Starting phenix.real_space_refine
on Fri Nov 15 08:33:52 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zqe_60384/11_2024/8zqe_60384.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zqe_60384/11_2024/8zqe_60384.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zqe_60384/11_2024/8zqe_60384.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zqe_60384/11_2024/8zqe_60384.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zqe_60384/11_2024/8zqe_60384.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zqe_60384/11_2024/8zqe_60384.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.032
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      64      5.16       5
     C    5602      2.51       5
     N    1490      2.21       5
     O    1611      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 8767
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1712
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1712
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 56
          Unresolved non-hydrogen dihedrals: 40
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 26
    Chain: "B"
      Number of atoms: 2590
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2590
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "C"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 438
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "S"
      Number of atoms: 1760
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1760
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "R"
      Number of atoms: 2192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2192
          Classifications: {'peptide': 276}
          Link IDs: {'PTRANS': 11, 'TRANS': 264}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 75
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 75
          Classifications: {'peptide': 10}
          Link IDs: {'PTRANS': 2, 'TRANS': 7}
  Time building chain proxies: 5.47, per 1000 atoms: 0.62
  Number of scatterers: 8767
  At special positions: 0
  Unit cell: (86.528, 117.312, 125.632, 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      64     16.00
     O    1611      8.00
     N    1490      7.00
     C    5602      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 183 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.46
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2116

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 14 sheets defined
      37.9% alpha, 22.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 3.576A  pdb=" N   GLU A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.590A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.459A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 281
    Processing helix  chain 'A' and resid 295 through 310
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 4 through 26
      removed outlier: 3.724A  pdb=" N   GLU B  10 " --> pdb=" O   GLN B   6 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.844A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 8 through 24
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 61 through 65
      removed outlier: 3.582A  pdb=" N   LYS S  65 " --> pdb=" O   ASP S  62 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.965A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 208 through 212
      removed outlier: 3.655A  pdb=" N   VAL S 212 " --> pdb=" O   ALA S 209 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 36 through 61
      removed outlier: 3.633A  pdb=" N   ALA R  42 " --> pdb=" O   VAL R  38 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 85
      removed outlier: 3.780A  pdb=" N   ILE R  70 " --> pdb=" O   ARG R  66 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   PHE R  71 " --> pdb=" O   LEU R  67 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   THR R  85 " --> pdb=" O   ILE R  81 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 85 through 95
      removed outlier: 3.985A  pdb=" N   TRP R  89 " --> pdb=" O   THR R  85 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   SER R  95 " --> pdb=" O   ASP R  91 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 102 through 137
      removed outlier: 3.590A  pdb=" N   SER R 110 " --> pdb=" O   CYS R 106 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 172
      Proline residue:  R 167  - end of helix
    Processing helix  chain 'R' and resid 189 through 202
    Processing helix  chain 'R' and resid 204 through 229
      removed outlier: 3.566A  pdb=" N   THR R 213 " --> pdb=" O   LEU R 209 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   SER R 229 " --> pdb=" O   HIS R 225 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 235 through 270
      removed outlier: 3.962A  pdb=" N   SER R 239 " --> pdb=" O   LYS R 235 " (cutoff:3.500A)
      Proline residue:  R 256  - end of helix
    Processing helix  chain 'R' and resid 278 through 288
    Processing helix  chain 'R' and resid 289 through 291
      No H-bonds generated for 'chain 'R' and resid 289 through 291'
    Processing helix  chain 'R' and resid 292 through 305
      removed outlier: 3.623A  pdb=" N   ASN R 298 " --> pdb=" O   ASN R 294 " (cutoff:3.500A)
      Proline residue:  R 299  - end of helix
    Processing helix  chain 'R' and resid 307 through 315
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.849A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.590A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.543A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52
      removed outlier: 6.229A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.119A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 5.163A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.719A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.990A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.621A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.971A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.621A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.971A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.545A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.181A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.639A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.716A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.418A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 3.754A  pdb=" N   THR S 118 " --> pdb=" O   GLY S  10 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   GLN S  39 " --> pdb=" O   MET S  93 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 130
    Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 135
      removed outlier: 3.520A  pdb=" N   TYR S 215 " --> pdb=" O   THR S 231 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'R' and resid 175 through 177

    442 hydrogen bonds defined for protein.
    1242 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.74

  Time building geometry restraints manager: 2.81 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: 2213
        1.33 -     1.45: 1854
        1.45 -     1.58: 4797
        1.58 -     1.70: 0
        1.70 -     1.82: 89
  Bond restraints: 8953
  Sorted by residual:
  bond pdb=" N   GLN B 175 "
       pdb=" CA  GLN B 175 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 9.00e-03 1.23e+04 1.44e+01
  bond pdb=" N   VAL L  74 "
       pdb=" CA  VAL L  74 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 9.10e-03 1.21e+04 1.34e+01
  bond pdb=" N   TRP R  89 "
       pdb=" CA  TRP R  89 "
    ideal  model  delta    sigma   weight residual
    1.459  1.502 -0.043 1.28e-02 6.10e+03 1.13e+01
  bond pdb=" N   VAL L  73 "
       pdb=" CA  VAL L  73 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.037 1.15e-02 7.56e+03 1.02e+01
  bond pdb=" N   ILE A 344 "
       pdb=" CA  ILE A 344 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 1.19e-02 7.06e+03 8.31e+00
  ... (remaining 8948 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 11617
        1.61 -     3.22: 422
        3.22 -     4.83: 72
        4.83 -     6.44: 13
        6.44 -     8.05: 6
  Bond angle restraints: 12130
  Sorted by residual:
  angle pdb=" C   SER R 229 "
        pdb=" CA  SER R 229 "
        pdb=" CB  SER R 229 "
      ideal   model   delta    sigma   weight residual
     116.63  110.91    5.72 1.16e+00 7.43e-01 2.43e+01
  angle pdb=" N   LEU R  36 "
        pdb=" CA  LEU R  36 "
        pdb=" C   LEU R  36 "
      ideal   model   delta    sigma   weight residual
     113.25  107.44    5.81 1.30e+00 5.92e-01 1.99e+01
  angle pdb=" N   PHE R  82 "
        pdb=" CA  PHE R  82 "
        pdb=" C   PHE R  82 "
      ideal   model   delta    sigma   weight residual
     111.36  106.96    4.40 1.09e+00 8.42e-01 1.63e+01
  angle pdb=" N   SER R 229 "
        pdb=" CA  SER R 229 "
        pdb=" C   SER R 229 "
      ideal   model   delta    sigma   weight residual
     108.08  114.70   -6.62 1.69e+00 3.50e-01 1.53e+01
  angle pdb=" N   PHE A 334 "
        pdb=" CA  PHE A 334 "
        pdb=" C   PHE A 334 "
      ideal   model   delta    sigma   weight residual
     111.07  107.04    4.03 1.07e+00 8.73e-01 1.42e+01
  ... (remaining 12125 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 4822
       17.86 -    35.72: 401
       35.72 -    53.58: 62
       53.58 -    71.44: 12
       71.44 -    89.30: 8
  Dihedral angle restraints: 5305
    sinusoidal: 2029
      harmonic: 3276
  Sorted by residual:
  dihedral pdb=" CA  GLU S 222 "
           pdb=" C   GLU S 222 "
           pdb=" N   TYR S 223 "
           pdb=" CA  TYR S 223 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.88  -25.12     0      5.00e+00 4.00e-02 2.52e+01
  dihedral pdb=" CB  CYS S 147 "
           pdb=" SG  CYS S 147 "
           pdb=" SG  CYS S 217 "
           pdb=" CB  CYS S 217 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   58.75   34.25     1      1.00e+01 1.00e-02 1.66e+01
  dihedral pdb=" CA  TRP B 332 "
           pdb=" C   TRP B 332 "
           pdb=" N   ASP B 333 "
           pdb=" CA  ASP B 333 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.51   16.49     0      5.00e+00 4.00e-02 1.09e+01
  ... (remaining 5302 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1094
       0.054 -    0.107: 232
       0.107 -    0.161: 48
       0.161 -    0.214: 11
       0.214 -    0.268: 1
  Chirality restraints: 1386
  Sorted by residual:
  chirality pdb=" CA  ILE R 309 "
            pdb=" N   ILE R 309 "
            pdb=" C   ILE R 309 "
            pdb=" CB  ILE R 309 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.70   -0.27 2.00e-01 2.50e+01 1.79e+00
  chirality pdb=" CA  ILE R 279 "
            pdb=" N   ILE R 279 "
            pdb=" C   ILE R 279 "
            pdb=" CB  ILE R 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 9.16e-01
  chirality pdb=" CA  VAL B 307 "
            pdb=" N   VAL B 307 "
            pdb=" C   VAL B 307 "
            pdb=" CB  VAL B 307 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 8.60e-01
  ... (remaining 1383 not shown)

  Planarity restraints: 1524
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP R 306 "    0.017 2.00e-02 2.50e+03   3.49e-02 1.22e+01
        pdb=" C   ASP R 306 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   ASP R 306 "    0.023 2.00e-02 2.50e+03
        pdb=" N   SER R 307 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 166 "    0.052 5.00e-02 4.00e+02   7.78e-02 9.68e+00
        pdb=" N   PRO R 167 "   -0.135 5.00e-02 4.00e+02
        pdb=" CA  PRO R 167 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO R 167 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP R  89 "   -0.010 2.00e-02 2.50e+03   2.07e-02 4.30e+00
        pdb=" C   TRP R  89 "    0.036 2.00e-02 2.50e+03
        pdb=" O   TRP R  89 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   VAL R  90 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1521 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 334
        2.72 -     3.26: 9201
        3.26 -     3.81: 14919
        3.81 -     4.35: 18338
        4.35 -     4.90: 31491
  Nonbonded interactions: 74283
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.169 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OE1 GLU R 173 "
            pdb=" NZ  LYS R 186 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" OG  SER S  52 "
            pdb=" O   SER S  55 "
     model   vdw
     2.266 3.040
  ... (remaining 74278 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.870
