Starting phenix.real_space_refine
on Wed May 21 19:12:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fnp_50601/05_2025/9fnp_50601.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fnp_50601/05_2025/9fnp_50601.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fnp_50601/05_2025/9fnp_50601.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fnp_50601/05_2025/9fnp_50601.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fnp_50601/05_2025/9fnp_50601.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fnp_50601/05_2025/9fnp_50601.cif"
  }
  resolution = 2.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     C   13853      2.51       5
     N    3766      2.21       5
     O    4291      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 21966
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 399, 3138
          Classifications: {'peptide': 399}
          Link IDs: {'PTRANS': 22, 'TRANS': 376}
          Chain breaks: 2
  Restraints were copied for chains:
    C, B, E, D, G, F
  Time building chain proxies: 8.68, per 1000 atoms: 0.40
  Number of scatterers: 21966
  At special positions: 0
  Unit cell: (175.13, 175.13, 114.54, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      56     16.00
     O    4291      8.00
     N    3766      7.00
     C   13853      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 159 " - pdb=" SG  CYS A 164 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 159 " - pdb=" SG  CYS C 164 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 159 " - pdb=" SG  CYS B 164 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 164 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 159 " - pdb=" SG  CYS D 164 " distance=2.04
    Simple disulfide: pdb=" SG  CYS G 159 " - pdb=" SG  CYS G 164 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 159 " - pdb=" SG  CYS F 164 " distance=2.04

  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: 4.64
  Conformation dependent library (CDL) restraints added in 2.7 seconds
  

  5502 Ramachandran restraints generated.
    2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5068

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 9 sheets defined
      20.1% alpha, 30.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 9
    Processing helix  chain 'A' and resid 28 through 34
      removed outlier: 3.626A  pdb=" N   VAL A  34 " --> pdb=" O   GLU A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 34 through 41
    Processing helix  chain 'A' and resid 97 through 107
    Processing helix  chain 'A' and resid 112 through 124
    Processing helix  chain 'A' and resid 354 through 361
    Processing helix  chain 'A' and resid 364 through 368
    Processing helix  chain 'A' and resid 372 through 381
      removed outlier: 3.572A  pdb=" N   THR A 376 " --> pdb=" O   ASP A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 393
    Processing helix  chain 'B' and resid 5 through 9
    Processing helix  chain 'B' and resid 28 through 34
      removed outlier: 3.627A  pdb=" N   VAL B  34 " --> pdb=" O   GLU B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 41
    Processing helix  chain 'B' and resid 97 through 107
    Processing helix  chain 'B' and resid 112 through 124
    Processing helix  chain 'B' and resid 354 through 361
    Processing helix  chain 'B' and resid 364 through 368
    Processing helix  chain 'B' and resid 372 through 381
      removed outlier: 3.572A  pdb=" N   THR B 376 " --> pdb=" O   ASP B 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 393
    Processing helix  chain 'C' and resid 5 through 9
    Processing helix  chain 'C' and resid 28 through 34
      removed outlier: 3.626A  pdb=" N   VAL C  34 " --> pdb=" O   GLU C  30 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 34 through 41
    Processing helix  chain 'C' and resid 97 through 107
    Processing helix  chain 'C' and resid 112 through 124
    Processing helix  chain 'C' and resid 354 through 361
    Processing helix  chain 'C' and resid 364 through 368
    Processing helix  chain 'C' and resid 372 through 381
      removed outlier: 3.572A  pdb=" N   THR C 376 " --> pdb=" O   ASP C 372 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 381 through 393
    Processing helix  chain 'D' and resid 5 through 9
    Processing helix  chain 'D' and resid 28 through 34
      removed outlier: 3.627A  pdb=" N   VAL D  34 " --> pdb=" O   GLU D  30 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 34 through 41
    Processing helix  chain 'D' and resid 97 through 107
    Processing helix  chain 'D' and resid 112 through 124
    Processing helix  chain 'D' and resid 354 through 361
    Processing helix  chain 'D' and resid 364 through 368
    Processing helix  chain 'D' and resid 372 through 381
      removed outlier: 3.572A  pdb=" N   THR D 376 " --> pdb=" O   ASP D 372 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 381 through 393
    Processing helix  chain 'E' and resid 5 through 9
    Processing helix  chain 'E' and resid 28 through 34
      removed outlier: 3.626A  pdb=" N   VAL E  34 " --> pdb=" O   GLU E  30 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 34 through 41
    Processing helix  chain 'E' and resid 97 through 107
    Processing helix  chain 'E' and resid 112 through 124
    Processing helix  chain 'E' and resid 354 through 361
    Processing helix  chain 'E' and resid 364 through 368
    Processing helix  chain 'E' and resid 372 through 381
      removed outlier: 3.572A  pdb=" N   THR E 376 " --> pdb=" O   ASP E 372 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 381 through 393
    Processing helix  chain 'F' and resid 5 through 9
    Processing helix  chain 'F' and resid 28 through 34
      removed outlier: 3.627A  pdb=" N   VAL F  34 " --> pdb=" O   GLU F  30 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 34 through 41
    Processing helix  chain 'F' and resid 97 through 107
    Processing helix  chain 'F' and resid 112 through 124
    Processing helix  chain 'F' and resid 354 through 361
    Processing helix  chain 'F' and resid 364 through 368
    Processing helix  chain 'F' and resid 372 through 381
      removed outlier: 3.571A  pdb=" N   THR F 376 " --> pdb=" O   ASP F 372 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 381 through 393
    Processing helix  chain 'G' and resid 5 through 9
    Processing helix  chain 'G' and resid 28 through 34
      removed outlier: 3.626A  pdb=" N   VAL G  34 " --> pdb=" O   GLU G  30 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 34 through 41
    Processing helix  chain 'G' and resid 97 through 107
    Processing helix  chain 'G' and resid 112 through 124
    Processing helix  chain 'G' and resid 354 through 361
    Processing helix  chain 'G' and resid 364 through 368
    Processing helix  chain 'G' and resid 372 through 381
      removed outlier: 3.571A  pdb=" N   THR G 376 " --> pdb=" O   ASP G 372 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 381 through 393
    Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 67
      removed outlier: 4.381A  pdb=" N   ASN A  72 " --> pdb=" O   ILE A  47 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 96
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 91 through 96
    current: chain 'A' and resid 148 through 153
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 169 through 179
    current: chain 'A' and resid 289 through 321
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 338 through 345
    current: chain 'B' and resid 148 through 153
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 169 through 179
    current: chain 'B' and resid 289 through 321
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 338 through 345
    current: chain 'C' and resid 148 through 153
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 169 through 179
    current: chain 'C' and resid 289 through 321
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 338 through 345
    current: chain 'D' and resid 148 through 153
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 169 through 179
    current: chain 'D' and resid 289 through 321
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 338 through 345
    current: chain 'E' and resid 148 through 153
  WARNING: can't find start of bonding for strands!
    previous: chain 'E' and resid 169 through 179
    current: chain 'E' and resid 289 through 321
  WARNING: can't find start of bonding for strands!
    previous: chain 'E' and resid 338 through 345
    current: chain 'F' and resid 148 through 153
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 169 through 179
    current: chain 'F' and resid 289 through 321
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 338 through 345
    current: chain 'G' and resid 148 through 153
  WARNING: can't find start of bonding for strands!
    previous: chain 'G' and resid 169 through 179
    current: chain 'G' and resid 289 through 321
    Processing sheet with id=AA3, first strand: chain 'A' and resid 215 through 243
    Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 67
      removed outlier: 4.381A  pdb=" N   ASN B  72 " --> pdb=" O   ILE B  47 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 65 through 67
      removed outlier: 4.381A  pdb=" N   ASN C  72 " --> pdb=" O   ILE C  47 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 65 through 67
      removed outlier: 4.381A  pdb=" N   ASN D  72 " --> pdb=" O   ILE D  47 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 65 through 67
      removed outlier: 4.381A  pdb=" N   ASN E  72 " --> pdb=" O   ILE E  47 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 65 through 67
      removed outlier: 4.380A  pdb=" N   ASN F  72 " --> pdb=" O   ILE F  47 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'G' and resid 65 through 67
      removed outlier: 4.381A  pdb=" N   ASN G  72 " --> pdb=" O   ILE G  47 " (cutoff:3.500A)

    819 hydrogen bonds defined for protein.
    2373 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: 6.31

