Starting phenix.real_space_refine
on Fri Aug 22 21:50:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jgf_36232/08_2025/8jgf_36232_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jgf_36232/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jgf_36232/08_2025/8jgf_36232_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jgf_36232/08_2025/8jgf_36232_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jgf_36232/08_2025/8jgf_36232.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jgf_36232/08_2025/8jgf_36232.map"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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, 'HIS:plan': 2, 'ASN:plan1': 1, 'ASP: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: {'ARG:plan': 8, 'ASP:plan': 5, 'TYR:plan': 2, 'PHE:plan': 2}
          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: {'ARG:plan': 2, 'TYR:plan': 1, 'GLU:plan': 1}
          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: {'ARG:plan': 2, 'GLU:plan': 1}
          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: {'ARG:plan': 1, 'GLU: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, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 49
  Time building chain proxies: 2.32, per 1000 atoms: 0.28
  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: 0.74
  Conformation dependent library (CDL) restraints added in 505.4 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.34
  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: 1.47

  Time building geometry restraints manager: 0.98 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:             0.820
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.400
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  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:6.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.470
-------------------------------------------------------------------------------
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 : 9.08
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.21 (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
 ARG   0.004   0.001   ARG E 191 
 TYR   0.028   0.002   TYR R  64 
 PHE   0.024   0.002   PHE B 240 
 TRP   0.017   0.002   TRP R 158 
 HIS   0.007   0.001   HIS B 147 

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

*********************** 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  : 0.336 
Fit side-chains
REVERT: A   49 ILE cc_start: 0.7450 (mt) cc_final: 0.7077 (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: 0.5885
  time to fit residues: 180.8786
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  : 0.369 
-------------------------------------------------------------------------------
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 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0060
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9980
   chunk 106 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.7798

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.115655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.106236 restraints weight = 12879.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 1.86
r_work: 0.3449 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3326 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.2438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8516  Z= 0.152
  Angle     :  0.570   7.220  11593  Z= 0.303
  Chirality :  0.042   0.159   1346
  Planarity :  0.005   0.056   1468
  Dihedral  :  4.410  20.977   1179
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 23.46 %
    Favored  : 71.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.91 (0.26), residues: 1081
  helix:  1.99 (0.26), residues: 370
  sheet: -0.20 (0.30), residues: 274
  loop :  0.05 (0.32), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 256 
 TYR   0.028   0.002   TYR L  17 
 PHE   0.023   0.002   PHE E  28 
 TRP   0.016   0.002   TRP B 174 
 HIS   0.003   0.001   HIS R 133 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 8515)
  covalent geometry    : angle       0.57036 (11591)
  SS BOND              : bond        0.00077 (    1)
  SS BOND              : angle       0.81398 (    2)
  hydrogen bonds       : bond        0.04018 (  458)
  hydrogen bonds       : angle       4.80379 ( 1275)

*********************** 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
  298 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 256
  time to evaluate  : 0.339 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8575 (mptm) cc_final: 0.8364 (mptm)
REVERT: A   43 ASN cc_start: 0.8556 (p0) cc_final: 0.8352 (p0)
REVERT: A   53 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7675 (mtm)
REVERT: A  192 ASP cc_start: 0.7481 (m-30) cc_final: 0.7166 (m-30)
REVERT: A  233 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8436 (tm)
REVERT: A  314 ASP cc_start: 0.8010 (m-30) cc_final: 0.7553 (m-30)
REVERT: B   18 GLN cc_start: 0.8252 (tm-30) cc_final: 0.7795 (tm-30)
REVERT: B   19 LEU cc_start: 0.8801 (mm) cc_final: 0.8193 (mm)
REVERT: B   35 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7996 (tp)
REVERT: B   37 GLN cc_start: 0.8270 (mt0) cc_final: 0.8020 (mt0)
REVERT: B  142 ARG cc_start: 0.8292 (ttm110) cc_final: 0.7712 (ttp-170)
REVERT: B  177 GLU cc_start: 0.8232 (tp30) cc_final: 0.7941 (tp30)
REVERT: B  191 ASP cc_start: 0.7967 (m-30) cc_final: 0.7708 (m-30)
REVERT: B  258 PHE cc_start: 0.8817 (m-80) cc_final: 0.8553 (m-80)
REVERT: B  263 ASP cc_start: 0.8152 (t70) cc_final: 0.7556 (t0)
REVERT: E   66 ARG cc_start: 0.8565 (mtm-85) cc_final: 0.8344 (mtp180)
REVERT: E  118 VAL cc_start: 0.8624 (t) cc_final: 0.8360 (m)
REVERT: E  213 THR cc_start: 0.8544 (t) cc_final: 0.8216 (p)
REVERT: R   47 VAL cc_start: 0.8746 (t) cc_final: 0.8457 (p)
REVERT: R  101 VAL cc_start: 0.8596 (OUTLIER) cc_final: 0.8311 (p)
REVERT: R  152 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8488 (tp)
REVERT: R  198 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7727 (tp)
REVERT: R  203 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8177 (mm)
REVERT: R  218 ILE cc_start: 0.8612 (mt) cc_final: 0.8358 (tt)
  outliers start: 42
  outliers final: 13
  residues processed: 277
  average time/residue: 0.4935
  time to fit residues: 147.0601
Evaluate side-chains
  270 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 250
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
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  233 LEU
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  198 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 24 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   chunk 62 optimal weight:    0.4980
   chunk 107 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 105 optimal weight:    4.9990
   overall best weight:    1.2786

