Starting phenix.real_space_refine
on Sat Aug 23 00:52:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xzh_38796/08_2025/8xzh_38796.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xzh_38796/08_2025/8xzh_38796.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xzh_38796/08_2025/8xzh_38796.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xzh_38796/08_2025/8xzh_38796.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xzh_38796/08_2025/8xzh_38796.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xzh_38796/08_2025/8xzh_38796.cif"
  }
  resolution = 2.6
  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=   0.002 sd=   0.006
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      72      5.16       5
     C    5767      2.51       5
     N    1532      2.21       5
     O    1677      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 77 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9048
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2419
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 303, 2419
          Classifications: {'peptide': 303}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 11, 'TRANS': 291}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 1743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1743
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "B"
      Number of atoms: 2592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2592
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "G"
      Number of atoms: 416
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 416
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "S"
      Number of atoms: 1773
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1773
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "L"
      Number of atoms: 105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 105
          Classifications: {'peptide': 13}
          Link IDs: {'PTRANS': 3, 'TRANS': 9}
  Time building chain proxies: 1.71, per 1000 atoms: 0.19
  Number of scatterers: 9048
  At special positions: 0
  Unit cell: (103, 131.016, 117.008, 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      72     16.00
     O    1677      8.00
     N    1532      7.00
     C    5767      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  19 " - pdb=" SG  CYS R 281 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 102 " - pdb=" SG  CYS R 181 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.05
    Simple disulfide: pdb=" SG  CYS L   1 " - pdb=" SG  CYS L   6 " distance=2.02

  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: 0.54
  Conformation dependent library (CDL) restraints added in 229.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2168

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 15 sheets defined
      40.3% alpha, 24.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'R' and resid 26 through 55
      Proline residue:  R  32  - end of helix
    Processing helix  chain 'R' and resid 64 through 80
    Processing helix  chain 'R' and resid 81 through 91
      removed outlier: 4.163A  pdb=" N   TRP R  85 " --> pdb=" O   THR R  81 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 97 through 132
      removed outlier: 4.147A  pdb=" N   PHE R 101 " --> pdb=" O   PHE R  97 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 137 through 145
    Processing helix  chain 'R' and resid 146 through 161
      removed outlier: 3.774A  pdb=" N   THR R 150 " --> pdb=" O   GLY R 146 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ALA R 161 " --> pdb=" O   ALA R 157 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 161 through 167
      removed outlier: 3.913A  pdb=" N   MET R 165 " --> pdb=" O   ALA R 161 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 190 through 192
      No H-bonds generated for 'chain 'R' and resid 190 through 192'
    Processing helix  chain 'R' and resid 193 through 210
      removed outlier: 3.734A  pdb=" N   TRP R 197 " --> pdb=" O   SER R 193 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 210 through 232
    Processing helix  chain 'R' and resid 236 through 274
      Proline residue:  R 263  - end of helix
    Processing helix  chain 'R' and resid 281 through 299
      Proline residue:  R 292  - end of helix
    Processing helix  chain 'R' and resid 300 through 310
      Proline residue:  R 306  - end of helix
    Processing helix  chain 'R' and resid 313 through 325
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.710A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
      removed outlier: 3.685A  pdb=" N   ILE A  49 " --> pdb=" O   GLY A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.651A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.481A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 232
      removed outlier: 4.251A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.873A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.811A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.618A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 3 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 9 through 24
      removed outlier: 3.821A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.512A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 208 through 212
      removed outlier: 3.797A  pdb=" N   VAL S 212 " --> pdb=" O   ALA S 209 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'R' and resid 168 through 171
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191
      removed outlier: 3.622A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.242A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.129A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.484A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.721A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.157A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.734A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.933A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.032A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.750A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.900A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.771A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.160A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.865A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.741A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.143A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.281A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.708A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.705A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.063A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.785A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12
      removed outlier: 4.211A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129
    Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136
      removed outlier: 6.201A  pdb=" N   VAL S 135 " --> pdb=" O   GLU S 234 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   LEU S 162 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   TYR S 178 " --> pdb=" O   LEU S 162 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'S' and resid 134 through 136
      removed outlier: 6.201A  pdb=" N   VAL S 135 " --> pdb=" O   GLU S 234 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   THR S 226 " --> pdb=" O   GLN S 219 " (cutoff:3.500A)

    482 hydrogen bonds defined for protein.
    1326 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: 1.10

