Starting phenix.real_space_refine
on Tue Mar  3 17:57:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vz8_65478/03_2026/9vz8_65478.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vz8_65478/03_2026/9vz8_65478.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vz8_65478/03_2026/9vz8_65478.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vz8_65478/03_2026/9vz8_65478.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vz8_65478/03_2026/9vz8_65478.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vz8_65478/03_2026/9vz8_65478.map"
  }
  resolution = 3.81
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.029
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      50      5.16       5
     C    4844      2.51       5
     N    1264      2.21       5
     O    1443      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7601
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 1001
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1001
          Classifications: {'peptide': 139}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 10, 'TRANS': 128}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 85
          Unresolved non-hydrogen angles: 105
          Unresolved non-hydrogen dihedrals: 73
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'TYR:plan': 2, 'ASP:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 47
    Chain: "D"
      Number of atoms: 2607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 344, 2607
          Classifications: {'peptide': 344}
          Incomplete info: {'truncation_to_alanine': 33}
          Link IDs: {'PTRANS': 22, 'TRANS': 321}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 124
          Unresolved non-hydrogen angles: 148
          Unresolved non-hydrogen dihedrals: 104
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 6, 'ARG:plan': 3, 'GLN:plan1': 3, 'ASN:plan1': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 75
    Chain: "E"
      Number of atoms: 2331
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 302, 2331
          Classifications: {'peptide': 302}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PTRANS': 18, 'TRANS': 283}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 104
          Unresolved non-hydrogen angles: 124
          Unresolved non-hydrogen dihedrals: 91
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 4, 'GLU:plan': 4, 'TYR:plan': 1, 'ARG:plan': 1, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 62
    Chain: "L"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 799
          Classifications: {'peptide': 111}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103}
          Unresolved non-hydrogen bonds: 62
          Unresolved non-hydrogen angles: 74
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4}
          Unresolved non-hydrogen planarities: 38
    Chain: "H"
      Number of atoms: 863
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 863
          Classifications: {'peptide': 119}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 4, 'TRANS': 114}
          Unresolved non-hydrogen bonds: 71
          Unresolved non-hydrogen angles: 85
          Unresolved non-hydrogen dihedrals: 57
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 36
  Time building chain proxies: 1.84, per 1000 atoms: 0.24
  Number of scatterers: 7601
  At special positions: 0
  Unit cell: (94, 97, 117, 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      50     16.00
     O    1443      8.00
     N    1264      7.00
     C    4844      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  92 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.51
  Conformation dependent library (CDL) restraints added in 250.3 milliseconds
  

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1884

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 20 sheets defined
      9.5% alpha, 24.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'C' and resid 235 through 241
    Processing helix  chain 'C' and resid 304 through 308
    Processing helix  chain 'D' and resid 234 through 240
    Processing helix  chain 'D' and resid 273 through 277
      removed outlier: 3.684A  pdb=" N   LEU D 276 " --> pdb=" O   PRO D 273 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 306 through 308
      No H-bonds generated for 'chain 'D' and resid 306 through 308'
    Processing helix  chain 'D' and resid 327 through 329
      No H-bonds generated for 'chain 'D' and resid 327 through 329'
    Processing helix  chain 'D' and resid 360 through 362
      No H-bonds generated for 'chain 'D' and resid 360 through 362'
    Processing helix  chain 'D' and resid 400 through 406
      removed outlier: 3.576A  pdb=" N   GLU D 404 " --> pdb=" O   SER D 400 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 462 through 466
    Processing helix  chain 'E' and resid 210 through 215
      removed outlier: 3.778A  pdb=" N   GLN E 215 " --> pdb=" O   PHE E 211 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 222 through 227
      removed outlier: 4.666A  pdb=" N   GLN E 227 " --> pdb=" O   LEU E 223 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 234 through 240
    Processing helix  chain 'E' and resid 327 through 329
      No H-bonds generated for 'chain 'E' and resid 327 through 329'
    Processing helix  chain 'E' and resid 360 through 362
      No H-bonds generated for 'chain 'E' and resid 360 through 362'
    Processing helix  chain 'E' and resid 462 through 465
    Processing helix  chain 'E' and resid 466 through 472
    Processing helix  chain 'L' and resid 83 through 87
      removed outlier: 4.026A  pdb=" N   THR L  87 " --> pdb=" O   GLU L  84 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.589A  pdb=" N   SER H  31 " --> pdb=" O   SER H  28 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 28 through 32'
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.527A  pdb=" N   SER H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 154 through 156
      removed outlier: 3.708A  pdb=" N   GLN C 154 " --> pdb=" O   GLN C 255 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLN C 255 " --> pdb=" O   GLN C 154 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 267 through 268
    Processing sheet with id=AA3, first strand: chain 'C' and resid 267 through 268
    Processing sheet with id=AA4, first strand: chain 'D' and resid 35 through 38
      removed outlier: 6.107A  pdb=" N   GLN D 381 " --> pdb=" O   CYS D 103 " (cutoff:3.500A)
      removed outlier: 5.443A  pdb=" N   CYS D 103 " --> pdb=" O   GLN D 381 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 250 through 255
      removed outlier: 3.639A  pdb=" N   CYS D 158 " --> pdb=" O   LEU D 251 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   GLN D 255 " --> pdb=" O   GLN D 154 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLN D 154 " --> pdb=" O   GLN D 255 " (cutoff:3.500A)
      removed outlier: 7.165A  pdb=" N   VAL D 453 " --> pdb=" O   VAL D  73 " (cutoff:3.500A)
      removed outlier: 5.961A  pdb=" N   ARG D  75 " --> pdb=" O   VAL D 453 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 119 through 124
      removed outlier: 4.818A  pdb=" N   PHE D 123 " --> pdb=" O   ASP D 146 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   ASP D 146 " --> pdb=" O   PHE D 123 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 166 through 172
    Processing sheet with id=AA8, first strand: chain 'D' and resid 201 through 202
      removed outlier: 6.774A  pdb=" N   MET D 201 " --> pdb=" O   LYS D 231 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'D' and resid 257 through 263
      removed outlier: 5.518A  pdb=" N   ALA D 258 " --> pdb=" O   SER D 299 " (cutoff:3.500A)
      removed outlier: 6.030A  pdb=" N   SER D 299 " --> pdb=" O   ALA D 258 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   HIS D 260 " --> pdb=" O   SER D 297 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 267 through 268
      removed outlier: 6.733A  pdb=" N   VAL D 267 " --> pdb=" O   GLN E 366 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 36 through 38
      removed outlier: 3.636A  pdb=" N   ILE E 379 " --> pdb=" O   GLY E 105 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 44 through 46
    Processing sheet with id=AB4, first strand: chain 'E' and resid 249 through 255
      removed outlier: 4.146A  pdb=" N   PHE E 249 " --> pdb=" O   LEU E 160 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   LEU E 160 " --> pdb=" O   PHE E 249 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 119 through 121
      removed outlier: 3.636A  pdb=" N   SER E 119 " --> pdb=" O   VAL E 150 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   HIS E 121 " --> pdb=" O   VAL E 148 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   VAL E 148 " --> pdb=" O   HIS E 121 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 192 through 195
      removed outlier: 3.768A  pdb=" N   HIS E 169 " --> pdb=" O   LYS E 192 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   THR E 194 " --> pdb=" O   GLY E 167 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   MET E 201 " --> pdb=" O   LYS E 231 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 258 through 263
      removed outlier: 6.617A  pdb=" N   SER E 297 " --> pdb=" O   ARG E 259 " (cutoff:3.500A)
      removed outlier: 5.543A  pdb=" N   PHE E 261 " --> pdb=" O   SER E 295 " (cutoff:3.500A)
      removed outlier: 7.296A  pdb=" N   SER E 295 " --> pdb=" O   PHE E 261 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'L' and resid 4 through 7
      removed outlier: 3.588A  pdb=" N   ALA L  19 " --> pdb=" O   ILE L  79 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ASN L  78 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   SER L  67 " --> pdb=" O   ASN L  78 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'L' and resid 11 through 13
      removed outlier: 6.499A  pdb=" N   TRP L  39 " --> pdb=" O   LEU L  51 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'H' and resid 4 through 5
      removed outlier: 3.829A  pdb=" N   VAL H  18 " --> pdb=" O   LEU H  83 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LEU H  83 " --> pdb=" O   VAL H  18 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   THR H  78 " --> pdb=" O   ASP H  73 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ASP H  73 " --> pdb=" O   THR H  78 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   THR H  69 " --> pdb=" O   GLN H  82 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'H' and resid 58 through 60
      removed outlier: 3.608A  pdb=" N   GLY H  44 " --> pdb=" O   ARG H  40 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   ARG H  40 " --> pdb=" O   GLY H  44 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   GLU H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   MET H  34 " --> pdb=" O   GLU H  50 " (cutoff:3.500A)