-------------------------------------------------------------------------------
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
E 171 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.113700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.104454 restraints weight = 12779.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 1.83
r_work: 0.3420 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3296 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.3038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8516  Z= 0.196
  Angle     :  0.558   8.904  11593  Z= 0.294
  Chirality :  0.043   0.166   1346
  Planarity :  0.005   0.064   1468
  Dihedral  :  4.294  20.132   1177
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 25.67 %
    Favored  : 69.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.19 (0.26), residues: 1081
  helix:  2.45 (0.26), residues: 365
  sheet: -0.21 (0.30), residues: 279
  loop :  0.15 (0.32), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  32 
 TYR   0.033   0.002   TYR L  17 
 PHE   0.028   0.002   PHE E  28 
 TRP   0.018   0.002   TRP A 211 
 HIS   0.011   0.001   HIS A 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 8515)
  covalent geometry    : angle       0.55823 (11591)
  SS BOND              : bond        0.00064 (    1)
  SS BOND              : angle       0.94079 (    2)
  hydrogen bonds       : bond        0.04036 (  458)
  hydrogen bonds       : angle       4.64213 ( 1275)

*********************** 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
  311 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 270
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.8886 (p0) cc_final: 0.8475 (p0)
REVERT: A  186 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6997 (tm-30)
REVERT: A  192 ASP cc_start: 0.7536 (m-30) cc_final: 0.6887 (m-30)
REVERT: A  198 MET cc_start: 0.8518 (ttm) cc_final: 0.8280 (ttp)
REVERT: A  205 ARG cc_start: 0.8734 (mtp-110) cc_final: 0.8406 (mtm-85)
REVERT: A  297 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6889 (mm-30)
REVERT: A  314 ASP cc_start: 0.8104 (m-30) cc_final: 0.7595 (m-30)
REVERT: A  337 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7573 (mp0)
REVERT: A  340 ARG cc_start: 0.8589 (tpp-160) cc_final: 0.7841 (tpt170)
REVERT: B   18 GLN cc_start: 0.8375 (tm-30) cc_final: 0.7917 (tm-30)
REVERT: B   19 LEU cc_start: 0.8894 (mm) cc_final: 0.8332 (mm)
REVERT: B   37 GLN cc_start: 0.8351 (mt0) cc_final: 0.8112 (mt0)
REVERT: B  191 ASP cc_start: 0.7942 (m-30) cc_final: 0.7529 (m-30)
REVERT: B  258 PHE cc_start: 0.8834 (m-80) cc_final: 0.8080 (m-80)
REVERT: B  263 ASP cc_start: 0.8093 (t70) cc_final: 0.7542 (t0)
REVERT: E   16 SER cc_start: 0.8560 (p) cc_final: 0.8265 (t)
REVERT: E   33 MET cc_start: 0.8328 (mmm) cc_final: 0.8120 (mmm)
REVERT: E   42 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8398 (mppt)
REVERT: E  118 VAL cc_start: 0.8631 (t) cc_final: 0.8393 (m)
REVERT: E  213 THR cc_start: 0.8511 (t) cc_final: 0.8225 (p)
REVERT: R   36 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8204 (mp)
REVERT: R   47 VAL cc_start: 0.8662 (t) cc_final: 0.8425 (p)
REVERT: R   84 LEU cc_start: 0.8329 (mt) cc_final: 0.8122 (mp)
REVERT: R  101 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8290 (p)
REVERT: R  117 SER cc_start: 0.8296 (t) cc_final: 0.8094 (t)
REVERT: R  152 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8474 (tp)
REVERT: R  203 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8153 (mm)
  outliers start: 41
  outliers final: 17
  residues processed: 285
  average time/residue: 0.4826
  time to fit residues: 148.0885
Evaluate side-chains
  272 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 249
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
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  186 GLU
Chi-restraints excluded: chain A residue  273 SER
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   36 ILE
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  196 LEU
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 48 optimal weight:    0.9990
   chunk 23 optimal weight:    0.3980
   chunk 2 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 64 optimal weight:    5.9990
   chunk 73 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 86 optimal weight:    0.5980
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.3658 r_free = 0.3658 target = 0.114927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.105542 restraints weight = 13013.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 1.87
r_work: 0.3432 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3308 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.3404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8516  Z= 0.132
  Angle     :  0.528   8.270  11593  Z= 0.277
  Chirality :  0.041   0.164   1346
  Planarity :  0.004   0.061   1468
  Dihedral  :  4.076  18.926   1177
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  5.23 %
    Allowed  : 27.41 %