  Time building geometry restraints manager: 5.57 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 6434
        1.34 -     1.46: 5147
        1.46 -     1.58: 10910
        1.58 -     1.70: 0
        1.70 -     1.83: 91
  Bond restraints: 22582
  Sorted by residual:
  bond pdb=" C   ARG C 336 "
       pdb=" O   ARG C 336 "
    ideal  model  delta    sigma   weight residual
    1.235  1.216  0.019 4.70e-03 4.53e+04 1.57e+01
  bond pdb=" C   ARG B 336 "
       pdb=" O   ARG B 336 "
    ideal  model  delta    sigma   weight residual
    1.235  1.217  0.018 4.70e-03 4.53e+04 1.46e+01
  bond pdb=" C   ARG E 336 "
       pdb=" O   ARG E 336 "
    ideal  model  delta    sigma   weight residual
    1.235  1.217  0.018 4.70e-03 4.53e+04 1.45e+01
  bond pdb=" C   ARG D 336 "
       pdb=" O   ARG D 336 "
    ideal  model  delta    sigma   weight residual
    1.235  1.217  0.018 4.70e-03 4.53e+04 1.41e+01
  bond pdb=" C   ARG F 336 "
       pdb=" O   ARG F 336 "
    ideal  model  delta    sigma   weight residual
    1.235  1.217  0.018 4.70e-03 4.53e+04 1.40e+01
  ... (remaining 22577 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.21: 26921
        1.21 -     2.43: 3084
        2.43 -     3.64: 699
        3.64 -     4.85: 96
        4.85 -     6.07: 35
  Bond angle restraints: 30835
  Sorted by residual:
  angle pdb=" N   LYS B 309 "
        pdb=" CA  LYS B 309 "
        pdb=" CB  LYS B 309 "
      ideal   model   delta    sigma   weight residual
     110.83  104.76    6.07 1.74e+00 3.30e-01 1.22e+01
  angle pdb=" N   LYS F 309 "
        pdb=" CA  LYS F 309 "
        pdb=" CB  LYS F 309 "
      ideal   model   delta    sigma   weight residual
     110.83  104.76    6.07 1.74e+00 3.30e-01 1.22e+01
  angle pdb=" N   LYS A 309 "
        pdb=" CA  LYS A 309 "
        pdb=" CB  LYS A 309 "
      ideal   model   delta    sigma   weight residual
     110.83  104.77    6.06 1.74e+00 3.30e-01 1.21e+01
  angle pdb=" N   LYS D 309 "
        pdb=" CA  LYS D 309 "
        pdb=" CB  LYS D 309 "
      ideal   model   delta    sigma   weight residual
     110.83  104.78    6.05 1.74e+00 3.30e-01 1.21e+01
  angle pdb=" N   LYS G 309 "
        pdb=" CA  LYS G 309 "
        pdb=" CB  LYS G 309 "
      ideal   model   delta    sigma   weight residual
     110.83  104.78    6.05 1.74e+00 3.30e-01 1.21e+01
  ... (remaining 30830 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.60: 12321
       17.60 -    35.19: 580
       35.19 -    52.79: 105
       52.79 -    70.39: 56
       70.39 -    87.99: 7
  Dihedral angle restraints: 13069
    sinusoidal: 5089
      harmonic: 7980
  Sorted by residual:
  dihedral pdb=" CA  TYR B 298 "
           pdb=" C   TYR B 298 "
           pdb=" N   LYS B 299 "
           pdb=" CA  LYS B 299 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.18   17.82     0      5.00e+00 4.00e-02 1.27e+01
  dihedral pdb=" CA  TYR C 298 "
           pdb=" C   TYR C 298 "
           pdb=" N   LYS C 299 "
           pdb=" CA  LYS C 299 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.18   17.82     0      5.00e+00 4.00e-02 1.27e+01
  dihedral pdb=" CA  TYR D 298 "
           pdb=" C   TYR D 298 "
           pdb=" N   LYS D 299 "
           pdb=" CA  LYS D 299 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.19   17.81     0      5.00e+00 4.00e-02 1.27e+01
  ... (remaining 13066 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 1659
       0.038 -    0.075: 1032
       0.075 -    0.113: 365
       0.113 -    0.150: 141
       0.150 -    0.188: 37
  Chirality restraints: 3234
  Sorted by residual:
  chirality pdb=" CA  ILE G 259 "
            pdb=" N   ILE G 259 "
            pdb=" C   ILE G 259 "
            pdb=" CB  ILE G 259 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.83e-01
  chirality pdb=" CA  ILE D 259 "
            pdb=" N   ILE D 259 "
            pdb=" C   ILE D 259 "
            pdb=" CB  ILE D 259 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.80e-01
  chirality pdb=" CA  ILE A 259 "
            pdb=" N   ILE A 259 "
            pdb=" C   ILE A 259 "
            pdb=" CB  ILE A 259 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.68e-01
  ... (remaining 3231 not shown)

  Planarity restraints: 4025
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  28 "    0.248 9.50e-02 1.11e+02   1.11e-01 7.61e+00
        pdb=" NE  ARG B  28 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  28 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  28 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  28 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG G  28 "   -0.248 9.50e-02 1.11e+02   1.11e-01 7.60e+00
        pdb=" NE  ARG G  28 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG G  28 "    0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG G  28 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG G  28 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG E  28 "    0.247 9.50e-02 1.11e+02   1.11e-01 7.59e+00
        pdb=" NE  ARG E  28 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG E  28 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG E  28 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG E  28 "    0.010 2.00e-02 2.50e+03
  ... (remaining 4022 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 4415
        2.80 -     3.32: 18545
        3.32 -     3.85: 36635
        3.85 -     4.37: 41807
        4.37 -     4.90: 70875
  Nonbonded interactions: 172277
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG E 220 "
            pdb=" OD2 ASP E 222 "
     model   vdw
     2.273 3.120
  nonbonded pdb=" NH1 ARG A 220 "
            pdb=" OD2 ASP A 222 "
     model   vdw
     2.273 3.120
  nonbonded pdb=" NH1 ARG F 220 "
            pdb=" OD2 ASP F 222 "
     model   vdw
     2.273 3.120
  nonbonded pdb=" NH1 ARG G 220 "
            pdb=" OD2 ASP G 222 "
     model   vdw
     2.273 3.120
  nonbonded pdb=" NH1 ARG D 220 "
            pdb=" OD2 ASP D 222 "
     model   vdw
     2.273 3.120
  ... (remaining 172272 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: 0.18
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.800
  Check model and map are aligned:         0.160
  Set scattering table:                    0.190
  Process input model:                     40.770
  Find NCS groups from input model:        0.420
  Set up NCS constraints:                  0.060
  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:11.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   57.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8832
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      :  0.006   0.039  22589  Z= 0.365
  Angle     :  0.885   6.067  30849  Z= 0.530
  Chirality :  0.057   0.188   3234
  Planarity :  0.009   0.111   4025
  Dihedral  : 11.822  87.986   7980
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 1.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  :  2.38 %
    Favored  : 96.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.15), residues: 2751
  helix: -0.27 (0.22), residues: 490
  sheet:  1.55 (0.16), residues: 980
  loop : -0.20 (0.16), residues: 1281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 329 
 HIS   0.005   0.002   HIS G 186 
 PHE   0.029   0.003   PHE D 321 
 TYR   0.019   0.003   TYR G 357 
 ARG   0.005   0.001   ARG D  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18950 (  819)
  hydrogen bonds       : angle       6.94705 ( 2373)
  SS BOND              : bond        0.00790 (    7)
  SS BOND              : angle       2.24680 (   14)
  covalent geometry    : bond        0.00578 (22582)
  covalent geometry    : angle       0.88400 (30835)

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

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

  5502 Ramachandran restraints generated.
    2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5502 Ramachandran restraints generated.
    2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 273
  time to evaluate  : 2.286 
Fit side-chains
REVERT: A    8 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7886 (mm-40)
REVERT: A   57 MET cc_start: 0.8100 (mtp) cc_final: 0.7695 (mtp)
REVERT: A   76 TYR cc_start: 0.7397 (OUTLIER) cc_final: 0.5754 (t80)
REVERT: A  171 LYS cc_start: 0.8881 (mttt) cc_final: 0.8661 (mttp)
REVERT: A  185 LYS cc_start: 0.8808 (mtpt) cc_final: 0.8232 (mttp)
REVERT: A  233 TYR cc_start: 0.7370 (m-80) cc_final: 0.6875 (t80)
REVERT: A  258 GLU cc_start: 0.8485 (tt0) cc_final: 0.8252 (tt0)
REVERT: B   57 MET cc_start: 0.8191 (mtp) cc_final: 0.7819 (mtp)
REVERT: B   76 TYR cc_start: 0.7492 (OUTLIER) cc_final: 0.6052 (t80)
REVERT: B  185 LYS cc_start: 0.8804 (mtpt) cc_final: 0.8334 (mttm)
REVERT: B  233 TYR cc_start: 0.7341 (m-80) cc_final: 0.6962 (t80)
REVERT: B  258 GLU cc_start: 0.8518 (tt0) cc_final: 0.8273 (tt0)
REVERT: C    8 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7789 (mm-40)
REVERT: C   76 TYR cc_start: 0.7329 (OUTLIER) cc_final: 0.6931 (t80)
REVERT: C  233 TYR cc_start: 0.7430 (m-80) cc_final: 0.6878 (t80)
REVERT: C  258 GLU cc_start: 0.8391 (tt0) cc_final: 0.8118 (tt0)
REVERT: D   76 TYR cc_start: 0.7449 (OUTLIER) cc_final: 0.5969 (t80)
REVERT: D  185 LYS cc_start: 0.8820 (mtpt) cc_final: 0.8363 (mttm)
REVERT: D  233 TYR cc_start: 0.7470 (m-80) cc_final: 0.6930 (t80)
REVERT: D  258 GLU cc_start: 0.8368 (tt0) cc_final: 0.8091 (tt0)
REVERT: E   45 TRP cc_start: 0.6063 (m100) cc_final: 0.5780 (m100)
REVERT: E   57 MET cc_start: 0.8118 (mtp) cc_final: 0.7875 (mtp)
REVERT: E   76 TYR cc_start: 0.7500 (OUTLIER) cc_final: 0.7085 (t80)
REVERT: E  233 TYR cc_start: 0.7345 (m-80) cc_final: 0.6828 (t80)
REVERT: F    2 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7797 (mt-10)
REVERT: F  185 LYS cc_start: 0.8817 (mtpt) cc_final: 0.8200 (mttp)
REVERT: F  233 TYR cc_start: 0.7362 (m-80) cc_final: 0.6825 (t80)
REVERT: F  258 GLU cc_start: 0.8469 (tt0) cc_final: 0.8183 (tt0)
REVERT: F  378 GLN cc_start: 0.8248 (mt0) cc_final: 0.7752 (mm110)
REVERT: G    2 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7646 (mt-10)
REVERT: G  233 TYR cc_start: 0.7464 (m-80) cc_final: 0.6955 (t80)
REVERT: G  258 GLU cc_start: 0.8428 (tt0) cc_final: 0.8137 (tt0)
REVERT: G  378 GLN cc_start: 0.8385 (mt0) cc_final: 0.7928 (mm110)
  outliers start: 28
  outliers final: 4
  residues processed: 298
  average time/residue: 1.5673
  time to fit residues: 520.6666
Evaluate side-chains
  182 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 173
  time to evaluate  : 2.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 TYR
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain B residue   76 TYR
Chi-restraints excluded: chain C residue   76 TYR
Chi-restraints excluded: chain D residue   76 TYR
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain E residue   76 TYR
Chi-restraints excluded: chain G residue   76 TYR
Chi-restraints excluded: chain G residue  312 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 273
   random chunks:
   chunk 230 optimal weight:    0.7980
   chunk 206 optimal weight:    6.9990
   chunk 114 optimal weight:    3.9990
   chunk 70 optimal weight:    0.7980
   chunk 139 optimal weight:    9.9990
   chunk 110 optimal weight:    2.9990
   chunk 213 optimal weight:    4.9990
   chunk 82 optimal weight:    2.9990
   chunk 130 optimal weight:    5.9990
   chunk 159 optimal weight:    6.9990
   chunk 247 optimal weight:    2.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 195 GLN
A 231 ASN
B   8 GLN
B  46 GLN
B 134 GLN
B 231 ASN
C  46 GLN
C 195 GLN
C 231 ASN
D   8 GLN
D 134 GLN
D 195 GLN
D 231 ASN
E   8 GLN
E 195 GLN
E 231 ASN
F   8 GLN
F 134 GLN
F 195 GLN
F 231 ASN
G   8 GLN
G 195 GLN
G 231 ASN