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2550
        1.33 -     1.45: 1829
        1.45 -     1.57: 4764
        1.57 -     1.69: 0
        1.69 -     1.82: 104
  Bond restraints: 9247
  Sorted by residual:
  bond pdb=" N   ILE B  37 "
       pdb=" CA  ILE B  37 "
    ideal  model  delta    sigma   weight residual
    1.461  1.498 -0.037 1.19e-02 7.06e+03 9.85e+00
  bond pdb=" N   ILE A 253 "
       pdb=" CA  ILE A 253 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.037 1.21e-02 6.83e+03 9.22e+00
  bond pdb=" N   LEU B 261 "
       pdb=" CA  LEU B 261 "
    ideal  model  delta    sigma   weight residual
    1.455  1.492 -0.037 1.29e-02 6.01e+03 8.38e+00
  bond pdb=" N   THR R  81 "
       pdb=" CA  THR R  81 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.034 1.18e-02 7.18e+03 8.36e+00
  bond pdb=" N   ILE A  49 "
       pdb=" CA  ILE A  49 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.034 1.19e-02 7.06e+03 8.02e+00
  ... (remaining 9242 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.15: 11981
        2.15 -     4.29: 493
        4.29 -     6.44: 50
        6.44 -     8.58: 7
        8.58 -    10.73: 3
  Bond angle restraints: 12534
  Sorted by residual:
  angle pdb=" N   ASP B  76 "
        pdb=" CA  ASP B  76 "
        pdb=" C   ASP B  76 "
      ideal   model   delta    sigma   weight residual
     113.02  103.47    9.55 1.20e+00 6.94e-01 6.33e+01
  angle pdb=" C   ASP B  38 "
        pdb=" N   PRO B  39 "
        pdb=" CA  PRO B  39 "
      ideal   model   delta    sigma   weight residual
     120.31  127.69   -7.38 9.80e-01 1.04e+00 5.67e+01
  angle pdb=" C   LEU R  30 "
        pdb=" N   ILE R  31 "
        pdb=" CA  ILE R  31 "
      ideal   model   delta    sigma   weight residual
     120.24  122.87   -2.63 6.30e-01 2.52e+00 1.75e+01
  angle pdb=" N   ARG B 197 "
        pdb=" CA  ARG B 197 "
        pdb=" C   ARG B 197 "
      ideal   model   delta    sigma   weight residual
     113.38  108.39    4.99 1.23e+00 6.61e-01 1.65e+01
  angle pdb=" N   LEU A 273 "
        pdb=" CA  LEU A 273 "
        pdb=" C   LEU A 273 "
      ideal   model   delta    sigma   weight residual
     111.28  106.87    4.41 1.09e+00 8.42e-01 1.64e+01
  ... (remaining 12529 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.26: 4953
       17.26 -    34.52: 411
       34.52 -    51.78: 74
       51.78 -    69.05: 20
       69.05 -    86.31: 8
  Dihedral angle restraints: 5466
    sinusoidal: 2104
      harmonic: 3362
  Sorted by residual:
  dihedral pdb=" CB  CYS L   1 "
           pdb=" SG  CYS L   1 "
           pdb=" SG  CYS L   6 "
           pdb=" CB  CYS L   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  172.92  -79.92     1      1.00e+01 1.00e-02 7.92e+01
  dihedral pdb=" CA  TYR S 223 "
           pdb=" C   TYR S 223 "
           pdb=" N   PRO S 224 "
           pdb=" CA  PRO S 224 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   30.75  -30.75     0      5.00e+00 4.00e-02 3.78e+01
  dihedral pdb=" CD  ARG S 179 "
           pdb=" NE  ARG S 179 "
           pdb=" CZ  ARG S 179 "
           pdb=" NH1 ARG S 179 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   44.78  -44.78     1      1.00e+01 1.00e-02 2.79e+01
  ... (remaining 5463 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 955
       0.060 -    0.121: 375
       0.121 -    0.181: 72
       0.181 -    0.241: 15
       0.241 -    0.302: 2
  Chirality restraints: 1419
  Sorted by residual:
  chirality pdb=" CB  VAL G  54 "
            pdb=" CA  VAL G  54 "
            pdb=" CG1 VAL G  54 "
            pdb=" CG2 VAL G  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.27e+00
  chirality pdb=" CA  ARG S 179 "
            pdb=" N   ARG S 179 "
            pdb=" C   ARG S 179 "
            pdb=" CB  ARG S 179 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.54e+00
  chirality pdb=" CB  VAL B 200 "
            pdb=" CA  VAL B 200 "
            pdb=" CG1 VAL B 200 "
            pdb=" CG2 VAL B 200 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.45e+00
  ... (remaining 1416 not shown)

