Starting phenix.real_space_refine
on Sun May 11 14:56:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jgf_36232/05_2025/8jgf_36232_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jgf_36232/05_2025/8jgf_36232.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jgf_36232/05_2025/8jgf_36232.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jgf_36232/05_2025/8jgf_36232.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jgf_36232/05_2025/8jgf_36232_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jgf_36232/05_2025/8jgf_36232_neut.cif"
  }
  resolution = 2.7
  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=   0.003 sd=   0.035
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      52      5.16       5
     C    5323      2.51       5
     N    1412      2.21       5
     O    1551      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8338
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1839
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1839
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 6, 'TRANS': 225}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 70
          Unresolved non-hydrogen angles: 82
          Unresolved non-hydrogen dihedrals: 62
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 42
    Chain: "B"
      Number of atoms: 2477
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2477
          Classifications: {'peptide': 336}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 110
          Unresolved non-hydrogen angles: 137
          Unresolved non-hydrogen dihedrals: 93
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 2, 'ARG:plan': 8, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 81
    Chain: "E"
      Number of atoms: 1742
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1742
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 49
          Unresolved non-hydrogen dihedrals: 36
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 21
    Chain: "G"
      Number of atoms: 384
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 384
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "L"
      Number of atoms: 110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 110
          Classifications: {'peptide': 12}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 1, 'TRANS': 10}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "R"
      Number of atoms: 1786
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1786
          Classifications: {'peptide': 236}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 6, 'TRANS': 229}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 103
          Unresolved non-hydrogen angles: 123
          Unresolved non-hydrogen dihedrals: 85
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 49
  Time building chain proxies: 4.98, per 1000 atoms: 0.60
  Number of scatterers: 8338
  At special positions: 0
  Unit cell: (94.64, 119.6, 112.32, 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      52     16.00
     O    1551      8.00
     N    1412      7.00
     C    5323      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  21 " - pdb=" SG  CYS E  95 " 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: 2.15
  Conformation dependent library (CDL) restraints added in 929.6 milliseconds
  

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2064

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 13 sheets defined
      37.9% alpha, 24.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.823A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   VAL A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 210 through 216
      removed outlier: 3.874A  pdb=" N   ASN A 216 " --> pdb=" O   GLN A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 245
    Processing helix  chain 'A' and resid 246 through 250
      removed outlier: 3.939A  pdb=" N   ARG A 250 " --> pdb=" O   ARG A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 271
    Processing helix  chain 'A' and resid 274 through 278
    Processing helix  chain 'A' and resid 279 through 285
    Processing helix  chain 'A' and resid 298 through 319
      removed outlier: 3.781A  pdb=" N   ILE A 315 " --> pdb=" O   GLU A 311 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   SER A 319 " --> pdb=" O   ILE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 358
    Processing helix  chain 'B' and resid 11 through 31
    Processing helix  chain 'B' and resid 34 through 40
    Processing helix  chain 'E' and resid 27 through 31
    Processing helix  chain 'E' and resid 86 through 90
    Processing helix  chain 'E' and resid 220 through 224
    Processing helix  chain 'G' and resid 10 through 23
    Processing helix  chain 'G' and resid 28 through 44
    Processing helix  chain 'R' and resid 26 through 28
      No H-bonds generated for 'chain 'R' and resid 26 through 28'
    Processing helix  chain 'R' and resid 29 through 55
      removed outlier: 3.796A  pdb=" N   CYS R  35 " --> pdb=" O   THR R  31 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 60 through 85
      removed outlier: 3.962A  pdb=" N   ASN R  67 " --> pdb=" O   ILE R  63 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 97 through 126
    Processing helix  chain 'R' and resid 126 through 133
    Processing helix  chain 'R' and resid 137 through 160
    Processing helix  chain 'R' and resid 175 through 205
    Processing helix  chain 'R' and resid 211 through 228
    Processing helix  chain 'R' and resid 229 through 239
      removed outlier: 4.459A  pdb=" N   GLY R 233 " --> pdb=" O   GLY R 229 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 245 through 252
    Processing helix  chain 'R' and resid 254 through 273
      Proline residue:  R 269  - end of helix
    Processing helix  chain 'R' and resid 273 through 278
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 9.092A  pdb=" N   ALA A 220 " --> pdb=" O   THR A  33 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   ILE A 222 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.268A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 8.557A  pdb=" N   ASP A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56
      removed outlier: 5.482A  pdb=" N   THR B  52 " --> pdb=" O   ASN B 345 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   ASN B 345 " --> pdb=" O   THR B  52 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68
      removed outlier: 3.534A  pdb=" N   ALA B  65 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   SER B  79 " --> pdb=" O   LYS B  83 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LYS B  83 " --> pdb=" O   SER B  79 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   LEU B  84 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   ALA B  97 " --> pdb=" O   LEU B  84 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ILE B  86 " --> pdb=" O   VAL B  95 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110
      removed outlier: 4.004A  pdb=" N   GLY B 121 " --> pdb=" O   ILE B 125 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   ILE B 125 " --> pdb=" O   GLY B 121 " (cutoff:3.500A)
      removed outlier: 5.832A  pdb=" N   CYS B 126 " --> pdb=" O   GLU B 143 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   GLU B 143 " --> pdb=" O   CYS B 126 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ILE B 128 " --> pdb=" O   SER B 141 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ARG B 139 " --> pdb=" O   ASN B 130 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 158
      removed outlier: 6.074A  pdb=" N   GLN B 161 " --> pdb=" O   LEU B 157 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   ASP B 175 " --> pdb=" O   GLN B 181 " (cutoff:3.500A)
      removed outlier: 5.906A  pdb=" N   GLN B 181 " --> pdb=" O   ASP B 175 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197
      removed outlier: 3.653A  pdb=" N   GLN B 225 " --> pdb=" O   LEU B 215 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   ASP B 217 " --> pdb=" O   CYS B 223 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   CYS B 223 " --> pdb=" O   ASP B 217 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239
      removed outlier: 6.527A  pdb=" N   CYS B 255 " --> pdb=" O   THR B 268 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   THR B 268 " --> pdb=" O   CYS B 255 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   LEU B 257 " --> pdb=" O   LEU B 266 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283
      removed outlier: 3.635A  pdb=" N   SER B 280 " --> pdb=" O   GLY B 293 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   ASP B 303 " --> pdb=" O   ARG B 309 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   ARG B 309 " --> pdb=" O   ASP B 303 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6
    Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11
      removed outlier: 5.888A  pdb=" N   GLY E   9 " --> pdb=" O   THR E 117 " (cutoff:3.500A)
      removed outlier: 5.687A  pdb=" N   ARG E  37 " --> pdb=" O   TRP E  46 " (cutoff:3.500A)
      removed outlier: 5.096A  pdb=" N   TRP E  46 " --> pdb=" O   ARG E  37 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11
      removed outlier: 5.888A  pdb=" N   GLY E   9 " --> pdb=" O   THR E 117 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   PHE E 109 " --> pdb=" O   ARG E  97 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148
      removed outlier: 3.951A  pdb=" N   GLU E 246 " --> pdb=" O   VAL E 147 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)

    462 hydrogen bonds defined for protein.