    160 hydrogen bonds defined for protein.
    390 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: 1.09

  Time building geometry restraints manager: 0.66 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1237
        1.32 -     1.44: 2266
        1.44 -     1.57: 4227
        1.57 -     1.69: 1
        1.69 -     1.82: 69
  Bond restraints: 7800
  Sorted by residual:
  bond pdb=" C   PRO E 354 "
       pdb=" O   PRO E 354 "
    ideal  model  delta    sigma   weight residual
    1.233  1.192  0.041 1.13e-02 7.83e+03 1.31e+01
  bond pdb=" N   SER H  31 "
       pdb=" CA  SER H  31 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.035 1.32e-02 5.74e+03 7.10e+00
  bond pdb=" N   VAL E 355 "
       pdb=" CA  VAL E 355 "
    ideal  model  delta    sigma   weight residual
    1.465  1.492 -0.027 1.02e-02 9.61e+03 7.08e+00
  bond pdb=" N   GLN E 352 "
       pdb=" CA  GLN E 352 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.032 1.23e-02 6.61e+03 6.95e+00
  bond pdb=" N   PRO D 183 "
       pdb=" CA  PRO D 183 "
    ideal  model  delta    sigma   weight residual
    1.467  1.435  0.031 1.21e-02 6.83e+03 6.78e+00
  ... (remaining 7795 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.33: 10451
        2.33 -     4.66: 172
        4.66 -     6.98: 19
        6.98 -     9.31: 1
        9.31 -    11.64: 1
  Bond angle restraints: 10644
  Sorted by residual:
  angle pdb=" N   PRO E 354 "
        pdb=" CA  PRO E 354 "
        pdb=" C   PRO E 354 "
      ideal   model   delta    sigma   weight residual
     110.80   99.16   11.64 1.51e+00 4.39e-01 5.94e+01
  angle pdb=" CA  LYS L  53 "
        pdb=" C   LYS L  53 "
        pdb=" O   LYS L  53 "
      ideal   model   delta    sigma   weight residual
     120.82  115.33    5.49 1.05e+00 9.07e-01 2.74e+01
  angle pdb=" CA  PRO E 354 "
        pdb=" C   PRO E 354 "
        pdb=" O   PRO E 354 "
      ideal   model   delta    sigma   weight residual
     121.03  115.41    5.62 1.14e+00 7.69e-01 2.43e+01
  angle pdb=" CA  LYS L  53 "
        pdb=" C   LYS L  53 "
        pdb=" N   TYR L  54 "
      ideal   model   delta    sigma   weight residual
     117.07  122.23   -5.16 1.14e+00 7.69e-01 2.05e+01
  angle pdb=" CA  TRP L  39 "
        pdb=" C   TRP L  39 "
        pdb=" O   TRP L  39 "
      ideal   model   delta    sigma   weight residual
     120.71  115.92    4.79 1.06e+00 8.90e-01 2.04e+01
  ... (remaining 10639 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 3932
       17.95 -    35.90: 463
       35.90 -    53.85: 105
       53.85 -    71.79: 16
       71.79 -    89.74: 10
  Dihedral angle restraints: 4526
    sinusoidal: 1595
      harmonic: 2931
  Sorted by residual:
  dihedral pdb=" CA  HIS L  80 "
           pdb=" C   HIS L  80 "
           pdb=" N   PRO L  81 "
           pdb=" CA  PRO L  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.64   18.36     0      5.00e+00 4.00e-02 1.35e+01
  dihedral pdb=" CD  ARG E 341 "
           pdb=" NE  ARG E 341 "
           pdb=" CZ  ARG E 341 "
           pdb=" NH1 ARG E 341 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   29.29  -29.29     1      1.00e+01 1.00e-02 1.23e+01
  dihedral pdb=" CA  ASP E 210 "
           pdb=" CB  ASP E 210 "
           pdb=" CG  ASP E 210 "
           pdb=" OD1 ASP E 210 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.35   58.35     1      2.00e+01 2.50e-03 1.14e+01
  ... (remaining 4523 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 911
       0.047 -    0.094: 174
       0.094 -    0.141: 88
       0.141 -    0.188: 5
       0.188 -    0.235: 2
  Chirality restraints: 1180
  Sorted by residual:
  chirality pdb=" CA  ASN E 353 "
            pdb=" N   ASN E 353 "
            pdb=" C   ASN E 353 "
            pdb=" CB  ASN E 353 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.24 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" CA  GLN D 182 "
            pdb=" N   GLN D 182 "
            pdb=" C   GLN D 182 "
            pdb=" CB  GLN D 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.00e-01
  chirality pdb=" CA  ILE L  52 "
            pdb=" N   ILE L  52 "
            pdb=" C   ILE L  52 "
            pdb=" CB  ILE L  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.83e-01
  ... (remaining 1177 not shown)