Total number of N/Q/H flips: 23

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.101173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.073596 restraints weight = 28567.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.2853 rms_B_bonded: 1.83
r_work: 0.2730 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2627 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.2627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8993
moved from start:          0.1692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  22589  Z= 0.217
  Angle     :  0.663   6.653  30849  Z= 0.380
  Chirality :  0.050   0.151   3234
  Planarity :  0.005   0.040   4025
  Dihedral  :  5.669  48.783   3039
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 1.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  :  5.70 %
    Favored  : 92.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.15), residues: 2751
  helix:  0.85 (0.22), residues: 490
  sheet:  1.48 (0.15), residues: 1029
  loop : -0.34 (0.16), residues: 1232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 370 
 HIS   0.006   0.002   HIS G 186 
 PHE   0.012   0.002   PHE D 321 
 TYR   0.024   0.002   TYR D  61 
 ARG   0.003   0.000   ARG A 323 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06653 (  819)
  hydrogen bonds       : angle       5.15037 ( 2373)
  SS BOND              : bond        0.00258 (    7)
  SS BOND              : angle       1.11177 (   14)
  covalent geometry    : bond        0.00423 (22582)
  covalent geometry    : angle       0.66279 (30835)

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

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

  5502 Ramachandran restraints generated.
    2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5502 Ramachandran restraints generated.
    2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 198
  time to evaluate  : 2.308 
Fit side-chains
REVERT: A    8 GLN cc_start: 0.8363 (mm-40) cc_final: 0.8070 (mm-40)
REVERT: A   57 MET cc_start: 0.8188 (mtp) cc_final: 0.7895 (mtp)
REVERT: A   76 TYR cc_start: 0.7614 (OUTLIER) cc_final: 0.5553 (t80)
REVERT: A  171 LYS cc_start: 0.9124 (mttt) cc_final: 0.8912 (mttp)
REVERT: A  185 LYS cc_start: 0.8925 (mtpt) cc_final: 0.8356 (mttp)
REVERT: A  233 TYR cc_start: 0.7506 (m-80) cc_final: 0.6745 (t80)
REVERT: A  258 GLU cc_start: 0.8517 (tt0) cc_final: 0.8257 (tt0)
REVERT: B   57 MET cc_start: 0.8202 (mtp) cc_final: 0.7908 (mtp)
REVERT: B   76 TYR cc_start: 0.7731 (OUTLIER) cc_final: 0.5894 (t80)
REVERT: B  233 TYR cc_start: 0.7446 (m-80) cc_final: 0.6802 (t80)
REVERT: B  258 GLU cc_start: 0.8522 (tt0) cc_final: 0.8261 (tt0)
REVERT: C    8 GLN cc_start: 0.8380 (mm-40) cc_final: 0.8010 (mm-40)
REVERT: C   57 MET cc_start: 0.8260 (mtm) cc_final: 0.8019 (mtp)
REVERT: C   76 TYR cc_start: 0.7680 (OUTLIER) cc_final: 0.5786 (t80)
REVERT: C  116 THR cc_start: 0.9218 (m) cc_final: 0.8836 (p)
REVERT: C  233 TYR cc_start: 0.7492 (m-80) cc_final: 0.6689 (t80)
REVERT: C  258 GLU cc_start: 0.8487 (tt0) cc_final: 0.8211 (tt0)
REVERT: D   76 TYR cc_start: 0.7602 (OUTLIER) cc_final: 0.5667 (t80)
REVERT: D  185 LYS cc_start: 0.8974 (mtpt) cc_final: 0.8549 (mttm)
REVERT: D  233 TYR cc_start: 0.7599 (m-80) cc_final: 0.6831 (t80)
REVERT: D  258 GLU cc_start: 0.8453 (tt0) cc_final: 0.8174 (tt0)
REVERT: E   45 TRP cc_start: 0.6648 (m100) cc_final: 0.6426 (m100)
REVERT: E  116 THR cc_start: 0.9210 (m) cc_final: 0.8881 (p)
REVERT: E  233 TYR cc_start: 0.7488 (m-80) cc_final: 0.6774 (t80)
REVERT: F  185 LYS cc_start: 0.8913 (mtpt) cc_final: 0.8450 (mttp)
REVERT: F  233 TYR cc_start: 0.7467 (m-80) cc_final: 0.6782 (t80)
REVERT: F  258 GLU cc_start: 0.8504 (tt0) cc_final: 0.8244 (tt0)
REVERT: F  378 GLN cc_start: 0.8311 (mt0) cc_final: 0.7875 (mm110)
REVERT: G   76 TYR cc_start: 0.7644 (OUTLIER) cc_final: 0.5710 (t80)
REVERT: G  233 TYR cc_start: 0.7541 (m-80) cc_final: 0.6752 (t80)
  outliers start: 37
  outliers final: 9
  residues processed: 228
  average time/residue: 1.2580
  time to fit residues: 328.7972
Evaluate side-chains
  183 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 169
  time to evaluate  : 2.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue   76 TYR
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain B residue    2 GLU
Chi-restraints excluded: chain B residue   76 TYR
Chi-restraints excluded: chain C residue   76 TYR
Chi-restraints excluded: chain D residue   56 ILE
Chi-restraints excluded: chain D residue   76 TYR
Chi-restraints excluded: chain E residue   56 ILE
Chi-restraints excluded: chain E residue  350 ASP
Chi-restraints excluded: chain F residue   56 ILE
Chi-restraints excluded: chain F residue  350 ASP
Chi-restraints excluded: chain G residue   76 TYR
Chi-restraints excluded: chain G residue   81 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 273
   random chunks:
   chunk 207 optimal weight:    7.9990
   chunk 259 optimal weight:    4.9990
   chunk 247 optimal weight:    0.9980
   chunk 216 optimal weight:    0.7980
   chunk 225 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 113 optimal weight:    3.9990
   chunk 165 optimal weight:    0.8980
   chunk 157 optimal weight:    5.9990
   chunk 261 optimal weight:    0.8980
   chunk 218 optimal weight:    5.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A 231 ASN
B   8 GLN
B  46 GLN
B 134 GLN
B 231 ASN
C  46 GLN
C 195 GLN
C 263 GLN
D   8 GLN
D 134 GLN
D 231 ASN
D 263 GLN
E   8 GLN
E 231 ASN
F   8 GLN
F 134 GLN
F 231 ASN
G   8 GLN
G 134 GLN
G 195 GLN
G 231 ASN
G 263 GLN

Total number of N/Q/H flips: 22

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.103361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.075920 restraints weight = 28473.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.2895 rms_B_bonded: 1.83
r_work: 0.2774 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2672 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8959
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  22589  Z= 0.142
  Angle     :  0.536   4.633  30849  Z= 0.305
  Chirality :  0.046   0.142   3234
  Planarity :  0.004   0.034   4025
  Dihedral  :  5.090  44.112   3035
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 1.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  6.21 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.15), residues: 2751
  helix:  1.39 (0.23), residues: 490
  sheet:  1.38 (0.15), residues: 1064
  loop : -0.23 (0.16), residues: 1197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 370 
 HIS   0.003   0.001   HIS G 186 
 PHE   0.015   0.001   PHE B 321 
 TYR   0.023   0.001   TYR E  61 
 ARG   0.003   0.000   ARG A  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04991 (  819)
  hydrogen bonds       : angle       4.73704 ( 2373)
  SS BOND              : bond        0.00112 (    7)
  SS BOND              : angle       0.58319 (   14)
  covalent geometry    : bond        0.00253 (22582)
  covalent geometry    : angle       0.53638 (30835)

