Starting phenix.real_space_refine
on Thu Jul  2 15:11:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vay_64909/07_2026/9vay_64909.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vay_64909/07_2026/9vay_64909.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vay_64909/07_2026/9vay_64909.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vay_64909/07_2026/9vay_64909.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vay_64909/07_2026/9vay_64909.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vay_64909/07_2026/9vay_64909.map"
  }
  resolution = 3.65
  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=  -0.009 sd=   0.078
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      61      5.16       5
     C    5711      2.51       5
     N    1528      2.21       5
     O    1669      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8969
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1751
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1751
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 2584
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2584
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "C"
      Number of atoms: 404
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 404
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "D"
      Number of atoms: 1762
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1762
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
          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: {'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 12
    Chain: "R"
      Number of atoms: 2415
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2415
          Classifications: {'peptide': 306}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 296}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 20
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "L"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 53
          Classifications: {'peptide': 6}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 4}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
  Time building chain proxies: 1.73, per 1000 atoms: 0.19
  Number of scatterers: 8969
  At special positions: 0
  Unit cell: (89.9167, 123.117, 132.8, 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      61     16.00
     O    1669      8.00
     N    1528      7.00
     C    5711      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 121 " - pdb=" SG  CYS B 149 " distance=2.86
    Simple disulfide: pdb=" SG  CYS D 147 " - pdb=" SG  CYS D 217 " distance=2.77

  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: 0.52
  Conformation dependent library (CDL) restraints added in 412.2 milliseconds
  

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2160

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 14 sheets defined
      39.5% alpha, 21.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.900A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 55
    Processing helix  chain 'A' and resid 202 through 204
      No H-bonds generated for 'chain 'A' and resid 202 through 204'
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.640A  pdb=" N   TRP A 211 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
      removed outlier: 5.034A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.821A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 4.347A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 270 through 281
    Processing helix  chain 'A' and resid 295 through 308
    Processing helix  chain 'A' and resid 329 through 351
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.835A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 10 through 24
      removed outlier: 3.552A  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 28 through 32
    Processing helix  chain 'D' and resid 52 through 56
      removed outlier: 3.611A  pdb=" N   SER D  55 " --> pdb=" O   SER D  52 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   GLY D  56 " --> pdb=" O   SER D  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 52 through 56'
    Processing helix  chain 'D' and resid 74 through 76
      No H-bonds generated for 'chain 'D' and resid 74 through 76'
    Processing helix  chain 'R' and resid 51 through 55
      removed outlier: 3.595A  pdb=" N   LEU R  54 " --> pdb=" O   SER R  51 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 59 through 92
      removed outlier: 3.894A  pdb=" N   LYS R  92 " --> pdb=" O   LEU R  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 97 through 128
      Proline residue:  R 121  - end of helix
      removed outlier: 3.610A  pdb=" N   TYR R 125 " --> pdb=" O   PRO R 121 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 136 through 172
    Processing helix  chain 'R' and resid 172 through 180
    Processing helix  chain 'R' and resid 181 through 200
      removed outlier: 3.643A  pdb=" N   ALA R 200 " --> pdb=" O   SER R 196 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 201 through 207
      removed outlier: 4.066A  pdb=" N   PHE R 205 " --> pdb=" O   VAL R 201 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   THR R 206 " --> pdb=" O   PRO R 202 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   MET R 207 " --> pdb=" O   MET R 203 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 201 through 207'
    Processing helix  chain 'R' and resid 229 through 245
      removed outlier: 4.170A  pdb=" N   VAL R 235 " --> pdb=" O   ALA R 231 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 245 through 272
    Processing helix  chain 'R' and resid 295 through 329
      removed outlier: 3.522A  pdb=" N   ARG R 306 " --> pdb=" O   VAL R 302 " (cutoff:3.500A)
      Proline residue:  R 318  - end of helix
    Processing helix  chain 'R' and resid 335 through 365
      Proline residue:  R 361  - end of helix
    Processing helix  chain 'R' and resid 366 through 369
      removed outlier: 3.852A  pdb=" N   ALA R 369 " --> pdb=" O   LEU R 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 366 through 369'
    Processing helix  chain 'R' and resid 370 through 375
      removed outlier: 4.508A  pdb=" N   ILE R 374 " --> pdb=" O   ASN R 370 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.925A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.744A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.378A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.534A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.245A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.750A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.962A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52
      removed outlier: 3.819A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.610A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 6.763A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151
      removed outlier: 3.600A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.653A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.099A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.911A  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: 6.424A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.329A  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: 6.811A  pdb=" N   MET D  34 " --> pdb=" O   TYR D  50 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   TYR D  50 " --> pdb=" O   MET D  34 " (cutoff:3.500A)
      removed outlier: 6.654A  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: 4.134A  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 130
      removed outlier: 3.585A  pdb=" N   ALA D 199 " --> pdb=" O   SER D 196 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 134 through 136
