Starting phenix.real_space_refine
on Wed Jan 15 21:35:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vy7_43647/01_2025/8vy7_43647.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vy7_43647/01_2025/8vy7_43647.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vy7_43647/01_2025/8vy7_43647.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vy7_43647/01_2025/8vy7_43647.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vy7_43647/01_2025/8vy7_43647.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vy7_43647/01_2025/8vy7_43647.cif"
  }
  resolution = 2.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.021
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C    5659      2.51       5
     N    1488      2.21       5
     O    1601      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 8811
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1753
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1753
          Classifications: {'peptide': 223}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 2, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 36
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 30
    Chain: "B"
      Number of atoms: 2564
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2564
          Classifications: {'peptide': 339}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 42
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 34
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 34
    Chain: "C"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 401
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "D"
      Number of atoms: 1743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1743
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 49
          Unresolved non-hydrogen dihedrals: 31
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 31
    Chain: "R"
      Number of atoms: 2299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2299
          Classifications: {'peptide': 287}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 3, 'TRANS': 283}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "R"
      Number of atoms: 51
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 51
          Unusual residues: {'A1AEI': 1, 'CLR': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.46, per 1000 atoms: 0.62
  Number of scatterers: 8811
  At special positions: 0
  Unit cell: (90.228, 120.888, 134.904, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      60     16.00
     F       3      9.00
     O    1601      8.00
     N    1488      7.00
     C    5659      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS D 147 " - pdb=" SG  CYS D 217 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.32
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2126

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 13 sheets defined
      39.4% alpha, 22.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.01
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.852A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 53
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.585A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.745A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 278
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.647A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.557A  pdb=" N   ALA A 299 " --> pdb=" O   THR A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 3 through 25
    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 'C' and resid 9 through 24
      removed outlier: 3.739A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'D' and resid 53 through 56
      removed outlier: 4.366A  pdb=" N   GLY D  56 " --> pdb=" O   SER D  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 53 through 56'
    Processing helix  chain 'D' and resid 87 through 91
      removed outlier: 3.658A  pdb=" N   THR D  91 " --> pdb=" O   SER D  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 2 through 37
    Processing helix  chain 'R' and resid 42 through 72
    Processing helix  chain 'R' and resid 72 through 77
    Processing helix  chain 'R' and resid 78 through 112
    Processing helix  chain 'R' and resid 116 through 124
    Processing helix  chain 'R' and resid 125 through 137
    Processing helix  chain 'R' and resid 137 through 158
      removed outlier: 3.606A  pdb=" N   LEU R 141 " --> pdb=" O   THR R 137 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 175 through 213
      removed outlier: 4.214A  pdb=" N   LEU R 181 " --> pdb=" O   SER R 177 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ILE R 189 " --> pdb=" O   VAL R 185 " (cutoff:3.500A)
      Proline residue:  R 190  - end of helix
    Processing helix  chain 'R' and resid 228 through 257
      removed outlier: 4.386A  pdb=" N   SER R 232 " --> pdb=" O   ARG R 228 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   LEU R 239 " --> pdb=" O   THR R 235 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   SER R 246 " --> pdb=" O   ILE R 242 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   LEU R 257 " --> pdb=" O   THR R 253 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 260 through 270
      removed outlier: 3.751A  pdb=" N   LEU R 264 " --> pdb=" O   ASN R 260 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   MET R 270 " --> pdb=" O   GLN R 266 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 270 through 282
      removed outlier: 4.624A  pdb=" N   SER R 277 " --> pdb=" O   PRO R 273 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   CYS R 278 " --> pdb=" O   SER R 274 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 284 through 302
      removed outlier: 3.791A  pdb=" N   ARG R 299 " --> pdb=" O   LEU R 295 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.545A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.421A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.285A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.705A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.695A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.969A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.778A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.070A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.278A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.621A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.009A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.468A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.711A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.744A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.370A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.491A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.666A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.024A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.628A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.023A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12
      removed outlier: 5.722A  pdb=" N   GLY D  10 " --> pdb=" O   THR D 118 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   MET D  34 " --> pdb=" O   TYR D  50 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   TYR D  50 " --> pdb=" O   MET D  34 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12
      removed outlier: 5.722A  pdb=" N   GLY D  10 " --> pdb=" O   THR D 118 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   PHE D 110 " --> pdb=" O   ARG D  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 128 through 129
      removed outlier: 3.911A  pdb=" N   ALA D 199 " --> pdb=" O   SER D 196 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 135 through 136
      removed outlier: 6.704A  pdb=" N   TRP D 164 " --> pdb=" O   LEU D 176 " (cutoff:3.500A)

    471 hydrogen bonds defined for protein.
