 453
    current: chain 'A' and resid 477 through 480
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 477 through 480
    current: chain 'A' and resid 505 through 517
      removed outlier: 7.507A  pdb=" N   ASN A 556 " --> pdb=" O   TYR A 584 " (cutoff:3.500A)
      removed outlier: 4.767A  pdb=" N   TYR A 584 " --> pdb=" O   ASN A 556 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   VAL A 558 " --> pdb=" O   ILE A 582 " (cutoff:3.500A)
      removed outlier: 4.819A  pdb=" N   ILE A 582 " --> pdb=" O   VAL A 558 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   THR A 560 " --> pdb=" O   GLY A 580 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   GLY A 580 " --> pdb=" O   THR A 560 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   VAL A 562 " --> pdb=" O   SER A 578 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   SER A 578 " --> pdb=" O   VAL A 562 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   SER A 564 " --> pdb=" O   ASN A 576 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   ASN A 576 " --> pdb=" O   SER A 564 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   ILE A 566 " --> pdb=" O   ARG A 574 " (cutoff:3.500A)
      removed outlier: 5.736A  pdb=" N   ARG A 574 " --> pdb=" O   ARG A 615 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   VAL A 607 " --> pdb=" O   ILE A 582 " (cutoff:3.500A)
      removed outlier: 7.093A  pdb=" N   TYR A 584 " --> pdb=" O   SER A 605 " (cutoff:3.500A)
      removed outlier: 5.656A  pdb=" N   SER A 605 " --> pdb=" O   TYR A 584 " (cutoff:3.500A)
      removed outlier: 6.114A  pdb=" N   ASP A 629 " --> pdb=" O   VAL A 635 " (cutoff:3.500A)
      removed outlier: 5.595A  pdb=" N   VAL A 635 " --> pdb=" O   ASP A 629 " (cutoff:3.500A)
      removed outlier: 5.651A  pdb=" N   ASP A 706 " --> pdb=" O   GLN A 712 " (cutoff:3.500A)
      removed outlier: 5.548A  pdb=" N   GLN A 712 " --> pdb=" O   ASP A 706 " (cutoff:3.500A)
      removed outlier: 13.167A  pdb=" N   LYS A 711 " --> pdb=" O   GLY A 738 " (cutoff:3.500A)
      removed outlier: 13.259A  pdb=" N   GLY A 738 " --> pdb=" O   LYS A 711 " (cutoff:3.500A)
      removed outlier: 8.532A  pdb=" N   ALA A 713 " --> pdb=" O   LEU A 736 " (cutoff:3.500A)
      removed outlier: 5.257A  pdb=" N   VAL A 747 " --> pdb=" O   ASN A 737 " (cutoff:3.500A)
      removed outlier: 4.934A  pdb=" N   TRP A 739 " --> pdb=" O   HIS A 745 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   HIS A 745 " --> pdb=" O   TRP A 739 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 63
      removed outlier: 6.825A  pdb=" N   MET B  36 " --> pdb=" O   LEU B  63 " (cutoff:3.500A)
      removed outlier: 5.795A  pdb=" N   LEU B  75 " --> pdb=" O   LEU B 109 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   LEU B 109 " --> pdb=" O   LEU B  75 " (cutoff:3.500A)
      removed outlier: 5.279A  pdb=" N   LEU B  77 " --> pdb=" O   THR B 107 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   THR B 107 " --> pdb=" O   LEU B  77 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   LYS B  79 " --> pdb=" O   ASN B 105 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   GLU B  97 " --> pdb=" O   ALA B  87 " (cutoff:3.500A)
      removed outlier: 6.137A  pdb=" N   VAL B  89 " --> pdb=" O   THR B  95 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   THR B  95 " --> pdb=" O   VAL B  89 " (cutoff:3.500A)

    305 hydrogen bonds defined for protein.