  Planarity restraints: 1366
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG E 341 "    0.529 9.50e-02 1.11e+02   2.37e-01 3.44e+01
        pdb=" NE  ARG E 341 "   -0.032 2.00e-02 2.50e+03
        pdb=" CZ  ARG E 341 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG E 341 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG E 341 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS L  80 "   -0.071 5.00e-02 4.00e+02   1.08e-01 1.86e+01
        pdb=" N   PRO L  81 "    0.187 5.00e-02 4.00e+02
        pdb=" CA  PRO L  81 "   -0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO L  81 "   -0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER L   7 "   -0.059 5.00e-02 4.00e+02   8.92e-02 1.27e+01
        pdb=" N   PRO L   8 "    0.154 5.00e-02 4.00e+02
        pdb=" CA  PRO L   8 "   -0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO L   8 "   -0.044 5.00e-02 4.00e+02
  ... (remaining 1363 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1757
        2.78 -     3.31: 6425
        3.31 -     3.84: 11553
        3.84 -     4.37: 12528
        4.37 -     4.90: 23034
  Nonbonded interactions: 55297
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN D 399 "
            pdb=" OG  SER D 401 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OD2 ASP D 200 "
            pdb=" NZ  LYS D 231 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" O   TYR D  49 "
            pdb=" NZ  LYS D  65 "
     model   vdw
     2.298 3.120
  nonbonded pdb=" OD1 ASP E 210 "
            pdb=" OG1 THR E 213 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" OG1 THR E 141 "
            pdb=" N   GLN E 142 "
     model   vdw
     2.310 3.120
  ... (remaining 55292 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.830
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.730
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.120   7802  Z= 0.226
  Angle     :  0.682  11.638  10648  Z= 0.403
  Chirality :  0.046   0.235   1180
  Planarity :  0.009   0.237   1366
  Dihedral  : 16.578  89.742   2636
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 30.13 %
    Favored  : 69.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.54 (0.27), residues: 969
  helix: -1.34 (0.71), residues: 40
  sheet: -0.75 (0.30), residues: 322
  loop : -1.15 (0.25), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG H  98 
 TYR   0.024   0.002   TYR H  32 
 PHE   0.031   0.001   PHE H  99 
 TRP   0.014   0.001   TRP H  33 
 HIS   0.010   0.001   HIS L  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 7800)
  covalent geometry    : angle       0.68236 (10644)
  SS BOND              : bond        0.00364 (    2)
  SS BOND              : angle       0.70017 (    4)
  hydrogen bonds       : bond        0.28291 (  158)
  hydrogen bonds       : angle       9.95348 (  390)

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.279 
Fit side-chains
REVERT: C  125 ASN cc_start: 0.8275 (t0) cc_final: 0.7845 (t0)
REVERT: C  255 GLN cc_start: 0.8867 (mt0) cc_final: 0.8465 (mt0)
REVERT: D  197 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8612 (mm-30)
REVERT: D  198 ASP cc_start: 0.8669 (t70) cc_final: 0.8468 (t0)
REVERT: D  238 MET cc_start: 0.9299 (mtp) cc_final: 0.8889 (mtp)
REVERT: E  472 PHE cc_start: 0.7997 (t80) cc_final: 0.7782 (t80)
REVERT: L   54 TYR cc_start: 0.8348 (m-80) cc_final: 0.8000 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.0689
  time to fit residues: 17.9030
Evaluate side-chains
  163 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.3980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.0570
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
D 255 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.160695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.125824 restraints weight = 10963.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.129673 restraints weight = 5809.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.132011 restraints weight = 3905.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.133560 restraints weight = 3069.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.134299 restraints weight = 2652.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.0985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   7802  Z= 0.116
  Angle     :  0.555   6.921  10648  Z= 0.281
  Chirality :  0.044   0.145   1180
  Planarity :  0.005   0.073   1366
  Dihedral  :  4.135  17.008   1075
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 28.33 %
    Favored  : 68.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.37 (0.27), residues: 969
  helix: -0.92 (0.77), residues: 40
  sheet: -0.68 (0.30), residues: 328
  loop : -1.03 (0.25), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 264 
 TYR   0.012   0.001   TYR L  91 
 PHE   0.010   0.001   PHE H  99 
 TRP   0.027   0.001   TRP C 170 
 HIS   0.004   0.001   HIS C 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 7800)
  covalent geometry    : angle       0.55539 (10644)
  SS BOND              : bond        0.00556 (    2)
  SS BOND              : angle       0.68326 (    4)
  hydrogen bonds       : bond        0.03645 (  158)
  hydrogen bonds       : angle       6.76590 (  390)