  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:          0.370
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     23.680
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:14.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7145
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8953  Z= 0.279
  Angle     :  0.714   8.053  12130  Z= 0.453
  Chirality :  0.049   0.268   1386
  Planarity :  0.005   0.078   1524
  Dihedral  : 13.699  89.299   3180
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.85 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.26), residues: 1111
  helix:  0.89 (0.26), residues: 391
  sheet: -0.11 (0.33), residues: 270
  loop : -0.89 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.007   0.001   HIS B 183 
 PHE   0.014   0.001   PHE A 334 
 TYR   0.020   0.002   TYR S 223 
 ARG   0.004   0.000   ARG S 190 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 279
  time to evaluate  : 0.953 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.8086 (mtmt) cc_final: 0.7853 (mtmt)
REVERT: A  243 MET cc_start: 0.7966 (tpp) cc_final: 0.7049 (tpp)
REVERT: A  249 LEU cc_start: 0.8387 (tp) cc_final: 0.8088 (tp)
REVERT: A  252 SER cc_start: 0.8467 (t) cc_final: 0.7858 (p)
REVERT: A  315 ASP cc_start: 0.7213 (p0) cc_final: 0.6969 (p0)
REVERT: B    8 ARG cc_start: 0.8210 (ptp90) cc_final: 0.7807 (ptp-110)
REVERT: B   33 ILE cc_start: 0.8317 (pt) cc_final: 0.7994 (mt)
REVERT: B  189 SER cc_start: 0.8297 (t) cc_final: 0.7991 (p)
REVERT: B  210 LEU cc_start: 0.8122 (tp) cc_final: 0.7882 (tt)
REVERT: B  260 GLU cc_start: 0.7136 (pt0) cc_final: 0.6907 (pt0)
REVERT: B  261 LEU cc_start: 0.8129 (mt) cc_final: 0.7878 (mm)
REVERT: B  262 MET cc_start: 0.7343 (mmt) cc_final: 0.7068 (mmm)
REVERT: B  263 THR cc_start: 0.8074 (m) cc_final: 0.7777 (t)
REVERT: C   20 LYS cc_start: 0.8362 (ttpt) cc_final: 0.8081 (ttpt)
REVERT: S    7 SER cc_start: 0.8340 (t) cc_final: 0.8096 (p)
REVERT: S   63 THR cc_start: 0.7866 (t) cc_final: 0.7512 (m)
REVERT: S   71 SER cc_start: 0.8281 (p) cc_final: 0.7903 (t)
REVERT: S   90 ASP cc_start: 0.7981 (m-30) cc_final: 0.7648 (m-30)
REVERT: S  116 THR cc_start: 0.8734 (t) cc_final: 0.8495 (m)
REVERT: S  160 THR cc_start: 0.7899 (m) cc_final: 0.7630 (t)
REVERT: S  218 MET cc_start: 0.7742 (ttp) cc_final: 0.7539 (ttp)
REVERT: R   55 MET cc_start: 0.6273 (mtm) cc_final: 0.5883 (mtm)
REVERT: R  124 LEU cc_start: 0.7036 (tp) cc_final: 0.6389 (mt)
REVERT: R  200 LEU cc_start: 0.7357 (tp) cc_final: 0.7145 (tt)
REVERT: R  300 PHE cc_start: 0.6486 (m-80) cc_final: 0.6240 (m-10)
  outliers start: 2
  outliers final: 2
  residues processed: 280
  average time/residue: 1.0436
  time to fit residues: 314.3872
Evaluate side-chains
  236 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 234
  time to evaluate  : 1.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain L residue   74 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 46 optimal weight:    0.4980
   chunk 28 optimal weight:    3.9990
   chunk 56 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9980
   chunk 86 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 99 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B  16 ASN
B 110 ASN
B 155 ASN
B 176 GLN
S 130 GLN
S 167 GLN
S 182 ASN
R 233 ASN
R 315 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   8953  Z= 0.254
  Angle     :  0.644   8.806  12130  Z= 0.330
  Chirality :  0.045   0.216   1386
  Planarity :  0.005   0.064   1524
  Dihedral  :  4.648  21.823   1219
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 13.53 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.26), residues: 1111
  helix:  1.18 (0.26), residues: 393
  sheet: -0.04 (0.32), residues: 277
  loop : -0.96 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B 183 
 PHE   0.019   0.002   PHE S  68 
 TYR   0.024   0.002   TYR S  59 
 ARG   0.007   0.001   ARG B 219 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 273
  time to evaluate  : 1.004 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 LYS cc_start: 0.7817 (mttm) cc_final: 0.7543 (mtpp)
REVERT: A  243 MET cc_start: 0.8121 (tpp) cc_final: 0.7315 (tpp)
REVERT: A  249 LEU cc_start: 0.8409 (tp) cc_final: 0.8116 (tp)
REVERT: A  252 SER cc_start: 0.8532 (t) cc_final: 0.8100 (p)
REVERT: A  271 LYS cc_start: 0.8202 (pttt) cc_final: 0.7594 (pttm)
REVERT: A  310 LEU cc_start: 0.8396 (mm) cc_final: 0.8195 (mm)
REVERT: B    8 ARG cc_start: 0.8206 (ptp90) cc_final: 0.7727 (ptt-90)
REVERT: B   17 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7365 (tm-30)
REVERT: B   19 ARG cc_start: 0.7559 (tmm160) cc_final: 0.7267 (ttp80)
REVERT: B   33 ILE cc_start: 0.8377 (pt) cc_final: 0.8021 (mt)
REVERT: B   74 SER cc_start: 0.7752 (p) cc_final: 0.7550 (p)
REVERT: B   96 ARG cc_start: 0.6790 (mpt90) cc_final: 0.6546 (mpt180)
REVERT: B  221 THR cc_start: 0.8231 (t) cc_final: 0.7899 (m)
REVERT: B  259 GLN cc_start: 0.8286 (pm20) cc_final: 0.8052 (pm20)
REVERT: B  261 LEU cc_start: 0.8214 (mt) cc_final: 0.7990 (mm)
REVERT: C   20 LYS cc_start: 0.8161 (ttpt) cc_final: 0.7864 (ttpt)
REVERT: C   21 MET cc_start: 0.7134 (ptm) cc_final: 0.6774 (ptm)
REVERT: S   50 TYR cc_start: 0.8177 (t80) cc_final: 0.7935 (t80)
REVERT: S   63 THR cc_start: 0.8200 (t) cc_final: 0.7867 (m)
REVERT: S  156 SER cc_start: 0.8209 (m) cc_final: 0.7986 (p)
REVERT: S  160 THR cc_start: 0.8016 (m) cc_final: 0.7753 (t)
REVERT: S  161 TYR cc_start: 0.8305 (m-80) cc_final: 0.8063 (m-80)
REVERT: S  201 THR cc_start: 0.8078 (p) cc_final: 0.7842 (t)
REVERT: S  205 SER cc_start: 0.8383 (t) cc_final: 0.8024 (t)
REVERT: S  216 TYR cc_start: 0.8372 (m-80) cc_final: 0.8170 (m-80)
REVERT: R   55 MET cc_start: 0.6259 (mtm) cc_final: 0.5931 (mtm)
REVERT: R  124 LEU cc_start: 0.7105 (tp) cc_final: 0.6521 (mt)
REVERT: R  222 LEU cc_start: 0.7917 (mp) cc_final: 0.7542 (mt)
REVERT: R  285 GLU cc_start: 0.6106 (OUTLIER) cc_final: 0.5601 (pm20)
REVERT: R  300 PHE cc_start: 0.6641 (m-80) cc_final: 0.6401 (m-10)
  outliers start: 43
  outliers final: 11
  residues processed: 285
  average time/residue: 0.9568
  time to fit residues: 295.0510
Evaluate side-chains
  272 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 259
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue   21 SER