    1275 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: 2.45

  Time building geometry restraints manager: 2.51 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1409
        1.31 -     1.44: 2371
        1.44 -     1.56: 4663
        1.56 -     1.69: 0
        1.69 -     1.81: 72
  Bond restraints: 8515
  Sorted by residual:
  bond pdb=" CA  PHE B 240 "
       pdb=" C   PHE B 240 "
    ideal  model  delta    sigma   weight residual
    1.523  1.430  0.092 1.28e-02 6.10e+03 5.22e+01
  bond pdb=" CA  LYS L  19 "
       pdb=" C   LYS L  19 "
    ideal  model  delta    sigma   weight residual
    1.524  1.427  0.096 1.35e-02 5.49e+03 5.09e+01
  bond pdb=" CA  SER R 176 "
       pdb=" C   SER R 176 "
    ideal  model  delta    sigma   weight residual
    1.524  1.440  0.083 1.32e-02 5.74e+03 3.99e+01
  bond pdb=" CA  TRP R  50 "
       pdb=" C   TRP R  50 "
    ideal  model  delta    sigma   weight residual
    1.524  1.454  0.071 1.24e-02 6.50e+03 3.24e+01
  bond pdb=" CA  VAL R  48 "
       pdb=" C   VAL R  48 "
    ideal  model  delta    sigma   weight residual
    1.524  1.451  0.072 1.30e-02 5.92e+03 3.10e+01
  ... (remaining 8510 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.67: 11379
        2.67 -     5.34: 173
        5.34 -     8.01: 22
        8.01 -    10.68: 14
       10.68 -    13.35: 3
  Bond angle restraints: 11591
  Sorted by residual:
  angle pdb=" N   TYR R  64 "
        pdb=" CA  TYR R  64 "
        pdb=" C   TYR R  64 "
      ideal   model   delta    sigma   weight residual
     114.04  100.69   13.35 1.24e+00 6.50e-01 1.16e+02
  angle pdb=" N   ILE R  63 "
        pdb=" CA  ILE R  63 "
        pdb=" C   ILE R  63 "
      ideal   model   delta    sigma   weight residual
     112.83  102.73   10.10 9.90e-01 1.02e+00 1.04e+02
  angle pdb=" C   GLY A  45 "
        pdb=" N   LYS A  46 "
        pdb=" CA  LYS A  46 "
      ideal   model   delta    sigma   weight residual
     120.38  132.21  -11.83 1.37e+00 5.33e-01 7.46e+01
  angle pdb=" N   LEU B 157 "
        pdb=" CA  LEU B 157 "
        pdb=" C   LEU B 157 "
      ideal   model   delta    sigma   weight residual
     113.97  103.28   10.69 1.28e+00 6.10e-01 6.97e+01
  angle pdb=" N   THR R 175 "
        pdb=" CA  THR R 175 "
        pdb=" C   THR R 175 "
      ideal   model   delta    sigma   weight residual
     113.30  102.75   10.55 1.34e+00 5.57e-01 6.20e+01
  ... (remaining 11586 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 4438
       17.84 -    35.68: 420
       35.68 -    53.52: 97
       53.52 -    71.36: 20
       71.36 -    89.21: 11
  Dihedral angle restraints: 4986
    sinusoidal: 1794
      harmonic: 3192
  Sorted by residual:
  dihedral pdb=" C   MET L  15 "
           pdb=" N   MET L  15 "
           pdb=" CA  MET L  15 "
           pdb=" CB  MET L  15 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -108.45  -14.15     0      2.50e+00 1.60e-01 3.21e+01
  dihedral pdb=" CA  PHE E  31 "
           pdb=" C   PHE E  31 "
           pdb=" N   GLY E  32 "
           pdb=" CA  GLY E  32 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.45   20.55     0      5.00e+00 4.00e-02 1.69e+01
  dihedral pdb=" C   PHE B 240 "
           pdb=" N   PHE B 240 "
           pdb=" CA  PHE B 240 "
           pdb=" CB  PHE B 240 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -112.58  -10.02     0      2.50e+00 1.60e-01 1.61e+01
  ... (remaining 4983 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1076
       0.052 -    0.104: 208
       0.104 -    0.156: 51
       0.156 -    0.207: 6
       0.207 -    0.259: 5
  Chirality restraints: 1346
  Sorted by residual:
  chirality pdb=" CA  ARG E 191 "
            pdb=" N   ARG E 191 "
            pdb=" C   ARG E 191 "
            pdb=" CB  ARG E 191 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.68e+00
  chirality pdb=" CA  LYS B  83 "
            pdb=" N   LYS B  83 "
            pdb=" C   LYS B  83 "
            pdb=" CB  LYS B  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" CA  MET L  15 "
            pdb=" N   MET L  15 "
            pdb=" C   MET L  15 "
            pdb=" CB  MET L  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.30e+00
  ... (remaining 1343 not shown)

  Planarity restraints: 1468
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU R 157 "   -0.018 2.00e-02 2.50e+03   3.54e-02 1.26e+01
        pdb=" C   GLU R 157 "    0.061 2.00e-02 2.50e+03
        pdb=" O   GLU R 157 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   TRP R 158 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 240 "    0.055 5.00e-02 4.00e+02   8.14e-02 1.06e+01
        pdb=" N   PRO B 241 "   -0.141 5.00e-02 4.00e+02
        pdb=" CA  PRO B 241 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO B 241 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN R  45 "    0.015 2.00e-02 2.50e+03   3.06e-02 9.37e+00
        pdb=" C   ASN R  45 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   ASN R  45 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ALA R  46 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1465 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1497
        2.76 -     3.29: 8373
        3.29 -     3.83: 14942
        3.83 -     4.36: 18121
        4.36 -     4.90: 30263
  Nonbonded interactions: 73196
  Sorted by model distance:
  nonbonded pdb=" O   ILE B  63 "
            pdb=" OG  SER B 321 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" OG  SER B 152 "
            pdb=" O   VAL B 192 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OE2 GLU B 265 "
            pdb=" OG1 THR B 268 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   THR B  91 "
            pdb=" OG1 THR B  92 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" O   HIS B  59 "
            pdb=" OG  SER B 339 "
     model   vdw
     2.285 3.040
  ... (remaining 73191 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:             0.390
  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:          0.300
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     21.590
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
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      :  0.008   0.096   8516  Z= 0.529
  Angle     :  0.860  13.354  11593  Z= 0.565
  Chirality :  0.047   0.259   1346
  Planarity :  0.005   0.081   1468
  Dihedral  : 15.546  89.206   2919
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 20.21 %
    Favored  : 79.21 %
  Cbeta Deviations :  0.10 %
  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:  0.21 (0.26), residues: 1081
  helix:  1.25 (0.28), residues: 362
  sheet: -0.50 (0.29), residues: 281
  loop : -0.22 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP R 158 
 HIS   0.007   0.001   HIS B 147 
 PHE   0.024   0.002   PHE B 240 
 TYR   0.028   0.002   TYR R  64 
 ARG   0.004   0.001   ARG E 191 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13482 (  458)
  hydrogen bonds       : angle       6.86372 ( 1275)
  SS BOND              : bond        0.00338 (    1)
  SS BOND              : angle       2.86236 (    2)
  covalent geometry    : bond        0.00756 ( 8515)
  covalent geometry    : angle       0.85953 (11591)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 287
  time to evaluate  : 0.918 
Fit side-chains
REVERT: A   49 ILE cc_start: 0.7450 (mt) cc_final: 0.7078 (OUTLIER)
REVERT: B   25 ASP cc_start: 0.6993 (m-30) cc_final: 0.6791 (m-30)