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 179
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
REVERT: C  125 ASN cc_start: 0.8448 (t0) cc_final: 0.8047 (t0)
REVERT: D  197 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8529 (mm-30)
REVERT: D  238 MET cc_start: 0.9087 (mtp) cc_final: 0.8615 (mtp)
REVERT: E  472 PHE cc_start: 0.8100 (t80) cc_final: 0.7742 (t80)
  outliers start: 26
  outliers final: 16
  residues processed: 194
  average time/residue: 0.0624
  time to fit residues: 17.9732
Evaluate side-chains
  185 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 169
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  166 ILE
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue  106 MET
Chi-restraints excluded: chain D residue  131 GLU
Chi-restraints excluded: chain D residue  335 THR
Chi-restraints excluded: chain E residue   63 VAL
Chi-restraints excluded: chain E residue  104 VAL
Chi-restraints excluded: chain E residue  116 ILE
Chi-restraints excluded: chain E residue  150 VAL
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain E residue  217 THR
Chi-restraints excluded: chain E residue  327 CYS
Chi-restraints excluded: chain E residue  357 SER
Chi-restraints excluded: chain E residue  371 VAL
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   20 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 87 optimal weight:    4.9990
   chunk 90 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 58 optimal weight:    0.3980
   chunk 4 optimal weight:    7.9990
   chunk 15 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    1.4786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.148922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.112752 restraints weight = 11060.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.116216 restraints weight = 6180.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.118380 restraints weight = 4295.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.119538 restraints weight = 3448.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.120481 restraints weight = 3042.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.1402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   7802  Z= 0.194
  Angle     :  0.589   6.574  10648  Z= 0.298
  Chirality :  0.045   0.171   1180
  Planarity :  0.005   0.059   1366
  Dihedral  :  4.384  19.079   1075
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  5.64 %
    Allowed  : 27.05 %
    Favored  : 67.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.27), residues: 969
  helix: -0.53 (0.83), residues: 40
  sheet: -0.66 (0.29), residues: 339
  loop : -1.17 (0.25), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 253 
 TYR   0.015   0.001   TYR L  91 
 PHE   0.012   0.002   PHE H  64 
 TRP   0.010   0.001   TRP H  47 
 HIS   0.004   0.001   HIS D  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 ( 7800)
  covalent geometry    : angle       0.58840 (10644)
  SS BOND              : bond        0.00544 (    2)
  SS BOND              : angle       0.92018 (    4)
  hydrogen bonds       : bond        0.03614 (  158)
  hydrogen bonds       : angle       6.00451 (  390)

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 170
  time to evaluate  : 0.264 
Fit side-chains
REVERT: C  125 ASN cc_start: 0.8555 (t0) cc_final: 0.8157 (t0)
REVERT: D  197 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8576 (mm-30)
REVERT: D  198 ASP cc_start: 0.8727 (t70) cc_final: 0.8514 (t0)
REVERT: D  238 MET cc_start: 0.9131 (mtp) cc_final: 0.8577 (mtp)
REVERT: D  247 MET cc_start: 0.6797 (ttt) cc_final: 0.6573 (ttt)
REVERT: E  125 ASN cc_start: 0.9137 (t0) cc_final: 0.8886 (t0)
REVERT: E  472 PHE cc_start: 0.8060 (t80) cc_final: 0.7719 (t80)
REVERT: L   80 HIS cc_start: 0.7169 (m-70) cc_final: 0.6883 (m-70)
  outliers start: 44
  outliers final: 33
  residues processed: 192
  average time/residue: 0.0629
  time to fit residues: 17.9239
Evaluate side-chains
  201 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 168
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  166 ILE
Chi-restraints excluded: chain D residue   53 VAL
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain D residue  131 GLU
Chi-restraints excluded: chain D residue  157 LEU
Chi-restraints excluded: chain D residue  204 THR
Chi-restraints excluded: chain D residue  309 LEU
Chi-restraints excluded: chain D residue  335 THR
Chi-restraints excluded: chain D residue  340 THR
Chi-restraints excluded: chain D residue  343 THR
Chi-restraints excluded: chain D residue  468 LEU
Chi-restraints excluded: chain E residue   63 VAL
Chi-restraints excluded: chain E residue  116 ILE
Chi-restraints excluded: chain E residue  150 VAL
Chi-restraints excluded: chain E residue  155 THR
Chi-restraints excluded: chain E residue  160 LEU
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain E residue  217 THR
Chi-restraints excluded: chain E residue  230 CYS
Chi-restraints excluded: chain E residue  327 CYS
Chi-restraints excluded: chain E residue  332 LEU
Chi-restraints excluded: chain E residue  348 CYS
Chi-restraints excluded: chain E residue  357 SER
Chi-restraints excluded: chain E residue  371 VAL
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   79 ILE
Chi-restraints excluded: chain L residue   98 ILE
Chi-restraints excluded: chain L residue  101 THR
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   58 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 36 optimal weight:    0.0060
   chunk 29 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 82 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.9400

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.153869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.117728 restraints weight = 11090.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.121476 restraints weight = 5945.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.123624 restraints weight = 4026.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.125267 restraints weight = 3213.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.126068 restraints weight = 2764.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.1533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7802  Z= 0.135
  Angle     :  0.548   6.821  10648  Z= 0.273
  Chirality :  0.045   0.148   1180
  Planarity :  0.004   0.070   1366
  Dihedral  :  4.193  18.801   1075
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 28.46 %
    Favored  : 67.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.33 (0.27), residues: 969
  helix: -0.44 (0.84), residues: 40
  sheet: -0.57 (0.29), residues: 328
  loop : -1.09 (0.25), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 253 
 TYR   0.011   0.001   TYR L  91 
 PHE   0.008   0.001   PHE C 248 
 TRP   0.011   0.001   TRP H  47 
 HIS   0.003   0.001   HIS D 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 7800)
  covalent geometry    : angle       0.54776 (10644)
  SS BOND              : bond        0.00441 (    2)
  SS BOND              : angle       0.74404 (    4)
  hydrogen bonds       : bond        0.02917 (  158)
  hydrogen bonds       : angle       5.69399 (  390)