      removed outlier: 6.805A  pdb=" N   LEU D 162 " --> pdb=" O   TYR D 178 " (cutoff:3.500A)
      removed outlier: 5.094A  pdb=" N   TYR D 178 " --> pdb=" O   LEU D 162 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   TRP D 164 " --> pdb=" O   LEU D 176 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'R' and resid 209 through 211

    471 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: 1.02

  Time building geometry restraints manager: 0.74 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: 1665
        1.33 -     1.45: 2384
        1.45 -     1.57: 5017
        1.57 -     1.69: 3
        1.69 -     1.82: 91
  Bond restraints: 9160
  Sorted by residual:
  bond pdb=" NE  ARG R  90 "
       pdb=" CZ  ARG R  90 "
    ideal  model  delta    sigma   weight residual
    1.326  1.661 -0.335 1.10e-02 8.26e+03 9.29e+02
  bond pdb=" CG  PHE R 174 "
       pdb=" CD1 PHE R 174 "
    ideal  model  delta    sigma   weight residual
    1.384  1.760 -0.376 2.10e-02 2.27e+03 3.21e+02
  bond pdb=" CG  PHE R 174 "
       pdb=" CD2 PHE R 174 "
    ideal  model  delta    sigma   weight residual
    1.384  1.221  0.163 2.10e-02 2.27e+03 6.00e+01
  bond pdb=" CB  SER R  52 "
       pdb=" OG  SER R  52 "
    ideal  model  delta    sigma   weight residual
    1.417  1.314  0.103 2.00e-02 2.50e+03 2.67e+01
  bond pdb=" CA  SER R 330 "
       pdb=" CB  SER R 330 "
    ideal  model  delta    sigma   weight residual
    1.529  1.463  0.066 1.58e-02 4.01e+03 1.74e+01
  ... (remaining 9155 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.75: 11352
        2.75 -     5.50: 1007
        5.50 -     8.26: 52
        8.26 -    11.01: 4
       11.01 -    13.76: 4
  Bond angle restraints: 12419
  Sorted by residual:
  angle pdb=" CD1 PHE R 174 "
        pdb=" CG  PHE R 174 "
        pdb=" CD2 PHE R 174 "
      ideal   model   delta    sigma   weight residual
     118.60  104.84   13.76 1.50e+00 4.44e-01 8.41e+01
  angle pdb=" CB  PHE R 174 "
        pdb=" CG  PHE R 174 "
        pdb=" CD2 PHE R 174 "
      ideal   model   delta    sigma   weight residual
     120.70  133.52  -12.82 1.70e+00 3.46e-01 5.69e+01
  angle pdb=" CG  PHE R 174 "
        pdb=" CD2 PHE R 174 "
        pdb=" CE2 PHE R 174 "
      ideal   model   delta    sigma   weight residual
     120.70  132.35  -11.65 1.70e+00 3.46e-01 4.70e+01
  angle pdb=" CB  PHE R 174 "
        pdb=" CG  PHE R 174 "
        pdb=" CD1 PHE R 174 "
      ideal   model   delta    sigma   weight residual
     120.70  109.36   11.34 1.70e+00 3.46e-01 4.45e+01
  angle pdb=" CD  ARG R  90 "
        pdb=" NE  ARG R  90 "
        pdb=" CZ  ARG R  90 "
      ideal   model   delta    sigma   weight residual
     124.40  132.60   -8.20 1.40e+00 5.10e-01 3.43e+01
  ... (remaining 12414 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.04: 5040
       16.04 -    32.09: 303
       32.09 -    48.13: 54
       48.13 -    64.17: 11
       64.17 -    80.22: 6
  Dihedral angle restraints: 5414
    sinusoidal: 2066
      harmonic: 3348
  Sorted by residual:
  dihedral pdb=" CB  CYS B 121 "
           pdb=" SG  CYS B 121 "
           pdb=" SG  CYS B 149 "
           pdb=" CB  CYS B 149 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  173.22  -80.22     1      1.00e+01 1.00e-02 7.97e+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  156.21   23.79     0      5.00e+00 4.00e-02 2.26e+01
  dihedral pdb=" C   ARG D 206 "
           pdb=" N   ARG D 206 "
           pdb=" CA  ARG D 206 "
           pdb=" CB  ARG D 206 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.44   10.84     0      2.50e+00 1.60e-01 1.88e+01
  ... (remaining 5411 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.131: 1169
       0.131 -    0.261: 225
       0.261 -    0.391: 22
       0.391 -    0.522: 1
       0.522 -    0.652: 1
  Chirality restraints: 1418
  Sorted by residual:
  chirality pdb=" CB  ILE R  60 "
            pdb=" CA  ILE R  60 "
            pdb=" CG1 ILE R  60 "
            pdb=" CG2 ILE R  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    1.99    0.65 2.00e-01 2.50e+01 1.06e+01
  chirality pdb=" CG  LEU R  71 "
            pdb=" CB  LEU R  71 "
            pdb=" CD1 LEU R  71 "
            pdb=" CD2 LEU R  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -3.06    0.47 2.00e-01 2.50e+01 5.62e+00
  chirality pdb=" CA  ARG D 206 "
            pdb=" N   ARG D 206 "
            pdb=" C   ARG D 206 "
            pdb=" CB  ARG D 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.67e+00
  ... (remaining 1415 not shown)

  Planarity restraints: 1566
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R 174 "   -0.100 2.00e-02 2.50e+03   9.69e-02 1.64e+02
        pdb=" CG  PHE R 174 "    0.223 2.00e-02 2.50e+03
        pdb=" CD1 PHE R 174 "   -0.049 2.00e-02 2.50e+03
        pdb=" CD2 PHE R 174 "   -0.042 2.00e-02 2.50e+03
        pdb=" CE1 PHE R 174 "    0.015 2.00e-02 2.50e+03
        pdb=" CE2 PHE R 174 "   -0.040 2.00e-02 2.50e+03
        pdb=" CZ  PHE R 174 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  99 "   -0.064 2.00e-02 2.50e+03   3.28e-02 2.69e+01
        pdb=" CG  TRP B  99 "    0.063 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  99 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  99 "    0.017 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  99 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  99 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  99 "    0.026 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  99 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  99 "    0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  99 "   -0.036 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG R  90 "    0.027 9.50e-02 1.11e+02   4.75e-02 2.64e+01
        pdb=" NE  ARG R  90 "   -0.027 2.00e-02 2.50e+03
        pdb=" CZ  ARG R  90 "    0.088 2.00e-02 2.50e+03
        pdb=" NH1 ARG R  90 "   -0.032 2.00e-02 2.50e+03
        pdb=" NH2 ARG R  90 "   -0.031 2.00e-02 2.50e+03
  ... (remaining 1563 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1177
        2.80 -     3.32: 8928
        3.32 -     3.85: 14648
        3.85 -     4.37: 17224
        4.37 -     4.90: 29901
  Nonbonded interactions: 71878
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   GLN B  75 "
            pdb=" OG  SER B  98 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" OD1 ASP A 251 "
            pdb=" ND2 ASN A 255 "
     model   vdw
     2.410 3.120
  nonbonded pdb=" O   ALA A  41 "
            pdb=" OG  SER A  44 "
     model   vdw
     2.416 3.040
  ... (remaining 71873 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.150
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.580
  Find NCS groups from input model:        0.030
  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:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
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      :  0.016   0.829   9162  Z= 0.917
  Angle     :  1.646  13.759  12423  Z= 1.096
  Chirality :  0.101   0.652   1418
  Planarity :  0.009   0.097   1566
  Dihedral  : 11.292  79.851   3248
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  5.47 %
    Favored  : 93.29 %
  Cbeta Deviations :  0.28 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.68 (0.23), residues: 1132
  helix:  0.77 (0.24), residues: 392
  sheet: -0.89 (0.31), residues: 257
  loop : -1.15 (0.27), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.089   0.004   ARG R  90 
 TYR   0.029   0.005   TYR D 103 
 PHE   0.223   0.007   PHE R 174 
 TRP   0.064   0.007   TRP B  99 
 HIS   0.015   0.004   HIS R 320 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01131 /  0.71 ( 9160)