REVERT: B  258 PHE cc_start: 0.8034 (m-80) cc_final: 0.7740 (m-80)
REVERT: B  263 ASP cc_start: 0.7212 (t70) cc_final: 0.6962 (t0)
REVERT: R   80 LEU cc_start: 0.7865 (tp) cc_final: 0.7507 (tt)
  outliers start: 5
  outliers final: 2
  residues processed: 289
  average time/residue: 1.0584
  time to fit residues: 325.9473
Evaluate side-chains
  227 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 226
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  234 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9990
   chunk 45 optimal weight:    0.3980
   chunk 27 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 84 optimal weight:    0.4980
   chunk 32 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 98 optimal weight:    0.9980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 259 ASN
B  37 GLN
B 137 ASN
B 180 GLN
B 264 GLN
E  76 ASN
E 171 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.115716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.106348 restraints weight = 12744.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 1.85
r_work: 0.3450 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3328 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.2498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8516  Z= 0.153
  Angle     :  0.566   7.247  11593  Z= 0.302
  Chirality :  0.042   0.155   1346
  Planarity :  0.005   0.056   1468
  Dihedral  :  4.399  21.011   1179
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 23.34 %
    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:  0.91 (0.26), residues: 1081
  helix:  1.99 (0.27), residues: 370
  sheet: -0.20 (0.30), residues: 273
  loop :  0.06 (0.32), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 174 
 HIS   0.003   0.001   HIS R 133 
 PHE   0.022   0.002   PHE E  28 
 TYR   0.028   0.002   TYR L  17 
 ARG   0.011   0.001   ARG B 256 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04013 (  458)
  hydrogen bonds       : angle       4.78439 ( 1275)
  SS BOND              : bond        0.00107 (    1)
  SS BOND              : angle       0.79542 (    2)
  covalent geometry    : bond        0.00326 ( 8515)
  covalent geometry    : angle       0.56631 (11591)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 266
  time to evaluate  : 0.846 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8565 (mptm) cc_final: 0.8353 (mptm)
REVERT: A   43 ASN cc_start: 0.8572 (p0) cc_final: 0.8369 (p0)
REVERT: A   53 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7657 (mtm)
REVERT: A  186 GLU cc_start: 0.7157 (tm-30) cc_final: 0.6943 (tm-30)
REVERT: A  192 ASP cc_start: 0.7488 (m-30) cc_final: 0.7172 (m-30)
REVERT: A  267 LYS cc_start: 0.8780 (ttmm) cc_final: 0.8500 (ttmt)
REVERT: A  314 ASP cc_start: 0.8021 (m-30) cc_final: 0.7552 (m-30)
REVERT: A  336 THR cc_start: 0.8295 (p) cc_final: 0.8046 (p)
REVERT: B   18 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7798 (tm-30)
REVERT: B   19 LEU cc_start: 0.8799 (mm) cc_final: 0.8193 (mm)
REVERT: B   35 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7997 (tp)
REVERT: B   37 GLN cc_start: 0.8272 (mt0) cc_final: 0.8025 (mt0)
REVERT: B  142 ARG cc_start: 0.8307 (ttm110) cc_final: 0.7728 (ttp-170)
REVERT: B  177 GLU cc_start: 0.8223 (tp30) cc_final: 0.7927 (tp30)
REVERT: B  191 ASP cc_start: 0.7963 (m-30) cc_final: 0.7700 (m-30)
REVERT: B  258 PHE cc_start: 0.8814 (m-80) cc_final: 0.8540 (m-80)
REVERT: B  263 ASP cc_start: 0.8144 (t70) cc_final: 0.7540 (t0)
REVERT: E   16 SER cc_start: 0.8676 (p) cc_final: 0.8339 (t)
REVERT: E  118 VAL cc_start: 0.8632 (t) cc_final: 0.8376 (m)
REVERT: E  213 THR cc_start: 0.8547 (t) cc_final: 0.8223 (p)
REVERT: R   36 ILE cc_start: 0.8479 (mp) cc_final: 0.8278 (mp)
REVERT: R   47 VAL cc_start: 0.8736 (t) cc_final: 0.8472 (p)
REVERT: R   98 LEU cc_start: 0.8182 (mm) cc_final: 0.7952 (tp)
REVERT: R  101 VAL cc_start: 0.8591 (OUTLIER) cc_final: 0.8309 (p)
REVERT: R  152 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8484 (tp)
REVERT: R  203 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8184 (mm)
  outliers start: 42
  outliers final: 13
  residues processed: 287
  average time/residue: 0.8748
  time to fit residues: 271.5329
Evaluate side-chains
  278 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 260
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  319 SER
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  152 LEU
Chi-restraints excluded: chain R residue  196 LEU
Chi-restraints excluded: chain R residue  203 LEU
Chi-restraints excluded: chain R residue  258 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 84 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 75 optimal weight:    3.9990
   chunk 88 optimal weight:    6.9990
   chunk 101 optimal weight:   10.0000
   chunk 89 optimal weight:    0.9980
   chunk 87 optimal weight:    3.9990
   chunk 102 optimal weight:    0.9990
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 259 ASN
A 338 ASN
A 354 ASN
B  21 ASN
B 225 GLN
B 264 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.115002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.105641 restraints weight = 12999.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.3532 rms_B_bonded: 1.86
r_work: 0.3436 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3311 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.3003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8516  Z= 0.144
  Angle     :  0.533   8.481  11593  Z= 0.280
  Chirality :  0.042   0.166   1346
  Planarity :  0.004   0.061   1468
  Dihedral  :  4.130  20.067   1177
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 26.60 %
    Favored  : 69.22 %
  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:  1.28 (0.26), residues: 1081
  helix:  2.51 (0.26), residues: 366
  sheet: -0.09 (0.30), residues: 277
  loop :  0.16 (0.32), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 211 
 HIS   0.010   0.001   HIS A 329 
 PHE   0.027   0.002   PHE E  28 
 TYR   0.034   0.001   TYR L  17 
 ARG   0.009   0.001   ARG B  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03783 (  458)
  hydrogen bonds       : angle       4.55258 ( 1275)
  SS BOND              : bond        0.00187 (    1)
  SS BOND              : angle       0.68229 (    2)
  covalent geometry    : bond        0.00317 ( 8515)
  covalent geometry    : angle       0.53269 (11591)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 263
  time to evaluate  : 0.917 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.8805 (p0) cc_final: 0.8408 (p0)
REVERT: A  186 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6938 (tm-30)
REVERT: A  205 ARG cc_start: 0.8728 (mtp-110) cc_final: 0.8401 (mtp-110)
REVERT: A  297 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6817 (mm-30)
REVERT: A  314 ASP cc_start: 0.8076 (m-30) cc_final: 0.7593 (m-30)
REVERT: A  329 HIS cc_start: 0.8516 (m-70) cc_final: 0.8313 (m170)
REVERT: A  331 THR cc_start: 0.8268 (p) cc_final: 0.8037 (t)
REVERT: A  337 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7627 (mp0)
REVERT: A  340 ARG cc_start: 0.8599 (tpp-160) cc_final: 0.8289 (tpt170)
REVERT: B   18 GLN cc_start: 0.8351 (tm-30) cc_final: 0.7887 (tm-30)
REVERT: B   19 LEU cc_start: 0.8853 (mm) cc_final: 0.8285 (mm)
REVERT: B   37 GLN cc_start: 0.8317 (mt0) cc_final: 0.8089 (mt0)
REVERT: B  191 ASP cc_start: 0.7950 (m-30) cc_final: 0.7645 (m-30)