    858 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.23

  Time building geometry restraints manager: 1.85 seconds

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

  Histogram of bond lengths:
        0.94 -     1.12: 6856
        1.12 -     1.30: 1271
        1.30 -     1.47: 2996
        1.47 -     1.65: 3057
        1.65 -     1.82: 52
  Bond restraints: 14232
  Sorted by residual:
  bond pdb=" N   SER A 185 "
       pdb=" H   SER A 185 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" CE2 TYR A 721 "
       pdb=" HE2 TYR A 721 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" N   SER A 226 "
       pdb=" H   SER A 226 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" CD1 PHE B 127 "
       pdb=" HD1 PHE B 127 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" CE1 PHE A 228 "
       pdb=" HE1 PHE A 228 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.70e+01
  ... (remaining 14227 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.37: 20767
        2.37 -     4.75: 3748
        4.75 -     7.12: 892
        7.12 -     9.49: 95
        9.49 -    11.87: 3
  Bond angle restraints: 25505
  Sorted by residual:
  angle pdb=" CA  ASP A 256 "
        pdb=" CB  ASP A 256 "
        pdb=" CG  ASP A 256 "
      ideal   model   delta    sigma   weight residual
     112.60  118.56   -5.96 1.00e+00 1.00e+00 3.55e+01
  angle pdb=" C   LYS A 123 "
        pdb=" N   GLY A 124 "
        pdb=" CA  GLY A 124 "
      ideal   model   delta    sigma   weight residual
     122.18  125.96   -3.78 6.90e-01 2.10e+00 3.00e+01
  angle pdb=" C   TYR A 411 "
        pdb=" N   GLY A 412 "
        pdb=" CA  GLY A 412 "
      ideal   model   delta    sigma   weight residual
     121.65  125.17   -3.52 6.80e-01 2.16e+00 2.68e+01
  angle pdb=" CB  HIS A  58 "
        pdb=" CG  HIS A  58 "
        pdb=" CD2 HIS A  58 "
      ideal   model   delta    sigma   weight residual
     131.20  124.74    6.46 1.30e+00 5.92e-01 2.47e+01
  angle pdb=" CA  PHE A 754 "
        pdb=" CB  PHE A 754 "
        pdb=" CG  PHE A 754 "
      ideal   model   delta    sigma   weight residual
     113.80  118.71   -4.91 1.00e+00 1.00e+00 2.41e+01
  ... (remaining 25500 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 6206
       17.88 -    35.77: 365
       35.77 -    53.65: 119
       53.65 -    71.53: 81
       71.53 -    89.41: 14
  Dihedral angle restraints: 6785
    sinusoidal: 3637
      harmonic: 3148
  Sorted by residual:
  dihedral pdb=" C   LYS A 131 "
           pdb=" N   LYS A 131 "
           pdb=" CA  LYS A 131 "
           pdb=" CB  LYS A 131 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.68   15.08     0      2.50e+00 1.60e-01 3.64e+01
  dihedral pdb=" CA  VAL A 104 "
           pdb=" C   VAL A 104 "
           pdb=" N   ASP A 105 "
           pdb=" CA  ASP A 105 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.15   28.85     0      5.00e+00 4.00e-02 3.33e+01
  dihedral pdb=" CA  ASP A 113 "
           pdb=" C   ASP A 113 "
           pdb=" N   ASP A 114 "
           pdb=" CA  ASP A 114 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.17  -26.83     0      5.00e+00 4.00e-02 2.88e+01
  ... (remaining 6782 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.108: 783
       0.108 -    0.216: 232
       0.216 -    0.323: 36
       0.323 -    0.431: 3
       0.431 -    0.539: 1
  Chirality restraints: 1055
  Sorted by residual:
  chirality pdb=" CA  LYS A 131 "
            pdb=" N   LYS A 131 "
            pdb=" C   LYS A 131 "
            pdb=" CB  LYS A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.26e+00
  chirality pdb=" CA  GLU A 159 "
            pdb=" N   GLU A 159 "
            pdb=" C   GLU A 159 "
            pdb=" CB  GLU A 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.17e+00
  chirality pdb=" CA  GLN B 131 "
            pdb=" N   GLN B 131 "
            pdb=" C   GLN B 131 "
            pdb=" CB  GLN B 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.90e+00
  ... (remaining 1052 not shown)

  Planarity restraints: 2161
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 157 "   -0.337 9.50e-02 1.11e+02   1.63e-01 3.25e+02
        pdb=" NE  ARG A 157 "   -0.094 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 157 "   -0.060 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 157 "   -0.101 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 157 "   -0.004 2.00e-02 2.50e+03
        pdb="HH11 ARG A 157 "    0.267 2.00e-02 2.50e+03
        pdb="HH12 ARG A 157 "   -0.134 2.00e-02 2.50e+03
        pdb="HH21 ARG A 157 "    0.110 2.00e-02 2.50e+03
        pdb="HH22 ARG A 157 "    0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 161 "    0.397 9.50e-02 1.11e+02   1.63e-01 2.18e+02
        pdb=" NE  ARG A 161 "    0.062 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 161 "    0.060 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 161 "    0.101 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 161 "   -0.014 2.00e-02 2.50e+03
        pdb="HH11 ARG A 161 "   -0.218 2.00e-02 2.50e+03
        pdb="HH12 ARG A 161 "    0.091 2.00e-02 2.50e+03
        pdb="HH21 ARG A 161 "   -0.077 2.00e-02 2.50e+03
        pdb="HH22 ARG A 161 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 465 "   -0.136 2.00e-02 2.50e+03   6.67e-02 1.78e+02