    1338 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: 2.94

  Time building geometry restraints manager: 2.69 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2778
        1.34 -     1.46: 1822
        1.46 -     1.57: 4307
        1.57 -     1.69: 2
        1.69 -     1.81: 90
  Bond restraints: 8999
  Sorted by residual:
  bond pdb=" C10 A1AEI R 501 "
       pdb=" N11 A1AEI R 501 "
    ideal  model  delta    sigma   weight residual
    1.364  1.459 -0.095 2.00e-02 2.50e+03 2.24e+01
  bond pdb=" C13 A1AEI R 501 "
       pdb=" C14 A1AEI R 501 "
    ideal  model  delta    sigma   weight residual
    1.461  1.529 -0.068 2.00e-02 2.50e+03 1.14e+01
  bond pdb=" N16 A1AEI R 501 "
       pdb=" N17 A1AEI R 501 "
    ideal  model  delta    sigma   weight residual
    1.275  1.333 -0.058 2.00e-02 2.50e+03 8.56e+00
  bond pdb=" C16 CLR R 502 "
       pdb=" C17 CLR R 502 "
    ideal  model  delta    sigma   weight residual
    1.554  1.607 -0.053 2.00e-02 2.50e+03 7.07e+00
  bond pdb=" C23 CLR R 502 "
       pdb=" C24 CLR R 502 "
    ideal  model  delta    sigma   weight residual
    1.525  1.574 -0.049 2.00e-02 2.50e+03 5.94e+00
  ... (remaining 8994 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.23: 11987
        2.23 -     4.45: 171
        4.45 -     6.68: 29
        6.68 -     8.90: 11
        8.90 -    11.13: 2
  Bond angle restraints: 12200
  Sorted by residual:
  angle pdb=" CA  LEU A 227 "
        pdb=" CB  LEU A 227 "
        pdb=" CG  LEU A 227 "
      ideal   model   delta    sigma   weight residual
     116.30  127.43  -11.13 3.50e+00 8.16e-02 1.01e+01
  angle pdb=" N   PRO D 224 "
        pdb=" CA  PRO D 224 "
        pdb=" C   PRO D 224 "
      ideal   model   delta    sigma   weight residual
     112.10  120.32   -8.22 2.60e+00 1.48e-01 9.99e+00
  angle pdb=" CA  TYR D 178 "
        pdb=" CB  TYR D 178 "
        pdb=" CG  TYR D 178 "
      ideal   model   delta    sigma   weight residual
     113.90  119.48   -5.58 1.80e+00 3.09e-01 9.62e+00
  angle pdb=" C22 CLR R 502 "
        pdb=" C23 CLR R 502 "
        pdb=" C24 CLR R 502 "
      ideal   model   delta    sigma   weight residual
     111.95  103.38    8.57 3.00e+00 1.11e-01 8.16e+00
  angle pdb=" CA  LEU R  51 "
        pdb=" CB  LEU R  51 "
        pdb=" CG  LEU R  51 "
      ideal   model   delta    sigma   weight residual
     116.30  126.28   -9.98 3.50e+00 8.16e-02 8.14e+00
  ... (remaining 12195 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.47: 4972
       22.47 -    44.95: 332
       44.95 -    67.42: 23
       67.42 -    89.90: 4
       89.90 -   112.37: 3
  Dihedral angle restraints: 5334
    sinusoidal: 2046
      harmonic: 3288
  Sorted by residual:
  dihedral pdb=" CA  LYS R 217 "
           pdb=" C   LYS R 217 "
           pdb=" N   ILE R 218 "
           pdb=" CA  ILE R 218 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -148.99  -31.01     0      5.00e+00 4.00e-02 3.85e+01
  dihedral pdb=" CA  ASP B 290 "
           pdb=" C   ASP B 290 "
           pdb=" N   ASP B 291 "
           pdb=" CA  ASP B 291 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.38   21.62     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.38   20.62     0      5.00e+00 4.00e-02 1.70e+01
  ... (remaining 5331 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1109
       0.055 -    0.109: 240
       0.109 -    0.164: 53
       0.164 -    0.218: 6
       0.218 -    0.273: 2
  Chirality restraints: 1410
  Sorted by residual:
  chirality pdb=" CB  THR R 224 "
            pdb=" CA  THR R 224 "
            pdb=" OG1 THR R 224 "
            pdb=" CG2 THR R 224 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.28    0.27 2.00e-01 2.50e+01 1.86e+00
  chirality pdb=" C17 CLR R 502 "
            pdb=" C13 CLR R 502 "
            pdb=" C16 CLR R 502 "
            pdb=" C20 CLR R 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.78   -0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" CB  VAL A 233 "
            pdb=" CA  VAL A 233 "
            pdb=" CG1 VAL A 233 "
            pdb=" CG2 VAL A 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.12e+00
  ... (remaining 1407 not shown)

  Planarity restraints: 1513
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R  90 "   -0.009 2.00e-02 2.50e+03   1.85e-02 3.44e+00
        pdb=" C   THR R  90 "    0.032 2.00e-02 2.50e+03
        pdb=" O   THR R  90 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   VAL R  91 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 193 "   -0.030 5.00e-02 4.00e+02   4.59e-02 3.37e+00
        pdb=" N   PRO B 194 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO B 194 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 194 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR R 240 "    0.020 2.00e-02 2.50e+03   1.29e-02 3.34e+00