  Planarity restraints: 1578
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG S 179 "   -0.767 9.50e-02 1.11e+02   3.44e-01 7.18e+01
        pdb=" NE  ARG S 179 "    0.045 2.00e-02 2.50e+03
        pdb=" CZ  ARG S 179 "    0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG S 179 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG S 179 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B  75 "    0.015 2.00e-02 2.50e+03   3.13e-02 9.80e+00
        pdb=" C   GLN B  75 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   GLN B  75 "    0.021 2.00e-02 2.50e+03
        pdb=" N   ASP B  76 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 274 "    0.011 2.00e-02 2.50e+03   2.30e-02 5.28e+00
        pdb=" C   THR B 274 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   THR B 274 "    0.015 2.00e-02 2.50e+03
        pdb=" N   SER B 275 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1575 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 538
        2.72 -     3.26: 8629
        3.26 -     3.81: 15032
        3.81 -     4.35: 19566
        4.35 -     4.90: 33280
  Nonbonded interactions: 77045
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.171 3.040
  nonbonded pdb=" NH2 ARG S  67 "
            pdb=" OD2 ASP S  90 "
     model   vdw
     2.198 3.120
  nonbonded pdb=" O   LEU R 108 "
            pdb=" ND2 ASN R 112 "
     model   vdw
     2.225 3.120
  nonbonded pdb=" O   PHE A 259 "
            pdb=" NZ  LYS A 317 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" O   CYS A 254 "
            pdb=" NZ  LYS A 317 "
     model   vdw
     2.273 3.120
  ... (remaining 77040 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.540
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:5.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.099   9252  Z= 0.553
  Angle     :  0.972  10.725  12544  Z= 0.592
  Chirality :  0.065   0.302   1419
  Planarity :  0.010   0.344   1578
  Dihedral  : 13.619  86.308   3283
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.21 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  5.30 %
    Favored  : 94.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.34 (0.23), residues: 1139
  helix: -0.92 (0.24), residues: 404
  sheet:  0.10 (0.28), residues: 297
  loop : -1.41 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 314 
 TYR   0.034   0.003   TYR B 105 
 PHE   0.025   0.003   PHE R  78 
 TRP   0.020   0.003   TRP B  99 
 HIS   0.009   0.002   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.01240 ( 9247)
  covalent geometry    : angle       0.97095 (12534)
  SS BOND              : bond        0.01124 (    5)
  SS BOND              : angle       1.84867 (   10)
  hydrogen bonds       : bond        0.15443 (  473)
  hydrogen bonds       : angle       6.96617 ( 1326)

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 186
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A  298 GLU cc_start: 0.7437 (tp30) cc_final: 0.7180 (tp30)
REVERT: A  306 GLN cc_start: 0.7557 (mm-40) cc_final: 0.7323 (mm-40)
REVERT: A  308 GLU cc_start: 0.7363 (mt-10) cc_final: 0.7149 (mt-10)
  outliers start: 6
  outliers final: 3
  residues processed: 191
  average time/residue: 0.6004
  time to fit residues: 120.8037
Evaluate side-chains
  168 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 165
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  280 LYS
Chi-restraints excluded: chain B residue   33 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    0.0980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    8.9990
   chunk 100 optimal weight:    0.9980
   chunk 106 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
R  46 ASN
A  52 GLN
A 188 HIS
A 204 GLN
A 213 HIS
A 306 GLN
A 322 HIS
** B  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  44 GLN
B 259 GLN
B 340 ASN
G  11 GLN
G  24 ASN
S 155 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.127350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.104049 restraints weight = 13217.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 2.32
r_work: 0.3242 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3108 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.1664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9252  Z= 0.122
  Angle     :  0.553   6.057  12544  Z= 0.301
  Chirality :  0.042   0.138   1419
  Planarity :  0.005   0.053   1578
  Dihedral  :  5.468  56.725   1266
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 10.60 %
    Favored  : 87.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.09 (0.24), residues: 1139
  helix:  0.89 (0.25), residues: 403
  sheet:  0.51 (0.29), residues: 273
  loop : -0.90 (0.28), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 219 
 TYR   0.011   0.001   TYR S 178 
 PHE   0.014   0.001   PHE B 199 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.002   0.001   HIS L   7 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 9247)
  covalent geometry    : angle       0.55198 (12534)
  SS BOND              : bond        0.00320 (    5)
  SS BOND              : angle       1.32849 (   10)
  hydrogen bonds       : bond        0.04310 (  473)
  hydrogen bonds       : angle       4.92346 ( 1326)