        pdb=" CG  TRP A 465 "   -0.055 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 465 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 465 "   -0.031 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 465 "    0.046 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 465 "   -0.031 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 465 "    0.028 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 465 "   -0.062 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 465 "    0.026 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 465 "   -0.036 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 465 "    0.043 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 465 "    0.126 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 465 "    0.090 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 465 "   -0.071 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 465 "    0.078 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 465 "   -0.037 2.00e-02 2.50e+03
  ... (remaining 2158 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 1114
        2.19 -     2.79: 24349
        2.79 -     3.39: 37529
        3.39 -     4.00: 52761
        4.00 -     4.60: 76112
  Nonbonded interactions: 191865
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 395 "
            pdb=" HH  TYR A 411 "
     model   vdw
     1.586 2.450
  nonbonded pdb=" OE1 GLU A 288 "
            pdb=" HH  TYR A 347 "
     model   vdw
     1.601 2.450
  nonbonded pdb=" OE2 GLU A 643 "
            pdb=" HH  TYR A 780 "
     model   vdw
     1.601 2.450
  nonbonded pdb=" HH  TYR A 248 "
            pdb=" OD2 ASP A 256 "
     model   vdw
     1.606 2.450
  nonbonded pdb=" HG  SER B  88 "
            pdb=" OE1 GLU B  97 "
     model   vdw
     1.616 2.450
  ... (remaining 191860 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.380
  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:             0.120
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     14.900
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:6.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
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      :  0.012   0.047   7376  Z= 0.748
  Angle     :  1.845   8.175  10020  Z= 1.237
  Chirality :  0.101   0.539   1055
  Planarity :  0.017   0.139   1318
  Dihedral  : 13.784  89.411   2708
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 0.14
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.63 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  2.56 %
    Favored  : 96.41 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  0.10 (0.26), residues: 875
  helix: -0.26 (0.50), residues: 82
  sheet:  1.00 (0.25), residues: 364
  loop : -0.67 (0.27), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 429 
 TYR   0.161   0.025   TYR A 537 
 PHE   0.082   0.011   PHE A 377 
 TRP   0.101   0.023   TRP A 311 
 HIS   0.014   0.005   HIS A 745 

Details of bonding type rmsd
  covalent geometry    : bond        0.01207 ( 7374)
  covalent geometry    : angle       1.84387 (10016)
  SS BOND              : bond        0.01847 (    2)
  SS BOND              : angle       3.77732 (    4)
  hydrogen bonds       : bond        0.15123 (  305)
  hydrogen bonds       : angle       7.51318 (  858)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 173
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 TRP cc_start: 0.7195 (t60) cc_final: 0.6746 (t60)
REVERT: A  139 ASP cc_start: 0.8047 (p0) cc_final: 0.7677 (m-30)
REVERT: A  150 LYS cc_start: 0.7707 (mtmm) cc_final: 0.7499 (ptpp)
REVERT: A  183 VAL cc_start: 0.8787 (t) cc_final: 0.8567 (t)
REVERT: A  202 ARG cc_start: 0.7808 (mtt90) cc_final: 0.7288 (mtm110)
REVERT: A  217 GLN cc_start: 0.7798 (mt0) cc_final: 0.7581 (mt0)
REVERT: A  495 ARG cc_start: 0.7548 (ttt180) cc_final: 0.7155 (ttp80)
REVERT: A  598 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7635 (mm-30)
REVERT: A  599 ASN cc_start: 0.8504 (m-40) cc_final: 0.8223 (m-40)
REVERT: A  602 LYS cc_start: 0.8015 (mttm) cc_final: 0.7458 (mmtm)
REVERT: A  615 ARG cc_start: 0.8027 (ttt90) cc_final: 0.7548 (tpt-90)
REVERT: A  650 ARG cc_start: 0.8103 (mtt90) cc_final: 0.7588 (mtt90)
REVERT: A  674 THR cc_start: 0.8736 (m) cc_final: 0.8357 (p)
REVERT: A  757 GLU cc_start: 0.8286 (tt0) cc_final: 0.7705 (mt-10)
REVERT: B   79 LYS cc_start: 0.8931 (tttt) cc_final: 0.8478 (ttpp)
REVERT: B  145 LYS cc_start: 0.8673 (tttt) cc_final: 0.8310 (tmtt)
REVERT: B  149 ASP cc_start: 0.8745 (m-30) cc_final: 0.8543 (m-30)
  outliers start: 8
  outliers final: 2
  residues processed: 177
  average time/residue: 1.2362
  time to fit residues: 230.6262
Evaluate side-chains
  102 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  593 ASP
Chi-restraints excluded: chain B residue   72 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
B  53 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.132248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.104106 restraints weight = 27600.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 2.14
r_work: 0.3354 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3254 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.2929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   7376  Z= 0.149
  Angle     :  0.605   4.623  10020  Z= 0.331