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

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

  5502 Ramachandran restraints generated.
    2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5502 Ramachandran restraints generated.
    2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 178
  time to evaluate  : 2.388 
Fit side-chains
REVERT: A    8 GLN cc_start: 0.8323 (mm-40) cc_final: 0.8027 (mm-40)
REVERT: A   57 MET cc_start: 0.8102 (mtp) cc_final: 0.7803 (mtp)
REVERT: A  185 LYS cc_start: 0.8914 (mtpt) cc_final: 0.8347 (mttp)
REVERT: A  233 TYR cc_start: 0.7376 (m-80) cc_final: 0.6522 (t80)
REVERT: A  258 GLU cc_start: 0.8415 (tt0) cc_final: 0.8173 (tt0)
REVERT: B   57 MET cc_start: 0.8192 (mtp) cc_final: 0.7914 (mtp)
REVERT: B  233 TYR cc_start: 0.7307 (m-80) cc_final: 0.6620 (t80)
REVERT: B  258 GLU cc_start: 0.8423 (tt0) cc_final: 0.8184 (tt0)
REVERT: B  263 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7561 (mp-120)
REVERT: C    8 GLN cc_start: 0.8356 (mm-40) cc_final: 0.8001 (mm-40)
REVERT: C   57 MET cc_start: 0.8231 (mtm) cc_final: 0.7996 (mtp)
REVERT: C  116 THR cc_start: 0.9184 (m) cc_final: 0.8783 (p)
REVERT: C  185 LYS cc_start: 0.8917 (mtmt) cc_final: 0.8494 (mttp)
REVERT: C  207 ASP cc_start: 0.9118 (OUTLIER) cc_final: 0.8813 (t70)
REVERT: C  233 TYR cc_start: 0.7390 (m-80) cc_final: 0.6526 (t80)
REVERT: C  258 GLU cc_start: 0.8388 (tt0) cc_final: 0.8112 (tt0)
REVERT: D  185 LYS cc_start: 0.8970 (mtpt) cc_final: 0.8544 (mttm)
REVERT: D  233 TYR cc_start: 0.7449 (m-80) cc_final: 0.6747 (t80)
REVERT: D  258 GLU cc_start: 0.8399 (tt0) cc_final: 0.8125 (tt0)
REVERT: E   76 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.5518 (t80)
REVERT: E  116 THR cc_start: 0.9197 (m) cc_final: 0.8854 (p)
REVERT: E  140 MET cc_start: 0.9051 (mmm) cc_final: 0.8642 (mmm)
REVERT: E  207 ASP cc_start: 0.9109 (OUTLIER) cc_final: 0.8794 (t0)
REVERT: E  233 TYR cc_start: 0.7322 (m-80) cc_final: 0.6684 (t80)
REVERT: F  185 LYS cc_start: 0.8900 (mtpt) cc_final: 0.8442 (mttp)
REVERT: F  233 TYR cc_start: 0.7292 (m-80) cc_final: 0.6607 (t80)
REVERT: F  258 GLU cc_start: 0.8438 (tt0) cc_final: 0.8184 (tt0)
REVERT: F  378 GLN cc_start: 0.8261 (mt0) cc_final: 0.7835 (mm110)
REVERT: G  185 LYS cc_start: 0.8959 (mtmt) cc_final: 0.8591 (mttm)
REVERT: G  233 TYR cc_start: 0.7403 (m-80) cc_final: 0.6573 (t80)
  outliers start: 35
  outliers final: 13
  residues processed: 199
  average time/residue: 1.2176
  time to fit residues: 278.8102
Evaluate side-chains
  183 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 166
  time to evaluate  : 2.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain B residue    2 GLU
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue  263 GLN
Chi-restraints excluded: chain B residue  350 ASP
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue  207 ASP
Chi-restraints excluded: chain C residue  350 ASP
Chi-restraints excluded: chain E residue    2 GLU
Chi-restraints excluded: chain E residue   56 ILE
Chi-restraints excluded: chain E residue   76 TYR
Chi-restraints excluded: chain E residue  207 ASP
Chi-restraints excluded: chain E residue  241 THR
Chi-restraints excluded: chain E residue  350 ASP
Chi-restraints excluded: chain F residue    2 GLU
Chi-restraints excluded: chain G residue   56 ILE
Chi-restraints excluded: chain G residue   81 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 273
   random chunks:
   chunk 153 optimal weight:    1.9990
   chunk 118 optimal weight:    4.9990
   chunk 173 optimal weight:    3.9990
   chunk 119 optimal weight:    6.9990
   chunk 48 optimal weight:    4.9990
   chunk 218 optimal weight:    5.9990
   chunk 113 optimal weight:    0.9980
   chunk 236 optimal weight:    7.9990
   chunk 60 optimal weight:    0.9980
   chunk 104 optimal weight:    0.3980
   chunk 21 optimal weight:    0.7980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 231 ASN
B   8 GLN
B  46 GLN
B 134 GLN
B 231 ASN
C 231 ASN
C 263 GLN
D   8 GLN
D 134 GLN
D 231 ASN
D 263 GLN
E   8 GLN
E 231 ASN
F   8 GLN
F 134 GLN
F 231 ASN
G   8 GLN
G 134 GLN
G 195 GLN
G 231 ASN

Total number of N/Q/H flips: 20

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.102935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.075388 restraints weight = 28833.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.2888 rms_B_bonded: 1.84
r_work: 0.2766 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2664 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8967
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017  22589  Z= 0.140
  Angle     :  0.525   4.681  30849  Z= 0.298
  Chirality :  0.046   0.138   3234
  Planarity :  0.004   0.033   4025
  Dihedral  :  4.452  15.547   3024
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 1.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  :  6.34 %
    Favored  : 92.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.15), residues: 2751
  helix:  1.38 (0.23), residues: 497
  sheet:  1.37 (0.15), residues: 1071
  loop : -0.25 (0.16), residues: 1183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 359 
 HIS   0.004   0.001   HIS G 186 
 PHE   0.014   0.001   PHE B 321 
 TYR   0.013   0.001   TYR G  61 
 ARG   0.001   0.000   ARG E 397 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04934 (  819)
  hydrogen bonds       : angle       4.53773 ( 2373)
  SS BOND              : bond        0.00083 (    7)
  SS BOND              : angle       0.47608 (   14)
  covalent geometry    : bond        0.00257 (22582)
  covalent geometry    : angle       0.52470 (30835)