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 179
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
REVERT: R   55 ARG cc_start: 0.7678 (mpt180) cc_final: 0.6179 (ppt170)
REVERT: R  254 VAL cc_start: 0.8453 (t) cc_final: 0.8140 (m)
REVERT: R  318 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7435 (mp10)
REVERT: R  321 THR cc_start: 0.7960 (m) cc_final: 0.7695 (m)
REVERT: A   52 GLN cc_start: 0.5718 (OUTLIER) cc_final: 0.5281 (mt0)
REVERT: A  272 ASP cc_start: 0.6557 (m-30) cc_final: 0.6195 (m-30)
REVERT: A  276 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.5973 (mp0)
REVERT: A  280 LYS cc_start: 0.7143 (OUTLIER) cc_final: 0.6687 (mmmt)
REVERT: A  298 GLU cc_start: 0.7194 (tp30) cc_final: 0.6875 (tp30)
REVERT: G   21 MET cc_start: 0.6395 (OUTLIER) cc_final: 0.6101 (ppp)
REVERT: G   62 ARG cc_start: 0.7022 (mtm-85) cc_final: 0.6666 (mtm-85)
REVERT: S  190 ARG cc_start: 0.7714 (mtm110) cc_final: 0.7513 (mtm110)
REVERT: S  206 ARG cc_start: 0.7183 (mtm110) cc_final: 0.6592 (ptt-90)
  outliers start: 20
  outliers final: 5
  residues processed: 191
  average time/residue: 0.5805
  time to fit residues: 117.2006
Evaluate side-chains
  170 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 160
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  318 GLN
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  280 LYS
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain G residue   21 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 42 optimal weight:   10.0000
   chunk 20 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0070
   chunk 50 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 91 optimal weight:    6.9990
   overall best weight:    0.9000

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
B  75 GLN
B 340 ASN
S 174 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.127435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.104195 restraints weight = 13233.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 2.33
r_work: 0.3250 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3115 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.1965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9252  Z= 0.119
  Angle     :  0.532   8.936  12544  Z= 0.287
  Chirality :  0.041   0.157   1419
  Planarity :  0.004   0.058   1578
  Dihedral  :  5.076  56.352   1264
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 12.03 %
    Favored  : 85.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.62 (0.25), residues: 1139
  helix:  1.62 (0.26), residues: 404
  sheet:  0.48 (0.29), residues: 281
  loop : -0.69 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 219 
 TYR   0.010   0.001   TYR S 178 
 PHE   0.014   0.001   PHE B 199 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 9247)
  covalent geometry    : angle       0.53122 (12534)
  SS BOND              : bond        0.00389 (    5)
  SS BOND              : angle       1.24688 (   10)
  hydrogen bonds       : bond        0.03973 (  473)
  hydrogen bonds       : angle       4.63181 ( 1326)

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 169
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   55 ARG cc_start: 0.7668 (mpt180) cc_final: 0.6187 (ppt170)
REVERT: R  242 LYS cc_start: 0.8244 (mmtm) cc_final: 0.8020 (mmtt)
REVERT: R  321 THR cc_start: 0.7964 (m) cc_final: 0.7702 (m)
REVERT: A   52 GLN cc_start: 0.5635 (OUTLIER) cc_final: 0.5178 (mt0)
REVERT: A  201 VAL cc_start: 0.8466 (p) cc_final: 0.8060 (m)
REVERT: A  276 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.5980 (mt-10)
REVERT: A  298 GLU cc_start: 0.7193 (tp30) cc_final: 0.6915 (tp30)
REVERT: B   40 VAL cc_start: 0.7690 (m) cc_final: 0.7456 (t)
REVERT: B  322 ASP cc_start: 0.8106 (m-30) cc_final: 0.7731 (m-30)
REVERT: G   21 MET cc_start: 0.6478 (OUTLIER) cc_final: 0.6182 (ppp)
REVERT: G   59 ASN cc_start: 0.7766 (t0) cc_final: 0.7464 (t0)
REVERT: G   62 ARG cc_start: 0.7065 (mtm-85) cc_final: 0.6744 (mtm-85)
  outliers start: 27
  outliers final: 12
  residues processed: 182
  average time/residue: 0.5822
  time to fit residues: 111.6654
Evaluate side-chains
  176 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 161
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  113 MET
Chi-restraints excluded: chain R residue  272 MET
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  318 GLN
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain G residue   21 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 15 optimal weight:    6.9990
   chunk 104 optimal weight:    4.9990
   chunk 76 optimal weight:    5.9990
   chunk 75 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9990
   chunk 71 optimal weight:    7.9990
   chunk 100 optimal weight:    9.9990
   chunk 19 optimal weight:    1.9990
   chunk 37 optimal weight:   10.0000
   chunk 79 optimal weight:    1.9990
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
B 340 ASN
G  59 ASN
S 174 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.125955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.102351 restraints weight = 13393.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 2.32
r_work: 0.3219 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9252  Z= 0.177
  Angle     :  0.579   7.757  12544  Z= 0.310
  Chirality :  0.043   0.141   1419
  Planarity :  0.005   0.057   1578
  Dihedral  :  5.104  58.329   1260
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 12.95 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.75 (0.25), residues: 1139
  helix:  1.74 (0.26), residues: 402
  sheet:  0.54 (0.28), residues: 296
  loop : -0.66 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 219 
 TYR   0.015   0.002   TYR S 103 
 PHE   0.015   0.002   PHE B 199 
 TRP   0.014   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 9247)
  covalent geometry    : angle       0.57783 (12534)
  SS BOND              : bond        0.00650 (    5)
  SS BOND              : angle       1.25913 (   10)
  hydrogen bonds       : bond        0.04405 (  473)
  hydrogen bonds       : angle       4.75444 ( 1326)