  Chirality :  0.047   0.160   1055
  Planarity :  0.005   0.064   1318
  Dihedral  :  6.489  75.222   1003
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 1.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  :  8.96 %
    Favored  : 88.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  0.18 (0.27), residues: 875
  helix:  0.38 (0.51), residues: 95
  sheet:  0.48 (0.24), residues: 440
  loop : -0.30 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 421 
 TYR   0.013   0.001   TYR A 537 
 PHE   0.011   0.001   PHE A 377 
 TRP   0.006   0.001   TRP A 444 
 HIS   0.003   0.001   HIS A 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 7374)
  covalent geometry    : angle       0.60425 (10016)
  SS BOND              : bond        0.00149 (    2)
  SS BOND              : angle       1.52187 (    4)
  hydrogen bonds       : bond        0.04486 (  305)
  hydrogen bonds       : angle       6.08650 (  858)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 LYS cc_start: 0.7458 (mtmm) cc_final: 0.7220 (ptpp)
REVERT: A  177 SER cc_start: 0.7399 (m) cc_final: 0.7024 (p)
REVERT: A  255 MET cc_start: 0.8730 (ptp) cc_final: 0.8392 (ptp)
REVERT: A  342 ASP cc_start: 0.8804 (m-30) cc_final: 0.8507 (m-30)
REVERT: A  495 ARG cc_start: 0.7445 (ttt180) cc_final: 0.6938 (ttp80)
REVERT: A  498 GLU cc_start: 0.7627 (mp0) cc_final: 0.7373 (mp0)
REVERT: A  598 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7430 (mp0)
REVERT: A  602 LYS cc_start: 0.8071 (mttm) cc_final: 0.7559 (mmtt)
REVERT: A  615 ARG cc_start: 0.7962 (ttt90) cc_final: 0.7724 (ttt90)
REVERT: A  650 ARG cc_start: 0.8107 (mtt90) cc_final: 0.7410 (mtt90)
REVERT: A  674 THR cc_start: 0.8470 (m) cc_final: 0.8111 (p)
REVERT: A  757 GLU cc_start: 0.8145 (tt0) cc_final: 0.7458 (mt-10)
REVERT: B   53 ASN cc_start: 0.8120 (t0) cc_final: 0.7849 (m-40)
REVERT: B   79 LYS cc_start: 0.8797 (tttt) cc_final: 0.8222 (ttpp)
REVERT: B  101 ILE cc_start: 0.9008 (tt) cc_final: 0.8445 (mp)
REVERT: B  145 LYS cc_start: 0.8361 (tttt) cc_final: 0.7882 (tmtt)
  outliers start: 21
  outliers final: 8
  residues processed: 136
  average time/residue: 1.1199
  time to fit residues: 161.3076
Evaluate side-chains
  110 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 102
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  281 GLN
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  579 VAL
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue   99 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0870
   chunk 32 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.1962

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

Flipped N/Q/H residues before XYZ refinement:
A 189 HIS
A 627 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.131219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.104034 restraints weight = 27679.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 2.08
r_work: 0.3341 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3243 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.3374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   7376  Z= 0.162
  Angle     :  0.556   4.767  10020  Z= 0.299
  Chirality :  0.046   0.149   1055
  Planarity :  0.005   0.049   1318
  Dihedral  :  5.316  18.654   1000
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 1.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 11.14 %
    Favored  : 86.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  0.06 (0.28), residues: 875
  helix:  0.99 (0.53), residues: 95
  sheet:  0.22 (0.24), residues: 446
  loop : -0.31 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 421 
 TYR   0.015   0.001   TYR A 537 
 PHE   0.010   0.001   PHE A 377 
 TRP   0.005   0.001   TRP A 272 
 HIS   0.002   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 7374)
  covalent geometry    : angle       0.55531 (10016)
  SS BOND              : bond        0.00106 (    2)
  SS BOND              : angle       1.02881 (    4)
  hydrogen bonds       : bond        0.03907 (  305)
  hydrogen bonds       : angle       5.76648 (  858)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
REVERT: A  142 MET cc_start: 0.8211 (mtt) cc_final: 0.7931 (mpp)
REVERT: A  177 SER cc_start: 0.7365 (m) cc_final: 0.6999 (p)
REVERT: A  495 ARG cc_start: 0.7531 (ttt180) cc_final: 0.7081 (ttp-170)
REVERT: A  598 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7464 (mp0)
REVERT: A  602 LYS cc_start: 0.8068 (mttm) cc_final: 0.7523 (mmtt)
REVERT: A  615 ARG cc_start: 0.7983 (ttt90) cc_final: 0.7717 (ttt90)
REVERT: A  650 ARG cc_start: 0.8056 (mtt90) cc_final: 0.7428 (mtt90)
REVERT: A  674 THR cc_start: 0.8459 (m) cc_final: 0.8056 (p)
REVERT: A  757 GLU cc_start: 0.8156 (tt0) cc_final: 0.7453 (mt-10)
REVERT: B   53 ASN cc_start: 0.8157 (t0) cc_final: 0.7887 (m-40)
REVERT: B   65 LYS cc_start: 0.7908 (ttmm) cc_final: 0.7654 (ttmm)
REVERT: B   66 GLU cc_start: 0.7342 (pp20) cc_final: 0.7113 (pm20)
REVERT: B   79 LYS cc_start: 0.8784 (tttt) cc_final: 0.8252 (ttpp)
REVERT: B  101 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8392 (mp)
REVERT: B  145 LYS cc_start: 0.8365 (tttt) cc_final: 0.7954 (tmtt)
  outliers start: 17
  outliers final: 10
  residues processed: 116
  average time/residue: 1.0451
  time to fit residues: 128.7344
Evaluate side-chains