  covalent geometry    : angle       1.64191 /  1.09 (12419)
  SS BOND              : bond        0.78518 / 39.63 (    2)
  SS BOND              : angle       6.80670 /  4.00 (    4)
  hydrogen bonds       : bond        0.18416 / 12.38 (  464)
  hydrogen bonds       : angle       7.46414 /  5.33 ( 1326)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  389 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 377
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
REVERT: A    9 ASP cc_start: 0.8002 (m-30) cc_final: 0.7734 (m-30)
REVERT: A   23 LEU cc_start: 0.9085 (mp) cc_final: 0.8512 (tt)
REVERT: A   29 LYS cc_start: 0.9320 (tptm) cc_final: 0.9110 (tppt)
REVERT: A  254 CYS cc_start: 0.9085 (t) cc_final: 0.8841 (p)
REVERT: A  256 ASN cc_start: 0.8923 (t0) cc_final: 0.8692 (t0)
REVERT: A  315 ASP cc_start: 0.8978 (p0) cc_final: 0.8569 (p0)
REVERT: A  328 ASP cc_start: 0.8271 (t0) cc_final: 0.7803 (p0)
REVERT: A  330 LYS cc_start: 0.9657 (mttt) cc_final: 0.9428 (mmtm)
REVERT: A  333 GLN cc_start: 0.9550 (tp40) cc_final: 0.9339 (tm-30)
REVERT: A  337 ASP cc_start: 0.9213 (t0) cc_final: 0.8721 (t0)
REVERT: B    6 GLN cc_start: 0.9670 (tt0) cc_final: 0.9110 (tm-30)
REVERT: B    7 LEU cc_start: 0.9468 (tp) cc_final: 0.9087 (tp)
REVERT: B   20 ASP cc_start: 0.9729 (t0) cc_final: 0.9221 (m-30)
REVERT: B  198 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8604 (pp)
REVERT: B  268 ASN cc_start: 0.9292 (m110) cc_final: 0.9074 (t0)
REVERT: B  335 PHE cc_start: 0.8912 (m-10) cc_final: 0.8595 (m-10)
REVERT: B  339 TRP cc_start: 0.8735 (m100) cc_final: 0.8300 (m100)
REVERT: D    6 GLU cc_start: 0.7541 (mp0) cc_final: 0.6772 (mp0)
REVERT: D   73 ASP cc_start: 0.8549 (t0) cc_final: 0.8329 (t0)
REVERT: D   87 ARG cc_start: 0.8897 (mtm180) cc_final: 0.8387 (mtp180)
REVERT: D  189 ASP cc_start: 0.8677 (p0) cc_final: 0.8398 (p0)
REVERT: D  215 TYR cc_start: 0.8223 (m-80) cc_final: 0.7954 (m-10)
REVERT: D  221 LEU cc_start: 0.8969 (tp) cc_final: 0.8146 (tp)
REVERT: D  232 LYS cc_start: 0.8825 (tttt) cc_final: 0.8536 (ttmm)
REVERT: R   85 LEU cc_start: 0.9664 (mt) cc_final: 0.9414 (tt)
REVERT: R   99 SER cc_start: 0.9415 (t) cc_final: 0.9188 (p)
REVERT: R  108 LEU cc_start: 0.8966 (tp) cc_final: 0.8747 (tp)
REVERT: R  110 LEU cc_start: 0.9439 (tp) cc_final: 0.9159 (tp)
REVERT: R  118 LEU cc_start: 0.8914 (mt) cc_final: 0.8588 (mt)
REVERT: R  151 CYS cc_start: 0.9068 (m) cc_final: 0.8599 (p)
REVERT: R  153 TYR cc_start: 0.8452 (m-80) cc_final: 0.8101 (m-10)
REVERT: R  187 LYS cc_start: 0.8695 (ttpt) cc_final: 0.8484 (tttt)
REVERT: R  243 MET cc_start: 0.9200 (mmm) cc_final: 0.8983 (mmm)
REVERT: R  262 LYS cc_start: 0.8834 (tptp) cc_final: 0.8539 (tppt)
REVERT: R  263 LEU cc_start: 0.8404 (mp) cc_final: 0.8108 (tt)
REVERT: R  324 LEU cc_start: 0.8554 (mt) cc_final: 0.8228 (pp)
REVERT: R  331 ASP cc_start: 0.8554 (p0) cc_final: 0.8210 (m-30)
  outliers start: 12
  outliers final: 3
  residues processed: 385
  average time/residue: 0.0925
  time to fit residues: 46.5558
Evaluate side-chains
  237 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 233
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain R residue   97 LEU
Chi-restraints excluded: chain L residue    8 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:   10.0000
   chunk 100 optimal weight:    5.9990
   chunk 106 optimal weight:    3.9990
   overall best weight:    2.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 188 HIS
A 244 HIS
B  75 GLN
B  88 ASN
B  91 HIS
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 130 GLN
D 159 ASN
** R  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 126 ASN
R 240 ASN
R 256 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.096751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.075147 restraints weight = 27622.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.077810 restraints weight = 13117.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.079615 restraints weight = 8334.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.080766 restraints weight = 6238.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.081506 restraints weight = 5161.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.3786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9162  Z= 0.164
  Angle     :  0.742  12.079  12423  Z= 0.382
  Chirality :  0.046   0.190   1418
  Planarity :  0.004   0.030   1566
  Dihedral  :  5.470  43.772   1256
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 14.45 %
    Favored  : 82.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.16 (0.24), residues: 1132
  helix:  1.11 (0.25), residues: 395
  sheet: -0.37 (0.30), residues: 265
  loop : -0.92 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG R 182 
 TYR   0.021   0.002   TYR D 178 
 PHE   0.036   0.002   PHE R 345 
 TRP   0.018   0.002   TRP B  99 
 HIS   0.017   0.002   HIS B 311 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00355 /  0.16 ( 9160)
  covalent geometry    : angle       0.73801 /  0.38 (12419)
  SS BOND              : bond        0.01960 /  1.02 (    2)
  SS BOND              : angle       4.13256 /  2.36 (    4)
  hydrogen bonds       : bond        0.05010 /  3.51 (  464)
  hydrogen bonds       : angle       5.55337 /  3.95 ( 1326)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 231
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
REVERT: A    9 ASP cc_start: 0.8677 (m-30) cc_final: 0.8113 (m-30)
REVERT: A   23 LEU cc_start: 0.9071 (mp) cc_final: 0.8661 (tt)
REVERT: A  251 ASP cc_start: 0.9126 (t0) cc_final: 0.8921 (t0)
REVERT: A  254 CYS cc_start: 0.8792 (t) cc_final: 0.8433 (p)
REVERT: A  256 ASN cc_start: 0.9392 (t0) cc_final: 0.9158 (t0)
REVERT: A  315 ASP cc_start: 0.8742 (p0) cc_final: 0.8301 (p0)
REVERT: A  348 LEU cc_start: 0.9345 (mt) cc_final: 0.8827 (mt)
REVERT: B    7 LEU cc_start: 0.9299 (tp) cc_final: 0.9087 (tp)
REVERT: B   16 ASN cc_start: 0.9062 (t0) cc_final: 0.8539 (t0)
REVERT: B  132 ASN cc_start: 0.8160 (p0) cc_final: 0.7922 (p0)
REVERT: B  170 ASP cc_start: 0.8153 (t70) cc_final: 0.7572 (p0)
REVERT: B  187 VAL cc_start: 0.8743 (OUTLIER) cc_final: 0.8529 (m)
REVERT: B  198 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8538 (pp)
REVERT: B  217 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7105 (pmm)
REVERT: B  303 ASP cc_start: 0.8580 (t0) cc_final: 0.8337 (t0)
REVERT: B  325 MET cc_start: 0.7992 (tpp) cc_final: 0.7724 (tpp)
REVERT: B  339 TRP cc_start: 0.8633 (m100) cc_final: 0.7846 (m100)
REVERT: C   13 ARG cc_start: 0.9132 (ttm110) cc_final: 0.8784 (mtm-85)
REVERT: D   86 LEU cc_start: 0.9366 (mt) cc_final: 0.9120 (mm)
REVERT: D  215 TYR cc_start: 0.8117 (m-80) cc_final: 0.7776 (m-10)
REVERT: D  221 LEU cc_start: 0.9195 (tp) cc_final: 0.8986 (tt)
REVERT: R   74 PHE cc_start: 0.9391 (t80) cc_final: 0.9180 (t80)
REVERT: R  103 TYR cc_start: 0.7313 (m-80) cc_final: 0.6999 (m-10)
REVERT: R  153 TYR cc_start: 0.8731 (m-80) cc_final: 0.8351 (m-80)
REVERT: R  243 MET cc_start: 0.8811 (mmm) cc_final: 0.8553 (mmm)
REVERT: R  262 LYS cc_start: 0.8701 (tptp) cc_final: 0.8363 (tppt)
REVERT: R  263 LEU cc_start: 0.8168 (mp) cc_final: 0.7957 (tt)
REVERT: R  324 LEU cc_start: 0.8318 (mt) cc_final: 0.8019 (pp)
  outliers start: 33
  outliers final: 14
  residues processed: 250
  average time/residue: 0.0875
  time to fit residues: 29.1776
Evaluate side-chains
  198 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 181
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain D residue   99 SER
Chi-restraints excluded: chain D residue  116 THR
Chi-restraints excluded: chain D residue  126 ILE
Chi-restraints excluded: chain R residue  198 LEU
Chi-restraints excluded: chain R residue  327 CYS