    Favored  : 67.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.30 (0.26), residues: 1081
  helix:  2.67 (0.26), residues: 366
  sheet: -0.04 (0.30), residues: 271
  loop : -0.02 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  54 
 TYR   0.032   0.001   TYR L  17 
 PHE   0.029   0.002   PHE E  28 
 TRP   0.015   0.001   TRP A 211 
 HIS   0.006   0.001   HIS A 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 8515)
  covalent geometry    : angle       0.52826 (11591)
  SS BOND              : bond        0.00287 (    1)
  SS BOND              : angle       0.83515 (    2)
  hydrogen bonds       : bond        0.03651 (  458)
  hydrogen bonds       : angle       4.48285 ( 1275)

*********************** 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
  308 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 263
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.8909 (p0) cc_final: 0.8506 (p0)
REVERT: A  186 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6920 (tm-30)
REVERT: A  192 ASP cc_start: 0.7495 (m-30) cc_final: 0.7049 (m-30)
REVERT: A  205 ARG cc_start: 0.8714 (mtp-110) cc_final: 0.8362 (mtm-85)
REVERT: A  297 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6711 (mm-30)
REVERT: A  298 ASP cc_start: 0.7860 (t0) cc_final: 0.7618 (t0)
REVERT: A  314 ASP cc_start: 0.8076 (m-30) cc_final: 0.7674 (m-30)
REVERT: A  329 HIS cc_start: 0.8492 (m-70) cc_final: 0.8278 (m170)
REVERT: A  337 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7517 (mp0)
REVERT: A  340 ARG cc_start: 0.8586 (tpp-160) cc_final: 0.8106 (tpp-160)
REVERT: B   11 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7954 (pp30)
REVERT: B   18 GLN cc_start: 0.8411 (tm-30) cc_final: 0.7937 (tm-30)
REVERT: B   19 LEU cc_start: 0.8892 (mm) cc_final: 0.8352 (mm)
REVERT: B   37 GLN cc_start: 0.8353 (mt0) cc_final: 0.8121 (mt0)
REVERT: B  191 ASP cc_start: 0.7952 (m-30) cc_final: 0.7555 (m-30)
REVERT: B  258 PHE cc_start: 0.8836 (m-80) cc_final: 0.8146 (m-80)
REVERT: B  263 ASP cc_start: 0.8104 (t70) cc_final: 0.7548 (t0)
REVERT: E   16 SER cc_start: 0.8512 (p) cc_final: 0.8216 (t)
REVERT: E   33 MET cc_start: 0.8297 (mmm) cc_final: 0.8073 (mmm)
REVERT: E   42 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8466 (mppt)
REVERT: E  203 PHE cc_start: 0.8533 (m-80) cc_final: 0.7852 (m-80)
REVERT: E  213 THR cc_start: 0.8519 (t) cc_final: 0.8232 (p)
REVERT: E  237 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8044 (mt)
REVERT: L   15 MET cc_start: 0.8374 (ttm) cc_final: 0.8172 (mtm)
REVERT: R   36 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8166 (mp)
REVERT: R   84 LEU cc_start: 0.8303 (mt) cc_final: 0.8100 (mp)
REVERT: R  101 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8269 (p)
REVERT: R  117 SER cc_start: 0.8332 (t) cc_final: 0.8098 (t)
REVERT: R  152 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8415 (tp)
REVERT: R  203 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8198 (mm)
  outliers start: 45
  outliers final: 19
  residues processed: 279
  average time/residue: 0.5003
  time to fit residues: 150.2546
Evaluate side-chains
  279 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 252
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
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  243 ILE
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   49 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   36 ILE
Chi-restraints excluded: chain R residue  101 VAL
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  258 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 107 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 82 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3664 r_free = 0.3664 target = 0.115208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.105754 restraints weight = 12740.808|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 1.85
r_work: 0.3436 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3313 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.3554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8516  Z= 0.143
  Angle     :  0.526   5.896  11593  Z= 0.276
  Chirality :  0.041   0.160   1346
  Planarity :  0.004   0.060   1468
  Dihedral  :  4.004  18.763   1177
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 28.11 %
    Favored  : 67.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.29 (0.26), residues: 1081
  helix:  2.67 (0.26), residues: 369
  sheet:  0.05 (0.31), residues: 271
  loop : -0.13 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 300 
 TYR   0.032   0.001   TYR L  17 
 PHE   0.031   0.002   PHE E  28 
 TRP   0.014   0.001   TRP A 211 
 HIS   0.004   0.001   HIS A 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 8515)
  covalent geometry    : angle       0.52631 (11591)
  SS BOND              : bond        0.00161 (    1)
  SS BOND              : angle       0.85650 (    2)
  hydrogen bonds       : bond        0.03691 (  458)
  hydrogen bonds       : angle       4.40653 ( 1275)