        pdb=" CG  TYR R 240 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD1 TYR R 240 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR R 240 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR R 240 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR R 240 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR R 240 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR R 240 "    0.006 2.00e-02 2.50e+03
  ... (remaining 1510 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.78: 1779
        2.78 -     3.31: 7653
        3.31 -     3.84: 15003
        3.84 -     4.37: 17000
        4.37 -     4.90: 30633
  Nonbonded interactions: 72068
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" OD2 ASP B  83 "
            pdb=" OG1 THR B  86 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OE2 GLU A  14 "
            pdb=" OG1 THR D  57 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" O   LEU R 133 "
            pdb=" OG1 THR R 137 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   ASN R  21 "
            pdb=" OG  SER R  25 "
     model   vdw
     2.294 3.040
  ... (remaining 72063 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:             1.190
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.640
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  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:14.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
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      :  0.005   0.095   8999  Z= 0.357
  Angle     :  0.708  11.125  12200  Z= 0.357
  Chirality :  0.049   0.273   1410
  Planarity :  0.004   0.046   1513
  Dihedral  : 14.098 112.369   3205
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.24), residues: 1120
  helix:  0.36 (0.22), residues: 414
  sheet:  0.59 (0.32), residues: 286
  loop : -1.15 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP R 297 
 HIS   0.005   0.001   HIS R  94 
 PHE   0.020   0.002   PHE A 267 
 TYR   0.030   0.002   TYR R 240 
 ARG   0.005   0.000   ARG D  67 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 0.948 
Fit side-chains
REVERT: A   26 ASP cc_start: 0.7783 (m-30) cc_final: 0.7396 (m-30)
REVERT: A  240 MET cc_start: 0.4803 (pmm) cc_final: 0.4514 (pmm)
REVERT: B  170 ASP cc_start: 0.7977 (t70) cc_final: 0.7591 (t0)
REVERT: B  191 SER cc_start: 0.8600 (t) cc_final: 0.8381 (p)
REVERT: D  144 SER cc_start: 0.8624 (m) cc_final: 0.8215 (t)
REVERT: R   16 GLU cc_start: 0.7587 (pt0) cc_final: 0.7327 (pt0)
REVERT: R   19 ILE cc_start: 0.8249 (mm) cc_final: 0.8025 (tp)
REVERT: R   87 ASN cc_start: 0.8530 (m-40) cc_final: 0.8285 (m-40)
REVERT: R   95 PHE cc_start: 0.7876 (m-10) cc_final: 0.7537 (m-80)
REVERT: R  301 MET cc_start: 0.4282 (tpt) cc_final: 0.3934 (tpt)
  outliers start: 0
  outliers final: 1
  residues processed: 230
  average time/residue: 1.0400
  time to fit residues: 257.4181
Evaluate side-chains
  202 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 201
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  261 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.5980
   chunk 84 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 44 optimal weight:    0.6980
   chunk 87 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 100 optimal weight:    0.6980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.127592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.111475 restraints weight = 12924.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 1.74
r_work: 0.3405 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3260 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.1305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8999  Z= 0.246
  Angle     :  0.564  10.568  12200  Z= 0.294
  Chirality :  0.042   0.155   1410
  Planarity :  0.004   0.037   1513
  Dihedral  :  5.230  58.483   1288
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 10.55 %
    Favored  : 87.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.25), residues: 1120
  helix:  1.72 (0.24), residues: 416
  sheet:  0.60 (0.30), residues: 280
  loop : -1.09 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 151 
 PHE   0.024   0.001   PHE R  82 
 TYR   0.020   0.001   TYR D 178 
 ARG   0.006   0.000   ARG B 219 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 204
  time to evaluate  : 1.019 
Fit side-chains
REVERT: A   26 ASP cc_start: 0.7934 (m-30) cc_final: 0.7579 (m-30)
REVERT: A  240 MET cc_start: 0.5108 (pmm) cc_final: 0.4809 (pmm)
REVERT: A  312 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8226 (mttm)
REVERT: A  345 LYS cc_start: 0.8299 (mmtt) cc_final: 0.8048 (mttp)
REVERT: B   52 ARG cc_start: 0.8376 (mtm-85) cc_final: 0.8065 (mtt-85)
REVERT: D   67 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8152 (ptm160)