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

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

  5502 Ramachandran restraints generated.
    2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5502 Ramachandran restraints generated.
    2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 168
  time to evaluate  : 2.610 
Fit side-chains
REVERT: A    8 GLN cc_start: 0.8304 (mm-40) cc_final: 0.8036 (mm-40)
REVERT: A   57 MET cc_start: 0.8123 (mtp) cc_final: 0.7883 (mtp)
REVERT: A  185 LYS cc_start: 0.8930 (mtpt) cc_final: 0.8364 (mttp)
REVERT: A  233 TYR cc_start: 0.7393 (m-80) cc_final: 0.6470 (t80)
REVERT: A  258 GLU cc_start: 0.8405 (tt0) cc_final: 0.8182 (tt0)
REVERT: B   57 MET cc_start: 0.8211 (mtp) cc_final: 0.7909 (mtm)
REVERT: B  233 TYR cc_start: 0.7363 (m-80) cc_final: 0.6636 (t80)
REVERT: B  258 GLU cc_start: 0.8370 (tt0) cc_final: 0.8116 (tt0)
REVERT: B  263 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7581 (mp-120)
REVERT: C    8 GLN cc_start: 0.8328 (mm-40) cc_final: 0.7934 (mm-40)
REVERT: C  116 THR cc_start: 0.9165 (m) cc_final: 0.8768 (p)
REVERT: C  185 LYS cc_start: 0.8921 (mtmt) cc_final: 0.8512 (mttm)
REVERT: C  207 ASP cc_start: 0.9111 (OUTLIER) cc_final: 0.8730 (t70)
REVERT: C  233 TYR cc_start: 0.7374 (m-80) cc_final: 0.6482 (t80)
REVERT: D  185 LYS cc_start: 0.8976 (mtpt) cc_final: 0.8555 (mttm)
REVERT: D  233 TYR cc_start: 0.7454 (m-80) cc_final: 0.6666 (t80)
REVERT: D  258 GLU cc_start: 0.8378 (tt0) cc_final: 0.8108 (tt0)
REVERT: E   76 TYR cc_start: 0.7687 (OUTLIER) cc_final: 0.5606 (t80)
REVERT: E  116 THR cc_start: 0.9196 (m) cc_final: 0.8850 (p)
REVERT: E  140 MET cc_start: 0.8994 (mmm) cc_final: 0.8631 (mmm)
REVERT: E  207 ASP cc_start: 0.9130 (OUTLIER) cc_final: 0.8732 (t0)
REVERT: E  233 TYR cc_start: 0.7366 (m-80) cc_final: 0.6657 (t80)
REVERT: F  185 LYS cc_start: 0.8888 (mtpt) cc_final: 0.8424 (mttp)
REVERT: F  233 TYR cc_start: 0.7323 (m-80) cc_final: 0.6614 (t80)
REVERT: F  258 GLU cc_start: 0.8423 (tt0) cc_final: 0.8172 (tt0)
REVERT: F  378 GLN cc_start: 0.8280 (mt0) cc_final: 0.7840 (mm110)
REVERT: G   50 LEU cc_start: 0.7284 (pt) cc_final: 0.7069 (pp)
REVERT: G  185 LYS cc_start: 0.8983 (mtmt) cc_final: 0.8610 (mttm)
REVERT: G  233 TYR cc_start: 0.7420 (m-80) cc_final: 0.6552 (t80)
  outliers start: 36
  outliers final: 14
  residues processed: 189
  average time/residue: 1.2552
  time to fit residues: 274.3716
Evaluate side-chains
  180 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 162
  time to evaluate  : 2.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain B residue    2 GLU
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue  263 GLN
Chi-restraints excluded: chain B residue  350 ASP
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue  147 ASP
Chi-restraints excluded: chain C residue  207 ASP
Chi-restraints excluded: chain C residue  350 ASP
Chi-restraints excluded: chain D residue  147 ASP
Chi-restraints excluded: chain E residue    2 GLU
Chi-restraints excluded: chain E residue   56 ILE
Chi-restraints excluded: chain E residue   76 TYR
Chi-restraints excluded: chain E residue  207 ASP
Chi-restraints excluded: chain E residue  350 ASP
Chi-restraints excluded: chain F residue   56 ILE
Chi-restraints excluded: chain F residue  350 ASP
Chi-restraints excluded: chain G residue   56 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 273
   random chunks:
   chunk 127 optimal weight:    5.9990
   chunk 139 optimal weight:    6.9990
   chunk 71 optimal weight:    4.9990
   chunk 130 optimal weight:    4.9990
   chunk 219 optimal weight:    5.9990
   chunk 192 optimal weight:    6.9990
   chunk 133 optimal weight:    0.7980
   chunk 168 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 203 optimal weight:    1.9990
   chunk 4 optimal weight:   10.0000
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 231 ASN
B   8 GLN
B 134 GLN
B 231 ASN
C 231 ASN
D   8 GLN
D 134 GLN
D 231 ASN
E   8 GLN
E 231 ASN
F   8 GLN
F 134 GLN
F 231 ASN
G   8 GLN
G 134 GLN
G 195 GLN
G 231 ASN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.099411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.071308 restraints weight = 28302.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.2813 rms_B_bonded: 1.86
r_work: 0.2689 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2587 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.2587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9030
moved from start:          0.2267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  22589  Z= 0.242
  Angle     :  0.663   5.581  30849  Z= 0.379
  Chirality :  0.051   0.180   3234
  Planarity :  0.005   0.038   4025
  Dihedral  :  4.923  16.241   3024
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 1.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  :  6.38 %
    Favored  : 91.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.15), residues: 2751
  helix:  1.16 (0.23), residues: 497
  sheet:  1.36 (0.15), residues: 1092
  loop : -0.51 (0.16), residues: 1162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 370 
 HIS   0.006   0.002   HIS B 186 
 PHE   0.011   0.002   PHE C 321 
 TYR   0.023   0.002   TYR C  61 
 ARG   0.005   0.001   ARG A 362 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07141 (  819)
  hydrogen bonds       : angle       4.65242 ( 2373)
  SS BOND              : bond        0.00184 (    7)
  SS BOND              : angle       0.69662 (   14)
  covalent geometry    : bond        0.00525 (22582)
  covalent geometry    : angle       0.66264 (30835)

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

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

  5502 Ramachandran restraints generated.
    2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5502 Ramachandran restraints generated.
    2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 158
  time to evaluate  : 2.309 
Fit side-chains
REVERT: A    8 GLN cc_start: 0.8328 (mm-40) cc_final: 0.8013 (mm-40)
REVERT: A   57 MET cc_start: 0.8288 (mtp) cc_final: 0.8066 (mtp)
REVERT: A  233 TYR cc_start: 0.7659 (m-80) cc_final: 0.6692 (t80)
REVERT: A  258 GLU cc_start: 0.8443 (tt0) cc_final: 0.8192 (tt0)
REVERT: B   57 MET cc_start: 0.8243 (mtp) cc_final: 0.7974 (mtm)
REVERT: B   76 TYR cc_start: 0.7822 (OUTLIER) cc_final: 0.5646 (t80)
REVERT: B  233 TYR cc_start: 0.7645 (m-80) cc_final: 0.6740 (t80)
REVERT: B  258 GLU cc_start: 0.8451 (tt0) cc_final: 0.8199 (tt0)
REVERT: C    8 GLN cc_start: 0.8407 (mm-40) cc_final: 0.8111 (mm-40)
REVERT: C   76 TYR cc_start: 0.7750 (OUTLIER) cc_final: 0.5568 (t80)
REVERT: C  116 THR cc_start: 0.9212 (m) cc_final: 0.8838 (p)
REVERT: C  185 LYS cc_start: 0.8948 (mtmt) cc_final: 0.8547 (mttm)
REVERT: C  207 ASP cc_start: 0.9164 (OUTLIER) cc_final: 0.8599 (t0)
REVERT: C  233 TYR cc_start: 0.7614 (m-80) cc_final: 0.6664 (t80)
REVERT: D   76 TYR cc_start: 0.7666 (OUTLIER) cc_final: 0.5495 (t80)
REVERT: D  185 LYS cc_start: 0.9021 (mtpt) cc_final: 0.8598 (mttp)
REVERT: D  233 TYR cc_start: 0.7756 (m-80) cc_final: 0.6773 (t80)
REVERT: D  258 GLU cc_start: 0.8413 (tt0) cc_final: 0.8136 (tt0)
REVERT: E   50 LEU cc_start: 0.7532 (pt) cc_final: 0.7301 (pp)
REVERT: E   76 TYR cc_start: 0.7652 (OUTLIER) cc_final: 0.5725 (t80)
REVERT: E  116 THR cc_start: 0.9223 (m) cc_final: 0.8882 (p)
REVERT: E  140 MET cc_start: 0.8955 (mmm) cc_final: 0.8704 (mmm)
REVERT: E  207 ASP cc_start: 0.9170 (OUTLIER) cc_final: 0.8545 (t0)
REVERT: E  233 TYR cc_start: 0.7642 (m-80) cc_final: 0.6739 (t80)
REVERT: F  185 LYS cc_start: 0.8939 (mtpt) cc_final: 0.8470 (mttp)
REVERT: F  233 TYR cc_start: 0.7657 (m-80) cc_final: 0.6722 (t80)
REVERT: F  258 GLU cc_start: 0.8495 (tt0) cc_final: 0.8242 (tt0)
REVERT: F  378 GLN cc_start: 0.8455 (mt0) cc_final: 0.7966 (mm110)
REVERT: G   76 TYR cc_start: 0.7665 (OUTLIER) cc_final: 0.5598 (t80)
REVERT: G  233 TYR cc_start: 0.7650 (m-80) cc_final: 0.6708 (t80)
  outliers start: 50
  outliers final: 26
  residues processed: 195
  average time/residue: 1.1928
  time to fit residues: 269.7691
Evaluate side-chains
  188 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 155
  time to evaluate  : 2.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  241 THR
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   76 TYR
Chi-restraints excluded: chain B residue  147 ASP
Chi-restraints excluded: chain B residue  207 ASP
Chi-restraints excluded: chain B residue  350 ASP
Chi-restraints excluded: chain C residue   42 MET
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   76 TYR
Chi-restraints excluded: chain C residue  147 ASP
Chi-restraints excluded: chain C residue  207 ASP
Chi-restraints excluded: chain C residue  241 THR
Chi-restraints excluded: chain D residue   56 ILE
Chi-restraints excluded: chain D residue   76 TYR
Chi-restraints excluded: chain D residue  147 ASP
Chi-restraints excluded: chain D residue  207 ASP
Chi-restraints excluded: chain E residue    2 GLU
Chi-restraints excluded: chain E residue    8 GLN
Chi-restraints excluded: chain E residue   56 ILE
Chi-restraints excluded: chain E residue   76 TYR
Chi-restraints excluded: chain E residue  147 ASP
Chi-restraints excluded: chain E residue  207 ASP
Chi-restraints excluded: chain E residue  241 THR
Chi-restraints excluded: chain F residue   56 ILE
Chi-restraints excluded: chain F residue  207 ASP
Chi-restraints excluded: chain F residue  241 THR
Chi-restraints excluded: chain G residue   56 ILE
Chi-restraints excluded: chain G residue   76 TYR
Chi-restraints excluded: chain G residue  241 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 273
   random chunks:
   chunk 69 optimal weight:    0.0030
   chunk 258 optimal weight:    7.9990
   chunk 190 optimal weight:    0.6980
   chunk 204 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 219 optimal weight:    7.9990
   chunk 58 optimal weight:    0.6980
   chunk 180 optimal weight:    7.9990
   chunk 244 optimal weight:    3.9990
   chunk 67 optimal weight:    0.5980
   overall best weight:    0.9992