  113 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  281 GLN
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  647 ASP
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain B residue   99 GLN
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  137 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 60 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 627 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.130838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.103964 restraints weight = 27758.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 2.06
r_work: 0.3340 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3243 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.3634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   7376  Z= 0.163
  Angle     :  0.532   4.640  10020  Z= 0.284
  Chirality :  0.045   0.148   1055
  Planarity :  0.005   0.080   1318
  Dihedral  :  5.079  17.589   1000
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 1.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 13.32 %
    Favored  : 84.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  0.00 (0.28), residues: 875
  helix:  1.28 (0.54), residues: 95
  sheet:  0.10 (0.24), residues: 447
  loop : -0.33 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 421 
 TYR   0.014   0.001   TYR A 537 
 PHE   0.009   0.001   PHE A 377 
 TRP   0.005   0.001   TRP A 272 
 HIS   0.002   0.001   HIS A 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 7374)
  covalent geometry    : angle       0.53187 (10016)
  SS BOND              : bond        0.00140 (    2)
  SS BOND              : angle       0.91188 (    4)
  hydrogen bonds       : bond        0.03661 (  305)
  hydrogen bonds       : angle       5.60963 (  858)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
REVERT: A  177 SER cc_start: 0.7366 (m) cc_final: 0.7008 (p)
REVERT: A  495 ARG cc_start: 0.7566 (ttt180) cc_final: 0.7134 (ttp80)
REVERT: A  598 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7487 (mp0)
REVERT: A  602 LYS cc_start: 0.8070 (mttm) cc_final: 0.7511 (mmtt)
REVERT: A  615 ARG cc_start: 0.7975 (ttt90) cc_final: 0.7685 (ttt90)
REVERT: A  650 ARG cc_start: 0.8037 (mtt90) cc_final: 0.7397 (mtt90)
REVERT: A  674 THR cc_start: 0.8431 (m) cc_final: 0.8045 (p)
REVERT: A  757 GLU cc_start: 0.8120 (tt0) cc_final: 0.7379 (mt-10)
REVERT: B   53 ASN cc_start: 0.8176 (t0) cc_final: 0.7921 (m-40)
REVERT: B   79 LYS cc_start: 0.8808 (tttt) cc_final: 0.8268 (ttpp)
REVERT: B  145 LYS cc_start: 0.8377 (tttt) cc_final: 0.7968 (tmtt)
  outliers start: 14
  outliers final: 10
  residues processed: 116
  average time/residue: 0.9559
  time to fit residues: 118.1296
Evaluate side-chains
  112 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  281 GLN
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  647 ASP
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain B residue   99 GLN
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  137 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0970
   chunk 26 optimal weight:    0.9980
   chunk 67 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  58 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.130599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.103758 restraints weight = 27975.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 2.07
r_work: 0.3334 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.3826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   7376  Z= 0.158
  Angle     :  0.525   4.615  10020  Z= 0.278
  Chirality :  0.045   0.148   1055
  Planarity :  0.005   0.047   1318
  Dihedral  :  4.897  17.543   1000
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 13.57 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.04 (0.28), residues: 875
  helix:  1.44 (0.55), residues: 95
  sheet:  0.02 (0.24), residues: 447
  loop : -0.33 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 421 
 TYR   0.014   0.001   TYR A 537 
 PHE   0.009   0.001   PHE A 377 
 TRP   0.006   0.001   TRP A 272 
 HIS   0.002   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 7374)
  covalent geometry    : angle       0.52467 (10016)
  SS BOND              : bond        0.00139 (    2)
  SS BOND              : angle       0.83035 (    4)
  hydrogen bonds       : bond        0.03548 (  305)
  hydrogen bonds       : angle       5.53148 (  858)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 MET cc_start: 0.5430 (tmt) cc_final: 0.5011 (mpt)
REVERT: A  177 SER cc_start: 0.7365 (m) cc_final: 0.7011 (p)
REVERT: A  495 ARG cc_start: 0.7545 (ttt180) cc_final: 0.7162 (ttp80)
REVERT: A  598 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7516 (mp0)
REVERT: A  602 LYS cc_start: 0.8093 (mttm) cc_final: 0.7510 (mmtt)
REVERT: A  615 ARG cc_start: 0.7991 (ttt90) cc_final: 0.7673 (ttt90)
REVERT: A  650 ARG cc_start: 0.7990 (mtt90) cc_final: 0.7370 (mtt90)
REVERT: A  674 THR cc_start: 0.8422 (m) cc_final: 0.8019 (p)
REVERT: A  757 GLU cc_start: 0.8124 (tt0) cc_final: 0.7384 (mt-10)
REVERT: B   53 ASN cc_start: 0.8191 (t0) cc_final: 0.7929 (m-40)
REVERT: B   79 LYS cc_start: 0.8814 (tttt) cc_final: 0.8273 (ttpp)
REVERT: B  145 LYS cc_start: 0.8360 (tttt) cc_final: 0.7945 (tmtt)
  outliers start: 15
  outliers final: 12
  residues processed: 111