REVERT: B  258 PHE cc_start: 0.8822 (m-80) cc_final: 0.8148 (m-80)
REVERT: B  263 ASP cc_start: 0.8101 (t70) cc_final: 0.7571 (t0)
REVERT: E   16 SER cc_start: 0.8559 (p) cc_final: 0.8256 (t)
REVERT: E   42 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8393 (mppt)
REVERT: E  118 VAL cc_start: 0.8616 (t) cc_final: 0.8387 (m)
REVERT: E  203 PHE cc_start: 0.8539 (m-80) cc_final: 0.7864 (m-80)
REVERT: E  213 THR cc_start: 0.8480 (t) cc_final: 0.8180 (p)
REVERT: R   36 ILE cc_start: 0.8527 (mp) cc_final: 0.8258 (mp)
REVERT: R   47 VAL cc_start: 0.8636 (t) cc_final: 0.8393 (p)
REVERT: R  101 VAL cc_start: 0.8550 (OUTLIER) cc_final: 0.8287 (p)
REVERT: R  152 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8467 (tp)
REVERT: R  203 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8172 (mm)
REVERT: R  218 ILE cc_start: 0.8467 (mt) cc_final: 0.8257 (tt)
  outliers start: 36
  outliers final: 17
  residues processed: 278
  average time/residue: 0.9434
  time to fit residues: 282.0810
Evaluate side-chains
  285 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 263
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain B residue   45 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain E residue   42 LYS
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain E residue  237 LEU
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  152 LEU
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  180 THR
Chi-restraints excluded: chain R residue  203 LEU
Chi-restraints excluded: chain R residue  258 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 103 optimal weight:    1.9990
   chunk 99 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 104 optimal weight:    0.0980
   chunk 21 optimal weight:    2.9990
   chunk 91 optimal weight:    0.0770
   chunk 33 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.9542

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

Flipped N/Q/H residues before XYZ refinement:
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 259 ASN
A 338 ASN
B  11 GLN
B 225 GLN
E 194 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.114670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.105234 restraints weight = 12940.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 1.86
r_work: 0.3429 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3304 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.3378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8516  Z= 0.156
  Angle     :  0.533   8.095  11593  Z= 0.279
  Chirality :  0.042   0.163   1346
  Planarity :  0.004   0.061   1468
  Dihedral  :  4.080  19.910   1177
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 27.41 %
    Favored  : 67.71 %
  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:  1.31 (0.26), residues: 1081
  helix:  2.61 (0.26), residues: 366
  sheet: -0.01 (0.30), residues: 271
  loop :  0.05 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 211 
 HIS   0.006   0.001   HIS A 329 
 PHE   0.028   0.002   PHE E  28 
 TYR   0.031   0.001   TYR L  17 
 ARG   0.008   0.001   ARG A 300 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03710 (  458)
  hydrogen bonds       : angle       4.43166 ( 1275)
  SS BOND              : bond        0.00160 (    1)
  SS BOND              : angle       0.68859 (    2)
  covalent geometry    : bond        0.00343 ( 8515)
  covalent geometry    : angle       0.53258 (11591)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 265
  time to evaluate  : 0.852 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.8912 (p0) cc_final: 0.8452 (p0)
REVERT: A  186 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6941 (tm-30)
REVERT: A  192 ASP cc_start: 0.7499 (m-30) cc_final: 0.7005 (m-30)
REVERT: A  205 ARG cc_start: 0.8717 (mtp-110) cc_final: 0.8382 (mtm-85)
REVERT: A  297 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6814 (mm-30)
REVERT: A  298 ASP cc_start: 0.7883 (t0) cc_final: 0.7679 (t0)
REVERT: A  314 ASP cc_start: 0.8078 (m-30) cc_final: 0.7686 (m-30)
REVERT: A  335 ASP cc_start: 0.7643 (m-30) cc_final: 0.7415 (t0)
REVERT: A  336 THR cc_start: 0.8452 (p) cc_final: 0.8252 (p)
REVERT: A  337 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7564 (mp0)
REVERT: A  340 ARG cc_start: 0.8588 (tpp-160) cc_final: 0.8116 (tpp-160)
REVERT: B   11 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7768 (pp30)
REVERT: B   18 GLN cc_start: 0.8405 (tm-30) cc_final: 0.7938 (tm-30)
REVERT: B   19 LEU cc_start: 0.8895 (mm) cc_final: 0.8338 (mm)
REVERT: B   37 GLN cc_start: 0.8347 (mt0) cc_final: 0.8107 (mt0)
REVERT: B  191 ASP cc_start: 0.7949 (m-30) cc_final: 0.7591 (m-30)
REVERT: B  258 PHE cc_start: 0.8849 (m-80) cc_final: 0.8246 (m-80)
REVERT: B  263 ASP cc_start: 0.8083 (t70) cc_final: 0.7539 (t0)
REVERT: E   16 SER cc_start: 0.8542 (p) cc_final: 0.8249 (t)
REVERT: E   42 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8459 (mppt)
REVERT: E  203 PHE cc_start: 0.8551 (m-80) cc_final: 0.7851 (m-80)
REVERT: E  213 THR cc_start: 0.8485 (t) cc_final: 0.8204 (p)
REVERT: R   36 ILE cc_start: 0.8516 (mp) cc_final: 0.8258 (mp)
REVERT: R  101 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8278 (p)
REVERT: R  152 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8427 (tp)
REVERT: R  203 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8190 (mm)
  outliers start: 42
  outliers final: 21
  residues processed: 283
  average time/residue: 0.8734
  time to fit residues: 266.9611
Evaluate side-chains
  273 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 246
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain B residue   11 GLN
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain E residue   42 LYS
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain E residue  237 LEU
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  152 LEU
Chi-restraints excluded: chain R residue  180 THR
Chi-restraints excluded: chain R residue  203 LEU
Chi-restraints excluded: chain R residue  240 LEU
Chi-restraints excluded: chain R residue  258 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 32 optimal weight:    3.9990
   chunk 95 optimal weight:    4.9990
   chunk 64 optimal weight:    7.9990
   chunk 37 optimal weight:    0.7980
   chunk 103 optimal weight:    0.6980
   chunk 102 optimal weight:    0.5980
   chunk 13 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   chunk 79 optimal weight:    4.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 259 ASN
A 338 ASN
B  11 GLN
B  21 ASN
B 225 GLN
B 264 GLN
E 142 GLN
E 194 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.115741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.106395 restraints weight = 12638.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3541 rms_B_bonded: 1.84
r_work: 0.3445 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3322 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.3566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8516  Z= 0.135
  Angle     :  0.534   8.030  11593  Z= 0.276
  Chirality :  0.042   0.161   1346
  Planarity :  0.004   0.060   1468
  Dihedral  :  4.004  19.066   1177
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 28.46 %
    Favored  : 66.55 %
  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:  1.36 (0.26), residues: 1081
  helix:  2.70 (0.26), residues: 366
  sheet:  0.04 (0.31), residues: 271
  loop :  0.01 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 211 