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

Flipped N/Q/H residues before XYZ refinement:
A 231 ASN
B   8 GLN
B 134 GLN
B 231 ASN
C  46 GLN
C 231 ASN
D   8 GLN
D 134 GLN
D 231 ASN
D 263 GLN
E   8 GLN
E 231 ASN
F   8 GLN
F 134 GLN
F 231 ASN
G   8 GLN
G 195 GLN
G 231 ASN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.102406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.074515 restraints weight = 28259.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.2870 rms_B_bonded: 1.86
r_work: 0.2748 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2647 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8979
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  22589  Z= 0.142
  Angle     :  0.533   4.760  30849  Z= 0.301
  Chirality :  0.046   0.139   3234
  Planarity :  0.004   0.032   4025
  Dihedral  :  4.543  16.072   3024
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 1.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  7.10 %
    Favored  : 91.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.15), residues: 2751
  helix:  1.28 (0.22), residues: 497
  sheet:  1.32 (0.15), residues: 1057
  loop : -0.33 (0.16), residues: 1197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 370 
 HIS   0.003   0.001   HIS E 186 
 PHE   0.016   0.001   PHE F 321 
 TYR   0.012   0.001   TYR E  61 
 ARG   0.002   0.000   ARG A  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04890 (  819)
  hydrogen bonds       : angle       4.51158 ( 2373)
  SS BOND              : bond        0.00073 (    7)
  SS BOND              : angle       0.35830 (   14)
  covalent geometry    : bond        0.00257 (22582)
  covalent geometry    : angle       0.53287 (30835)

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

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

  5502 Ramachandran restraints generated.
    2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5502 Ramachandran restraints generated.
    2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 159
  time to evaluate  : 2.285 
Fit side-chains
REVERT: A    8 GLN cc_start: 0.8331 (mm-40) cc_final: 0.8060 (mm-40)
REVERT: A   57 MET cc_start: 0.8255 (mtp) cc_final: 0.8038 (mtp)
REVERT: A  185 LYS cc_start: 0.8940 (mtpt) cc_final: 0.8389 (mttp)
REVERT: A  233 TYR cc_start: 0.7520 (m-80) cc_final: 0.6546 (t80)
REVERT: B   29 GLU cc_start: 0.7420 (mp0) cc_final: 0.7210 (mp0)
REVERT: B   57 MET cc_start: 0.8202 (mtp) cc_final: 0.7968 (mtp)
REVERT: B  233 TYR cc_start: 0.7455 (m-80) cc_final: 0.6613 (t80)
REVERT: B  258 GLU cc_start: 0.8420 (tt0) cc_final: 0.8168 (tt0)
REVERT: C    8 GLN cc_start: 0.8333 (mm-40) cc_final: 0.8032 (mm-40)
REVERT: C  116 THR cc_start: 0.9177 (m) cc_final: 0.8774 (p)
REVERT: C  185 LYS cc_start: 0.8937 (mtmt) cc_final: 0.8546 (mttm)
REVERT: C  207 ASP cc_start: 0.9125 (OUTLIER) cc_final: 0.8632 (t0)
REVERT: C  233 TYR cc_start: 0.7434 (m-80) cc_final: 0.6485 (t80)
REVERT: D  185 LYS cc_start: 0.8997 (mtpt) cc_final: 0.8580 (mttp)
REVERT: D  233 TYR cc_start: 0.7569 (m-80) cc_final: 0.6669 (t80)
REVERT: D  258 GLU cc_start: 0.8390 (tt0) cc_final: 0.8110 (tt0)
REVERT: E   76 TYR cc_start: 0.7711 (OUTLIER) cc_final: 0.5442 (t80)
REVERT: E  116 THR cc_start: 0.9185 (m) cc_final: 0.8839 (p)
REVERT: E  207 ASP cc_start: 0.9138 (OUTLIER) cc_final: 0.8563 (t0)
REVERT: E  233 TYR cc_start: 0.7478 (m-80) cc_final: 0.6658 (t80)
REVERT: F  185 LYS cc_start: 0.8913 (mtpt) cc_final: 0.8453 (mttp)
REVERT: F  233 TYR cc_start: 0.7495 (m-80) cc_final: 0.6618 (t80)
REVERT: F  258 GLU cc_start: 0.8444 (tt0) cc_final: 0.8196 (tt0)
REVERT: F  378 GLN cc_start: 0.8398 (mt0) cc_final: 0.7906 (mm110)
REVERT: G  233 TYR cc_start: 0.7548 (m-80) cc_final: 0.6600 (t80)
  outliers start: 35
  outliers final: 15
  residues processed: 184
  average time/residue: 1.2290
  time to fit residues: 261.1263
Evaluate side-chains
  175 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 157
  time to evaluate  : 2.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue  207 ASP
Chi-restraints excluded: chain B residue  350 ASP
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue  207 ASP
Chi-restraints excluded: chain C residue  350 ASP
Chi-restraints excluded: chain D residue   56 ILE
Chi-restraints excluded: chain E residue    2 GLU
Chi-restraints excluded: chain E residue   56 ILE
Chi-restraints excluded: chain E residue   76 TYR
Chi-restraints excluded: chain E residue  207 ASP
Chi-restraints excluded: chain E residue  241 THR
Chi-restraints excluded: chain E residue  350 ASP
Chi-restraints excluded: chain F residue   56 ILE
Chi-restraints excluded: chain F residue  207 ASP
Chi-restraints excluded: chain G residue   56 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 273
   random chunks:
   chunk 249 optimal weight:    7.9990
   chunk 106 optimal weight:    0.4980
   chunk 6 optimal weight:    0.0870
   chunk 187 optimal weight:    0.0370
   chunk 217 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9990
   chunk 190 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   chunk 225 optimal weight:    3.9990
   chunk 85 optimal weight:    4.9990
   chunk 234 optimal weight:    0.0050
   overall best weight:    0.3252

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

Flipped N/Q/H residues before XYZ refinement:
A 231 ASN
B   8 GLN
B 134 GLN
B 231 ASN
C 231 ASN
D   8 GLN
D 134 GLN
D 231 ASN
E   8 GLN
E 231 ASN
F   8 GLN
F 134 GLN
F 231 ASN
G   8 GLN
G 134 GLN
G 231 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.106170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.078589 restraints weight = 28452.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.2942 rms_B_bonded: 1.86
r_work: 0.2825 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2726 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8918
moved from start:          0.2687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050  22589  Z= 0.100
  Angle     :  0.462   6.332  30849  Z= 0.258
  Chirality :  0.044   0.138   3234
  Planarity :  0.004   0.030   4025
  Dihedral  :  4.121  14.449   3024
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 1.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  7.74 %
    Favored  : 91.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.15), residues: 2751
  helix:  1.61 (0.23), residues: 497
  sheet:  1.36 (0.15), residues: 1071
  loop : -0.19 (0.17), residues: 1183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 103 
 HIS   0.002   0.001   HIS E 186 
 PHE   0.017   0.001   PHE F 321 
 TYR   0.008   0.001   TYR C  61 
 ARG   0.003   0.000   ARG D  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03425 (  819)
  hydrogen bonds       : angle       4.35631 ( 2373)
  SS BOND              : bond        0.00011 (    7)
  SS BOND              : angle       0.14931 (   14)
  covalent geometry    : bond        0.00177 (22582)
  covalent geometry    : angle       0.46206 (30835)

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

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

  5502 Ramachandran restraints generated.
    2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5502 Ramachandran restraints generated.
    2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 203
  time to evaluate  : 2.960 
Fit side-chains
REVERT: A    8 GLN cc_start: 0.8300 (mm-40) cc_final: 0.8089 (mm-40)
REVERT: A   57 MET cc_start: 0.8231 (mtp) cc_final: 0.8025 (mtp)
REVERT: A  185 LYS cc_start: 0.8904 (mtpt) cc_final: 0.8355 (mttp)
REVERT: A  233 TYR cc_start: 0.7270 (m-80) cc_final: 0.6345 (t80)
REVERT: B   57 MET cc_start: 0.8154 (mtp) cc_final: 0.7913 (mtp)
REVERT: B  233 TYR cc_start: 0.7270 (m-80) cc_final: 0.6491 (t80)
REVERT: B  258 GLU cc_start: 0.8263 (tt0) cc_final: 0.7997 (tt0)
REVERT: C    8 GLN cc_start: 0.8276 (mm-40) cc_final: 0.7985 (mm-40)
REVERT: C  116 THR cc_start: 0.9135 (m) cc_final: 0.8723 (p)
REVERT: C  185 LYS cc_start: 0.8918 (mtmt) cc_final: 0.8526 (mttm)
REVERT: C  207 ASP cc_start: 0.9127 (OUTLIER) cc_final: 0.8743 (t70)
REVERT: C  233 TYR cc_start: 0.7210 (m-80) cc_final: 0.6370 (t80)
REVERT: D  185 LYS cc_start: 0.8967 (mtpt) cc_final: 0.8553 (mttp)
REVERT: D  233 TYR cc_start: 0.7363 (m-80) cc_final: 0.6482 (t80)
REVERT: D  258 GLU cc_start: 0.8286 (tt0) cc_final: 0.8012 (tt0)
REVERT: E  116 THR cc_start: 0.9146 (m) cc_final: 0.8787 (p)
REVERT: E  233 TYR cc_start: 0.7256 (m-80) cc_final: 0.6517 (t80)
REVERT: F  185 LYS cc_start: 0.8885 (mtpt) cc_final: 0.8433 (mttp)
REVERT: F  233 TYR cc_start: 0.7231 (m-80) cc_final: 0.6425 (t80)
REVERT: F  242 LYS cc_start: 0.7586 (tttt) cc_final: 0.7282 (ttmp)
REVERT: F  258 GLU cc_start: 0.8365 (tt0) cc_final: 0.8112 (tt0)
REVERT: F  378 GLN cc_start: 0.8347 (mt0) cc_final: 0.7860 (mm110)
REVERT: G  233 TYR cc_start: 0.7307 (m-80) cc_final: 0.6413 (t80)
  outliers start: 25
  outliers final: 11
  residues processed: 222
  average time/residue: 1.1429
  time to fit residues: 295.8763
Evaluate side-chains
  183 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 171
  time to evaluate  : 2.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain B residue   36 SER
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue  207 ASP
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue  207 ASP
Chi-restraints excluded: chain D residue   56 ILE
Chi-restraints excluded: chain E residue   56 ILE
Chi-restraints excluded: chain E residue  350 ASP
Chi-restraints excluded: chain F residue   56 ILE
Chi-restraints excluded: chain F residue  207 ASP
Chi-restraints excluded: chain G residue   56 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 273
   random chunks:
   chunk 238 optimal weight:    0.8980
   chunk 199 optimal weight:    1.9990
   chunk 118 optimal weight:    7.9990
   chunk 222 optimal weight:    1.9990
   chunk 184 optimal weight:    0.1980
   chunk 229 optimal weight:    5.9990
   chunk 88 optimal weight:    5.9990
   chunk 6 optimal weight:    4.9990
   chunk 230 optimal weight:    0.9990
   chunk 185 optimal weight:    2.9990
   chunk 96 optimal weight:    1.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
A 231 ASN
B   8 GLN
B 231 ASN
C 231 ASN
C 263 GLN
D   8 GLN
D 134 GLN
D 231 ASN
D 263 GLN
E 231 ASN
F   8 GLN
F 134 GLN
F 231 ASN
G   8 GLN
G 195 GLN
G 231 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.102071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.074630 restraints weight = 28615.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.2873 rms_B_bonded: 1.82
r_work: 0.2753 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2652 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8979
moved from start:          0.2591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  22589  Z= 0.142
  Angle     :  0.529   7.494  30849  Z= 0.297
  Chirality :  0.046   0.140   3234
  Planarity :  0.004   0.032   4025
  Dihedral  :  4.382  14.888   3024
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 1.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  8.21 %
    Favored  : 90.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.15), residues: 2751
  helix:  1.52 (0.23), residues: 497
  sheet:  1.34 (0.15), residues: 1071
  loop : -0.23 (0.16), residues: 1183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 329 
 HIS   0.005   0.001   HIS G 186 
 PHE   0.013   0.001   PHE F 321 
 TYR   0.012   0.001   TYR C  61 
 ARG   0.002   0.000   ARG F 144 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05050 (  819)
  hydrogen bonds       : angle       4.31992 ( 2373)
  SS BOND              : bond        0.00068 (    7)
  SS BOND              : angle       0.30673 (   14)
  covalent geometry    : bond        0.00272 (22582)
  covalent geometry    : angle       0.52868 (30835)