  average time/residue: 0.8898
  time to fit residues: 105.8817
Evaluate side-chains
  115 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  281 GLN
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  647 ASP
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain B residue   99 GLN
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  137 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 87 optimal weight:    0.0670
   chunk 68 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.2124

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

Flipped N/Q/H residues before XYZ refinement:
** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.130059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.103383 restraints weight = 27798.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 2.06
r_work: 0.3335 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.3917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   7376  Z= 0.161
  Angle     :  0.521   4.533  10020  Z= 0.276
  Chirality :  0.045   0.149   1055
  Planarity :  0.005   0.046   1318
  Dihedral  :  4.837  17.486   1000
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 1.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 13.70 %
    Favored  : 84.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.10 (0.28), residues: 875
  helix:  1.49 (0.55), residues: 95
  sheet: -0.05 (0.24), residues: 448
  loop : -0.37 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 421 
 TYR   0.014   0.001   TYR A 537 
 PHE   0.009   0.001   PHE A 377 
 TRP   0.007   0.001   TRP A 272 
 HIS   0.002   0.001   HIS A 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 7374)
  covalent geometry    : angle       0.52055 (10016)
  SS BOND              : bond        0.00165 (    2)
  SS BOND              : angle       0.80291 (    4)
  hydrogen bonds       : bond        0.03492 (  305)
  hydrogen bonds       : angle       5.50065 (  858)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 GLN cc_start: 0.7536 (mt0) cc_final: 0.7256 (mp10)
REVERT: A  177 SER cc_start: 0.7365 (m) cc_final: 0.7019 (p)
REVERT: A  495 ARG cc_start: 0.7529 (ttt180) cc_final: 0.7230 (ttp80)
REVERT: A  598 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7536 (mp0)
REVERT: A  602 LYS cc_start: 0.8098 (mttm) cc_final: 0.7515 (mmtt)
REVERT: A  615 ARG cc_start: 0.7986 (ttt90) cc_final: 0.7681 (ttt90)
REVERT: A  650 ARG cc_start: 0.7989 (mtt90) cc_final: 0.7381 (mtt90)
REVERT: A  674 THR cc_start: 0.8424 (m) cc_final: 0.8020 (p)
REVERT: A  757 GLU cc_start: 0.8106 (tt0) cc_final: 0.7360 (mt-10)
REVERT: B   53 ASN cc_start: 0.8144 (t0) cc_final: 0.7912 (m-40)
REVERT: B   79 LYS cc_start: 0.8771 (tttt) cc_final: 0.8230 (ttpp)
REVERT: B   99 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8634 (tp-100)
REVERT: B  145 LYS cc_start: 0.8367 (tttt) cc_final: 0.7955 (tmtt)
  outliers start: 16
  outliers final: 11
  residues processed: 113
  average time/residue: 0.9450
  time to fit residues: 114.5188
Evaluate side-chains
  109 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  366 GLN
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  647 ASP
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue   99 GLN
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  137 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 71 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 81 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 85 optimal weight:    1.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
A 599 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.129743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.102947 restraints weight = 27859.230|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 2.05
r_work: 0.3317 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3220 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.4012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7376  Z= 0.178
  Angle     :  0.533   5.996  10020  Z= 0.282
  Chirality :  0.045   0.149   1055
  Planarity :  0.005   0.046   1318
  Dihedral  :  4.830  17.637   1000
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 13.70 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.19 (0.28), residues: 875
  helix:  1.49 (0.55), residues: 95
  sheet: -0.11 (0.24), residues: 448
  loop : -0.43 (0.32), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 421 
 TYR   0.015   0.001   TYR A 537 
 PHE   0.010   0.001   PHE A 377 
 TRP   0.006   0.001   TRP A 272 
 HIS   0.002   0.001   HIS A 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 7374)
  covalent geometry    : angle       0.53326 (10016)
  SS BOND              : bond        0.00181 (    2)
  SS BOND              : angle       0.79331 (    4)
  hydrogen bonds       : bond        0.03551 (  305)
  hydrogen bonds       : angle       5.53026 (  858)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: A  177 SER cc_start: 0.7351 (m) cc_final: 0.6988 (p)
REVERT: A  495 ARG cc_start: 0.7527 (ttt180) cc_final: 0.7219 (ttp80)
REVERT: A  598 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7544 (mp0)
REVERT: A  602 LYS cc_start: 0.8124 (mttm) cc_final: 0.7524 (mmtt)
REVERT: A  615 ARG cc_start: 0.7999 (ttt90) cc_final: 0.7736 (ttt90)
REVERT: A  650 ARG cc_start: 0.8032 (mtt90) cc_final: 0.7428 (mtt90)