 HIS   0.004   0.001   HIS A 329 
 PHE   0.031   0.002   PHE E  28 
 TYR   0.031   0.001   TYR L  17 
 ARG   0.009   0.000   ARG A 300 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03655 (  458)
  hydrogen bonds       : angle       4.37516 ( 1275)
  SS BOND              : bond        0.00149 (    1)
  SS BOND              : angle       0.55442 (    2)
  covalent geometry    : bond        0.00297 ( 8515)
  covalent geometry    : angle       0.53359 (11591)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 256
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ASN cc_start: 0.8886 (p0) cc_final: 0.8506 (p0)
REVERT: A  186 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6901 (tm-30)
REVERT: A  192 ASP cc_start: 0.7527 (m-30) cc_final: 0.7030 (m-30)
REVERT: A  205 ARG cc_start: 0.8708 (mtp-110) cc_final: 0.8384 (mtm-85)
REVERT: A  267 LYS cc_start: 0.8508 (ttmm) cc_final: 0.8229 (ptmt)
REVERT: A  297 GLU cc_start: 0.7369 (mm-30) cc_final: 0.6831 (mm-30)
REVERT: A  298 ASP cc_start: 0.7839 (t0) cc_final: 0.7624 (t0)
REVERT: A  314 ASP cc_start: 0.8013 (m-30) cc_final: 0.7640 (m-30)
REVERT: A  337 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7534 (mp0)
REVERT: A  340 ARG cc_start: 0.8572 (tpp-160) cc_final: 0.8108 (tpp-160)
REVERT: B   18 GLN cc_start: 0.8417 (tm-30) cc_final: 0.7948 (tm-30)
REVERT: B   19 LEU cc_start: 0.8918 (mm) cc_final: 0.8347 (mm)
REVERT: B   37 GLN cc_start: 0.8354 (mt0) cc_final: 0.8138 (mt0)
REVERT: B   66 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7809 (ttp)
REVERT: B  191 ASP cc_start: 0.7978 (m-30) cc_final: 0.7644 (m-30)
REVERT: B  258 PHE cc_start: 0.8834 (m-80) cc_final: 0.8123 (m-80)
REVERT: B  263 ASP cc_start: 0.8063 (t70) cc_final: 0.7516 (t0)
REVERT: E   16 SER cc_start: 0.8504 (p) cc_final: 0.8209 (t)
REVERT: E   42 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8646 (mtpt)
REVERT: E  139 VAL cc_start: 0.8520 (t) cc_final: 0.8282 (p)
REVERT: E  203 PHE cc_start: 0.8551 (m-80) cc_final: 0.7860 (m-80)
REVERT: E  206 SER cc_start: 0.8571 (t) cc_final: 0.8205 (p)
REVERT: E  213 THR cc_start: 0.8443 (OUTLIER) cc_final: 0.8072 (p)
REVERT: E  237 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8070 (mt)
REVERT: R   36 ILE cc_start: 0.8510 (mp) cc_final: 0.8277 (mp)
REVERT: R   52 LEU cc_start: 0.8711 (mt) cc_final: 0.8483 (mm)
REVERT: R  101 VAL cc_start: 0.8552 (OUTLIER) cc_final: 0.8268 (p)
REVERT: R  152 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8410 (tp)
REVERT: R  239 PHE cc_start: 0.8485 (m-10) cc_final: 0.8236 (m-10)
  outliers start: 43
  outliers final: 18
  residues processed: 269
  average time/residue: 0.9295
  time to fit residues: 269.2484
Evaluate side-chains
  276 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 251
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain B residue   11 GLN
Chi-restraints excluded: chain B residue   66 MET
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain E residue   42 LYS
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  213 THR
Chi-restraints excluded: chain E residue  237 LEU
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  152 LEU
Chi-restraints excluded: chain R residue  180 THR
Chi-restraints excluded: chain R residue  258 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 106 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 89 optimal weight:    0.6980
   chunk 75 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9980
   chunk 104 optimal weight:    0.9980
   chunk 97 optimal weight:    2.9990
   chunk 88 optimal weight:    0.8980
   chunk 74 optimal weight:    0.0570
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 259 ASN
A 338 ASN
B  11 GLN
B 225 GLN
B 264 GLN
E 194 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.117060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.107750 restraints weight = 12432.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 1.80
r_work: 0.3461 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3340 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.3724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8516  Z= 0.131
  Angle     :  0.544   8.205  11593  Z= 0.279
  Chirality :  0.042   0.158   1346
  Planarity :  0.004   0.059   1468
  Dihedral  :  4.010  19.077   1177
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 28.11 %
    Favored  : 67.13 %
  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:  1.38 (0.26), residues: 1081
  helix:  2.74 (0.26), residues: 367
  sheet:  0.08 (0.31), residues: 271
  loop : -0.03 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 211 
 HIS   0.003   0.001   HIS A 329 
 PHE   0.034   0.002   PHE E  28 
 TYR   0.028   0.001   TYR L  17 
 ARG   0.008   0.001   ARG A 300 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03617 (  458)
  hydrogen bonds       : angle       4.36275 ( 1275)
  SS BOND              : bond        0.00026 (    1)
  SS BOND              : angle       0.53673 (    2)
  covalent geometry    : bond        0.00290 ( 8515)
  covalent geometry    : angle       0.54372 (11591)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 254
  time to evaluate  : 0.902 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.8590 (ttmm) cc_final: 0.8369 (ttmm)
REVERT: A   43 ASN cc_start: 0.8882 (p0) cc_final: 0.8597 (p0)
REVERT: A  192 ASP cc_start: 0.7590 (m-30) cc_final: 0.7142 (m-30)
REVERT: A  205 ARG cc_start: 0.8688 (mtp-110) cc_final: 0.8379 (mtm-85)
REVERT: A  267 LYS cc_start: 0.8490 (ttmm) cc_final: 0.8193 (ptmt)
REVERT: A  297 GLU cc_start: 0.7391 (mm-30) cc_final: 0.6871 (mm-30)
REVERT: A  314 ASP cc_start: 0.7975 (m-30) cc_final: 0.7601 (m-30)
REVERT: A  337 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7463 (mp0)
REVERT: B   18 GLN cc_start: 0.8401 (tm-30) cc_final: 0.7966 (tm-30)
REVERT: B   19 LEU cc_start: 0.8932 (mm) cc_final: 0.8380 (mm)
REVERT: B   37 GLN cc_start: 0.8366 (mt0) cc_final: 0.8152 (mt0)
REVERT: B   66 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7730 (ttp)
REVERT: B  191 ASP cc_start: 0.7970 (m-30) cc_final: 0.7647 (m-30)
REVERT: B  263 ASP cc_start: 0.8068 (t70) cc_final: 0.7556 (t0)
REVERT: B  291 LEU cc_start: 0.8514 (mp) cc_final: 0.8307 (mt)
REVERT: E   16 SER cc_start: 0.8490 (p) cc_final: 0.8200 (t)
REVERT: E   20 SER cc_start: 0.8171 (m) cc_final: 0.7861 (t)
REVERT: E   42 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8657 (mtpt)
REVERT: E   68 THR cc_start: 0.8878 (OUTLIER) cc_final: 0.8657 (p)
REVERT: E  139 VAL cc_start: 0.8475 (t) cc_final: 0.8229 (p)
REVERT: E  141 THR cc_start: 0.8500 (m) cc_final: 0.8225 (p)
REVERT: E  203 PHE cc_start: 0.8545 (m-80) cc_final: 0.7888 (m-80)
REVERT: E  206 SER cc_start: 0.8535 (t) cc_final: 0.8216 (p)
REVERT: E  213 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8072 (p)
REVERT: E  224 VAL cc_start: 0.8383 (t) cc_final: 0.8108 (p)
REVERT: E  237 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8082 (mt)
REVERT: R   36 ILE cc_start: 0.8502 (mp) cc_final: 0.8269 (mp)
REVERT: R   52 LEU cc_start: 0.8603 (mt) cc_final: 0.8379 (mm)
REVERT: R  101 VAL cc_start: 0.8593 (t) cc_final: 0.8335 (p)
REVERT: R  125 LEU cc_start: 0.8907 (mp) cc_final: 0.8704 (mt)
REVERT: R  152 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8332 (tp)
REVERT: R  203 LEU cc_start: 0.8649 (mm) cc_final: 0.8351 (mm)
REVERT: R  250 PHE cc_start: 0.8519 (t80) cc_final: 0.8271 (t80)
  outliers start: 41