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 166
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
REVERT: R   55 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.6120 (ppt170)
REVERT: R  318 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7463 (mp10)
REVERT: R  321 THR cc_start: 0.7971 (m) cc_final: 0.7715 (m)
REVERT: A   52 GLN cc_start: 0.5707 (OUTLIER) cc_final: 0.5196 (mt0)
REVERT: A  201 VAL cc_start: 0.8523 (p) cc_final: 0.8122 (m)
REVERT: A  276 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.6058 (mt-10)
REVERT: A  298 GLU cc_start: 0.7178 (tp30) cc_final: 0.6816 (tp30)
REVERT: B  322 ASP cc_start: 0.8136 (m-30) cc_final: 0.7755 (m-30)
REVERT: G   21 MET cc_start: 0.6383 (OUTLIER) cc_final: 0.6082 (ppp)
REVERT: G   47 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7255 (mp0)
REVERT: G   62 ARG cc_start: 0.7020 (mtm-85) cc_final: 0.6717 (mtm-85)
  outliers start: 30
  outliers final: 15
  residues processed: 181
  average time/residue: 0.5689
  time to fit residues: 108.7805
Evaluate side-chains
  182 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 162
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   55 ARG
Chi-restraints excluded: chain R residue   80 VAL
Chi-restraints excluded: chain R residue  180 GLN
Chi-restraints excluded: chain R residue  272 MET
Chi-restraints excluded: chain R residue  288 MET
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  318 GLN
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  286 CYS
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain G residue   21 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 65 optimal weight:    6.9990
   chunk 71 optimal weight:    0.5980
   chunk 50 optimal weight:    0.5980
   chunk 41 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 100 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   chunk 103 optimal weight:    7.9990
   chunk 29 optimal weight:    0.6980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
B 340 ASN
G  59 ASN
S 174 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.127190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.104313 restraints weight = 13355.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 2.29
r_work: 0.3250 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3118 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.2097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9252  Z= 0.126
  Angle     :  0.525   7.120  12544  Z= 0.282
  Chirality :  0.041   0.130   1419
  Planarity :  0.004   0.055   1578
  Dihedral  :  4.864  54.721   1260
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 14.17 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.90 (0.25), residues: 1139
  helix:  1.96 (0.26), residues: 401
  sheet:  0.65 (0.29), residues: 281
  loop : -0.65 (0.29), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 219 
 TYR   0.010   0.001   TYR S 103 
 PHE   0.014   0.001   PHE B 199 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 9247)
  covalent geometry    : angle       0.52443 (12534)
  SS BOND              : bond        0.00470 (    5)
  SS BOND              : angle       1.20499 (   10)
  hydrogen bonds       : bond        0.03898 (  473)
  hydrogen bonds       : angle       4.55987 ( 1326)

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 174
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  318 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7460 (mp10)
REVERT: R  321 THR cc_start: 0.7933 (m) cc_final: 0.7667 (m)
REVERT: A   52 GLN cc_start: 0.5601 (OUTLIER) cc_final: 0.5158 (mt0)
REVERT: A  201 VAL cc_start: 0.8460 (p) cc_final: 0.8069 (m)
REVERT: A  276 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6089 (mt-10)
REVERT: A  298 GLU cc_start: 0.7198 (tp30) cc_final: 0.6915 (tp30)
REVERT: B   40 VAL cc_start: 0.7718 (m) cc_final: 0.7504 (t)
REVERT: B  322 ASP cc_start: 0.8068 (m-30) cc_final: 0.7694 (m-30)
REVERT: G   21 MET cc_start: 0.6474 (OUTLIER) cc_final: 0.6172 (ppp)
REVERT: G   47 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7284 (mp0)
REVERT: G   62 ARG cc_start: 0.7032 (mtm-85) cc_final: 0.6715 (mtm-85)
REVERT: S    6 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7352 (mp0)
REVERT: S  212 VAL cc_start: 0.8149 (m) cc_final: 0.7835 (t)
  outliers start: 31
  outliers final: 14
  residues processed: 188
  average time/residue: 0.6168
  time to fit residues: 122.2147
Evaluate side-chains
  190 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 171
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   80 VAL
Chi-restraints excluded: chain R residue  113 MET
Chi-restraints excluded: chain R residue  272 MET
Chi-restraints excluded: chain R residue  288 MET
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  318 GLN
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain S residue    6 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 83 optimal weight:    7.9990
   chunk 12 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 93 optimal weight:    0.0570
   chunk 49 optimal weight:    0.9990
   chunk 45 optimal weight:   20.0000
   chunk 90 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 15 optimal weight:    7.9990
   chunk 65 optimal weight:    6.9990
   chunk 79 optimal weight:    4.9990
   overall best weight:    3.2106