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  203 THR
Chi-restraints excluded: chain S residue  231 THR
Chi-restraints excluded: chain R residue  193 LEU
Chi-restraints excluded: chain R residue  241 LYS
Chi-restraints excluded: chain R residue  284 MET
Chi-restraints excluded: chain R residue  285 GLU
Chi-restraints excluded: chain R residue  297 VAL
Chi-restraints excluded: chain R residue  301 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 100 optimal weight:    0.9980
   chunk 108 optimal weight:    2.9990
   chunk 89 optimal weight:    0.8980
   chunk 99 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 80 optimal weight:    3.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
B 183 HIS
B 311 HIS
S 167 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.3035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   8953  Z= 0.276
  Angle     :  0.622   8.777  12130  Z= 0.320
  Chirality :  0.044   0.184   1386
  Planarity :  0.005   0.058   1524
  Dihedral  :  4.485  23.404   1216
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 18.08 %
    Favored  : 78.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.26), residues: 1111
  helix:  1.27 (0.26), residues: 393
  sheet: -0.27 (0.31), residues: 290
  loop : -0.80 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.020   0.002   PHE R 204 
 TYR   0.035   0.002   TYR S  59 
 ARG   0.010   0.001   ARG S 168 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 261
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 LYS cc_start: 0.7844 (mttm) cc_final: 0.7213 (mtpp)
REVERT: A  243 MET cc_start: 0.8212 (tpp) cc_final: 0.7403 (tpp)
REVERT: A  249 LEU cc_start: 0.8395 (tp) cc_final: 0.8009 (tp)
REVERT: A  252 SER cc_start: 0.8546 (t) cc_final: 0.8074 (p)
REVERT: A  271 LYS cc_start: 0.8350 (pttt) cc_final: 0.7761 (pttm)
REVERT: A  330 LYS cc_start: 0.7889 (mppt) cc_final: 0.7546 (mppt)
REVERT: B    8 ARG cc_start: 0.8158 (ptp90) cc_final: 0.7766 (ptp-110)
REVERT: B   17 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7399 (tm-30)
REVERT: B   22 ARG cc_start: 0.7112 (mtt180) cc_final: 0.6840 (mtt-85)
REVERT: B   74 SER cc_start: 0.7723 (p) cc_final: 0.7516 (m)
REVERT: B  137 ARG cc_start: 0.7044 (mmm160) cc_final: 0.6812 (mmm160)
REVERT: B  171 ILE cc_start: 0.7729 (mm) cc_final: 0.7498 (mm)
REVERT: B  221 THR cc_start: 0.8278 (t) cc_final: 0.7965 (m)
REVERT: B  253 PHE cc_start: 0.8461 (m-80) cc_final: 0.8106 (m-80)
REVERT: C   20 LYS cc_start: 0.8112 (ttpt) cc_final: 0.7811 (ttpt)
REVERT: C   21 MET cc_start: 0.7135 (ptm) cc_final: 0.6811 (ptm)
REVERT: S   58 ILE cc_start: 0.8528 (mm) cc_final: 0.8307 (OUTLIER)
REVERT: S   63 THR cc_start: 0.8421 (t) cc_final: 0.8135 (m)
REVERT: S  156 SER cc_start: 0.8313 (m) cc_final: 0.8092 (p)
REVERT: S  171 GLN cc_start: 0.8104 (mt0) cc_final: 0.7839 (mt0)
REVERT: S  201 THR cc_start: 0.8065 (p) cc_final: 0.7804 (t)
REVERT: S  205 SER cc_start: 0.8305 (t) cc_final: 0.7970 (t)
REVERT: R   55 MET cc_start: 0.6252 (mtm) cc_final: 0.5917 (mtm)
REVERT: R   71 PHE cc_start: 0.7565 (m-10) cc_final: 0.7096 (m-10)
REVERT: R  124 LEU cc_start: 0.7161 (tp) cc_final: 0.6852 (tp)
REVERT: R  300 PHE cc_start: 0.6695 (m-80) cc_final: 0.6468 (m-10)
REVERT: R  301 ILE cc_start: 0.8554 (mm) cc_final: 0.8334 (mp)
  outliers start: 33
  outliers final: 16
  residues processed: 267
  average time/residue: 1.0421
  time to fit residues: 299.1038
Evaluate side-chains
  276 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 260
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  198 THR
Chi-restraints excluded: chain S residue  231 THR
Chi-restraints excluded: chain R residue  113 ILE
Chi-restraints excluded: chain R residue  241 LYS
Chi-restraints excluded: chain R residue  284 MET
Chi-restraints excluded: chain R residue  297 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0980
   chunk 11 optimal weight:    0.8980
   chunk 47 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9980
   chunk 106 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 95 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
B 176 GLN
B 230 ASN
** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 167 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7341
moved from start:          0.3346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8953  Z= 0.209
  Angle     :  0.572   8.022  12130  Z= 0.294
  Chirality :  0.043   0.215   1386
  Planarity :  0.004   0.057   1524
  Dihedral  :  4.332  22.226   1216
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 21.14 %
    Favored  : 75.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.26), residues: 1111
  helix:  1.31 (0.26), residues: 393
  sheet: -0.18 (0.31), residues: 288
  loop : -0.82 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.019   0.001   PHE R 204 
 TYR   0.028   0.002   TYR S  59 
 ARG   0.008   0.001   ARG B  68 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 273
  time to evaluate  : 1.011 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 LYS cc_start: 0.7640 (mttm) cc_final: 0.7379 (mtpp)
REVERT: A  243 MET cc_start: 0.8240 (tpp) cc_final: 0.7402 (tpp)
REVERT: A  249 LEU cc_start: 0.8387 (tp) cc_final: 0.8028 (tp)
REVERT: A  252 SER cc_start: 0.8506 (t) cc_final: 0.8126 (p)
REVERT: A  271 LYS cc_start: 0.8360 (pttt) cc_final: 0.7744 (pttm)
REVERT: A  275 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7491 (mm-30)
REVERT: A  330 LYS cc_start: 0.7926 (mppt) cc_final: 0.7564 (mppt)
REVERT: B    8 ARG cc_start: 0.8150 (ptp90) cc_final: 0.7769 (ptp-110)
REVERT: B   17 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7427 (tm-30)
REVERT: B   50 THR cc_start: 0.8065 (m) cc_final: 0.7857 (t)
REVERT: B  171 ILE cc_start: 0.7740 (mm) cc_final: 0.7465 (mm)
REVERT: B  221 THR cc_start: 0.8234 (t) cc_final: 0.7936 (m)
REVERT: B  253 PHE cc_start: 0.8437 (m-80) cc_final: 0.8072 (m-80)
REVERT: B  263 THR cc_start: 0.8251 (m) cc_final: 0.8007 (t)
REVERT: C   20 LYS cc_start: 0.8107 (ttpt) cc_final: 0.7789 (ttpt)
REVERT: C   21 MET cc_start: 0.7103 (ptm) cc_final: 0.6783 (ptm)
REVERT: S   63 THR cc_start: 0.8454 (t) cc_final: 0.8140 (m)
REVERT: S   95 TYR cc_start: 0.7663 (m-80) cc_final: 0.7337 (m-80)
REVERT: S  171 GLN cc_start: 0.8055 (mt0) cc_final: 0.7796 (mt0)