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 169
  time to evaluate  : 0.304 
Fit side-chains
REVERT: C  125 ASN cc_start: 0.8574 (t0) cc_final: 0.8185 (t0)
REVERT: C  156 GLN cc_start: 0.8354 (mt0) cc_final: 0.8003 (tt0)
REVERT: C  247 MET cc_start: 0.2561 (OUTLIER) cc_final: 0.1668 (tmt)
REVERT: D  197 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8557 (mm-30)
REVERT: D  198 ASP cc_start: 0.8667 (t70) cc_final: 0.8464 (t0)
REVERT: D  238 MET cc_start: 0.9065 (mtp) cc_final: 0.8520 (mtp)
REVERT: D  247 MET cc_start: 0.7001 (ttt) cc_final: 0.6791 (ttt)
REVERT: E  472 PHE cc_start: 0.8083 (t80) cc_final: 0.7744 (t80)
  outliers start: 34
  outliers final: 28
  residues processed: 187
  average time/residue: 0.0619
  time to fit residues: 17.1958
Evaluate side-chains
  195 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 166
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  166 ILE
Chi-restraints excluded: chain C residue  247 MET
Chi-restraints excluded: chain D residue   53 VAL
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   76 VAL
Chi-restraints excluded: chain D residue  106 MET
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain D residue  131 GLU
Chi-restraints excluded: chain D residue  204 THR
Chi-restraints excluded: chain D residue  212 SER
Chi-restraints excluded: chain D residue  335 THR
Chi-restraints excluded: chain D residue  468 LEU
Chi-restraints excluded: chain E residue   63 VAL
Chi-restraints excluded: chain E residue  116 ILE
Chi-restraints excluded: chain E residue  150 VAL
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain E residue  217 THR
Chi-restraints excluded: chain E residue  327 CYS
Chi-restraints excluded: chain E residue  348 CYS
Chi-restraints excluded: chain E residue  357 SER
Chi-restraints excluded: chain E residue  371 VAL
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   79 ILE
Chi-restraints excluded: chain L residue   98 ILE
Chi-restraints excluded: chain L residue  101 THR
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   58 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 6 optimal weight:    7.9990
   chunk 86 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 20 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9980
   overall best weight:    1.3784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.152004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.115702 restraints weight = 11079.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.119359 restraints weight = 5963.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.121505 restraints weight = 4061.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.123099 restraints weight = 3245.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.123850 restraints weight = 2801.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.1760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7802  Z= 0.180
  Angle     :  0.572   7.114  10648  Z= 0.286
  Chirality :  0.045   0.161   1180
  Planarity :  0.004   0.067   1366
  Dihedral  :  4.330  18.000   1075
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 27.18 %
    Favored  : 66.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.41 (0.27), residues: 969
  helix:  0.45 (0.94), residues: 34
  sheet: -0.64 (0.28), residues: 341
  loop : -1.20 (0.25), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 253 
 TYR   0.011   0.001   TYR L  91 
 PHE   0.010   0.001   PHE D 310 
 TRP   0.012   0.001   TRP H  47 
 HIS   0.004   0.001   HIS D  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 7800)
  covalent geometry    : angle       0.57170 (10644)
  SS BOND              : bond        0.00472 (    2)
  SS BOND              : angle       0.82036 (    4)
  hydrogen bonds       : bond        0.03028 (  158)
  hydrogen bonds       : angle       5.57082 (  390)

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 169
  time to evaluate  : 0.276 
Fit side-chains
REVERT: C  125 ASN cc_start: 0.8569 (t0) cc_final: 0.8212 (t0)
REVERT: C  247 MET cc_start: 0.2513 (OUTLIER) cc_final: 0.1573 (tmt)
REVERT: D  197 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8562 (mm-30)
REVERT: D  238 MET cc_start: 0.9116 (mtp) cc_final: 0.8551 (mtp)
REVERT: E  472 PHE cc_start: 0.7964 (t80) cc_final: 0.7616 (t80)
  outliers start: 52
  outliers final: 42
  residues processed: 197
  average time/residue: 0.0629
  time to fit residues: 18.2511
Evaluate side-chains
  211 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 168
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  166 ILE
Chi-restraints excluded: chain C residue  247 MET
Chi-restraints excluded: chain D residue   53 VAL
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   76 VAL
Chi-restraints excluded: chain D residue  106 MET
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain D residue  157 LEU
Chi-restraints excluded: chain D residue  194 THR
Chi-restraints excluded: chain D residue  204 THR
Chi-restraints excluded: chain D residue  212 SER
Chi-restraints excluded: chain D residue  217 THR
Chi-restraints excluded: chain D residue  309 LEU
Chi-restraints excluded: chain D residue  335 THR
Chi-restraints excluded: chain D residue  340 THR
Chi-restraints excluded: chain D residue  343 THR
Chi-restraints excluded: chain D residue  346 THR
Chi-restraints excluded: chain D residue  468 LEU
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue   63 VAL
Chi-restraints excluded: chain E residue  116 ILE
Chi-restraints excluded: chain E residue  150 VAL
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain E residue  217 THR
Chi-restraints excluded: chain E residue  326 ILE
Chi-restraints excluded: chain E residue  327 CYS
Chi-restraints excluded: chain E residue  332 LEU
Chi-restraints excluded: chain E residue  348 CYS
Chi-restraints excluded: chain E residue  351 THR
Chi-restraints excluded: chain E residue  357 SER
Chi-restraints excluded: chain E residue  371 VAL
Chi-restraints excluded: chain E residue  463 LEU
Chi-restraints excluded: chain E residue  468 LEU
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   79 ILE
Chi-restraints excluded: chain L residue   98 ILE
Chi-restraints excluded: chain L residue  101 THR
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   58 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 24 optimal weight:    0.0050
   chunk 91 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 74 optimal weight:    0.5980
   chunk 39 optimal weight:    0.6980
   chunk 28 optimal weight:    4.9990
   chunk 97 optimal weight:    2.9990
   overall best weight:    1.0396