REVERT: D  144 SER cc_start: 0.8643 (m) cc_final: 0.8309 (t)
REVERT: D  226 THR cc_start: 0.8621 (OUTLIER) cc_final: 0.8409 (p)
REVERT: R   19 ILE cc_start: 0.8245 (mm) cc_final: 0.8019 (tp)
REVERT: R   24 ASN cc_start: 0.7790 (m-40) cc_final: 0.7510 (m-40)
REVERT: R   31 ASN cc_start: 0.7275 (m110) cc_final: 0.6982 (m110)
REVERT: R   95 PHE cc_start: 0.7979 (m-10) cc_final: 0.7672 (m-80)
REVERT: R  116 ASN cc_start: 0.7754 (t0) cc_final: 0.7478 (t0)
REVERT: R  144 ASN cc_start: 0.8470 (t0) cc_final: 0.8218 (t0)
REVERT: R  212 MET cc_start: 0.8315 (mmm) cc_final: 0.8069 (mmm)
REVERT: R  301 MET cc_start: 0.4517 (tpt) cc_final: 0.4151 (tpt)
  outliers start: 15
  outliers final: 4
  residues processed: 205
  average time/residue: 1.0228
  time to fit residues: 225.9968
Evaluate side-chains
  197 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 190
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 LYS
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain D residue   67 ARG
Chi-restraints excluded: chain D residue  183 LEU
Chi-restraints excluded: chain D residue  226 THR
Chi-restraints excluded: chain R residue  188 PHE
Chi-restraints excluded: chain R residue  261 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 77 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   chunk 75 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9990
   chunk 10 optimal weight:    5.9990
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.126978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.110831 restraints weight = 13011.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.3500 rms_B_bonded: 1.74
r_work: 0.3393 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3249 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.1595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8999  Z= 0.287
  Angle     :  0.555   9.808  12200  Z= 0.291
  Chirality :  0.043   0.212   1410
  Planarity :  0.003   0.036   1513
  Dihedral  :  5.125  55.113   1288
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 14.61 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.25), residues: 1120
  helix:  2.09 (0.25), residues: 417
  sheet:  0.59 (0.30), residues: 281
  loop : -1.01 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.005   0.001   HIS R 151 
 PHE   0.025   0.002   PHE R  26 
 TYR   0.023   0.002   TYR D 178 
 ARG   0.005   0.001   ARG B 214 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 196
  time to evaluate  : 1.005 
Fit side-chains
REVERT: A   26 ASP cc_start: 0.7909 (m-30) cc_final: 0.7559 (m-30)
REVERT: A  240 MET cc_start: 0.5117 (pmm) cc_final: 0.4819 (pmm)
REVERT: A  312 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8233 (mttm)
REVERT: B  136 SER cc_start: 0.8432 (m) cc_final: 0.8202 (p)
REVERT: B  170 ASP cc_start: 0.8035 (t70) cc_final: 0.7633 (t0)
REVERT: B  217 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8176 (pmm)
REVERT: D  144 SER cc_start: 0.8600 (m) cc_final: 0.8288 (t)
REVERT: D  226 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.8398 (p)
REVERT: R   31 ASN cc_start: 0.7423 (m110) cc_final: 0.7097 (m110)
REVERT: R   95 PHE cc_start: 0.7971 (m-10) cc_final: 0.7666 (m-80)
REVERT: R  212 MET cc_start: 0.8268 (mmm) cc_final: 0.8023 (mmm)
REVERT: R  247 PHE cc_start: 0.6258 (OUTLIER) cc_final: 0.5998 (m-10)
REVERT: R  301 MET cc_start: 0.4559 (tpt) cc_final: 0.4213 (tpt)
  outliers start: 24
  outliers final: 9
  residues processed: 205
  average time/residue: 1.0417
  time to fit residues: 230.0076
Evaluate side-chains
  199 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 186
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  312 LYS
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain D residue  172 SER
Chi-restraints excluded: chain D residue  183 LEU
Chi-restraints excluded: chain D residue  212 VAL
Chi-restraints excluded: chain D residue  226 THR
Chi-restraints excluded: chain R residue   49 THR
Chi-restraints excluded: chain R residue  188 PHE
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  247 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 110 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 40 optimal weight:    0.4980
   chunk 95 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 59 optimal weight:    0.1980
   chunk 7 optimal weight:    0.2980
   overall best weight:    0.5580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.127634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.111414 restraints weight = 13005.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 1.75
r_work: 0.3403 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3257 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.1742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8999  Z= 0.211