*********************** 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
  301 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 259
  time to evaluate  : 0.407 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.8914 (p0) cc_final: 0.8644 (p0)
REVERT: A  186 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6900 (tm-30)
REVERT: A  192 ASP cc_start: 0.7549 (m-30) cc_final: 0.7036 (m-30)
REVERT: A  205 ARG cc_start: 0.8703 (mtp-110) cc_final: 0.8370 (mtm-85)
REVERT: A  267 LYS cc_start: 0.8579 (ttmm) cc_final: 0.8209 (ptpt)
REVERT: A  297 GLU cc_start: 0.7342 (mm-30) cc_final: 0.6787 (mm-30)
REVERT: A  298 ASP cc_start: 0.7842 (t0) cc_final: 0.7637 (t0)
REVERT: A  314 ASP cc_start: 0.8073 (m-30) cc_final: 0.7689 (m-30)
REVERT: A  337 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7502 (mp0)
REVERT: A  340 ARG cc_start: 0.8583 (tpp-160) cc_final: 0.8117 (tpp-160)
REVERT: B   18 GLN cc_start: 0.8433 (tm-30) cc_final: 0.7961 (tm-30)
REVERT: B   19 LEU cc_start: 0.8932 (mm) cc_final: 0.8375 (mm)
REVERT: B   37 GLN cc_start: 0.8343 (mt0) cc_final: 0.8109 (mt0)
REVERT: B  191 ASP cc_start: 0.7981 (m-30) cc_final: 0.7616 (m-30)
REVERT: B  258 PHE cc_start: 0.8827 (m-80) cc_final: 0.8162 (m-80)
REVERT: B  263 ASP cc_start: 0.8100 (t70) cc_final: 0.7531 (t0)
REVERT: E   16 SER cc_start: 0.8477 (p) cc_final: 0.8189 (t)
REVERT: E   33 MET cc_start: 0.8348 (mmm) cc_final: 0.8140 (mmm)
REVERT: E   42 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8643 (mtpt)
REVERT: E  139 VAL cc_start: 0.8521 (t) cc_final: 0.8285 (p)
REVERT: E  203 PHE cc_start: 0.8547 (m-80) cc_final: 0.7845 (m-80)
REVERT: E  206 SER cc_start: 0.8568 (t) cc_final: 0.8211 (p)
REVERT: E  213 THR cc_start: 0.8460 (OUTLIER) cc_final: 0.8099 (p)
REVERT: E  237 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8099 (mt)
REVERT: R   36 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8174 (mp)
REVERT: R   52 LEU cc_start: 0.8719 (mt) cc_final: 0.8494 (mm)
REVERT: R   84 LEU cc_start: 0.8341 (mt) cc_final: 0.8131 (mp)
REVERT: R  101 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8275 (p)
REVERT: R  152 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8410 (tp)
REVERT: R  255 LEU cc_start: 0.8511 (mm) cc_final: 0.8302 (mm)
  outliers start: 42
  outliers final: 22
  residues processed: 273
  average time/residue: 0.5033
  time to fit residues: 147.5873
Evaluate side-chains
  279 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 250
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
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  243 ILE
Chi-restraints excluded: chain A residue  253 SER
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  222 MET
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  144 THR
Chi-restraints excluded: chain E residue  154 SER
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   36 ILE
Chi-restraints excluded: chain R residue  101 VAL
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 98 optimal weight:    0.8980
   chunk 91 optimal weight:    0.0060
   chunk 103 optimal weight:    0.0020
   chunk 8 optimal weight:    0.7980
   chunk 105 optimal weight:    0.8980
   chunk 99 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   overall best weight:    0.4804