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.151877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.115230 restraints weight = 11022.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.118896 restraints weight = 5958.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.121263 restraints weight = 4051.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.122544 restraints weight = 3222.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.123539 restraints weight = 2816.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.1859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7802  Z= 0.142
  Angle     :  0.563   8.093  10648  Z= 0.276
  Chirality :  0.045   0.196   1180
  Planarity :  0.004   0.070   1366
  Dihedral  :  4.241  22.221   1075
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 27.82 %
    Favored  : 66.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.34 (0.27), residues: 969
  helix:  0.46 (0.93), residues: 34
  sheet: -0.58 (0.29), residues: 325
  loop : -1.15 (0.25), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 253 
 TYR   0.010   0.001   TYR L  91 
 PHE   0.009   0.001   PHE C 248 
 TRP   0.013   0.001   TRP H  47 
 HIS   0.003   0.001   HIS D 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 7800)
  covalent geometry    : angle       0.56284 (10644)
  SS BOND              : bond        0.00422 (    2)
  SS BOND              : angle       0.76507 (    4)
  hydrogen bonds       : bond        0.02740 (  158)
  hydrogen bonds       : angle       5.44492 (  390)

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 174
  time to evaluate  : 0.303 
Fit side-chains
REVERT: C  247 MET cc_start: 0.2647 (OUTLIER) cc_final: 0.1677 (tmt)
REVERT: D  238 MET cc_start: 0.9073 (mtp) cc_final: 0.8523 (mtp)
REVERT: E  472 PHE cc_start: 0.7876 (t80) cc_final: 0.7544 (t80)
  outliers start: 48
  outliers final: 43
  residues processed: 200
  average time/residue: 0.0598
  time to fit residues: 17.8559
Evaluate side-chains
  209 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 165
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  166 ILE
Chi-restraints excluded: chain C residue  247 MET
Chi-restraints excluded: chain D residue   53 VAL
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   76 VAL
Chi-restraints excluded: chain D residue  106 MET
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain D residue  131 GLU
Chi-restraints excluded: chain D residue  157 LEU
Chi-restraints excluded: chain D residue  194 THR
Chi-restraints excluded: chain D residue  204 THR
Chi-restraints excluded: chain D residue  212 SER
Chi-restraints excluded: chain D residue  217 THR
Chi-restraints excluded: chain D residue  335 THR
Chi-restraints excluded: chain D residue  340 THR
Chi-restraints excluded: chain D residue  342 SER
Chi-restraints excluded: chain D residue  343 THR
Chi-restraints excluded: chain D residue  346 THR
Chi-restraints excluded: chain D residue  468 LEU
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue   63 VAL
Chi-restraints excluded: chain E residue  104 VAL
Chi-restraints excluded: chain E residue  116 ILE
Chi-restraints excluded: chain E residue  150 VAL
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain E residue  217 THR
Chi-restraints excluded: chain E residue  326 ILE
Chi-restraints excluded: chain E residue  327 CYS
Chi-restraints excluded: chain E residue  332 LEU
Chi-restraints excluded: chain E residue  348 CYS
Chi-restraints excluded: chain E residue  351 THR
Chi-restraints excluded: chain E residue  371 VAL
Chi-restraints excluded: chain E residue  463 LEU
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   62 VAL
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   79 ILE
Chi-restraints excluded: chain L residue   98 ILE
Chi-restraints excluded: chain L residue  101 THR
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   58 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 93 optimal weight:    0.0970
   chunk 24 optimal weight:    0.0870
   chunk 22 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 8 optimal weight:    9.9990
   chunk 85 optimal weight:    9.9990
   chunk 52 optimal weight:    0.9990
   chunk 43 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 97 optimal weight:    5.9990
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.5558

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.157283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.121225 restraints weight = 10931.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.124992 restraints weight = 5877.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.127397 restraints weight = 3976.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.128917 restraints weight = 3133.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.129633 restraints weight = 2709.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.1982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   7802  Z= 0.101
  Angle     :  0.541   7.986  10648  Z= 0.265
  Chirality :  0.044   0.238   1180
  Planarity :  0.004   0.070   1366
  Dihedral  :  4.055  19.707   1075
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 29.10 %
    Favored  : 65.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.27 (0.27), residues: 969
  helix:  0.37 (0.92), residues: 34
  sheet: -0.52 (0.30), residues: 325
  loop : -1.10 (0.25), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 253 
 TYR   0.009   0.001   TYR L  91 
 PHE   0.010   0.001   PHE C 248 
 TRP   0.014   0.001   TRP H  47 
 HIS   0.008   0.001   HIS D 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 7800)
  covalent geometry    : angle       0.54063 (10644)
  SS BOND              : bond        0.00362 (    2)
  SS BOND              : angle       0.57925 (    4)
  hydrogen bonds       : bond        0.02469 (  158)
  hydrogen bonds       : angle       5.28567 (  390)