  Angle     :  0.527   8.826  12200  Z= 0.275
  Chirality :  0.041   0.153   1410
  Planarity :  0.003   0.033   1513
  Dihedral  :  5.013  55.701   1286
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 15.35 %
    Favored  : 82.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.25), residues: 1120
  helix:  2.29 (0.25), residues: 417
  sheet:  0.62 (0.30), residues: 279
  loop : -1.03 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 151 
 PHE   0.021   0.001   PHE R  72 
 TYR   0.022   0.001   TYR D 178 
 ARG   0.004   0.000   ARG B 214 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 194
  time to evaluate  : 0.954 
Fit side-chains
REVERT: A   26 ASP cc_start: 0.7932 (m-30) cc_final: 0.7573 (m-30)
REVERT: A  240 MET cc_start: 0.5040 (pmm) cc_final: 0.4760 (pmm)
REVERT: B  136 SER cc_start: 0.8427 (m) cc_final: 0.8226 (p)
REVERT: B  217 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8158 (pmm)
REVERT: D  144 SER cc_start: 0.8597 (m) cc_final: 0.8304 (t)
REVERT: D  226 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8340 (p)
REVERT: R   19 ILE cc_start: 0.8300 (mt) cc_final: 0.8005 (tp)
REVERT: R   31 ASN cc_start: 0.7365 (m110) cc_final: 0.7036 (m110)
REVERT: R   95 PHE cc_start: 0.7988 (m-10) cc_final: 0.7687 (m-80)
REVERT: R  247 PHE cc_start: 0.6383 (OUTLIER) cc_final: 0.6139 (m-10)
REVERT: R  301 MET cc_start: 0.4549 (tpt) cc_final: 0.4203 (tpt)
  outliers start: 23
  outliers final: 10
  residues processed: 201
  average time/residue: 1.0105
  time to fit residues: 219.0201
Evaluate side-chains
  199 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 186
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain D residue  172 SER
Chi-restraints excluded: chain D residue  226 THR
Chi-restraints excluded: chain R residue   49 THR
Chi-restraints excluded: chain R residue  188 PHE
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  247 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 110 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   chunk 93 optimal weight:    0.7980
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.8580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.126783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.110804 restraints weight = 12956.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 1.72
r_work: 0.3397 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3254 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.1820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8999  Z= 0.294
  Angle     :  0.560   9.660  12200  Z= 0.290
  Chirality :  0.043   0.157   1410
  Planarity :  0.003   0.035   1513
  Dihedral  :  5.104  55.968   1286
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 17.80 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.25), residues: 1120
  helix:  2.27 (0.24), residues: 417
  sheet:  0.52 (0.30), residues: 281
  loop : -1.04 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R  94 
 PHE   0.018   0.001   PHE R  82 
 TYR   0.026   0.002   TYR D 178 
 ARG   0.004   0.000   ARG R  83 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 185
  time to evaluate  : 1.100 
Fit side-chains
REVERT: A   26 ASP cc_start: 0.7924 (m-30) cc_final: 0.7563 (m-30)
REVERT: A  240 MET cc_start: 0.5078 (pmm) cc_final: 0.4781 (pmm)
REVERT: B  217 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8168 (pmm)
REVERT: D  144 SER cc_start: 0.8581 (m) cc_final: 0.8285 (t)
REVERT: R   95 PHE cc_start: 0.7986 (m-10) cc_final: 0.7654 (m-80)
REVERT: R  247 PHE cc_start: 0.6462 (OUTLIER) cc_final: 0.6223 (m-10)
REVERT: R  301 MET cc_start: 0.4571 (tpt) cc_final: 0.4228 (tpt)
  outliers start: 19
  outliers final: 9
  residues processed: 190
  average time/residue: 1.0846
  time to fit residues: 222.1012
Evaluate side-chains
  189 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 178
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain D residue  172 SER
Chi-restraints excluded: chain D residue  183 LEU
Chi-restraints excluded: chain R residue  188 PHE
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  247 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 85 optimal weight:    0.9980
   chunk 96 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   chunk 75 optimal weight:    0.2980
   chunk 56 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 108 optimal weight:    1.9990
   chunk 84 optimal weight:    0.7980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.127117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.111025 restraints weight = 12975.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 1.73
r_work: 0.3395 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8999  Z= 0.240
  Angle     :  0.546   9.568  12200  Z= 0.281
  Chirality :  0.042   0.169   1410
  Planarity :  0.003   0.035   1513