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
B  32 GLN
B 340 ASN
G  59 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.125383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.096045 restraints weight = 13283.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 1.79
r_work: 0.3225 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3101 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.1797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061   9252  Z= 0.262
  Angle     :  0.650   7.558  12544  Z= 0.344
  Chirality :  0.047   0.146   1419
  Planarity :  0.005   0.058   1578
  Dihedral  :  5.345  59.953   1260
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 15.09 %
    Favored  : 81.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.25), residues: 1139
  helix:  1.61 (0.26), residues: 400
  sheet:  0.53 (0.28), residues: 305
  loop : -0.72 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 219 
 TYR   0.019   0.002   TYR S 103 
 PHE   0.018   0.002   PHE R 101 
 TRP   0.013   0.002   TRP R 279 
 HIS   0.008   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00636 ( 9247)
  covalent geometry    : angle       0.64939 (12534)
  SS BOND              : bond        0.00840 (    5)
  SS BOND              : angle       1.39141 (   10)
  hydrogen bonds       : bond        0.04901 (  473)
  hydrogen bonds       : angle       4.92922 ( 1326)

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 172
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  318 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7395 (mp10)
REVERT: A   52 GLN cc_start: 0.5829 (OUTLIER) cc_final: 0.5250 (mt0)
REVERT: A  276 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6162 (mt-10)
REVERT: A  298 GLU cc_start: 0.7296 (tp30) cc_final: 0.6965 (tp30)
REVERT: B  322 ASP cc_start: 0.8080 (m-30) cc_final: 0.7692 (m-30)
REVERT: G   47 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7292 (mp0)
REVERT: G   62 ARG cc_start: 0.7021 (mtm-85) cc_final: 0.6658 (mtm-85)
REVERT: S    6 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7553 (mp0)
  outliers start: 31
  outliers final: 17
  residues processed: 189
  average time/residue: 0.5973
  time to fit residues: 118.8679
Evaluate side-chains
  194 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 173
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   55 ARG
Chi-restraints excluded: chain R residue   80 VAL
Chi-restraints excluded: chain R residue  180 GLN
Chi-restraints excluded: chain R residue  272 MET
Chi-restraints excluded: chain R residue  288 MET
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  318 GLN
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  286 CYS
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain S residue    6 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 112 optimal weight:    3.9990
   chunk 68 optimal weight:    5.9990
   chunk 34 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 37 optimal weight:    7.9990
   chunk 56 optimal weight:    0.8980
   chunk 35 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 45 optimal weight:    9.9990
   chunk 1 optimal weight:    0.3980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
R 112 ASN
B  32 GLN
G  59 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.127188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.104277 restraints weight = 13380.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 2.28
r_work: 0.3250 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3119 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.2141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9252  Z= 0.123
  Angle     :  0.529   6.565  12544  Z= 0.284
  Chirality :  0.041   0.176   1419
  Planarity :  0.004   0.055   1578
  Dihedral  :  4.988  54.703   1260
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 16.21 %
    Favored  : 81.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.25), residues: 1139
  helix:  1.89 (0.26), residues: 402
  sheet:  0.65 (0.29), residues: 283
  loop : -0.65 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 219 
 TYR   0.011   0.001   TYR S 178 
 PHE   0.015   0.001   PHE B 199 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 9247)
  covalent geometry    : angle       0.52820 (12534)
  SS BOND              : bond        0.00439 (    5)
  SS BOND              : angle       1.21640 (   10)
  hydrogen bonds       : bond        0.03866 (  473)
  hydrogen bonds       : angle       4.58213 ( 1326)