  outliers final: 25
  residues processed: 272
  average time/residue: 0.9186
  time to fit residues: 269.3790
Evaluate side-chains
  276 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 245
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain B residue   11 GLN
Chi-restraints excluded: chain B residue   66 MET
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain E residue   42 LYS
Chi-restraints excluded: chain E residue   68 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain E residue  213 THR
Chi-restraints excluded: chain E residue  237 LEU
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  152 LEU
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  180 THR
Chi-restraints excluded: chain R residue  202 ILE
Chi-restraints excluded: chain R residue  249 LEU
Chi-restraints excluded: chain R residue  258 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   chunk 54 optimal weight:    0.7980
   chunk 103 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   chunk 12 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 95 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 43 optimal weight:    0.6980
   chunk 79 optimal weight:    7.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 259 ASN
A 338 ASN
A 354 ASN
B  11 GLN
B 225 GLN
B 264 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.117170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.107870 restraints weight = 12479.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 1.81
r_work: 0.3464 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3342 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.3838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8516  Z= 0.132
  Angle     :  0.545  10.789  11593  Z= 0.280
  Chirality :  0.042   0.157   1346
  Planarity :  0.004   0.059   1468
  Dihedral  :  3.996  18.934   1177
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 28.22 %
    Favored  : 67.60 %
  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:  1.35 (0.26), residues: 1081
  helix:  2.78 (0.26), residues: 370
  sheet:  0.06 (0.31), residues: 271
  loop : -0.14 (0.31), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 211 
 HIS   0.003   0.001   HIS A 329 
 PHE   0.035   0.002   PHE E  28 
 TYR   0.012   0.001   TYR E 190 
 ARG   0.010   0.001   ARG A 300 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03653 (  458)
  hydrogen bonds       : angle       4.35063 ( 1275)
  SS BOND              : bond        0.00081 (    1)
  SS BOND              : angle       0.55441 (    2)
  covalent geometry    : bond        0.00292 ( 8515)
  covalent geometry    : angle       0.54527 (11591)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 258
  time to evaluate  : 0.923 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.8869 (p0) cc_final: 0.8514 (p0)
REVERT: A  192 ASP cc_start: 0.7556 (m-30) cc_final: 0.7109 (m-30)
REVERT: A  205 ARG cc_start: 0.8677 (mtp-110) cc_final: 0.8380 (mtm-85)
REVERT: A  297 GLU cc_start: 0.7370 (mm-30) cc_final: 0.6813 (mm-30)
REVERT: A  314 ASP cc_start: 0.7979 (m-30) cc_final: 0.7609 (m-30)
REVERT: A  337 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7470 (mp0)
REVERT: B   10 ASP cc_start: 0.7066 (OUTLIER) cc_final: 0.4247 (t70)
REVERT: B   18 GLN cc_start: 0.8412 (tm-30) cc_final: 0.7996 (tm-30)
REVERT: B   19 LEU cc_start: 0.8957 (mm) cc_final: 0.8387 (mm)
REVERT: B   37 GLN cc_start: 0.8388 (mt0) cc_final: 0.8176 (mt0)
REVERT: B  191 ASP cc_start: 0.7976 (m-30) cc_final: 0.7640 (m-30)
REVERT: B  263 ASP cc_start: 0.8056 (t0) cc_final: 0.7556 (t0)
REVERT: B  291 LEU cc_start: 0.8515 (mp) cc_final: 0.8301 (mt)
REVERT: E   16 SER cc_start: 0.8485 (p) cc_final: 0.8193 (t)
REVERT: E   20 SER cc_start: 0.8239 (m) cc_final: 0.7908 (t)
REVERT: E   42 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8656 (mtpt)
REVERT: E   68 THR cc_start: 0.8869 (OUTLIER) cc_final: 0.8647 (p)
REVERT: E  139 VAL cc_start: 0.8465 (t) cc_final: 0.8209 (p)
REVERT: E  174 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8274 (tm)
REVERT: E  203 PHE cc_start: 0.8537 (m-80) cc_final: 0.7872 (m-80)
REVERT: E  206 SER cc_start: 0.8541 (t) cc_final: 0.8189 (p)
REVERT: E  213 THR cc_start: 0.8442 (OUTLIER) cc_final: 0.8058 (p)
REVERT: E  237 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8139 (mt)
REVERT: R   36 ILE cc_start: 0.8518 (mp) cc_final: 0.8276 (mp)
REVERT: R   52 LEU cc_start: 0.8579 (mt) cc_final: 0.8371 (mm)
REVERT: R  101 VAL cc_start: 0.8597 (t) cc_final: 0.8341 (p)
REVERT: R  103 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7187 (mpt)
REVERT: R  125 LEU cc_start: 0.8907 (mp) cc_final: 0.8693 (mt)
REVERT: R  152 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8315 (tp)
  outliers start: 36
  outliers final: 22
  residues processed: 277
  average time/residue: 1.0081
  time to fit residues: 298.8846
Evaluate side-chains
  283 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 253
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain B residue   10 ASP
Chi-restraints excluded: chain B residue   11 GLN
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain E residue   42 LYS
Chi-restraints excluded: chain E residue   68 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  174 LEU
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain E residue  213 THR
Chi-restraints excluded: chain E residue  237 LEU
Chi-restraints excluded: chain R residue  102 MET
Chi-restraints excluded: chain R residue  103 MET
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  152 LEU
Chi-restraints excluded: chain R residue  180 THR
Chi-restraints excluded: chain R residue  249 LEU
Chi-restraints excluded: chain R residue  258 ILE
Chi-restraints excluded: chain R residue  275 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9990
   chunk 56 optimal weight:    6.9990
   chunk 102 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 54 optimal weight:    0.6980
   chunk 71 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 338 ASN
A 354 ASN
B  11 GLN
B  93 ASN
B 225 GLN
B 264 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.115998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.106701 restraints weight = 12598.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3541 rms_B_bonded: 1.82
r_work: 0.3449 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3327 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.3874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8516  Z= 0.175
  Angle     :  0.557   6.425  11593  Z= 0.290
  Chirality :  0.043   0.175   1346
  Planarity :  0.004   0.060   1468
  Dihedral  :  4.088  19.309   1177
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 29.38 %
    Favored  : 66.09 %
  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:  1.27 (0.26), residues: 1081
  helix:  2.69 (0.26), residues: 371
  sheet:  0.01 (0.31), residues: 271
  loop : -0.17 (0.31), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 211 
 HIS   0.004   0.001   HIS A 329 
 PHE   0.037   0.002   PHE E  28 
 TYR   0.020   0.001   TYR L  17 
 ARG   0.009   0.001   ARG B  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03795 (  458)
  hydrogen bonds       : angle       4.38211 ( 1275)
  SS BOND              : bond        0.00093 (    1)
  SS BOND              : angle       0.77601 (    2)
  covalent geometry    : bond        0.00385 ( 8515)
  covalent geometry    : angle       0.55712 (11591)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 255