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

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

  5502 Ramachandran restraints generated.
    2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5502 Ramachandran restraints generated.
    2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 167
  time to evaluate  : 2.663 
Fit side-chains
REVERT: A    8 GLN cc_start: 0.8335 (mm-40) cc_final: 0.8071 (mm-40)
REVERT: A  233 TYR cc_start: 0.7455 (m-80) cc_final: 0.6438 (t80)
REVERT: B   57 MET cc_start: 0.8179 (mtp) cc_final: 0.7947 (mtp)
REVERT: B  233 TYR cc_start: 0.7460 (m-80) cc_final: 0.6646 (t80)
REVERT: B  258 GLU cc_start: 0.8313 (tt0) cc_final: 0.8072 (tt0)
REVERT: C    8 GLN cc_start: 0.8283 (mm-40) cc_final: 0.8018 (mm-40)
REVERT: C  116 THR cc_start: 0.9166 (m) cc_final: 0.8760 (p)
REVERT: C  185 LYS cc_start: 0.8929 (mtmt) cc_final: 0.8533 (mttm)
REVERT: C  207 ASP cc_start: 0.9137 (OUTLIER) cc_final: 0.8732 (t70)
REVERT: C  233 TYR cc_start: 0.7399 (m-80) cc_final: 0.6471 (t80)
REVERT: D  185 LYS cc_start: 0.8977 (mtpt) cc_final: 0.8563 (mttp)
REVERT: D  233 TYR cc_start: 0.7473 (m-80) cc_final: 0.6580 (t80)
REVERT: D  258 GLU cc_start: 0.8338 (tt0) cc_final: 0.8071 (tt0)
REVERT: E   50 LEU cc_start: 0.7251 (pt) cc_final: 0.7018 (pp)
REVERT: E  116 THR cc_start: 0.9172 (m) cc_final: 0.8820 (p)
REVERT: E  207 ASP cc_start: 0.9131 (OUTLIER) cc_final: 0.8625 (t70)
REVERT: E  233 TYR cc_start: 0.7418 (m-80) cc_final: 0.6588 (t80)
REVERT: F  185 LYS cc_start: 0.8912 (mtpt) cc_final: 0.8459 (mttp)
REVERT: F  233 TYR cc_start: 0.7441 (m-80) cc_final: 0.6620 (t80)
REVERT: F  242 LYS cc_start: 0.7632 (tttt) cc_final: 0.7362 (ttmp)
REVERT: F  258 GLU cc_start: 0.8430 (tt0) cc_final: 0.8184 (tt0)
REVERT: F  378 GLN cc_start: 0.8415 (mt0) cc_final: 0.7911 (mm110)
REVERT: G  233 TYR cc_start: 0.7448 (m-80) cc_final: 0.6542 (t80)
  outliers start: 26
  outliers final: 14
  residues processed: 187
  average time/residue: 1.2248
  time to fit residues: 265.6469
Evaluate side-chains
  180 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 164
  time to evaluate  : 2.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain B residue   36 SER
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue  147 ASP
Chi-restraints excluded: chain B residue  207 ASP
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue  207 ASP
Chi-restraints excluded: chain C residue  350 ASP
Chi-restraints excluded: chain D residue   56 ILE
Chi-restraints excluded: chain E residue    2 GLU
Chi-restraints excluded: chain E residue   56 ILE
Chi-restraints excluded: chain E residue  207 ASP
Chi-restraints excluded: chain E residue  350 ASP
Chi-restraints excluded: chain F residue   56 ILE
Chi-restraints excluded: chain F residue  207 ASP
Chi-restraints excluded: chain G residue   56 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 273
   random chunks:
   chunk 69 optimal weight:    5.9990
   chunk 87 optimal weight:    0.6980
   chunk 175 optimal weight:    4.9990
   chunk 119 optimal weight:    6.9990
   chunk 241 optimal weight:    1.9990
   chunk 102 optimal weight:    2.9990
   chunk 181 optimal weight:    5.9990
   chunk 249 optimal weight:    3.9990
   chunk 169 optimal weight:    1.9990
   chunk 266 optimal weight:    0.3980
   chunk 229 optimal weight:    3.9990
   overall best weight:    1.6186

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

Flipped N/Q/H residues before XYZ refinement:
A 231 ASN
B   8 GLN
B 231 ASN
C 231 ASN
D   8 GLN
D 134 GLN
D 231 ASN
E 231 ASN
F   8 GLN
F 134 GLN
F 231 ASN
G   8 GLN
G 134 GLN
G 195 GLN
G 231 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.100769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.073366 restraints weight = 28517.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.2851 rms_B_bonded: 1.82
r_work: 0.2730 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2628 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8997
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  22589  Z= 0.164
  Angle     :  0.563   9.973  30849  Z= 0.317
  Chirality :  0.047   0.141   3234
  Planarity :  0.004   0.033   4025
  Dihedral  :  4.546  15.766   3024
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 1.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  8.38 %
    Favored  : 90.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.15), residues: 2751
  helix:  1.40 (0.23), residues: 497
  sheet:  1.37 (0.15), residues: 1057
  loop : -0.26 (0.16), residues: 1197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 370 
 HIS   0.004   0.001   HIS B 186 
 PHE   0.013   0.002   PHE B 321 
 TYR   0.017   0.001   TYR A  61 
 ARG   0.003   0.000   ARG G  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05601 (  819)
  hydrogen bonds       : angle       4.40320 ( 2373)
  SS BOND              : bond        0.00085 (    7)
  SS BOND              : angle       0.34719 (   14)
  covalent geometry    : bond        0.00321 (22582)
  covalent geometry    : angle       0.56260 (30835)