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 179
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  318 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7437 (mp10)
REVERT: A  201 VAL cc_start: 0.8435 (p) cc_final: 0.8160 (m)
REVERT: A  276 GLU cc_start: 0.6695 (OUTLIER) cc_final: 0.6072 (mt-10)
REVERT: A  298 GLU cc_start: 0.7111 (tp30) cc_final: 0.6832 (tp30)
REVERT: B  322 ASP cc_start: 0.8071 (m-30) cc_final: 0.7675 (m-30)
REVERT: G   47 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7276 (mp0)
REVERT: G   62 ARG cc_start: 0.6984 (mtm-85) cc_final: 0.6608 (mtm-85)
REVERT: S    6 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7316 (mp0)
REVERT: S  212 VAL cc_start: 0.8157 (m) cc_final: 0.7851 (t)
  outliers start: 22
  outliers final: 14
  residues processed: 192
  average time/residue: 0.5767
  time to fit residues: 116.9134
Evaluate side-chains
  192 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 175
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   80 VAL
Chi-restraints excluded: chain R residue  113 MET
Chi-restraints excluded: chain R residue  180 GLN
Chi-restraints excluded: chain R residue  272 MET
Chi-restraints excluded: chain R residue  288 MET
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  318 GLN
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  286 CYS
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain S residue    6 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 101 optimal weight:    7.9990
   chunk 51 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 61 optimal weight:    0.6980
   chunk 50 optimal weight:    0.5980
   chunk 53 optimal weight:   10.0000
   chunk 83 optimal weight:    7.9990
   chunk 73 optimal weight:    9.9990
   chunk 63 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.127479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.104025 restraints weight = 13323.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 2.13
r_work: 0.3267 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9252  Z= 0.120
  Angle     :  0.526   6.379  12544  Z= 0.281
  Chirality :  0.041   0.158   1419
  Planarity :  0.004   0.057   1578
  Dihedral  :  4.419  22.035   1257
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 16.41 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.25), residues: 1139
  helix:  2.01 (0.26), residues: 402
  sheet:  0.67 (0.30), residues: 282
  loop : -0.60 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 219 
 TYR   0.017   0.001   TYR R 182 
 PHE   0.015   0.001   PHE B 199 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 9247)
  covalent geometry    : angle       0.52523 (12534)
  SS BOND              : bond        0.00516 (    5)
  SS BOND              : angle       1.15897 (   10)
  hydrogen bonds       : bond        0.03751 (  473)
  hydrogen bonds       : angle       4.51435 ( 1326)

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 177
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 VAL cc_start: 0.8450 (p) cc_final: 0.8152 (m)
REVERT: A  276 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6179 (mt-10)
REVERT: A  298 GLU cc_start: 0.7125 (tp30) cc_final: 0.6831 (tp30)
REVERT: A  350 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7644 (t0)
REVERT: B   40 VAL cc_start: 0.7748 (m) cc_final: 0.7546 (t)
REVERT: B  322 ASP cc_start: 0.8044 (m-30) cc_final: 0.7673 (m-30)
REVERT: G   47 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7258 (mp0)
REVERT: G   62 ARG cc_start: 0.6997 (mtm-85) cc_final: 0.6622 (mtm-85)
REVERT: S    6 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7402 (mp0)
REVERT: S  212 VAL cc_start: 0.8164 (m) cc_final: 0.7850 (t)
  outliers start: 25
  outliers final: 16
  residues processed: 193
  average time/residue: 0.6034
  time to fit residues: 123.0579
Evaluate side-chains
  191 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 172
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   80 VAL
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  113 MET
Chi-restraints excluded: chain R residue  180 GLN
Chi-restraints excluded: chain R residue  272 MET
Chi-restraints excluded: chain R residue  288 MET
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  286 CYS
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue  147 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 81 optimal weight:    6.9990
   chunk 29 optimal weight:    0.6980
   chunk 88 optimal weight:    0.9990
   chunk 71 optimal weight:   10.0000
   chunk 70 optimal weight:    3.9990
   chunk 36 optimal weight:    7.9990
   chunk 44 optimal weight:    7.9990
   chunk 91 optimal weight:    7.9990
   chunk 90 optimal weight:    0.0570
   overall best weight:    1.3504

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
B 340 ASN
G  59 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.127026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.103882 restraints weight = 13281.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 2.31
r_work: 0.3243 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3112 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.2235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9252  Z= 0.138
  Angle     :  0.542   6.252  12544  Z= 0.290
  Chirality :  0.042   0.155   1419
  Planarity :  0.004   0.056   1578
  Dihedral  :  4.483  22.163   1257
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 16.41 %
    Favored  : 80.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.96 (0.25), residues: 1139
  helix:  1.96 (0.26), residues: 402
  sheet:  0.67 (0.29), residues: 288
  loop : -0.58 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 219 
 TYR   0.011   0.001   TYR S 103 
 PHE   0.016   0.001   PHE B 199 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 9247)
  covalent geometry    : angle       0.54131 (12534)
  SS BOND              : bond        0.00568 (    5)
  SS BOND              : angle       1.26900 (   10)
  hydrogen bonds       : bond        0.03897 (  473)
  hydrogen bonds       : angle       4.58069 ( 1326)