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 169
  time to evaluate  : 0.291 
Fit side-chains
REVERT: C  247 MET cc_start: 0.2704 (OUTLIER) cc_final: 0.1704 (tmt)
REVERT: D  238 MET cc_start: 0.8974 (mtp) cc_final: 0.8368 (mtp)
REVERT: E  152 TYR cc_start: 0.9011 (m-10) cc_final: 0.8786 (m-10)
REVERT: E  472 PHE cc_start: 0.7759 (t80) cc_final: 0.7444 (t80)
  outliers start: 41
  outliers final: 33
  residues processed: 191
  average time/residue: 0.0617
  time to fit residues: 17.6483
Evaluate side-chains
  198 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 164
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  166 ILE
Chi-restraints excluded: chain C residue  247 MET
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue  106 MET
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain D residue  131 GLU
Chi-restraints excluded: chain D residue  157 LEU
Chi-restraints excluded: chain D residue  212 SER
Chi-restraints excluded: chain D residue  217 THR
Chi-restraints excluded: chain D residue  229 ILE
Chi-restraints excluded: chain D residue  309 LEU
Chi-restraints excluded: chain D residue  335 THR
Chi-restraints excluded: chain D residue  340 THR
Chi-restraints excluded: chain D residue  343 THR
Chi-restraints excluded: chain D residue  346 THR
Chi-restraints excluded: chain D residue  468 LEU
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue   63 VAL
Chi-restraints excluded: chain E residue  116 ILE
Chi-restraints excluded: chain E residue  150 VAL
Chi-restraints excluded: chain E residue  217 THR
Chi-restraints excluded: chain E residue  327 CYS
Chi-restraints excluded: chain E residue  348 CYS
Chi-restraints excluded: chain E residue  371 VAL
Chi-restraints excluded: chain E residue  463 LEU
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   79 ILE
Chi-restraints excluded: chain L residue  101 THR
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   58 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 89 optimal weight:   20.0000
   chunk 8 optimal weight:    9.9990
   chunk 19 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0370
   chunk 66 optimal weight:    3.9990
   chunk 3 optimal weight:    0.0050
   chunk 73 optimal weight:    2.9990
   overall best weight:    1.3876

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.153463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.117553 restraints weight = 10992.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.121150 restraints weight = 5897.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.123508 restraints weight = 4020.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.124813 restraints weight = 3164.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.125773 restraints weight = 2756.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.2033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7802  Z= 0.182
  Angle     :  0.585   8.473  10648  Z= 0.289
  Chirality :  0.045   0.200   1180
  Planarity :  0.004   0.073   1366
  Dihedral  :  4.277  19.028   1075
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 29.10 %
    Favored  : 65.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.35 (0.27), residues: 969
  helix:  0.33 (0.90), residues: 34
  sheet: -0.59 (0.29), residues: 328
  loop : -1.16 (0.25), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 253 
 TYR   0.010   0.001   TYR H  95 
 PHE   0.010   0.001   PHE H  64 
 TRP   0.013   0.001   TRP H  47 
 HIS   0.007   0.001   HIS D 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 7800)
  covalent geometry    : angle       0.58444 (10644)
  SS BOND              : bond        0.00449 (    2)
  SS BOND              : angle       0.85832 (    4)
  hydrogen bonds       : bond        0.02876 (  158)
  hydrogen bonds       : angle       5.33723 (  390)

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 164
  time to evaluate  : 0.289 
Fit side-chains
REVERT: C  247 MET cc_start: 0.2649 (OUTLIER) cc_final: 0.1675 (tmt)
REVERT: D  238 MET cc_start: 0.9089 (mtp) cc_final: 0.8647 (mtp)
REVERT: E  472 PHE cc_start: 0.7747 (t80) cc_final: 0.7402 (t80)
  outliers start: 45
  outliers final: 41
  residues processed: 189
  average time/residue: 0.0634
  time to fit residues: 17.7291
Evaluate side-chains
  206 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 164
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  166 ILE
Chi-restraints excluded: chain C residue  247 MET
Chi-restraints excluded: chain D residue   53 VAL
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   76 VAL
Chi-restraints excluded: chain D residue  106 MET
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain D residue  157 LEU
Chi-restraints excluded: chain D residue  204 THR
Chi-restraints excluded: chain D residue  212 SER
Chi-restraints excluded: chain D residue  217 THR
Chi-restraints excluded: chain D residue  335 THR
Chi-restraints excluded: chain D residue  340 THR
Chi-restraints excluded: chain D residue  343 THR
Chi-restraints excluded: chain D residue  346 THR
Chi-restraints excluded: chain D residue  455 LEU
Chi-restraints excluded: chain D residue  468 LEU
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue   63 VAL
Chi-restraints excluded: chain E residue  116 ILE
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain E residue  150 VAL
Chi-restraints excluded: chain E residue  214 LEU
Chi-restraints excluded: chain E residue  217 THR
Chi-restraints excluded: chain E residue  326 ILE
Chi-restraints excluded: chain E residue  327 CYS
Chi-restraints excluded: chain E residue  332 LEU
Chi-restraints excluded: chain E residue  348 CYS
Chi-restraints excluded: chain E residue  351 THR
Chi-restraints excluded: chain E residue  357 SER
Chi-restraints excluded: chain E residue  371 VAL
Chi-restraints excluded: chain E residue  463 LEU
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   62 VAL
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   79 ILE
Chi-restraints excluded: chain L residue  101 THR
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   58 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 39 optimal weight:    0.0670
   chunk 51 optimal weight:    0.3980
   chunk 80 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 81 optimal weight:    0.2980
   chunk 52 optimal weight:    0.0020
   chunk 60 optimal weight:    0.5980
   chunk 98 optimal weight:    4.9990
   chunk 7 optimal weight:    0.8980
   chunk 12 optimal weight:    0.1980
   chunk 73 optimal weight:    0.9980
   overall best weight:    0.1926

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.161111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.125887 restraints weight = 10749.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.129615 restraints weight = 5695.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.132037 restraints weight = 3848.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.133520 restraints weight = 3019.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.134288 restraints weight = 2601.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   7802  Z= 0.087
  Angle     :  0.533   7.910  10648  Z= 0.260
  Chirality :  0.043   0.143   1180
  Planarity :  0.004   0.072   1366
  Dihedral  :  3.875  20.109   1075
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 31.79 %
    Favored  : 65.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.17 (0.27), residues: 969
  helix:  0.26 (0.88), residues: 34
  sheet: -0.51 (0.30), residues: 314
  loop : -0.98 (0.25), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 253 
 TYR   0.010   0.001   TYR D 294 
 PHE   0.006   0.001   PHE D 333 
 TRP   0.016   0.001   TRP H  47 
 HIS   0.004   0.001   HIS D 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00201 ( 7800)
  covalent geometry    : angle       0.53281 (10644)
  SS BOND              : bond        0.00325 (    2)
  SS BOND              : angle       0.47339 (    4)
  hydrogen bonds       : bond        0.02240 (  158)
  hydrogen bonds       : angle       5.14325 (  390)