Chi-restraints excluded: chain R residue  367 VAL
Chi-restraints excluded: chain L residue    8 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 24 optimal weight:    0.0020
   chunk 74 optimal weight:    6.9990
   chunk 46 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9990
   chunk 34 optimal weight:    5.9990
   chunk 4 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 101 optimal weight:    0.0570
   chunk 0 optimal weight:   20.0000
   chunk 89 optimal weight:    7.9990
   chunk 47 optimal weight:    8.9990
   overall best weight:    2.0112

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 294 ASN
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 159 ASN
** R  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 158 ASN
R 172 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.095625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.074059 restraints weight = 27663.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.076693 restraints weight = 13362.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.078474 restraints weight = 8558.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.079594 restraints weight = 6410.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.080220 restraints weight = 5346.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.4575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9162  Z= 0.143
  Angle     :  0.685  10.242  12423  Z= 0.352
  Chirality :  0.045   0.197   1418
  Planarity :  0.004   0.031   1566
  Dihedral  :  5.015  35.384   1254
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 13.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 15.58 %
    Favored  : 80.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.25), residues: 1132
  helix:  1.05 (0.26), residues: 396
  sheet: -0.11 (0.30), residues: 289
  loop : -0.86 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R 268 
 TYR   0.017   0.002   TYR D 178 
 PHE   0.026   0.001   PHE R 345 
 TRP   0.014   0.001   TRP B 339 
 HIS   0.009   0.001   HIS B 311 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.14 ( 9160)
  covalent geometry    : angle       0.68457 /  0.35 (12419)
  SS BOND              : bond        0.00677 /  0.35 (    2)
  SS BOND              : angle       1.08243 /  0.56 (    4)
  hydrogen bonds       : bond        0.04539 /  3.15 (  464)
  hydrogen bonds       : angle       5.24086 /  3.70 ( 1326)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 199
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
REVERT: A    9 ASP cc_start: 0.8646 (m-30) cc_final: 0.8053 (m-30)
REVERT: A   21 ARG cc_start: 0.8943 (ttm110) cc_final: 0.8604 (mtp-110)
REVERT: A   23 LEU cc_start: 0.9209 (mp) cc_final: 0.8858 (tt)
REVERT: A  198 MET cc_start: 0.9033 (ttp) cc_final: 0.8828 (mtp)
REVERT: A  254 CYS cc_start: 0.8944 (t) cc_final: 0.8510 (p)
REVERT: A  256 ASN cc_start: 0.9365 (t0) cc_final: 0.9123 (t0)
REVERT: A  315 ASP cc_start: 0.8763 (p0) cc_final: 0.8292 (p0)
REVERT: A  348 LEU cc_start: 0.9294 (mt) cc_final: 0.8810 (mt)
REVERT: B   14 LEU cc_start: 0.9435 (mt) cc_final: 0.9227 (mt)
REVERT: B   16 ASN cc_start: 0.8956 (t0) cc_final: 0.8705 (t0)
REVERT: B  142 HIS cc_start: 0.7256 (OUTLIER) cc_final: 0.6871 (t70)
REVERT: B  198 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8519 (pp)
REVERT: B  303 ASP cc_start: 0.8744 (t0) cc_final: 0.8410 (t0)
REVERT: B  318 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8773 (pp)
REVERT: C   13 ARG cc_start: 0.9120 (ttm110) cc_final: 0.8758 (mtm-85)
REVERT: C   19 LEU cc_start: 0.9655 (mt) cc_final: 0.9231 (tp)
REVERT: D   81 LEU cc_start: 0.8552 (tp) cc_final: 0.8341 (mt)
REVERT: D   83 MET cc_start: 0.7465 (mtm) cc_final: 0.7123 (ptm)
REVERT: D  148 ARG cc_start: 0.8643 (ptp90) cc_final: 0.8361 (ptp90)
REVERT: R  243 MET cc_start: 0.8837 (mmm) cc_final: 0.8579 (mmm)
REVERT: R  262 LYS cc_start: 0.8567 (tptp) cc_final: 0.8321 (tppt)
  outliers start: 38
  outliers final: 22
  residues processed: 222
  average time/residue: 0.0830
  time to fit residues: 24.7947
Evaluate side-chains
  206 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 181
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue   99 SER
Chi-restraints excluded: chain D residue  116 THR
Chi-restraints excluded: chain D residue  177 ILE
Chi-restraints excluded: chain R residue   85 LEU
Chi-restraints excluded: chain R residue  158 ASN
Chi-restraints excluded: chain R residue  198 LEU
Chi-restraints excluded: chain R residue  327 CYS
Chi-restraints excluded: chain R residue  367 VAL
Chi-restraints excluded: chain L residue    8 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 65 optimal weight:    8.9990
   chunk 20 optimal weight:    5.9990
   chunk 68 optimal weight:   10.0000
   chunk 33 optimal weight:    9.9990
   chunk 80 optimal weight:    9.9990
   chunk 61 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 41 optimal weight:    9.9990
   chunk 37 optimal weight:    9.9990
   chunk 55 optimal weight:   20.0000
   chunk 87 optimal weight:    8.9990
   overall best weight:    5.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 102 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.091385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.069777 restraints weight = 28320.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.072238 restraints weight = 13889.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.073892 restraints weight = 8997.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.074966 restraints weight = 6842.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.075569 restraints weight = 5729.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.5144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   9162  Z= 0.248
  Angle     :  0.747  12.219  12423  Z= 0.387
  Chirality :  0.046   0.200   1418
  Planarity :  0.004   0.039   1566
  Dihedral  :  5.267  35.254   1254
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 14.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 16.41 %
    Favored  : 78.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.25), residues: 1132
  helix:  0.81 (0.24), residues: 401
  sheet:  0.03 (0.32), residues: 266
  loop : -0.72 (0.29), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  19 
 TYR   0.017   0.002   TYR D 178 
 PHE   0.032   0.002   PHE D 227 
 TRP   0.019   0.002   TRP B 339 
 HIS   0.008   0.002   HIS B 311 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00552 /  0.25 ( 9160)
  covalent geometry    : angle       0.74618 /  0.39 (12419)
  SS BOND              : bond        0.00660 /  0.35 (    2)
  SS BOND              : angle       1.82835 /  1.00 (    4)
  hydrogen bonds       : bond        0.04741 /  3.31 (  464)
  hydrogen bonds       : angle       5.28313 /  3.74 ( 1326)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 189
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
REVERT: A    9 ASP cc_start: 0.8868 (m-30) cc_final: 0.8284 (m-30)
REVERT: A   18 MET cc_start: 0.8231 (tpp) cc_final: 0.8030 (tpp)
REVERT: A   23 LEU cc_start: 0.9235 (mp) cc_final: 0.8882 (tt)
REVERT: A   39 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8363 (mp)
REVERT: A  198 MET cc_start: 0.9080 (ttp) cc_final: 0.8828 (mtp)
REVERT: A  315 ASP cc_start: 0.8735 (p0) cc_final: 0.8299 (p0)
REVERT: A  348 LEU cc_start: 0.9338 (mt) cc_final: 0.8853 (mt)
REVERT: B   14 LEU cc_start: 0.9475 (mt) cc_final: 0.9267 (mt)
REVERT: B  142 HIS cc_start: 0.7793 (OUTLIER) cc_final: 0.6750 (t-90)
REVERT: B  178 THR cc_start: 0.7990 (OUTLIER) cc_final: 0.7566 (p)
REVERT: B  198 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8711 (pp)
REVERT: B  303 ASP cc_start: 0.8909 (t0) cc_final: 0.8507 (t0)