  Dihedral  :  5.031  55.039   1286
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 18.34 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.25), residues: 1120
  helix:  2.39 (0.25), residues: 417
  sheet:  0.61 (0.30), residues: 277
  loop : -1.06 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R  94 
 PHE   0.017   0.001   PHE R  82 
 TYR   0.023   0.001   TYR D 178 
 ARG   0.007   0.000   ARG R  83 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 182
  time to evaluate  : 0.940 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7476 (mt-10)
REVERT: A   26 ASP cc_start: 0.7935 (m-30) cc_final: 0.7579 (m-30)
REVERT: A  240 MET cc_start: 0.5074 (pmm) cc_final: 0.4787 (pmm)
REVERT: B   52 ARG cc_start: 0.8384 (mtm-85) cc_final: 0.8084 (mtt-85)
REVERT: B  217 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8163 (pmm)
REVERT: D  144 SER cc_start: 0.8566 (m) cc_final: 0.8280 (t)
REVERT: R   19 ILE cc_start: 0.8284 (mt) cc_final: 0.8008 (tp)
REVERT: R   95 PHE cc_start: 0.7962 (m-10) cc_final: 0.7659 (m-80)
REVERT: R  120 LEU cc_start: 0.8606 (mp) cc_final: 0.8353 (mm)
REVERT: R  247 PHE cc_start: 0.6519 (OUTLIER) cc_final: 0.6268 (m-10)
REVERT: R  301 MET cc_start: 0.4536 (tpt) cc_final: 0.4202 (tpt)
  outliers start: 21
  outliers final: 9
  residues processed: 189
  average time/residue: 1.0193
  time to fit residues: 208.0830
Evaluate side-chains
  199 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 187
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain D residue  172 SER
Chi-restraints excluded: chain R residue  188 PHE
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  247 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 37 optimal weight:    0.5980
   chunk 11 optimal weight:    0.5980
   chunk 13 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 104 optimal weight:    3.9990
   chunk 101 optimal weight:    0.2980
   chunk 97 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0980
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.4380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.128081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.111723 restraints weight = 12991.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 1.74
r_work: 0.3408 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3262 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8999  Z= 0.183
  Angle     :  0.528  11.099  12200  Z= 0.271
  Chirality :  0.041   0.204   1410
  Planarity :  0.003   0.031   1513
  Dihedral  :  4.945  56.639   1286
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 19.40 %
    Favored  : 78.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.25), residues: 1120
  helix:  2.56 (0.25), residues: 420
  sheet:  0.75 (0.31), residues: 271
  loop : -0.99 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R  94 
 PHE   0.025   0.001   PHE R  72 
 TYR   0.020   0.001   TYR D 178 
 ARG   0.007   0.000   ARG B 214 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 192
  time to evaluate  : 0.984 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7427 (mt-10)
REVERT: A   26 ASP cc_start: 0.7938 (m-30) cc_final: 0.7573 (m-30)
REVERT: A  240 MET cc_start: 0.5030 (pmm) cc_final: 0.4759 (pmm)
REVERT: B   52 ARG cc_start: 0.8373 (mtm-85) cc_final: 0.8094 (mtt-85)
REVERT: B  217 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8164 (pmm)
REVERT: B  254 ASP cc_start: 0.7824 (t70) cc_final: 0.7550 (t70)
REVERT: D  144 SER cc_start: 0.8559 (m) cc_final: 0.8278 (t)
REVERT: D  226 THR cc_start: 0.8623 (m) cc_final: 0.8341 (p)
REVERT: R   19 ILE cc_start: 0.8256 (mt) cc_final: 0.7965 (tp)
REVERT: R   95 PHE cc_start: 0.7960 (m-10) cc_final: 0.7664 (m-80)
REVERT: R  120 LEU cc_start: 0.8607 (mp) cc_final: 0.8356 (mm)
REVERT: R  301 MET cc_start: 0.4516 (tpt) cc_final: 0.4194 (tpt)
  outliers start: 20
  outliers final: 10
  residues processed: 198
  average time/residue: 1.0140
  time to fit residues: 216.8272
Evaluate side-chains
  200 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 188
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain D residue  172 SER
Chi-restraints excluded: chain R residue   21 ASN
Chi-restraints excluded: chain R residue  188 PHE
Chi-restraints excluded: chain R residue  204 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 100 optimal weight:    0.1980
   chunk 49 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 36 optimal weight:    0.0980
   chunk 21 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 96 optimal weight:    0.6980
   chunk 7 optimal weight:    0.0970
   chunk 19 optimal weight:    0.0270
   chunk 47 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    0.2236