REVERT: S  190 ARG cc_start: 0.7203 (mtm180) cc_final: 0.6552 (ptt-90)
REVERT: S  205 SER cc_start: 0.8265 (t) cc_final: 0.7925 (t)
REVERT: R   55 MET cc_start: 0.6223 (mtm) cc_final: 0.5903 (mtm)
REVERT: R   71 PHE cc_start: 0.7534 (m-10) cc_final: 0.7054 (m-10)
REVERT: R   82 PHE cc_start: 0.7541 (t80) cc_final: 0.7257 (t80)
REVERT: R  124 LEU cc_start: 0.7134 (tp) cc_final: 0.6842 (mt)
REVERT: R  222 LEU cc_start: 0.7943 (mp) cc_final: 0.7652 (mt)
REVERT: R  285 GLU cc_start: 0.6265 (OUTLIER) cc_final: 0.5779 (pm20)
REVERT: R  300 PHE cc_start: 0.6766 (m-80) cc_final: 0.6530 (m-10)
REVERT: R  301 ILE cc_start: 0.8563 (mm) cc_final: 0.8361 (mp)
  outliers start: 31
  outliers final: 18
  residues processed: 284
  average time/residue: 1.0003
  time to fit residues: 305.9655
Evaluate side-chains
  285 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 265
  time to evaluate  : 1.047 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  198 THR
Chi-restraints excluded: chain S residue  231 THR
Chi-restraints excluded: chain R residue   73 ILE
Chi-restraints excluded: chain R residue   83 LEU
Chi-restraints excluded: chain R residue  113 ILE
Chi-restraints excluded: chain R residue  128 SER
Chi-restraints excluded: chain R residue  193 LEU
Chi-restraints excluded: chain R residue  284 MET
Chi-restraints excluded: chain R residue  285 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 60 optimal weight:    5.9990
   chunk 1 optimal weight:    0.5980
   chunk 79 optimal weight:    5.9990
   chunk 43 optimal weight:    0.1980
   chunk 90 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 95 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
B  75 GLN
B 230 ASN
B 340 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
moved from start:          0.3715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8953  Z= 0.272
  Angle     :  0.612   8.057  12130  Z= 0.315
  Chirality :  0.045   0.214   1386
  Planarity :  0.005   0.056   1524
  Dihedral  :  4.455  19.797   1216
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 22.30 %
    Favored  : 73.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.26), residues: 1111
  helix:  1.35 (0.26), residues: 392
  sheet: -0.36 (0.30), residues: 297
  loop : -0.87 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  82 
 HIS   0.004   0.001   HIS A 213 
 PHE   0.019   0.002   PHE R 204 
 TYR   0.043   0.002   TYR S  59 
 ARG   0.010   0.001   ARG S 168 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 268
  time to evaluate  : 1.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 LYS cc_start: 0.7692 (mttm) cc_final: 0.7445 (mtpp)
REVERT: A  243 MET cc_start: 0.8290 (tpp) cc_final: 0.7508 (tpp)
REVERT: A  249 LEU cc_start: 0.8406 (tp) cc_final: 0.7997 (tp)
REVERT: A  252 SER cc_start: 0.8499 (t) cc_final: 0.8082 (p)
REVERT: A  275 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7446 (mt-10)
REVERT: A  330 LYS cc_start: 0.8021 (mppt) cc_final: 0.7653 (mppt)
REVERT: B    8 ARG cc_start: 0.8156 (ptp90) cc_final: 0.7775 (ptp-110)
REVERT: B   17 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7433 (tm-30)
REVERT: B  135 VAL cc_start: 0.8455 (t) cc_final: 0.8170 (m)
REVERT: B  172 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6626 (mp0)
REVERT: B  221 THR cc_start: 0.8281 (t) cc_final: 0.7959 (m)
REVERT: B  253 PHE cc_start: 0.8443 (m-80) cc_final: 0.8059 (m-80)
REVERT: B  269 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8241 (pt)
REVERT: C   20 LYS cc_start: 0.8098 (ttpt) cc_final: 0.7787 (ttpt)
REVERT: C   21 MET cc_start: 0.7122 (ptm) cc_final: 0.6813 (ptm)
REVERT: S   18 ARG cc_start: 0.7966 (tpp-160) cc_final: 0.7525 (mmt-90)
REVERT: S   63 THR cc_start: 0.8504 (t) cc_final: 0.8236 (m)
REVERT: S  160 THR cc_start: 0.8026 (m) cc_final: 0.7819 (t)
REVERT: S  171 GLN cc_start: 0.8084 (mt0) cc_final: 0.7859 (mt0)
REVERT: S  205 SER cc_start: 0.8248 (t) cc_final: 0.7914 (t)
REVERT: S  223 TYR cc_start: 0.7450 (OUTLIER) cc_final: 0.7206 (t80)
REVERT: R   55 MET cc_start: 0.6229 (mtm) cc_final: 0.5898 (mtm)
REVERT: R   71 PHE cc_start: 0.7646 (m-10) cc_final: 0.7144 (m-10)
REVERT: R   75 LEU cc_start: 0.7798 (tm) cc_final: 0.7485 (tp)
REVERT: R   82 PHE cc_start: 0.7635 (t80) cc_final: 0.7317 (t80)
REVERT: R  121 VAL cc_start: 0.8078 (t) cc_final: 0.7676 (p)
REVERT: R  124 LEU cc_start: 0.7127 (tp) cc_final: 0.6783 (mt)
REVERT: R  222 LEU cc_start: 0.7964 (mp) cc_final: 0.7644 (mt)
REVERT: R  285 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.5910 (pm20)
REVERT: R  297 VAL cc_start: 0.7965 (p) cc_final: 0.7702 (m)
REVERT: R  300 PHE cc_start: 0.6735 (m-80) cc_final: 0.6498 (m-10)
  outliers start: 38
  outliers final: 17
  residues processed: 282
  average time/residue: 1.0120
  time to fit residues: 307.6242
Evaluate side-chains
  286 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 265
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  180 MET
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  198 THR
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain R residue   73 ILE
Chi-restraints excluded: chain R residue   83 LEU
Chi-restraints excluded: chain R residue  113 ILE
Chi-restraints excluded: chain R residue  193 LEU
Chi-restraints excluded: chain R residue  284 MET
Chi-restraints excluded: chain R residue  285 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 95 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 106 optimal weight:    9.9990
   chunk 88 optimal weight:    6.9990
   chunk 49 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
B 230 ASN
** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 167 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7368
moved from start:          0.3908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8953  Z= 0.236
  Angle     :  0.598   7.947  12130  Z= 0.307
  Chirality :  0.044   0.202   1386
  Planarity :  0.005   0.056   1524
  Dihedral  :  4.422  26.068   1216
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 22.62 %
    Favored  : 72.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.25), residues: 1111
  helix:  1.36 (0.26), residues: 394
  sheet: -0.31 (0.31), residues: 276
  loop : -0.96 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.022   0.002   PHE S  68 