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 167
  time to evaluate  : 0.293 
Fit side-chains
REVERT: C  156 GLN cc_start: 0.8250 (mt0) cc_final: 0.7829 (tt0)
REVERT: C  247 MET cc_start: 0.2636 (OUTLIER) cc_final: 0.1720 (tmt)
REVERT: D  238 MET cc_start: 0.8893 (mtp) cc_final: 0.8432 (mtp)
REVERT: E  152 TYR cc_start: 0.8959 (m-10) cc_final: 0.8738 (m-10)
REVERT: E  472 PHE cc_start: 0.7502 (t80) cc_final: 0.7220 (t80)
REVERT: L   65 ARG cc_start: 0.7519 (ttm110) cc_final: 0.7080 (ttp80)
REVERT: H   39 GLN cc_start: 0.7686 (tp40) cc_final: 0.7120 (tp40)
  outliers start: 22
  outliers final: 19
  residues processed: 180
  average time/residue: 0.0653
  time to fit residues: 17.3016
Evaluate side-chains
  182 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 162
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  166 ILE
Chi-restraints excluded: chain C residue  247 MET
Chi-restraints excluded: chain D residue   76 VAL
Chi-restraints excluded: chain D residue  106 MET
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain D residue  157 LEU
Chi-restraints excluded: chain D residue  335 THR
Chi-restraints excluded: chain D residue  343 THR
Chi-restraints excluded: chain D residue  346 THR
Chi-restraints excluded: chain D residue  468 LEU
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue  116 ILE
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain E residue  150 VAL
Chi-restraints excluded: chain E residue  327 CYS
Chi-restraints excluded: chain E residue  351 THR
Chi-restraints excluded: chain E residue  371 VAL
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   62 VAL
Chi-restraints excluded: chain L residue   73 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 39 optimal weight:    0.3980
   chunk 17 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
D 193 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.158120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.122746 restraints weight = 10937.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.126404 restraints weight = 5881.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.128736 restraints weight = 4004.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.130084 restraints weight = 3167.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.131078 restraints weight = 2753.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.2165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7802  Z= 0.155
  Angle     :  0.572   9.781  10648  Z= 0.281
  Chirality :  0.045   0.175   1180
  Planarity :  0.004   0.072   1366
  Dihedral  :  4.058  20.052   1075
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 32.18 %
    Favored  : 65.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.27), residues: 969
  helix:  0.30 (0.90), residues: 34
  sheet: -0.56 (0.30), residues: 326
  loop : -1.10 (0.25), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 253 
 TYR   0.020   0.001   TYR H 100 
 PHE   0.009   0.001   PHE H  64 
 TRP   0.013   0.001   TRP H  47 
 HIS   0.006   0.001   HIS D 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 7800)
  covalent geometry    : angle       0.57143 (10644)
  SS BOND              : bond        0.00426 (    2)
  SS BOND              : angle       0.77382 (    4)
  hydrogen bonds       : bond        0.02646 (  158)
  hydrogen bonds       : angle       5.13868 (  390)

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 163
  time to evaluate  : 0.276 
Fit side-chains
REVERT: C  247 MET cc_start: 0.2586 (OUTLIER) cc_final: 0.1605 (tmt)
REVERT: D  238 MET cc_start: 0.9055 (mtp) cc_final: 0.8621 (mtp)
REVERT: E  472 PHE cc_start: 0.7598 (t80) cc_final: 0.7261 (t80)
REVERT: L   65 ARG cc_start: 0.7568 (ttm110) cc_final: 0.7071 (ttp80)
REVERT: H   39 GLN cc_start: 0.7621 (tp40) cc_final: 0.7009 (tp40)
  outliers start: 20
  outliers final: 18
  residues processed: 175
  average time/residue: 0.0585
  time to fit residues: 15.2747
Evaluate side-chains
  183 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 164
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  166 ILE
Chi-restraints excluded: chain C residue  247 MET
Chi-restraints excluded: chain D residue   76 VAL
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain D residue  157 LEU
Chi-restraints excluded: chain D residue  335 THR
Chi-restraints excluded: chain D residue  342 SER
Chi-restraints excluded: chain D residue  343 THR
Chi-restraints excluded: chain D residue  346 THR
Chi-restraints excluded: chain D residue  468 LEU
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue  116 ILE
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain E residue  150 VAL
Chi-restraints excluded: chain E residue  327 CYS
Chi-restraints excluded: chain E residue  351 THR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   62 VAL
Chi-restraints excluded: chain L residue   73 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 8 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 42 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   chunk 70 optimal weight:    0.4980
   chunk 90 optimal weight:    3.9990
   chunk 56 optimal weight:    0.7980
   chunk 41 optimal weight:    9.9990
   chunk 44 optimal weight:    0.6980
   overall best weight:    1.3984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.153811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.117811 restraints weight = 10924.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.121436 restraints weight = 5942.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.123650 restraints weight = 4069.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.125134 restraints weight = 3228.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.125543 restraints weight = 2813.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.2219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7802  Z= 0.180
  Angle     :  0.586   8.745  10648  Z= 0.290
  Chirality :  0.046   0.185   1180
  Planarity :  0.005   0.073   1366
  Dihedral  :  4.210  19.649   1075
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 31.15 %
    Favored  : 65.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.35 (0.27), residues: 969
  helix:  0.31 (0.91), residues: 34
  sheet: -0.63 (0.29), residues: 326
  loop : -1.13 (0.25), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 253 
 TYR   0.019   0.001   TYR H 100 
 PHE   0.010   0.001   PHE H  64 
 TRP   0.043   0.001   TRP C 170 
 HIS   0.006   0.001   HIS D 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 7800)
  covalent geometry    : angle       0.58540 (10644)
  SS BOND              : bond        0.00443 (    2)
  SS BOND              : angle       0.82605 (    4)
  hydrogen bonds       : bond        0.02846 (  158)
  hydrogen bonds       : angle       5.20578 (  390)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1348.71 seconds
wall clock time: 23 minutes 52.18 seconds (1432.18 seconds total)