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.129523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.113256 restraints weight = 13175.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 1.76
r_work: 0.3429 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3284 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.2130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8999  Z= 0.141
  Angle     :  0.516   9.873  12200  Z= 0.264
  Chirality :  0.041   0.247   1410
  Planarity :  0.003   0.031   1513
  Dihedral  :  4.785  58.652   1286
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 20.58 %
    Favored  : 78.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.26), residues: 1120
  helix:  2.71 (0.25), residues: 420
  sheet:  0.80 (0.31), residues: 268
  loop : -0.97 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R  94 
 PHE   0.014   0.001   PHE R  82 
 TYR   0.017   0.001   TYR D 178 
 ARG   0.005   0.000   ARG R  83 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 195
  time to evaluate  : 1.017 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7388 (mt-10)
REVERT: A   26 ASP cc_start: 0.7925 (m-30) cc_final: 0.7563 (m-30)
REVERT: A  240 MET cc_start: 0.5052 (pmm) cc_final: 0.4777 (pmm)
REVERT: B   52 ARG cc_start: 0.8344 (mtm-85) cc_final: 0.8053 (mtt-85)
REVERT: B  197 ARG cc_start: 0.7827 (mtt-85) cc_final: 0.7567 (mtt-85)
REVERT: B  214 ARG cc_start: 0.8571 (mpt-90) cc_final: 0.8262 (mmt90)
REVERT: B  217 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8174 (pmm)
REVERT: B  254 ASP cc_start: 0.7790 (t70) cc_final: 0.7532 (t70)
REVERT: D  144 SER cc_start: 0.8551 (m) cc_final: 0.8292 (t)
REVERT: D  226 THR cc_start: 0.8634 (m) cc_final: 0.8368 (p)
REVERT: R   95 PHE cc_start: 0.7944 (m-10) cc_final: 0.7675 (m-80)
REVERT: R  120 LEU cc_start: 0.8562 (mp) cc_final: 0.8309 (mm)
REVERT: R  301 MET cc_start: 0.4493 (tpt) cc_final: 0.4200 (tpt)
  outliers start: 12
  outliers final: 5
  residues processed: 196
  average time/residue: 1.0082
  time to fit residues: 213.3314
Evaluate side-chains
  198 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 191
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain D residue  172 SER
Chi-restraints excluded: chain R residue   21 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 87 optimal weight:    0.6980
   chunk 88 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 101 optimal weight:    0.0870
   chunk 80 optimal weight:    0.5980
   chunk 15 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 76 optimal weight:    0.8980
   chunk 103 optimal weight:    8.9990
   overall best weight:    0.5958

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.128022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.111728 restraints weight = 13042.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 1.75
r_work: 0.3407 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3262 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.2118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8999  Z= 0.228
  Angle     :  0.553  12.738  12200  Z= 0.281
  Chirality :  0.043   0.266   1410
  Planarity :  0.003   0.032   1513
  Dihedral  :  4.891  58.989   1286
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 20.58 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.26), residues: 1120
  helix:  2.67 (0.25), residues: 420
  sheet:  0.78 (0.31), residues: 272
  loop : -0.97 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R  94 
 PHE   0.023   0.001   PHE R  72 
 TYR   0.022   0.001   TYR D 178 
 ARG   0.005   0.000   ARG R  83 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 193
  time to evaluate  : 1.010 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7443 (mt-10)
REVERT: A   26 ASP cc_start: 0.7903 (m-30) cc_final: 0.7543 (m-30)
REVERT: A  240 MET cc_start: 0.5109 (pmm) cc_final: 0.4809 (pmm)
REVERT: A  243 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7868 (ttp)
REVERT: B  197 ARG cc_start: 0.7827 (mtt-85) cc_final: 0.7579 (mtt-85)
REVERT: B  214 ARG cc_start: 0.8572 (mpt-90) cc_final: 0.8264 (mmt90)
REVERT: B  217 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8147 (pmm)
REVERT: B  254 ASP cc_start: 0.7833 (t70) cc_final: 0.7557 (t70)
REVERT: D   67 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7177 (ptm-80)
REVERT: D  144 SER cc_start: 0.8539 (m) cc_final: 0.8283 (t)
REVERT: D  226 THR cc_start: 0.8613 (m) cc_final: 0.8341 (p)
REVERT: R   19 ILE cc_start: 0.8278 (mt) cc_final: 0.7998 (tp)
REVERT: R   95 PHE cc_start: 0.7951 (m-10) cc_final: 0.7648 (m-80)
REVERT: R  120 LEU cc_start: 0.8595 (mp) cc_final: 0.8336 (mm)
REVERT: R  301 MET cc_start: 0.4481 (tpt) cc_final: 0.4171 (tpt)
  outliers start: 13
  outliers final: 7
  residues processed: 197
  average time/residue: 1.0745
  time to fit residues: 227.8324
Evaluate side-chains
  201 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 190