 TYR   0.035   0.002   TYR S  59 
 ARG   0.009   0.001   ARG S 168 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 270
  time to evaluate  : 1.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 LYS cc_start: 0.7665 (mttm) cc_final: 0.7391 (mtpp)
REVERT: A  243 MET cc_start: 0.8324 (tpp) cc_final: 0.7497 (tpp)
REVERT: A  275 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7429 (mt-10)
REVERT: A  330 LYS cc_start: 0.8021 (mppt) cc_final: 0.7636 (mppt)
REVERT: B    8 ARG cc_start: 0.8148 (ptp90) cc_final: 0.7771 (ptp-110)
REVERT: B  135 VAL cc_start: 0.8457 (t) cc_final: 0.8167 (m)
REVERT: B  172 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6597 (mp0)
REVERT: B  221 THR cc_start: 0.8236 (t) cc_final: 0.7951 (m)
REVERT: B  253 PHE cc_start: 0.8473 (m-80) cc_final: 0.8039 (m-80)
REVERT: B  269 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8237 (pt)
REVERT: C   20 LYS cc_start: 0.8103 (ttpt) cc_final: 0.7796 (ttpt)
REVERT: C   21 MET cc_start: 0.7107 (ptm) cc_final: 0.6792 (ptm)
REVERT: S   63 THR cc_start: 0.8450 (t) cc_final: 0.8129 (m)
REVERT: S   83 MET cc_start: 0.7635 (mtm) cc_final: 0.7360 (mtp)
REVERT: S  171 GLN cc_start: 0.8086 (mt0) cc_final: 0.7877 (mt0)
REVERT: S  190 ARG cc_start: 0.7322 (mtm-85) cc_final: 0.6634 (ptt-90)
REVERT: S  205 SER cc_start: 0.8211 (t) cc_final: 0.7875 (t)
REVERT: S  223 TYR cc_start: 0.7354 (OUTLIER) cc_final: 0.7015 (t80)
REVERT: R   55 MET cc_start: 0.6192 (mtm) cc_final: 0.5875 (mtm)
REVERT: R   71 PHE cc_start: 0.7629 (m-10) cc_final: 0.7228 (m-10)
REVERT: R   75 LEU cc_start: 0.7818 (tm) cc_final: 0.7523 (tp)
REVERT: R   82 PHE cc_start: 0.7756 (t80) cc_final: 0.7483 (t80)
REVERT: R  121 VAL cc_start: 0.8040 (t) cc_final: 0.7633 (p)
REVERT: R  124 LEU cc_start: 0.7142 (tp) cc_final: 0.6823 (mt)
REVERT: R  222 LEU cc_start: 0.7960 (mp) cc_final: 0.7632 (mt)
REVERT: R  285 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.5907 (pm20)
REVERT: R  297 VAL cc_start: 0.7973 (p) cc_final: 0.7730 (m)
REVERT: R  300 PHE cc_start: 0.6743 (m-80) cc_final: 0.6502 (m-10)
  outliers start: 42
  outliers final: 25
  residues processed: 283
  average time/residue: 1.0778
  time to fit residues: 327.8192
Evaluate side-chains
  291 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 263
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain S residue   21 SER
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  175 LEU
Chi-restraints excluded: chain S residue  198 THR
Chi-restraints excluded: chain S residue  202 LEU
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain R residue   72 ILE
Chi-restraints excluded: chain R residue   73 ILE
Chi-restraints excluded: chain R residue   83 LEU
Chi-restraints excluded: chain R residue  128 SER
Chi-restraints excluded: chain R residue  193 LEU
Chi-restraints excluded: chain R residue  284 MET
Chi-restraints excluded: chain R residue  285 GLU
Chi-restraints excluded: chain R residue  301 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 11 optimal weight:    0.4980
   chunk 60 optimal weight:    5.9990
   chunk 77 optimal weight:    0.3980
   chunk 89 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   chunk 106 optimal weight:    6.9990
   chunk 66 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9980
   chunk 48 optimal weight:    0.3980
   chunk 65 optimal weight:    0.7980
   chunk 42 optimal weight:    0.0770
   overall best weight:    0.4338

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
B 230 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  82 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.4016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8953  Z= 0.171
  Angle     :  0.579   6.912  12130  Z= 0.296
  Chirality :  0.043   0.187   1386
  Planarity :  0.005   0.056   1524
  Dihedral  :  4.304  24.350   1216
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 24.21 %
    Favored  : 71.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.25), residues: 1111
  helix:  1.42 (0.26), residues: 393
  sheet: -0.31 (0.31), residues: 276
  loop : -0.92 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.002   0.000   HIS S  35 
 PHE   0.017   0.001   PHE R 204 
 TYR   0.033   0.002   TYR S  59 
 ARG   0.009   0.000   ARG S 168 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 268
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 LYS cc_start: 0.7625 (mttm) cc_final: 0.7350 (mtpp)
REVERT: A  243 MET cc_start: 0.8344 (tpp) cc_final: 0.7514 (tpp)
REVERT: A  252 SER cc_start: 0.8419 (t) cc_final: 0.8108 (p)
REVERT: A  271 LYS cc_start: 0.8409 (pttt) cc_final: 0.8152 (pttp)
REVERT: A  275 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7415 (mt-10)
REVERT: A  330 LYS cc_start: 0.7968 (mppt) cc_final: 0.7583 (mppt)
REVERT: B    8 ARG cc_start: 0.8145 (ptp90) cc_final: 0.7768 (ptp-110)
REVERT: B  119 ASN cc_start: 0.7771 (m-40) cc_final: 0.7462 (m-40)
REVERT: B  135 VAL cc_start: 0.8448 (t) cc_final: 0.8170 (m)
REVERT: B  221 THR cc_start: 0.8197 (t) cc_final: 0.7907 (m)
REVERT: C   20 LYS cc_start: 0.8120 (ttpt) cc_final: 0.7806 (ttpt)
REVERT: C   21 MET cc_start: 0.7095 (ptm) cc_final: 0.6788 (ptm)
REVERT: C   46 LYS cc_start: 0.8509 (mtpp) cc_final: 0.8295 (mtpp)
REVERT: S   63 THR cc_start: 0.8353 (t) cc_final: 0.8017 (m)
REVERT: S   68 PHE cc_start: 0.7952 (m-10) cc_final: 0.7691 (m-10)
REVERT: S   83 MET cc_start: 0.7655 (mtm) cc_final: 0.7073 (mtm)
REVERT: S   93 MET cc_start: 0.6961 (tmm) cc_final: 0.6438 (tmm)
REVERT: S   95 TYR cc_start: 0.7811 (m-80) cc_final: 0.7139 (m-80)
REVERT: S  190 ARG cc_start: 0.7303 (mtm-85) cc_final: 0.6774 (ptt-90)
REVERT: S  205 SER cc_start: 0.8149 (t) cc_final: 0.7835 (t)
REVERT: S  223 TYR cc_start: 0.7187 (OUTLIER) cc_final: 0.6840 (t80)
REVERT: R   55 MET cc_start: 0.6146 (mtm) cc_final: 0.5832 (mtm)
REVERT: R   71 PHE cc_start: 0.7600 (m-10) cc_final: 0.7206 (m-10)
REVERT: R   75 LEU cc_start: 0.7886 (tm) cc_final: 0.7606 (tp)
REVERT: R   82 PHE cc_start: 0.7972 (t80) cc_final: 0.7668 (t80)
REVERT: R  124 LEU cc_start: 0.7103 (tp) cc_final: 0.6773 (mt)
REVERT: R  222 LEU cc_start: 0.7945 (mp) cc_final: 0.7601 (mt)
REVERT: R  285 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.5864 (pm20)