REVERT: C   13 ARG cc_start: 0.9097 (ttm110) cc_final: 0.8698 (mtm-85)
REVERT: C   19 LEU cc_start: 0.9657 (mt) cc_final: 0.9443 (mt)
REVERT: D   73 ASP cc_start: 0.8324 (t0) cc_final: 0.7577 (t0)
REVERT: D   83 MET cc_start: 0.7764 (mtm) cc_final: 0.6975 (ptp)
REVERT: D   90 ASP cc_start: 0.8713 (m-30) cc_final: 0.8023 (m-30)
REVERT: D  222 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8116 (mm-30)
REVERT: R  103 TYR cc_start: 0.7399 (m-80) cc_final: 0.7013 (m-10)
REVERT: R  153 TYR cc_start: 0.8690 (m-80) cc_final: 0.8490 (m-80)
REVERT: R  243 MET cc_start: 0.8891 (mmm) cc_final: 0.8678 (mmm)
REVERT: R  262 LYS cc_start: 0.8543 (tptp) cc_final: 0.8198 (tppt)
REVERT: R  347 MET cc_start: 0.8078 (ptp) cc_final: 0.7866 (ptp)
  outliers start: 47
  outliers final: 28
  residues processed: 225
  average time/residue: 0.0824
  time to fit residues: 24.5658
Evaluate side-chains
  201 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 169
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain D residue   99 SER
Chi-restraints excluded: chain D residue  116 THR
Chi-restraints excluded: chain D residue  126 ILE
Chi-restraints excluded: chain D residue  177 ILE
Chi-restraints excluded: chain R residue  198 LEU
Chi-restraints excluded: chain R residue  241 THR
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain R residue  327 CYS
Chi-restraints excluded: chain R residue  365 ASN
Chi-restraints excluded: chain R residue  367 VAL
Chi-restraints excluded: chain L residue    8 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 93 optimal weight:    0.9980
   chunk 84 optimal weight:    6.9990
   chunk 13 optimal weight:    3.9990
   chunk 18 optimal weight:    9.9990
   chunk 38 optimal weight:   10.0000
   chunk 103 optimal weight:    5.9990
   chunk 54 optimal weight:    9.9990
   chunk 15 optimal weight:    2.9990
   chunk 100 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 56 optimal weight:    9.9990
   overall best weight:    2.3786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 295 ASN
** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.093486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.072277 restraints weight = 27987.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.074754 restraints weight = 13910.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.076430 restraints weight = 9051.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.077503 restraints weight = 6871.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.078215 restraints weight = 5746.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.5450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9162  Z= 0.147
  Angle     :  0.714  13.849  12423  Z= 0.359
  Chirality :  0.044   0.240   1418
  Planarity :  0.004   0.040   1566
  Dihedral  :  5.010  36.856   1254
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 12.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 17.75 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.25), residues: 1132
  helix:  1.17 (0.26), residues: 402
  sheet:  0.12 (0.32), residues: 284
  loop : -0.72 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  24 
 TYR   0.014   0.001   TYR D 178 
 PHE   0.023   0.001   PHE R 345 
 TRP   0.016   0.002   TRP B 339 
 HIS   0.008   0.001   HIS B 311 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.15 ( 9160)
  covalent geometry    : angle       0.71348 /  0.36 (12419)
  SS BOND              : bond        0.00543 /  0.27 (    2)
  SS BOND              : angle       0.91458 /  0.47 (    4)
  hydrogen bonds       : bond        0.04328 /  3.04 (  464)
  hydrogen bonds       : angle       5.07196 /  3.58 ( 1326)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 189
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
REVERT: A    9 ASP cc_start: 0.8653 (m-30) cc_final: 0.8053 (m-30)
REVERT: A   23 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8820 (tt)
REVERT: A   37 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7834 (tt)
REVERT: A   39 LEU cc_start: 0.8652 (mt) cc_final: 0.8308 (mt)
REVERT: A  198 MET cc_start: 0.8907 (ttp) cc_final: 0.8677 (ttm)
REVERT: A  315 ASP cc_start: 0.8693 (p0) cc_final: 0.8343 (p0)
REVERT: A  348 LEU cc_start: 0.9314 (mt) cc_final: 0.8821 (mt)
REVERT: B    7 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9172 (mt)
REVERT: B   14 LEU cc_start: 0.9486 (mt) cc_final: 0.9284 (mt)
REVERT: B   89 LYS cc_start: 0.8974 (mmtp) cc_final: 0.8704 (mmtm)
REVERT: B  142 HIS cc_start: 0.7443 (OUTLIER) cc_final: 0.7163 (t70)
REVERT: B  198 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8783 (pp)
REVERT: B  209 LYS cc_start: 0.8171 (mttt) cc_final: 0.7920 (mmtm)
REVERT: B  303 ASP cc_start: 0.8737 (t0) cc_final: 0.8336 (t0)
REVERT: C   13 ARG cc_start: 0.9027 (ttm110) cc_final: 0.8683 (mtm-85)
REVERT: D   83 MET cc_start: 0.7387 (mtm) cc_final: 0.6612 (ptp)
REVERT: D   90 ASP cc_start: 0.8545 (m-30) cc_final: 0.8134 (m-30)
REVERT: D  234 GLU cc_start: 0.7158 (pm20) cc_final: 0.6579 (pm20)
REVERT: R  103 TYR cc_start: 0.7200 (m-80) cc_final: 0.6844 (m-10)
REVERT: R  146 PHE cc_start: 0.8635 (t80) cc_final: 0.8406 (t80)
REVERT: R  243 MET cc_start: 0.8805 (mmm) cc_final: 0.8529 (mmm)
REVERT: R  262 LYS cc_start: 0.8529 (tptp) cc_final: 0.8256 (tppt)
  outliers start: 39
  outliers final: 18
  residues processed: 218
  average time/residue: 0.0878
  time to fit residues: 25.6639
Evaluate side-chains
  187 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 164
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain D residue   99 SER
Chi-restraints excluded: chain D residue  126 ILE
Chi-restraints excluded: chain D residue  177 ILE
Chi-restraints excluded: chain R residue  198 LEU
Chi-restraints excluded: chain R residue  305 LEU
Chi-restraints excluded: chain R residue  327 CYS
Chi-restraints excluded: chain R residue  367 VAL
Chi-restraints excluded: chain L residue    8 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 94 optimal weight:    7.9990
   chunk 5 optimal weight:    0.8980
   chunk 20 optimal weight:    7.9990
   chunk 51 optimal weight:   10.0000
   chunk 74 optimal weight:    1.9990
   chunk 90 optimal weight:   30.0000
   chunk 68 optimal weight:    8.9990
   chunk 103 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    1.7788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.094725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.073853 restraints weight = 27862.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.076333 restraints weight = 13740.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.078002 restraints weight = 8912.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.079093 restraints weight = 6758.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.079728 restraints weight = 5640.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.5722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9162  Z= 0.137
  Angle     :  0.726  14.784  12423  Z= 0.361
  Chirality :  0.044   0.249   1418
  Planarity :  0.004   0.034   1566
  Dihedral  :  4.874  36.644   1254
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 12.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 20.74 %
    Favored  : 75.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.25 (0.25), residues: 1132
  helix:  1.16 (0.26), residues: 403
  sheet:  0.36 (0.32), residues: 266
  loop : -0.78 (0.29), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG R 268 
 TYR   0.012   0.001   TYR D 178 
 PHE   0.016   0.001   PHE D 227 
 TRP   0.015   0.001   TRP R 316 
 HIS   0.007   0.001   HIS B 311 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.14 ( 9160)