REVERT: A  674 THR cc_start: 0.8446 (m) cc_final: 0.8023 (p)
REVERT: A  757 GLU cc_start: 0.8110 (tt0) cc_final: 0.7298 (mt-10)
REVERT: B   53 ASN cc_start: 0.8154 (t0) cc_final: 0.7896 (m-40)
REVERT: B   79 LYS cc_start: 0.8803 (tttt) cc_final: 0.8253 (ttpp)
REVERT: B  145 LYS cc_start: 0.8341 (tttt) cc_final: 0.7920 (tmtt)
  outliers start: 18
  outliers final: 14
  residues processed: 107
  average time/residue: 0.8488
  time to fit residues: 97.3469
Evaluate side-chains
  110 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 SER
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  366 GLN
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  535 SER
Chi-restraints excluded: chain A residue  647 ASP
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue   99 GLN
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  137 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 74 optimal weight:    0.5980
   chunk 82 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.131459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.104984 restraints weight = 27712.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 2.05
r_work: 0.3352 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3257 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.4125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7376  Z= 0.121
  Angle     :  0.502   6.052  10020  Z= 0.264
  Chirality :  0.045   0.147   1055
  Planarity :  0.004   0.047   1318
  Dihedral  :  4.616  17.257   1000
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 15.11 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.16 (0.28), residues: 875
  helix:  1.60 (0.56), residues: 95
  sheet: -0.14 (0.24), residues: 445
  loop : -0.37 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 421 
 TYR   0.013   0.001   TYR A 537 
 PHE   0.008   0.001   PHE A 377 
 TRP   0.005   0.001   TRP A 272 
 HIS   0.002   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 7374)
  covalent geometry    : angle       0.50194 (10016)
  SS BOND              : bond        0.00122 (    2)
  SS BOND              : angle       0.77680 (    4)
  hydrogen bonds       : bond        0.03198 (  305)
  hydrogen bonds       : angle       5.33555 (  858)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.436 
Fit side-chains
REVERT: A   83 GLN cc_start: 0.7641 (mt0) cc_final: 0.7389 (mp10)
REVERT: A  177 SER cc_start: 0.7311 (m) cc_final: 0.6965 (p)
REVERT: A  495 ARG cc_start: 0.7513 (ttt180) cc_final: 0.7242 (ttp80)
REVERT: A  592 ASP cc_start: 0.7869 (t0) cc_final: 0.6983 (t0)
REVERT: A  598 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7551 (mp0)
REVERT: A  602 LYS cc_start: 0.8121 (mttm) cc_final: 0.7539 (mmtt)
REVERT: A  615 ARG cc_start: 0.7959 (ttt90) cc_final: 0.7659 (ttt90)
REVERT: A  650 ARG cc_start: 0.8029 (mtt90) cc_final: 0.7454 (mtt90)
REVERT: A  674 THR cc_start: 0.8405 (m) cc_final: 0.8007 (p)
REVERT: A  757 GLU cc_start: 0.7996 (tt0) cc_final: 0.7328 (mt-10)
REVERT: B   53 ASN cc_start: 0.8160 (t0) cc_final: 0.7923 (m-40)
REVERT: B   79 LYS cc_start: 0.8801 (tttt) cc_final: 0.8262 (ttpp)
REVERT: B  145 LYS cc_start: 0.8344 (tttt) cc_final: 0.7939 (tmtt)
  outliers start: 14
  outliers final: 7
  residues processed: 109
  average time/residue: 0.9848
  time to fit residues: 114.9490
Evaluate side-chains
  106 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  647 ASP
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain B residue  119 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 22 optimal weight:    0.3980
   chunk 47 optimal weight:    2.9990
   chunk 56 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0870
   chunk 74 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 82 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
A 680 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.132430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.105986 restraints weight = 27762.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 2.06
r_work: 0.3371 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3275 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.4247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   7376  Z= 0.100
  Angle     :  0.491   6.261  10020  Z= 0.257
  Chirality :  0.044   0.144   1055
  Planarity :  0.004   0.051   1318
  Dihedral  :  4.428  16.676   1000
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 1.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 15.11 %
    Favored  : 83.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.08 (0.28), residues: 875
  helix:  1.70 (0.56), residues: 95
  sheet: -0.11 (0.24), residues: 443
  loop : -0.29 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 421 
 TYR   0.015   0.001   TYR A 388 
 PHE   0.007   0.001   PHE A 377 
 TRP   0.005   0.001   TRP A 325 
 HIS   0.002   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 7374)
  covalent geometry    : angle       0.49104 (10016)
  SS BOND              : bond        0.00081 (    2)
  SS BOND              : angle       0.77296 (    4)
  hydrogen bonds       : bond        0.02978 (  305)
  hydrogen bonds       : angle       5.16860 (  858)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.454 
Fit side-chains
REVERT: A   83 GLN cc_start: 0.7626 (mt0) cc_final: 0.7332 (mp10)