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  243 MET
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain D residue   67 ARG
Chi-restraints excluded: chain D residue  172 SER
Chi-restraints excluded: chain R residue   21 ASN
Chi-restraints excluded: chain R residue  204 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 95 optimal weight:    0.8980
   chunk 47 optimal weight:    0.6980
   chunk 90 optimal weight:    0.8980
   chunk 65 optimal weight:    0.0020
   chunk 75 optimal weight:    0.3980
   chunk 80 optimal weight:    0.7980
   chunk 55 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 10 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.5588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.128164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.111887 restraints weight = 13085.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 1.75
r_work: 0.3409 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3265 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8999  Z= 0.218
  Angle     :  0.559  13.470  12200  Z= 0.283
  Chirality :  0.042   0.255   1410
  Planarity :  0.003   0.041   1513
  Dihedral  :  4.909  58.883   1286
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 20.90 %
    Favored  : 77.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.26), residues: 1120
  helix:  2.67 (0.25), residues: 420
  sheet:  0.72 (0.31), residues: 276
  loop : -0.99 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R  94 
 PHE   0.015   0.001   PHE R  82 
 TYR   0.021   0.001   TYR D 178 
 ARG   0.008   0.000   ARG R  83 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 186
  time to evaluate  : 0.930 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7437 (mt-10)
REVERT: A   26 ASP cc_start: 0.7910 (m-30) cc_final: 0.7555 (m-30)
REVERT: A  240 MET cc_start: 0.5147 (pmm) cc_final: 0.4801 (pmm)
REVERT: B   52 ARG cc_start: 0.8312 (mtm-85) cc_final: 0.8078 (mtt-85)
REVERT: B  197 ARG cc_start: 0.7788 (mtt-85) cc_final: 0.7567 (mtt-85)
REVERT: B  214 ARG cc_start: 0.8598 (mpt-90) cc_final: 0.8351 (mmt90)
REVERT: B  217 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8146 (pmm)
REVERT: B  254 ASP cc_start: 0.7825 (t70) cc_final: 0.7546 (t70)
REVERT: D   67 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.7192 (ptm-80)
REVERT: D  144 SER cc_start: 0.8523 (m) cc_final: 0.8268 (t)
REVERT: D  226 THR cc_start: 0.8594 (m) cc_final: 0.8305 (p)
REVERT: R   19 ILE cc_start: 0.8278 (mt) cc_final: 0.8006 (tp)
REVERT: R   95 PHE cc_start: 0.7941 (m-10) cc_final: 0.7639 (m-80)
REVERT: R  120 LEU cc_start: 0.8603 (mp) cc_final: 0.8336 (mm)
REVERT: R  301 MET cc_start: 0.4448 (tpt) cc_final: 0.4159 (tpt)
  outliers start: 13
  outliers final: 8
  residues processed: 190
  average time/residue: 1.0950
  time to fit residues: 224.4583
Evaluate side-chains
  196 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 185
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  243 MET
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain D residue   67 ARG
Chi-restraints excluded: chain D residue  172 SER
Chi-restraints excluded: chain R residue   21 ASN
Chi-restraints excluded: chain R residue  297 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 99 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 83 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0770
   chunk 21 optimal weight:    0.6980
   chunk 95 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 76 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9980
   chunk 74 optimal weight:    0.3980
   overall best weight:    0.5338

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.128254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.111962 restraints weight = 13134.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 1.76
r_work: 0.3411 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3266 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8999  Z= 0.212
  Angle     :  0.557  13.219  12200  Z= 0.282
  Chirality :  0.042   0.252   1410
  Planarity :  0.003   0.038   1513
  Dihedral  :  4.892  59.589   1286
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 21.22 %
    Favored  : 77.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.26), residues: 1120
  helix:  2.70 (0.25), residues: 420
  sheet:  0.77 (0.31), residues: 270
  loop : -1.03 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R  94 
 PHE   0.025   0.001   PHE R  72 
 TYR   0.021   0.001   TYR D 178 
 ARG   0.008   0.000   ARG R  83 
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.

===============================================================================
Job complete
usr+sys time: 7455.42 seconds
wall clock time: 131 minutes 40.81 seconds (7900.81 seconds total)