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ASN cc_start: 0.8900 (p0) cc_final: 0.8636 (p0)
REVERT: A  192 ASP cc_start: 0.7534 (m-30) cc_final: 0.7204 (m-30)
REVERT: A  205 ARG cc_start: 0.8691 (mtp-110) cc_final: 0.8361 (mtm-85)
REVERT: A  267 LYS cc_start: 0.8428 (ttmm) cc_final: 0.8155 (ptpt)
REVERT: A  297 GLU cc_start: 0.7413 (mm-30) cc_final: 0.6889 (mm-30)
REVERT: A  314 ASP cc_start: 0.8026 (m-30) cc_final: 0.7646 (m-30)
REVERT: A  337 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7476 (mp0)
REVERT: B   10 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.4085 (t70)
REVERT: B   18 GLN cc_start: 0.8425 (tm-30) cc_final: 0.7995 (tm-30)
REVERT: B   19 LEU cc_start: 0.8988 (mm) cc_final: 0.8398 (mm)
REVERT: B   37 GLN cc_start: 0.8380 (mt0) cc_final: 0.8163 (mt0)
REVERT: B   93 ASN cc_start: 0.8125 (m-40) cc_final: 0.7922 (m110)
REVERT: B  191 ASP cc_start: 0.7998 (m-30) cc_final: 0.7625 (m-30)
REVERT: B  263 ASP cc_start: 0.8075 (t0) cc_final: 0.7569 (t0)
REVERT: B  291 LEU cc_start: 0.8525 (mp) cc_final: 0.8309 (mt)
REVERT: E   16 SER cc_start: 0.8442 (p) cc_final: 0.8168 (t)
REVERT: E   20 SER cc_start: 0.8244 (m) cc_final: 0.7892 (p)
REVERT: E   42 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8644 (mtpt)
REVERT: E   68 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8673 (p)
REVERT: E  139 VAL cc_start: 0.8498 (t) cc_final: 0.8216 (p)
REVERT: E  174 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8306 (tm)
REVERT: E  213 THR cc_start: 0.8460 (OUTLIER) cc_final: 0.8164 (p)
REVERT: R   36 ILE cc_start: 0.8522 (mp) cc_final: 0.8282 (mp)
REVERT: R   52 LEU cc_start: 0.8571 (mt) cc_final: 0.8358 (mm)
REVERT: R  101 VAL cc_start: 0.8614 (t) cc_final: 0.8361 (p)
REVERT: R  125 LEU cc_start: 0.8874 (mp) cc_final: 0.8658 (mt)
REVERT: R  152 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8344 (tp)
REVERT: R  250 PHE cc_start: 0.8274 (t80) cc_final: 0.7971 (t80)
  outliers start: 39
  outliers final: 27
  residues processed: 276
  average time/residue: 0.9774
  time to fit residues: 289.4848
Evaluate side-chains
  282 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 249
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  188 LYS
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain B residue   10 ASP
Chi-restraints excluded: chain B residue   11 GLN
Chi-restraints excluded: chain B residue   49 GLN
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain E residue   42 LYS
Chi-restraints excluded: chain E residue   68 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  154 SER
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  174 LEU
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain E residue  213 THR
Chi-restraints excluded: chain G residue   45 LYS
Chi-restraints excluded: chain R residue  102 MET
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  152 LEU
Chi-restraints excluded: chain R residue  180 THR
Chi-restraints excluded: chain R residue  249 LEU
Chi-restraints excluded: chain R residue  258 ILE
Chi-restraints excluded: chain R residue  275 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 15 optimal weight:    0.6980
   chunk 94 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   chunk 21 optimal weight:    0.6980
   chunk 80 optimal weight:    0.7980
   chunk 83 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 101 optimal weight:    0.4980
   chunk 104 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 338 ASN
B  11 GLN
B 225 GLN
B 264 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.117238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.107938 restraints weight = 12587.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 1.82
r_work: 0.3463 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3342 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.3982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8516  Z= 0.134
  Angle     :  0.559  11.354  11593  Z= 0.287
  Chirality :  0.043   0.215   1346
  Planarity :  0.004   0.045   1468
  Dihedral  :  4.040  19.466   1177
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 30.43 %
    Favored  : 65.85 %
  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:  1.32 (0.26), residues: 1081
  helix:  2.75 (0.26), residues: 371
  sheet:  0.02 (0.31), residues: 271
  loop : -0.15 (0.31), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 211 
 HIS   0.003   0.001   HIS A 329 
 PHE   0.038   0.002   PHE E  28 
 TYR   0.019   0.001   TYR L  17 
 ARG   0.010   0.001   ARG B  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03702 (  458)
  hydrogen bonds       : angle       4.34596 ( 1275)
  SS BOND              : bond        0.00030 (    1)
  SS BOND              : angle       0.57527 (    2)
  covalent geometry    : bond        0.00298 ( 8515)
  covalent geometry    : angle       0.55864 (11591)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 258
  time to evaluate  : 0.850 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8523 (mptm) cc_final: 0.8293 (mptm)
REVERT: A   21 LYS cc_start: 0.8587 (ttmm) cc_final: 0.8358 (ttmm)
REVERT: A   43 ASN cc_start: 0.8891 (p0) cc_final: 0.8572 (p0)
REVERT: A  192 ASP cc_start: 0.7513 (m-30) cc_final: 0.6943 (m-30)
REVERT: A  205 ARG cc_start: 0.8694 (mtp-110) cc_final: 0.8380 (mtm-85)
REVERT: A  267 LYS cc_start: 0.8370 (ttmm) cc_final: 0.8124 (ptpt)
REVERT: A  297 GLU cc_start: 0.7369 (mm-30) cc_final: 0.6802 (mm-30)
REVERT: A  314 ASP cc_start: 0.7991 (m-30) cc_final: 0.7613 (m-30)
REVERT: A  337 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7460 (mp0)
REVERT: A  340 ARG cc_start: 0.8554 (tpp-160) cc_final: 0.7574 (tpt170)
REVERT: B   10 ASP cc_start: 0.7002 (OUTLIER) cc_final: 0.3957 (t70)
REVERT: B   18 GLN cc_start: 0.8416 (tm-30) cc_final: 0.7999 (tm-30)
REVERT: B   19 LEU cc_start: 0.8987 (mm) cc_final: 0.8415 (mm)
REVERT: B   37 GLN cc_start: 0.8395 (mt0) cc_final: 0.8179 (mt0)
REVERT: B  191 ASP cc_start: 0.7993 (m-30) cc_final: 0.7626 (m-30)
REVERT: B  263 ASP cc_start: 0.8044 (t0) cc_final: 0.7537 (t0)
REVERT: B  291 LEU cc_start: 0.8512 (mp) cc_final: 0.8297 (mt)
REVERT: E   16 SER cc_start: 0.8389 (p) cc_final: 0.8135 (t)
REVERT: E   20 SER cc_start: 0.8210 (m) cc_final: 0.7884 (t)
REVERT: E   42 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8651 (mtpt)
REVERT: E   68 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8649 (p)
REVERT: E  139 VAL cc_start: 0.8454 (t) cc_final: 0.8169 (p)
REVERT: E  141 THR cc_start: 0.8507 (OUTLIER) cc_final: 0.8238 (p)
REVERT: E  174 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8224 (tm)
REVERT: E  206 SER cc_start: 0.8562 (t) cc_final: 0.8240 (p)
REVERT: E  213 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8065 (p)
REVERT: R   36 ILE cc_start: 0.8524 (mp) cc_final: 0.8280 (mp)
REVERT: R  101 VAL cc_start: 0.8587 (t) cc_final: 0.8335 (p)
REVERT: R  152 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8318 (tp)
  outliers start: 32
  outliers final: 23
  residues processed: 276
  average time/residue: 0.9711
  time to fit residues: 287.5007
Evaluate side-chains
  280 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 250
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LYS
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain B residue   10 ASP
Chi-restraints excluded: chain B residue   11 GLN
Chi-restraints excluded: chain B residue   49 GLN