REVERT: R  300 PHE cc_start: 0.6770 (m-80) cc_final: 0.6528 (m-10)
  outliers start: 38
  outliers final: 17
  residues processed: 279
  average time/residue: 1.0120
  time to fit residues: 304.2167
Evaluate side-chains
  286 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 267
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain R residue   72 ILE
Chi-restraints excluded: chain R residue   73 ILE
Chi-restraints excluded: chain R residue  128 SER
Chi-restraints excluded: chain R residue  193 LEU
Chi-restraints excluded: chain R residue  284 MET
Chi-restraints excluded: chain R residue  285 GLU
Chi-restraints excluded: chain R residue  301 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 63 optimal weight:    0.0040
   chunk 31 optimal weight:    0.1980
   chunk 20 optimal weight:    1.9990
   chunk 67 optimal weight:    5.9990
   chunk 72 optimal weight:    3.9990
   chunk 52 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 83 optimal weight:    6.9990
   chunk 96 optimal weight:    0.6980
   chunk 101 optimal weight:    0.9980
   chunk 92 optimal weight:    5.9990
   overall best weight:    0.4992

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
B 230 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  82 GLN
R  74 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7333
moved from start:          0.4186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8953  Z= 0.180
  Angle     :  0.588   8.714  12130  Z= 0.299
  Chirality :  0.043   0.186   1386
  Planarity :  0.005   0.059   1524
  Dihedral  :  4.309  25.977   1216
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 26.11 %
    Favored  : 70.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.26), residues: 1111
  helix:  1.51 (0.26), residues: 392
  sheet: -0.32 (0.31), residues: 281
  loop : -0.87 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.016   0.001   PHE R 204 
 TYR   0.031   0.002   TYR S  59 
 ARG   0.009   0.001   ARG S 168 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 263
  time to evaluate  : 1.024 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 LYS cc_start: 0.7629 (mttm) cc_final: 0.7403 (mtpp)
REVERT: A  243 MET cc_start: 0.8345 (tpp) cc_final: 0.7517 (tpp)
REVERT: A  252 SER cc_start: 0.8423 (t) cc_final: 0.8108 (p)
REVERT: A  271 LYS cc_start: 0.8442 (pttt) cc_final: 0.8184 (pttp)
REVERT: A  275 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7412 (mt-10)
REVERT: A  330 LYS cc_start: 0.7967 (mppt) cc_final: 0.7582 (mppt)
REVERT: B    8 ARG cc_start: 0.8154 (ptp90) cc_final: 0.7778 (mtm110)
REVERT: B  221 THR cc_start: 0.8188 (t) cc_final: 0.7900 (m)
REVERT: C   20 LYS cc_start: 0.8115 (ttpt) cc_final: 0.7802 (ttpt)
REVERT: C   21 MET cc_start: 0.7088 (ptm) cc_final: 0.6773 (ptm)
REVERT: C   46 LYS cc_start: 0.8523 (mtpp) cc_final: 0.8299 (mtpp)
REVERT: S   59 TYR cc_start: 0.8315 (m-80) cc_final: 0.8072 (m-80)
REVERT: S   63 THR cc_start: 0.8332 (t) cc_final: 0.8036 (m)
REVERT: S   68 PHE cc_start: 0.7935 (m-10) cc_final: 0.7682 (m-10)
REVERT: S   83 MET cc_start: 0.7668 (mtm) cc_final: 0.6993 (mtm)
REVERT: S   93 MET cc_start: 0.6999 (tmm) cc_final: 0.6463 (tmm)
REVERT: S   95 TYR cc_start: 0.7777 (m-80) cc_final: 0.7037 (m-80)
REVERT: S  205 SER cc_start: 0.8131 (t) cc_final: 0.7813 (t)
REVERT: S  223 TYR cc_start: 0.7134 (OUTLIER) cc_final: 0.6912 (t80)
REVERT: R   55 MET cc_start: 0.6100 (mtm) cc_final: 0.5799 (mtm)
REVERT: R   71 PHE cc_start: 0.7593 (m-10) cc_final: 0.7198 (m-10)
REVERT: R   75 LEU cc_start: 0.7911 (tm) cc_final: 0.7640 (tp)
REVERT: R   82 PHE cc_start: 0.7835 (t80) cc_final: 0.7621 (t80)
REVERT: R  124 LEU cc_start: 0.7121 (tp) cc_final: 0.6803 (mt)
REVERT: R  222 LEU cc_start: 0.7922 (mp) cc_final: 0.7588 (mt)
REVERT: R  285 GLU cc_start: 0.6415 (OUTLIER) cc_final: 0.5934 (pm20)
REVERT: R  297 VAL cc_start: 0.8002 (p) cc_final: 0.7758 (m)
REVERT: R  300 PHE cc_start: 0.6762 (m-80) cc_final: 0.6508 (m-10)
  outliers start: 30
  outliers final: 16
  residues processed: 275
  average time/residue: 1.0288
  time to fit residues: 304.3020
Evaluate side-chains
  277 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 259
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  175 LEU
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain R residue   72 ILE
Chi-restraints excluded: chain R residue   73 ILE
Chi-restraints excluded: chain R residue  128 SER
Chi-restraints excluded: chain R residue  193 LEU
Chi-restraints excluded: chain R residue  284 MET
Chi-restraints excluded: chain R residue  285 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 101 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 89 optimal weight:    0.8980
   chunk 93 optimal weight:    0.0670
   chunk 64 optimal weight:    0.7980
   chunk 104 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   overall best weight:    0.7520

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
moved from start:          0.4324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8953  Z= 0.224
  Angle     :  0.623   8.988  12130  Z= 0.315
  Chirality :  0.044   0.192   1386
  Planarity :  0.005   0.060   1524
  Dihedral  :  4.383  22.618   1216
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 26.53 %
    Favored  : 70.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.26), residues: 1111
  helix:  1.48 (0.26), residues: 393
  sheet: -0.25 (0.31), residues: 286
  loop : -0.89 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 339 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.016   0.001   PHE R 204 
 TYR   0.029   0.002   TYR S  59 
 ARG   0.008   0.001   ARG S 168 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 267
  time to evaluate  : 1.101 
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: A  197 LYS cc_start: 0.7620 (mttm) cc_final: 0.7350 (mtpp)
REVERT: A  243 MET cc_start: 0.8357 (tpp) cc_final: 0.7543 (tpp)
REVERT: A  271 LYS cc_start: 0.8461 (pttt) cc_final: 0.8198 (pttp)
REVERT: A  275 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7425 (mt-10)
REVERT: A  330 LYS cc_start: 0.7998 (mppt) cc_final: 0.7606 (mppt)
REVERT: B    8 ARG cc_start: 0.8141 (ptp90) cc_final: 0.7764 (mtm110)
REVERT: B  221 THR cc_start: 0.8213 (t) cc_final: 0.7914 (m)
REVERT: B  283 ARG cc_start: 0.8393 (tpp80) cc_final: 0.8008 (tpt90)