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 174
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   55 ARG cc_start: 0.7800 (mpt180) cc_final: 0.6286 (ppt170)
REVERT: A  201 VAL cc_start: 0.8471 (p) cc_final: 0.8196 (m)
REVERT: A  276 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.6137 (mt-10)
REVERT: A  298 GLU cc_start: 0.7092 (tp30) cc_final: 0.6796 (tp30)
REVERT: A  350 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7672 (t0)
REVERT: B   40 VAL cc_start: 0.7743 (m) cc_final: 0.7529 (t)
REVERT: B  322 ASP cc_start: 0.8133 (m-30) cc_final: 0.7705 (m-30)
REVERT: G   47 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7314 (mp0)
REVERT: G   59 ASN cc_start: 0.7620 (t0) cc_final: 0.7412 (t0)
REVERT: G   62 ARG cc_start: 0.7008 (mtm-85) cc_final: 0.6622 (mtm-85)
REVERT: S  212 VAL cc_start: 0.8160 (m) cc_final: 0.7863 (t)
  outliers start: 26
  outliers final: 19
  residues processed: 187
  average time/residue: 0.6054
  time to fit residues: 119.3636
Evaluate side-chains
  192 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 171
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   80 VAL
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  113 MET
Chi-restraints excluded: chain R residue  180 GLN
Chi-restraints excluded: chain R residue  272 MET
Chi-restraints excluded: chain R residue  288 MET
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  318 GLN
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  286 CYS
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain S residue  147 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 103 optimal weight:   10.0000
   chunk 24 optimal weight:    0.6980
   chunk 63 optimal weight:    0.7980
   chunk 85 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 37 optimal weight:    9.9990
   chunk 58 optimal weight:    6.9990
   chunk 64 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 99 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.127471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.103930 restraints weight = 13274.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 2.15
r_work: 0.3264 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3137 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.2303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9252  Z= 0.122
  Angle     :  0.528   6.230  12544  Z= 0.282
  Chirality :  0.041   0.150   1419
  Planarity :  0.004   0.056   1578
  Dihedral  :  4.430  24.582   1257
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 17.13 %
    Favored  : 80.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.25), residues: 1139
  helix:  2.03 (0.26), residues: 402
  sheet:  0.65 (0.30), residues: 288
  loop : -0.54 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 219 
 TYR   0.010   0.001   TYR S 103 
 PHE   0.015   0.001   PHE B 199 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 9247)
  covalent geometry    : angle       0.52715 (12534)
  SS BOND              : bond        0.00536 (    5)
  SS BOND              : angle       1.21459 (   10)
  hydrogen bonds       : bond        0.03736 (  473)
  hydrogen bonds       : angle       4.51658 ( 1326)

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 170
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  183 MET cc_start: 0.8052 (mmm) cc_final: 0.7847 (mtt)
REVERT: A  201 VAL cc_start: 0.8430 (p) cc_final: 0.8159 (m)
REVERT: A  276 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.6186 (mt-10)
REVERT: A  298 GLU cc_start: 0.7123 (tp30) cc_final: 0.6836 (tp30)
REVERT: A  350 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7634 (t0)
REVERT: B   46 ARG cc_start: 0.5927 (mpp-170) cc_final: 0.5621 (mpp-170)
REVERT: B  322 ASP cc_start: 0.8137 (m-30) cc_final: 0.7744 (m-30)
REVERT: G   47 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7291 (mp0)
REVERT: G   62 ARG cc_start: 0.7067 (mtm-85) cc_final: 0.6711 (mtm-85)
REVERT: S  212 VAL cc_start: 0.8193 (m) cc_final: 0.7896 (t)
  outliers start: 23
  outliers final: 18
  residues processed: 182
  average time/residue: 0.6121
  time to fit residues: 117.6721
Evaluate side-chains
  188 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 168
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   80 VAL
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  113 MET
Chi-restraints excluded: chain R residue  180 GLN
Chi-restraints excluded: chain R residue  272 MET
Chi-restraints excluded: chain R residue  288 MET
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  318 GLN
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  286 CYS
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain S residue  147 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 103 optimal weight:    9.9990
   chunk 44 optimal weight:   10.0000
   chunk 76 optimal weight:    4.9990
   chunk 90 optimal weight:    2.9990
   chunk 111 optimal weight:    8.9990
   chunk 23 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 14 optimal weight:    9.9990
   chunk 65 optimal weight:    6.9990
   chunk 31 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
B  32 GLN
G  59 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.125254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.101307 restraints weight = 13091.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 2.14
r_work: 0.3220 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3088 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.1981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   9252  Z= 0.232
  Angle     :  0.637   6.639  12544  Z= 0.337
  Chirality :  0.046   0.162   1419
  Planarity :  0.005   0.057   1578
  Dihedral  :  4.857  22.657   1257
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 17.13 %
    Favored  : 80.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.81 (0.25), residues: 1139
  helix:  1.70 (0.26), residues: 403
  sheet:  0.58 (0.28), residues: 304
  loop : -0.56 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 219 
 TYR   0.017   0.002   TYR S 103 
 PHE   0.018   0.002   PHE B 199 
 TRP   0.013   0.002   TRP R 279 
 HIS   0.006   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00561 ( 9247)
  covalent geometry    : angle       0.63580 (12534)
  SS BOND              : bond        0.00839 (    5)
  SS BOND              : angle       1.45076 (   10)
  hydrogen bonds       : bond        0.04634 (  473)
  hydrogen bonds       : angle       4.85894 ( 1326)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4062.60 seconds
wall clock time: 69 minutes 36.44 seconds (4176.44 seconds total)