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain E residue   42 LYS
Chi-restraints excluded: chain E residue   68 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  154 SER
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  174 LEU
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain E residue  213 THR
Chi-restraints excluded: chain R residue  102 MET
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  152 LEU
Chi-restraints excluded: chain R residue  180 THR
Chi-restraints excluded: chain R residue  258 ILE
Chi-restraints excluded: chain R residue  275 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 82 optimal weight:    2.9990
   chunk 100 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 29 optimal weight:    2.9990
   chunk 56 optimal weight:    6.9990
   chunk 88 optimal weight:    0.9980
   chunk 14 optimal weight:    4.9990
   chunk 64 optimal weight:    5.9990
   chunk 50 optimal weight:    0.5980
   chunk 5 optimal weight:    6.9990
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 338 ASN
B  11 GLN
B 225 GLN
B 264 GLN
B 345 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.115078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.105705 restraints weight = 12701.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3520 rms_B_bonded: 1.83
r_work: 0.3426 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3304 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.3993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8516  Z= 0.197
  Angle     :  0.579   6.544  11593  Z= 0.302
  Chirality :  0.044   0.169   1346
  Planarity :  0.004   0.044   1468
  Dihedral  :  4.190  20.091   1177
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 30.43 %
    Favored  : 65.97 %
  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:  1.21 (0.26), residues: 1081
  helix:  2.58 (0.25), residues: 373
  sheet:  0.01 (0.31), residues: 277
  loop : -0.18 (0.31), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP L  13 
 HIS   0.003   0.001   HIS A 329 
 PHE   0.039   0.002   PHE E  28 
 TYR   0.021   0.002   TYR L  17 
 ARG   0.009   0.001   ARG B  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03884 (  458)
  hydrogen bonds       : angle       4.41573 ( 1275)
  SS BOND              : bond        0.00142 (    1)
  SS BOND              : angle       0.79741 (    2)
  covalent geometry    : bond        0.00433 ( 8515)
  covalent geometry    : angle       0.57852 (11591)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 257
  time to evaluate  : 0.969 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ASN cc_start: 0.8916 (p0) cc_final: 0.8498 (p0)
REVERT: A  192 ASP cc_start: 0.7528 (m-30) cc_final: 0.6895 (m-30)
REVERT: A  205 ARG cc_start: 0.8721 (mtp-110) cc_final: 0.8357 (mtm-85)
REVERT: A  267 LYS cc_start: 0.8416 (ttmm) cc_final: 0.8141 (ptpt)
REVERT: A  297 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6811 (mm-30)
REVERT: A  314 ASP cc_start: 0.8080 (m-30) cc_final: 0.7700 (m-30)
REVERT: A  336 THR cc_start: 0.8633 (p) cc_final: 0.8397 (p)
REVERT: A  337 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7510 (mp0)
REVERT: A  340 ARG cc_start: 0.8568 (tpp-160) cc_final: 0.7549 (tpt170)
REVERT: B   10 ASP cc_start: 0.6967 (OUTLIER) cc_final: 0.3874 (t70)
REVERT: B   18 GLN cc_start: 0.8465 (tm-30) cc_final: 0.8025 (tm-30)
REVERT: B   19 LEU cc_start: 0.8971 (mm) cc_final: 0.8383 (mm)
REVERT: B   37 GLN cc_start: 0.8396 (mt0) cc_final: 0.8169 (mt0)
REVERT: B  191 ASP cc_start: 0.7997 (m-30) cc_final: 0.7573 (m-30)
REVERT: B  263 ASP cc_start: 0.8087 (t0) cc_final: 0.7579 (t0)
REVERT: B  291 LEU cc_start: 0.8537 (mp) cc_final: 0.8318 (mt)
REVERT: B  345 ASN cc_start: 0.7847 (OUTLIER) cc_final: 0.7575 (t0)
REVERT: E   16 SER cc_start: 0.8438 (p) cc_final: 0.8167 (t)
REVERT: E   20 SER cc_start: 0.8270 (m) cc_final: 0.7943 (t)
REVERT: E   42 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8651 (mtpt)
REVERT: E   68 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8638 (p)
REVERT: E  139 VAL cc_start: 0.8530 (t) cc_final: 0.8258 (p)
REVERT: E  174 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8250 (tm)
REVERT: E  213 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8141 (p)
REVERT: R   36 ILE cc_start: 0.8541 (mp) cc_final: 0.8254 (mp)
REVERT: R  101 VAL cc_start: 0.8573 (t) cc_final: 0.8320 (p)
REVERT: R  152 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8358 (tp)
  outliers start: 31
  outliers final: 23
  residues processed: 277
  average time/residue: 0.9934
  time to fit residues: 294.8975
Evaluate side-chains
  278 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 248
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LYS
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain B residue   10 ASP
Chi-restraints excluded: chain B residue   11 GLN
Chi-restraints excluded: chain B residue   49 GLN
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain B residue  345 ASN
Chi-restraints excluded: chain E residue   42 LYS
Chi-restraints excluded: chain E residue   68 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  154 SER
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  174 LEU
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain E residue  213 THR
Chi-restraints excluded: chain R residue  102 MET
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  152 LEU
Chi-restraints excluded: chain R residue  180 THR
Chi-restraints excluded: chain R residue  196 LEU
Chi-restraints excluded: chain R residue  258 ILE
Chi-restraints excluded: chain R residue  275 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   chunk 56 optimal weight:    4.9990
   chunk 98 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 97 optimal weight:    0.8980
   chunk 75 optimal weight:    4.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 338 ASN
B  11 GLN
B  41 ASN
B 115 ASN
B 225 GLN
B 235 ASN
B 264 GLN
B 300 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.116872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.107678 restraints weight = 12640.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 1.81
r_work: 0.3461 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3339 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.4092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8516  Z= 0.157
  Angle     :  0.587  11.004  11593  Z= 0.301
  Chirality :  0.044   0.200   1346
  Planarity :  0.004   0.045   1468
  Dihedral  :  4.162  20.395   1177
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 31.01 %
    Favored  : 65.51 %
  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:  1.22 (0.26), residues: 1081
  helix:  2.60 (0.25), residues: 375
  sheet: -0.01 (0.31), residues: 277
  loop : -0.19 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.002   TRP L  13 
 HIS   0.004   0.001   HIS R 243 
 PHE   0.039   0.002   PHE E  28 
 TYR   0.021   0.001   TYR L  17 
 ARG   0.012   0.001   ARG B  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03824 (  458)
  hydrogen bonds       : angle       4.41550 ( 1275)
  SS BOND              : bond        0.00015 (    1)
  SS BOND              : angle       0.57394 (    2)
  covalent geometry    : bond        0.00348 ( 8515)
  covalent geometry    : angle       0.58716 (11591)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7443.72 seconds
wall clock time: 128 minutes 32.58 seconds (7712.58 seconds total)