REVERT: A  495 ARG cc_start: 0.7463 (ttt180) cc_final: 0.7053 (ttp80)
REVERT: A  592 ASP cc_start: 0.7802 (t0) cc_final: 0.7031 (t0)
REVERT: A  598 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7502 (mp0)
REVERT: A  602 LYS cc_start: 0.8112 (mttm) cc_final: 0.7515 (mmtt)
REVERT: A  615 ARG cc_start: 0.7905 (ttt90) cc_final: 0.7630 (ttt90)
REVERT: A  650 ARG cc_start: 0.7992 (mtt90) cc_final: 0.7334 (mtt90)
REVERT: A  674 THR cc_start: 0.8361 (m) cc_final: 0.7969 (p)
REVERT: A  757 GLU cc_start: 0.7949 (tt0) cc_final: 0.7371 (mt-10)
REVERT: B   79 LYS cc_start: 0.8782 (tttt) cc_final: 0.8235 (ttpp)
REVERT: B  101 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8419 (mp)
REVERT: B  145 LYS cc_start: 0.8336 (tttt) cc_final: 0.7897 (tmtt)
  outliers start: 10
  outliers final: 6
  residues processed: 110
  average time/residue: 1.0054
  time to fit residues: 118.2971
Evaluate side-chains
  103 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  119 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 75 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 5 optimal weight:    7.9990
   chunk 66 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
A 599 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.129360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.102551 restraints weight = 27975.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 2.05
r_work: 0.3319 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3223 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.4210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7376  Z= 0.196
  Angle     :  0.544   7.701  10020  Z= 0.287
  Chirality :  0.045   0.154   1055
  Planarity :  0.005   0.052   1318
  Dihedral  :  4.707  16.935   1000
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 15.62 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.18 (0.28), residues: 875
  helix:  1.60 (0.55), residues: 95
  sheet: -0.15 (0.24), residues: 448
  loop : -0.38 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 409 
 TYR   0.024   0.002   TYR A 388 
 PHE   0.010   0.001   PHE A 541 
 TRP   0.008   0.001   TRP A 272 
 HIS   0.002   0.001   HIS A 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 7374)
  covalent geometry    : angle       0.54404 (10016)
  SS BOND              : bond        0.00188 (    2)
  SS BOND              : angle       0.75908 (    4)
  hydrogen bonds       : bond        0.03566 (  305)
  hydrogen bonds       : angle       5.44017 (  858)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
REVERT: A  177 SER cc_start: 0.7404 (m) cc_final: 0.7058 (p)
REVERT: A  495 ARG cc_start: 0.7462 (ttt180) cc_final: 0.7035 (ttp80)
REVERT: A  592 ASP cc_start: 0.7900 (t0) cc_final: 0.7066 (t0)
REVERT: A  598 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7595 (mp0)
REVERT: A  602 LYS cc_start: 0.8122 (mttm) cc_final: 0.7501 (mmtt)
REVERT: A  615 ARG cc_start: 0.7950 (ttt90) cc_final: 0.7686 (ttt90)
REVERT: A  650 ARG cc_start: 0.8023 (mtt90) cc_final: 0.7366 (mtt90)
REVERT: A  674 THR cc_start: 0.8408 (m) cc_final: 0.7985 (p)
REVERT: A  757 GLU cc_start: 0.8038 (tt0) cc_final: 0.7339 (mt-10)
REVERT: B   79 LYS cc_start: 0.8745 (tttt) cc_final: 0.8198 (ttpp)
REVERT: B  145 LYS cc_start: 0.8284 (tttt) cc_final: 0.7868 (tmtt)
  outliers start: 10
  outliers final: 7
  residues processed: 99
  average time/residue: 0.9910
  time to fit residues: 104.9185
Evaluate side-chains
  103 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  765 TYR
Chi-restraints excluded: chain B residue  119 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 86 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 81 optimal weight:    0.4980
   chunk 74 optimal weight:    0.4980
   chunk 13 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A  83 GLN
A 217 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.129912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.103292 restraints weight = 27922.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 2.04
r_work: 0.3329 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3234 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.4255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7376  Z= 0.159
  Angle     :  0.523   6.957  10020  Z= 0.275
  Chirality :  0.045   0.151   1055
  Planarity :  0.004   0.053   1318
  Dihedral  :  4.646  16.874   1000
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 1.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 15.36 %
    Favored  : 83.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.18 (0.28), residues: 875
  helix:  1.66 (0.55), residues: 95
  sheet: -0.16 (0.24), residues: 445
  loop : -0.39 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 421 
 TYR   0.023   0.001   TYR A 388 
 PHE   0.009   0.001   PHE A 377 
 TRP   0.007   0.001   TRP A 125 
 HIS   0.002   0.001   HIS A 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 7374)
  covalent geometry    : angle       0.52246 (10016)
  SS BOND              : bond        0.00170 (    2)
  SS BOND              : angle       0.75691 (    4)
  hydrogen bonds       : bond        0.03390 (  305)
  hydrogen bonds       : angle       5.38980 (  858)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5217.66 seconds
wall clock time: 88 minutes 55.96 seconds (5335.96 seconds total)