  covalent geometry    : angle       0.72627 /  0.36 (12419)
  SS BOND              : bond        0.00709 /  0.36 (    2)
  SS BOND              : angle       0.85188 /  0.47 (    4)
  hydrogen bonds       : bond        0.04268 /  2.99 (  464)
  hydrogen bonds       : angle       5.03563 /  3.54 ( 1326)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 179
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
REVERT: A    9 ASP cc_start: 0.8562 (m-30) cc_final: 0.7954 (m-30)
REVERT: A   23 LEU cc_start: 0.9227 (mp) cc_final: 0.8874 (tt)
REVERT: A   39 LEU cc_start: 0.8615 (mt) cc_final: 0.8306 (mp)
REVERT: A   49 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8911 (tt)
REVERT: A  315 ASP cc_start: 0.8684 (p0) cc_final: 0.8409 (p0)
REVERT: A  348 LEU cc_start: 0.9308 (mt) cc_final: 0.8810 (mt)
REVERT: B   14 LEU cc_start: 0.9441 (mt) cc_final: 0.9235 (mt)
REVERT: B   45 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7477 (ttp)
REVERT: B  142 HIS cc_start: 0.7471 (OUTLIER) cc_final: 0.7229 (t70)
REVERT: B  198 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8744 (pp)
REVERT: B  209 LYS cc_start: 0.8163 (mttt) cc_final: 0.7934 (mmtm)
REVERT: B  303 ASP cc_start: 0.8651 (t0) cc_final: 0.8434 (t0)
REVERT: C   13 ARG cc_start: 0.8918 (ttm110) cc_final: 0.8470 (mtm-85)
REVERT: C   21 MET cc_start: 0.8853 (ptp) cc_final: 0.8610 (ptp)
REVERT: D   90 ASP cc_start: 0.8391 (m-30) cc_final: 0.8059 (m-30)
REVERT: D   98 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.7005 (ptt90)
REVERT: R  103 TYR cc_start: 0.7280 (m-80) cc_final: 0.6912 (m-10)
REVERT: R  203 MET cc_start: 0.7865 (tpp) cc_final: 0.7043 (tmm)
REVERT: R  243 MET cc_start: 0.8792 (mmm) cc_final: 0.8540 (mmm)
REVERT: R  262 LYS cc_start: 0.8572 (tptp) cc_final: 0.8209 (tppt)
REVERT: R  355 VAL cc_start: 0.9601 (t) cc_final: 0.9372 (p)
  outliers start: 33
  outliers final: 20
  residues processed: 201
  average time/residue: 0.0819
  time to fit residues: 22.6339
Evaluate side-chains
  188 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 163
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain D residue   98 ARG
Chi-restraints excluded: chain D residue   99 SER
Chi-restraints excluded: chain D residue  126 ILE
Chi-restraints excluded: chain D residue  177 ILE
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain R residue  198 LEU
Chi-restraints excluded: chain R residue  259 ILE
Chi-restraints excluded: chain R residue  327 CYS
Chi-restraints excluded: chain R residue  365 ASN
Chi-restraints excluded: chain R residue  367 VAL
Chi-restraints excluded: chain L residue    8 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 40 optimal weight:    0.4980
   chunk 57 optimal weight:    7.9990
   chunk 84 optimal weight:   10.0000
   chunk 65 optimal weight:    8.9990
   chunk 111 optimal weight:    0.5980
   chunk 83 optimal weight:    5.9990
   chunk 32 optimal weight:    5.9990
   chunk 67 optimal weight:    8.9990
   chunk 78 optimal weight:    5.9990
   chunk 52 optimal weight:    9.9990
   overall best weight:    3.8186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 331 ASN
B  13 GLN
** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.092512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.071414 restraints weight = 28494.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.073810 restraints weight = 14413.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.075414 restraints weight = 9514.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.076445 restraints weight = 7325.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.077115 restraints weight = 6190.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.5908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9162  Z= 0.186
  Angle     :  0.759  14.485  12423  Z= 0.380
  Chirality :  0.045   0.226   1418
  Planarity :  0.004   0.042   1566
  Dihedral  :  5.022  43.842   1254
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 14.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 21.47 %
    Favored  : 74.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.25), residues: 1132
  helix:  1.12 (0.26), residues: 403
  sheet:  0.23 (0.33), residues: 267
  loop : -0.75 (0.30), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG R 268 
 TYR   0.019   0.002   TYR A 302 
 PHE   0.019   0.002   PHE R 345 
 TRP   0.018   0.002   TRP B 339 
 HIS   0.006   0.001   HIS B 311 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00426 /  0.19 ( 9160)
  covalent geometry    : angle       0.75899 /  0.38 (12419)
  SS BOND              : bond        0.00678 /  0.35 (    2)
  SS BOND              : angle       1.15427 /  0.59 (    4)
  hydrogen bonds       : bond        0.04414 /  3.07 (  464)
  hydrogen bonds       : angle       5.10273 /  3.58 ( 1326)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 168
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
REVERT: A   23 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8810 (tt)
REVERT: A   39 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8441 (mp)
REVERT: A   49 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8926 (tt)
REVERT: A  315 ASP cc_start: 0.8557 (p0) cc_final: 0.8270 (p0)
REVERT: A  348 LEU cc_start: 0.9326 (mt) cc_final: 0.8833 (mt)
REVERT: B   89 LYS cc_start: 0.8924 (mmtp) cc_final: 0.8623 (mmtm)
REVERT: B  142 HIS cc_start: 0.7674 (OUTLIER) cc_final: 0.7041 (t-90)
REVERT: B  198 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8798 (pp)
REVERT: B  209 LYS cc_start: 0.8308 (mttt) cc_final: 0.8083 (mmtm)
REVERT: B  303 ASP cc_start: 0.8638 (t0) cc_final: 0.8357 (t0)
REVERT: C   13 ARG cc_start: 0.8928 (ttm110) cc_final: 0.8485 (mtm-85)
REVERT: D   90 ASP cc_start: 0.8362 (m-30) cc_final: 0.8040 (m-30)
REVERT: D   98 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7164 (ptt90)
REVERT: R  103 TYR cc_start: 0.7370 (m-80) cc_final: 0.6989 (m-10)
REVERT: R  146 PHE cc_start: 0.8566 (t80) cc_final: 0.8344 (t80)
REVERT: R  153 TYR cc_start: 0.8602 (m-80) cc_final: 0.8143 (m-80)
REVERT: R  243 MET cc_start: 0.8734 (mmm) cc_final: 0.8322 (mmm)
REVERT: R  262 LYS cc_start: 0.8626 (tptp) cc_final: 0.8318 (tppt)
REVERT: R  355 VAL cc_start: 0.9583 (t) cc_final: 0.9336 (p)
  outliers start: 36
  outliers final: 23
  residues processed: 191
  average time/residue: 0.0790
  time to fit residues: 20.5713
Evaluate side-chains
  184 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 155
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain D residue   98 ARG
Chi-restraints excluded: chain D residue   99 SER
Chi-restraints excluded: chain D residue  126 ILE
Chi-restraints excluded: chain D residue  177 ILE
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain R residue  198 LEU
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain R residue  327 CYS
Chi-restraints excluded: chain R residue  362 ILE
Chi-restraints excluded: chain R residue  367 VAL
Chi-restraints excluded: chain L residue    8 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 104 optimal weight:   10.0000
   chunk 38 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 94 optimal weight:    0.2980
   chunk 75 optimal weight:    7.9990
   chunk 90 optimal weight:    8.9990
   chunk 30 optimal weight:    5.9990
   chunk 102 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 3 optimal weight:    7.9990
   chunk 69 optimal weight:    2.9990
   overall best weight:    2.4588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  98 GLN
** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.093373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.072226 restraints weight = 28348.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.074667 restraints weight = 14199.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.076320 restraints weight = 9334.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.077383 restraints weight = 7150.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.077982 restraints weight = 6015.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.6083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9162  Z= 0.150
  Angle     :  0.764  13.887  12423  Z= 0.377
  Chirality :  0.045   0.325   1418
  Planarity :  0.004   0.046   1566
  Dihedral  :  4.957  52.128   1254
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 22.29 %
    Favored  : 73.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.25), residues: 1132
  helix:  1.17 (0.26), residues: 402
  sheet:  0.35 (0.33), residues: 262
  loop : -0.69 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  24 
 TYR   0.016   0.001   TYR A 302 
 PHE   0.018   0.001   PHE R 345 
 TRP   0.018   0.002   TRP B 339 
 HIS   0.006   0.001   HIS B 311 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00342 /  0.15 ( 9160)
  covalent geometry    : angle       0.76407 /  0.38 (12419)
  SS BOND              : bond        0.00620 /  0.32 (    2)
  SS BOND              : angle       0.90536 /  0.45 (    4)
  hydrogen bonds       : bond        0.04222 /  2.92 (  464)
  hydrogen bonds       : angle       5.05187 /  3.54 ( 1326)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 167
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
REVERT: A   23 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8844 (tt)
REVERT: A   39 LEU cc_start: 0.8715 (mt) cc_final: 0.8341 (mp)
REVERT: A   49 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8938 (tt)
REVERT: A  315 ASP cc_start: 0.8603 (p0) cc_final: 0.8328 (p0)
REVERT: A  348 LEU cc_start: 0.9317 (mt) cc_final: 0.8829 (mt)
REVERT: B   89 LYS cc_start: 0.8909 (mmtp) cc_final: 0.8616 (mmtm)
REVERT: B  142 HIS cc_start: 0.7606 (OUTLIER) cc_final: 0.7358 (t70)
REVERT: B  198 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8821 (pp)
REVERT: B  209 LYS cc_start: 0.8258 (mttt) cc_final: 0.8021 (mmtm)
REVERT: C   13 ARG cc_start: 0.9045 (ttm110) cc_final: 0.8534 (mtm-85)
REVERT: D   90 ASP cc_start: 0.8497 (m-30) cc_final: 0.8208 (m-30)
REVERT: D   98 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7106 (ptt90)
REVERT: R  103 TYR cc_start: 0.7177 (m-80) cc_final: 0.6851 (m-10)
REVERT: R  146 PHE cc_start: 0.8717 (t80) cc_final: 0.8483 (t80)
REVERT: R  153 TYR cc_start: 0.8468 (m-80) cc_final: 0.8189 (m-80)
REVERT: R  243 MET cc_start: 0.8774 (mmm) cc_final: 0.8475 (mmm)
REVERT: R  262 LYS cc_start: 0.8598 (tptp) cc_final: 0.8319 (tppt)
REVERT: R  355 VAL cc_start: 0.9600 (t) cc_final: 0.9376 (p)
  outliers start: 37
  outliers final: 24
  residues processed: 189
  average time/residue: 0.0851
  time to fit residues: 21.9271
Evaluate side-chains
  187 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 158
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain D residue   98 ARG
Chi-restraints excluded: chain D residue   99 SER
Chi-restraints excluded: chain D residue  126 ILE
Chi-restraints excluded: chain D residue  129 THR
Chi-restraints excluded: chain D residue  177 ILE
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain R residue   98 GLN
Chi-restraints excluded: chain R residue  198 LEU
Chi-restraints excluded: chain R residue  241 THR
Chi-restraints excluded: chain R residue  327 CYS
Chi-restraints excluded: chain R residue  362 ILE
Chi-restraints excluded: chain R residue  367 VAL
Chi-restraints excluded: chain L residue    8 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 84 optimal weight:    5.9990
   chunk 70 optimal weight:   20.0000
   chunk 90 optimal weight:    5.9990
   chunk 93 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 10 optimal weight:    9.9990
   chunk 3 optimal weight:    4.9990
   chunk 74 optimal weight:    9.9990
   chunk 110 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0000
   overall best weight:    1.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  16 ASN
** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  98 GLN
R 172 HIS
R 256 ASN
R 343 HIS
R 350 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.094217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.073202 restraints weight = 28381.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.075646 restraints weight = 14186.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.077306 restraints weight = 9292.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.078401 restraints weight = 7072.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.079137 restraints weight = 5913.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.6227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9162  Z= 0.142
  Angle     :  0.785  14.503  12423  Z= 0.389
  Chirality :  0.046   0.268   1418
  Planarity :  0.004   0.049   1566
  Dihedral  :  5.084  72.765   1254
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 22.70 %
    Favored  : 74.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.25), residues: 1132
  helix:  1.18 (0.26), residues: 403
  sheet:  0.40 (0.33), residues: 262
  loop : -0.79 (0.29), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  24 
 TYR   0.014   0.001   TYR A 302 
 PHE   0.016   0.001   PHE R 345 
 TRP   0.016   0.001   TRP R 316 
 HIS   0.006   0.001   HIS B 311 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00322 /  0.14 ( 9160)
  covalent geometry    : angle       0.78508 /  0.39 (12419)
  SS BOND              : bond        0.00581 /  0.30 (    2)
  SS BOND              : angle       0.80884 /  0.40 (    4)
  hydrogen bonds       : bond        0.04179 /  2.90 (  464)
  hydrogen bonds       : angle       5.06782 /  3.55 ( 1326)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 170
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
REVERT: A   23 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8886 (tt)
REVERT: A   39 LEU cc_start: 0.8707 (mt) cc_final: 0.8383 (mp)
REVERT: A   49 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8951 (tt)
REVERT: A  256 ASN cc_start: 0.9481 (t0) cc_final: 0.9061 (t0)
REVERT: A  315 ASP cc_start: 0.8573 (p0) cc_final: 0.8316 (p0)
REVERT: A  348 LEU cc_start: 0.9318 (mt) cc_final: 0.8825 (mt)
REVERT: B   15 LYS cc_start: 0.9170 (mmtm) cc_final: 0.8903 (mmtm)
REVERT: B   20 ASP cc_start: 0.8510 (m-30) cc_final: 0.8174 (m-30)
REVERT: B   45 MET cc_start: 0.7718 (ttm) cc_final: 0.7445 (mtp)
REVERT: B  142 HIS cc_start: 0.7495 (OUTLIER) cc_final: 0.7279 (t70)
REVERT: B  198 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8801 (pp)
REVERT: B  209 LYS cc_start: 0.8258 (mttt) cc_final: 0.8038 (mmtm)
REVERT: C   13 ARG cc_start: 0.8999 (ttm110) cc_final: 0.8519 (mtm-85)
REVERT: C   21 MET cc_start: 0.8755 (ptp) cc_final: 0.8540 (ptp)
REVERT: D   90 ASP cc_start: 0.8493 (m-30) cc_final: 0.8154 (m-30)
REVERT: D   98 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7110 (ptt90)
REVERT: R  103 TYR cc_start: 0.7187 (m-80) cc_final: 0.6861 (m-10)
REVERT: R  151 CYS cc_start: 0.9027 (m) cc_final: 0.8416 (p)
REVERT: R  153 TYR cc_start: 0.8422 (m-80) cc_final: 0.8161 (m-80)
REVERT: R  243 MET cc_start: 0.8770 (mmm) cc_final: 0.8424 (mmm)
REVERT: R  262 LYS cc_start: 0.8556 (tptp) cc_final: 0.8306 (tppt)
REVERT: R  355 VAL cc_start: 0.9608 (t) cc_final: 0.9389 (p)
  outliers start: 31
  outliers final: 24
  residues processed: 190
  average time/residue: 0.0835
  time to fit residues: 21.3170
Evaluate side-chains
  193 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 164
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  296 TYR