REVERT: C   20 LYS cc_start: 0.8106 (ttpt) cc_final: 0.7809 (ttpt)
REVERT: C   21 MET cc_start: 0.7086 (ptm) cc_final: 0.6778 (ptm)
REVERT: C   46 LYS cc_start: 0.8522 (mtpp) cc_final: 0.8290 (mtpp)
REVERT: S   59 TYR cc_start: 0.8307 (m-80) cc_final: 0.8065 (m-80)
REVERT: S   63 THR cc_start: 0.8403 (t) cc_final: 0.8105 (m)
REVERT: S   93 MET cc_start: 0.7003 (tmm) cc_final: 0.6446 (tmm)
REVERT: S   95 TYR cc_start: 0.7869 (m-80) cc_final: 0.7164 (m-80)
REVERT: S  205 SER cc_start: 0.8119 (t) cc_final: 0.7819 (t)
REVERT: R   55 MET cc_start: 0.6104 (mtm) cc_final: 0.5810 (mtm)
REVERT: R   71 PHE cc_start: 0.7650 (m-10) cc_final: 0.7236 (m-10)
REVERT: R  124 LEU cc_start: 0.7108 (tp) cc_final: 0.6849 (mt)
REVERT: R  222 LEU cc_start: 0.7930 (mp) cc_final: 0.7621 (mt)
REVERT: R  285 GLU cc_start: 0.6440 (OUTLIER) cc_final: 0.5932 (pm20)
REVERT: R  300 PHE cc_start: 0.6777 (m-80) cc_final: 0.6516 (m-10)
  outliers start: 29
  outliers final: 19
  residues processed: 275
  average time/residue: 1.0490
  time to fit residues: 310.6953
Evaluate side-chains
  283 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 263
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  118 THR
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  175 LEU
Chi-restraints excluded: chain S residue  198 THR
Chi-restraints excluded: chain R residue   72 ILE
Chi-restraints excluded: chain R residue  128 SER
Chi-restraints excluded: chain R residue  193 LEU
Chi-restraints excluded: chain R residue  284 MET
Chi-restraints excluded: chain R residue  285 GLU
Chi-restraints excluded: chain R residue  301 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 72 optimal weight:    5.9990
   chunk 109 optimal weight:    9.9990
   chunk 100 optimal weight:    0.7980
   chunk 87 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   chunk 67 optimal weight:    3.9990
   chunk 53 optimal weight:    0.6980
   chunk 69 optimal weight:    0.8980
   chunk 92 optimal weight:    0.0980
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7337
moved from start:          0.4417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8953  Z= 0.203
  Angle     :  0.626   9.574  12130  Z= 0.315
  Chirality :  0.044   0.194   1386
  Planarity :  0.005   0.059   1524
  Dihedral  :  4.456  23.826   1216
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 27.70 %
    Favored  : 69.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.25), residues: 1111
  helix:  1.47 (0.26), residues: 395
  sheet: -0.27 (0.31), residues: 280
  loop : -0.98 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.069   0.002   PHE S  68 
 TYR   0.030   0.002   TYR S 223 
 ARG   0.009   0.001   ARG S 168 

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 258
  time to evaluate  : 1.071 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 MET cc_start: 0.8355 (tpp) cc_final: 0.7542 (tpp)
REVERT: A  271 LYS cc_start: 0.8470 (pttt) cc_final: 0.8211 (pttp)
REVERT: A  275 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7445 (mt-10)
REVERT: A  330 LYS cc_start: 0.7995 (mppt) cc_final: 0.7601 (mppt)
REVERT: B    8 ARG cc_start: 0.8141 (ptp90) cc_final: 0.7773 (mtm110)
REVERT: B  221 THR cc_start: 0.8190 (t) cc_final: 0.7887 (m)
REVERT: B  283 ARG cc_start: 0.8377 (tpp80) cc_final: 0.8073 (tpt170)
REVERT: C   20 LYS cc_start: 0.8098 (ttpt) cc_final: 0.7805 (ttpt)
REVERT: C   21 MET cc_start: 0.7081 (ptm) cc_final: 0.6773 (ptm)
REVERT: C   46 LYS cc_start: 0.8529 (mtpp) cc_final: 0.8291 (mtpp)
REVERT: S   34 MET cc_start: 0.7670 (mmm) cc_final: 0.7398 (mmt)
REVERT: S   63 THR cc_start: 0.8113 (t) cc_final: 0.7745 (m)
REVERT: S   93 MET cc_start: 0.6973 (tmm) cc_final: 0.6416 (tmm)
REVERT: S   95 TYR cc_start: 0.7784 (m-80) cc_final: 0.7021 (m-80)
REVERT: S  205 SER cc_start: 0.8106 (t) cc_final: 0.7801 (t)
REVERT: S  208 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7045 (mt-10)
REVERT: R   55 MET cc_start: 0.6090 (mtm) cc_final: 0.5813 (mtm)
REVERT: R   71 PHE cc_start: 0.7640 (m-10) cc_final: 0.7246 (m-10)
REVERT: R  124 LEU cc_start: 0.7110 (tp) cc_final: 0.6868 (mt)
REVERT: R  222 LEU cc_start: 0.7933 (mp) cc_final: 0.7611 (mt)
REVERT: R  285 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.5919 (pm20)
REVERT: R  300 PHE cc_start: 0.6780 (m-80) cc_final: 0.6519 (m-10)
  outliers start: 24
  outliers final: 19
  residues processed: 267
  average time/residue: 0.8337
  time to fit residues: 240.8941
Evaluate side-chains
  269 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 249
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  175 LEU
Chi-restraints excluded: chain R residue   72 ILE
Chi-restraints excluded: chain R residue  128 SER
Chi-restraints excluded: chain R residue  193 LEU
Chi-restraints excluded: chain R residue  284 MET
Chi-restraints excluded: chain R residue  285 GLU
Chi-restraints excluded: chain R residue  301 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 12 optimal weight:    0.3980
   chunk 24 optimal weight:    0.5980
   chunk 87 optimal weight:    0.8980
   chunk 36 optimal weight:    0.4980
   chunk 89 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 76 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.146410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.123958 restraints weight = 13215.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 2.16
r_work: 0.3537 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3385 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.4528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8953  Z= 0.200
  Angle     :  0.641   9.069  12130  Z= 0.323
  Chirality :  0.044   0.187   1386
  Planarity :  0.005   0.060   1524
  Dihedral  :  4.486  24.262   1216
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 27.70 %
    Favored  : 69.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.25), residues: 1111
  helix:  1.43 (0.26), residues: 395
  sheet: -0.25 (0.31), residues: 279
  loop : -0.96 (0.30), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.046   0.002   PHE S  68 
 TYR   0.042   0.002   TYR S  59 
 ARG   0.009   0.000   ARG S 168 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4844.05 seconds
wall clock time: 88 minutes 33.84 seconds (5313.84 seconds total)