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

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

  5502 Ramachandran restraints generated.
    2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5502 Ramachandran restraints generated.
    2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 162
  time to evaluate  : 2.377 
Fit side-chains
REVERT: A    8 GLN cc_start: 0.8336 (mm-40) cc_final: 0.8104 (mm-40)
REVERT: A  233 TYR cc_start: 0.7544 (m-80) cc_final: 0.6538 (t80)
REVERT: B   57 MET cc_start: 0.8244 (mtp) cc_final: 0.8002 (mtp)
REVERT: B  233 TYR cc_start: 0.7553 (m-80) cc_final: 0.6681 (t80)
REVERT: B  258 GLU cc_start: 0.8349 (tt0) cc_final: 0.8109 (tt0)
REVERT: C    8 GLN cc_start: 0.8337 (mm-40) cc_final: 0.8066 (mm-40)
REVERT: C  116 THR cc_start: 0.9183 (m) cc_final: 0.8783 (p)
REVERT: C  185 LYS cc_start: 0.8941 (mtmt) cc_final: 0.8548 (mttm)
REVERT: C  207 ASP cc_start: 0.9137 (OUTLIER) cc_final: 0.8661 (t0)
REVERT: C  233 TYR cc_start: 0.7464 (m-80) cc_final: 0.6532 (t80)
REVERT: D  185 LYS cc_start: 0.8998 (mtpt) cc_final: 0.8579 (mttp)
REVERT: D  233 TYR cc_start: 0.7611 (m-80) cc_final: 0.6661 (t80)
REVERT: D  258 GLU cc_start: 0.8375 (tt0) cc_final: 0.8117 (tt0)
REVERT: E   50 LEU cc_start: 0.7222 (pt) cc_final: 0.6992 (pp)
REVERT: E  116 THR cc_start: 0.9181 (m) cc_final: 0.8830 (p)
REVERT: E  207 ASP cc_start: 0.9143 (OUTLIER) cc_final: 0.8598 (t0)
REVERT: E  233 TYR cc_start: 0.7541 (m-80) cc_final: 0.6742 (t80)
REVERT: F  185 LYS cc_start: 0.8927 (mtpt) cc_final: 0.8464 (mttp)
REVERT: F  233 TYR cc_start: 0.7585 (m-80) cc_final: 0.6669 (t80)
REVERT: F  258 GLU cc_start: 0.8427 (tt0) cc_final: 0.8199 (tt0)
REVERT: F  378 GLN cc_start: 0.8436 (mt0) cc_final: 0.7886 (mm110)
REVERT: G   50 LEU cc_start: 0.6998 (tp) cc_final: 0.6282 (pt)
REVERT: G  233 TYR cc_start: 0.7612 (m-80) cc_final: 0.6628 (t80)
  outliers start: 26
  outliers final: 15
  residues processed: 182
  average time/residue: 1.2087
  time to fit residues: 254.1384
Evaluate side-chains
  175 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 158
  time to evaluate  : 2.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue  147 ASP
Chi-restraints excluded: chain B residue  207 ASP
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue  207 ASP
Chi-restraints excluded: chain C residue  350 ASP
Chi-restraints excluded: chain D residue   56 ILE
Chi-restraints excluded: chain D residue  207 ASP
Chi-restraints excluded: chain E residue    2 GLU
Chi-restraints excluded: chain E residue   56 ILE
Chi-restraints excluded: chain E residue  207 ASP
Chi-restraints excluded: chain E residue  241 THR
Chi-restraints excluded: chain F residue   56 ILE
Chi-restraints excluded: chain F residue  207 ASP
Chi-restraints excluded: chain G residue   56 ILE
Chi-restraints excluded: chain G residue  241 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 273
   random chunks:
   chunk 216 optimal weight:    0.7980
   chunk 87 optimal weight:    0.5980
   chunk 10 optimal weight:    5.9990
   chunk 58 optimal weight:    0.4980
   chunk 17 optimal weight:    3.9990
   chunk 184 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 189 optimal weight:    3.9990
   chunk 260 optimal weight:    2.9990
   chunk 148 optimal weight:    0.0000
   chunk 221 optimal weight:    0.8980
   overall best weight:    0.5584

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

Flipped N/Q/H residues before XYZ refinement:
A 231 ASN
B   8 GLN
B 231 ASN
C 231 ASN
D   8 GLN
D 134 GLN
D 231 ASN
D 263 GLN
E 231 ASN
F   8 GLN
F 134 GLN
F 231 ASN
G   8 GLN
G 134 GLN
G 195 GLN
G 231 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.103529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.076345 restraints weight = 28693.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 1.82
r_work: 0.2785 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2685 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8952
moved from start:          0.2712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  22589  Z= 0.117
  Angle     :  0.493   9.550  30849  Z= 0.275
  Chirality :  0.045   0.138   3234
  Planarity :  0.004   0.031   4025
  Dihedral  :  4.262  14.961   3024
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 1.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  8.84 %
    Favored  : 90.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.15), residues: 2751
  helix:  1.58 (0.23), residues: 497
  sheet:  1.34 (0.15), residues: 1071
  loop : -0.20 (0.17), residues: 1183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP G  45 
 HIS   0.003   0.001   HIS B 186 
 PHE   0.016   0.001   PHE F 321 
 TYR   0.012   0.001   TYR A  61 
 ARG   0.001   0.000   ARG D 152 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04120 (  819)
  hydrogen bonds       : angle       4.32603 ( 2373)
  SS BOND              : bond        0.00024 (    7)
  SS BOND              : angle       0.20976 (   14)
  covalent geometry    : bond        0.00203 (22582)
  covalent geometry    : angle       0.49317 (30835)

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

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

  5502 Ramachandran restraints generated.
    2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5502 Ramachandran restraints generated.
    2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 166
  time to evaluate  : 2.305 
Fit side-chains
REVERT: A    8 GLN cc_start: 0.8310 (mm-40) cc_final: 0.8096 (mm-40)
REVERT: A  185 LYS cc_start: 0.8918 (mtpt) cc_final: 0.8370 (mttp)
REVERT: A  233 TYR cc_start: 0.7410 (m-80) cc_final: 0.6429 (t80)
REVERT: B   57 MET cc_start: 0.8227 (mtp) cc_final: 0.7968 (mtp)
REVERT: B  233 TYR cc_start: 0.7423 (m-80) cc_final: 0.6610 (t80)
REVERT: B  258 GLU cc_start: 0.8239 (tt0) cc_final: 0.8010 (tt0)
REVERT: C    8 GLN cc_start: 0.8285 (mm-40) cc_final: 0.8054 (mm-40)
REVERT: C  116 THR cc_start: 0.9137 (m) cc_final: 0.8726 (p)
REVERT: C  185 LYS cc_start: 0.8929 (mtmt) cc_final: 0.8539 (mttm)
REVERT: C  207 ASP cc_start: 0.9130 (OUTLIER) cc_final: 0.8754 (t70)
REVERT: C  233 TYR cc_start: 0.7326 (m-80) cc_final: 0.6412 (t80)
REVERT: D  185 LYS cc_start: 0.8968 (mtpt) cc_final: 0.8556 (mttp)
REVERT: D  233 TYR cc_start: 0.7441 (m-80) cc_final: 0.6602 (t80)
REVERT: D  258 GLU cc_start: 0.8333 (tt0) cc_final: 0.8068 (tt0)
REVERT: E   50 LEU cc_start: 0.7091 (pt) cc_final: 0.6877 (pp)
REVERT: E  116 THR cc_start: 0.9147 (m) cc_final: 0.8796 (p)
REVERT: E  233 TYR cc_start: 0.7337 (m-80) cc_final: 0.6559 (t80)
REVERT: F  185 LYS cc_start: 0.8909 (mtpt) cc_final: 0.8450 (mttp)
REVERT: F  233 TYR cc_start: 0.7398 (m-80) cc_final: 0.6584 (t80)
REVERT: F  242 LYS cc_start: 0.7607 (tttt) cc_final: 0.7343 (ttmp)
REVERT: F  258 GLU cc_start: 0.8382 (tt0) cc_final: 0.8150 (tt0)
REVERT: F  378 GLN cc_start: 0.8389 (mt0) cc_final: 0.7887 (mm110)
REVERT: G  233 TYR cc_start: 0.7403 (m-80) cc_final: 0.6498 (t80)
  outliers start: 15
  outliers final: 8
  residues processed: 178
  average time/residue: 1.2307
  time to fit residues: 254.4282
Evaluate side-chains
  173 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 164
  time to evaluate  : 2.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue  207 ASP
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue  207 ASP
Chi-restraints excluded: chain D residue   56 ILE
Chi-restraints excluded: chain E residue   56 ILE
Chi-restraints excluded: chain F residue   56 ILE
Chi-restraints excluded: chain F residue  207 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 273
   random chunks:
   chunk 145 optimal weight:    5.9990
   chunk 218 optimal weight:    3.9990
   chunk 85 optimal weight:    0.3980
   chunk 28 optimal weight:    0.7980
   chunk 205 optimal weight:    5.9990
   chunk 236 optimal weight:    9.9990
   chunk 70 optimal weight:    0.3980
   chunk 31 optimal weight:    3.9990
   chunk 43 optimal weight:    7.9990
   chunk 238 optimal weight:    0.9980
   chunk 19 optimal weight:    5.9990
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
A 231 ASN
B   8 GLN
B 231 ASN
C 231 ASN
D   8 GLN
D 134 GLN
D 231 ASN
E 231 ASN
F   8 GLN
F 134 GLN
F 231 ASN
G   8 GLN
G 195 GLN
G 231 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.101676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.074369 restraints weight = 28604.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 1.82
r_work: 0.2748 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2647 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8983
moved from start:          0.2642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  22589  Z= 0.145
  Angle     :  0.535   9.507  30849  Z= 0.300
  Chirality :  0.046   0.139   3234
  Planarity :  0.004   0.031   4025
  Dihedral  :  4.414  15.295   3024
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 1.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  8.63 %
    Favored  : 90.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.15), residues: 2751
  helix:  1.49 (0.23), residues: 497
  sheet:  1.38 (0.15), residues: 1057
  loop : -0.22 (0.16), residues: 1197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP G 370 
 HIS   0.004   0.001   HIS G 186 
 PHE   0.014   0.001   PHE F 321 
 TYR   0.016   0.001   TYR A  61 
 ARG   0.002   0.000   ARG D 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05108 (  819)
  hydrogen bonds       : angle       4.33038 ( 2373)
  SS BOND              : bond        0.00064 (    7)
  SS BOND              : angle       0.25871 (   14)
  covalent geometry    : bond        0.00278 (22582)
  covalent geometry    : angle       0.53483 (30835)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 18808.23 seconds
wall clock time: 325 minutes 12.61 seconds (19512.61 seconds total)