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue    9 GLN
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain D residue   98 ARG
Chi-restraints excluded: chain D residue   99 SER
Chi-restraints excluded: chain D residue  126 ILE
Chi-restraints excluded: chain D residue  129 THR
Chi-restraints excluded: chain D residue  177 ILE
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain R residue   98 GLN
Chi-restraints excluded: chain R residue  198 LEU
Chi-restraints excluded: chain R residue  259 ILE
Chi-restraints excluded: chain R residue  327 CYS
Chi-restraints excluded: chain R residue  367 VAL
Chi-restraints excluded: chain L residue    8 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 105 optimal weight:    5.9990
   chunk 94 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 38 optimal weight:    0.0050
   chunk 41 optimal weight:   10.0000
   chunk 83 optimal weight:    8.9990
   chunk 24 optimal weight:   20.0000
   chunk 60 optimal weight:    7.9990
   chunk 27 optimal weight:    2.9990
   chunk 69 optimal weight:    6.9990
   chunk 68 optimal weight:    5.9990
   overall best weight:    4.2002

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  98 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.092236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.070968 restraints weight = 28311.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.073443 restraints weight = 13938.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.075069 restraints weight = 9055.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.076193 restraints weight = 6899.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.076899 restraints weight = 5754.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.6278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   9162  Z= 0.199
  Angle     :  0.825  14.012  12423  Z= 0.412
  Chirality :  0.047   0.363   1418
  Planarity :  0.004   0.051   1566
  Dihedral  :  5.351  81.016   1254
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 14.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 23.01 %
    Favored  : 73.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.25), residues: 1132
  helix:  1.07 (0.25), residues: 403
  sheet:  0.13 (0.33), residues: 271
  loop : -0.66 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  24 
 TYR   0.018   0.002   TYR A 302 
 PHE   0.019   0.002   PHE R 345 
 TRP   0.014   0.002   TRP R 316 
 HIS   0.006   0.001   HIS B 142 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00455 /  0.20 ( 9160)
  covalent geometry    : angle       0.82527 /  0.41 (12419)
  SS BOND              : bond        0.00827 /  0.41 (    2)
  SS BOND              : angle       1.16915 /  0.59 (    4)
  hydrogen bonds       : bond        0.04457 /  3.10 (  464)
  hydrogen bonds       : angle       5.17538 /  3.65 ( 1326)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 167
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS L   8 " (corrupted residue). Skipping it.
REVERT: A   18 MET cc_start: 0.8357 (tpp) cc_final: 0.8092 (tpp)
REVERT: A   23 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8869 (tt)
REVERT: A   39 LEU cc_start: 0.8844 (mt) cc_final: 0.8529 (mt)
REVERT: A   49 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8946 (tt)
REVERT: A  256 ASN cc_start: 0.9581 (t0) cc_final: 0.9113 (t0)
REVERT: A  315 ASP cc_start: 0.8691 (p0) cc_final: 0.8423 (p0)
REVERT: A  318 GLU cc_start: 0.7429 (mp0) cc_final: 0.7048 (mp0)
REVERT: A  348 LEU cc_start: 0.9301 (mt) cc_final: 0.8790 (mt)
REVERT: B  142 HIS cc_start: 0.7695 (OUTLIER) cc_final: 0.6956 (t-90)
REVERT: B  198 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8861 (pp)
REVERT: B  209 LYS cc_start: 0.8247 (mttt) cc_final: 0.7981 (mmtm)
REVERT: C   13 ARG cc_start: 0.9088 (ttm110) cc_final: 0.8580 (mtm-85)
REVERT: C   21 MET cc_start: 0.8857 (ptp) cc_final: 0.8615 (ptp)
REVERT: D   90 ASP cc_start: 0.8729 (m-30) cc_final: 0.8472 (m-30)
REVERT: D   98 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.7029 (ptt90)
REVERT: R  103 TYR cc_start: 0.7103 (m-80) cc_final: 0.6767 (m-10)
REVERT: R  146 PHE cc_start: 0.8686 (t80) cc_final: 0.8450 (t80)
REVERT: R  151 CYS cc_start: 0.9108 (m) cc_final: 0.8462 (p)
REVERT: R  153 TYR cc_start: 0.8519 (m-80) cc_final: 0.8239 (m-80)
REVERT: R  243 MET cc_start: 0.8820 (mmm) cc_final: 0.8340 (mmm)
REVERT: R  262 LYS cc_start: 0.8609 (tptp) cc_final: 0.8376 (tppt)
REVERT: R  269 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8390 (tm-30)
REVERT: R  355 VAL cc_start: 0.9628 (t) cc_final: 0.9425 (p)
  outliers start: 31
  outliers final: 25
  residues processed: 189
  average time/residue: 0.0817
  time to fit residues: 21.3504
Evaluate side-chains
  196 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 166
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  296 TYR
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain D residue   98 ARG
Chi-restraints excluded: chain D residue   99 SER
Chi-restraints excluded: chain D residue  126 ILE
Chi-restraints excluded: chain D residue  129 THR
Chi-restraints excluded: chain D residue  177 ILE
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain R residue   98 GLN
Chi-restraints excluded: chain R residue  198 LEU
Chi-restraints excluded: chain R residue  241 THR
Chi-restraints excluded: chain R residue  327 CYS
Chi-restraints excluded: chain R residue  367 VAL
Chi-restraints excluded: chain L residue    8 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 76 optimal weight:    0.2980
   chunk 96 optimal weight:    0.9990
   chunk 83 optimal weight:   10.0000
   chunk 105 optimal weight:    6.9990
   chunk 106 optimal weight:    7.9990
   chunk 28 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 79 optimal weight:    6.9990
   chunk 86 optimal weight:   30.0000
   chunk 27 optimal weight:    1.9990
   chunk 6 optimal weight:    6.9990
   overall best weight:    1.4386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  98 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.094863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.073994 restraints weight = 27868.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.076448 restraints weight = 14030.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.078099 restraints weight = 9206.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.079223 restraints weight = 7031.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.079869 restraints weight = 5870.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.6382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9162  Z= 0.143
  Angle     :  0.831  14.709  12423  Z= 0.407
  Chirality :  0.047   0.370   1418
  Planarity :  0.004   0.051   1566
  Dihedral  :  5.320  83.743   1254
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 23.43 %
    Favored  : 73.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.29 (0.26), residues: 1132
  helix:  1.14 (0.26), residues: 403
  sheet:  0.28 (0.32), residues: 276
  loop : -0.65 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  24 
 TYR   0.013   0.001   TYR D 102 
 PHE   0.016   0.001   PHE R 345 
 TRP   0.020   0.002   TRP B  82 
 HIS   0.007   0.001   HIS B 311 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.14 ( 9160)
  covalent geometry    : angle       0.83057 /  0.41 (12419)
  SS BOND              : bond        0.00728 /  0.36 (    2)
  SS BOND              : angle       0.67738 /  0.33 (    4)
  hydrogen bonds       : bond        0.04256 /  2.96 (  464)
  hydrogen bonds       : angle       5.13212 /  3.61 ( 1326)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1338.59 seconds
wall clock time: 23 minutes 55.79 seconds (1435.79 seconds total)