-------------------------------------------------------------------------------
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  93 ASN
B 225 GLN
B 264 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 = 0.3695 r_free = 0.3695 target = 0.117610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.108301 restraints weight = 12449.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 1.81
r_work: 0.3466 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3344 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.3773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8516  Z= 0.113
  Angle     :  0.524   6.231  11593  Z= 0.273
  Chirality :  0.041   0.159   1346
  Planarity :  0.004   0.059   1468
  Dihedral  :  3.936  18.646   1177
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 28.11 %
    Favored  : 66.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.40 (0.26), residues: 1081
  helix:  2.81 (0.26), residues: 369
  sheet:  0.13 (0.31), residues: 271
  loop : -0.12 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 247 
 TYR   0.027   0.001   TYR L  17 
 PHE   0.033   0.002   PHE E  28 
 TRP   0.013   0.001   TRP A 211 
 HIS   0.003   0.001   HIS A 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 8515)
  covalent geometry    : angle       0.52440 (11591)
  SS BOND              : bond        0.00200 (    1)
  SS BOND              : angle       0.59646 (    2)
  hydrogen bonds       : bond        0.03531 (  458)
  hydrogen bonds       : angle       4.31447 ( 1275)

*********************** 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
  314 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 266
  time to evaluate  : 0.353 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.8593 (ttmm) cc_final: 0.8375 (ttmm)
REVERT: A   43 ASN cc_start: 0.8878 (p0) cc_final: 0.8581 (p0)
REVERT: A  186 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6836 (tm-30)
REVERT: A  192 ASP cc_start: 0.7546 (m-30) cc_final: 0.7051 (m-30)
REVERT: A  205 ARG cc_start: 0.8668 (mtp-110) cc_final: 0.8366 (mtm-85)
REVERT: A  267 LYS cc_start: 0.8484 (ttmm) cc_final: 0.8142 (ptpt)
REVERT: A  297 GLU cc_start: 0.7359 (mm-30) cc_final: 0.6816 (mm-30)
REVERT: A  314 ASP cc_start: 0.7975 (m-30) cc_final: 0.7602 (m-30)
REVERT: A  337 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7414 (mp0)
REVERT: A  340 ARG cc_start: 0.8540 (tpp-160) cc_final: 0.8120 (tpp-160)
REVERT: B   10 ASP cc_start: 0.7015 (OUTLIER) cc_final: 0.4240 (t70)
REVERT: B   18 GLN cc_start: 0.8409 (tm-30) cc_final: 0.7973 (tm-30)
REVERT: B   19 LEU cc_start: 0.8952 (mm) cc_final: 0.8379 (mm)
REVERT: B   37 GLN cc_start: 0.8352 (mt0) cc_final: 0.8144 (mt0)
REVERT: B   93 ASN cc_start: 0.8154 (m-40) cc_final: 0.7931 (m110)
REVERT: B  191 ASP cc_start: 0.7966 (m-30) cc_final: 0.7620 (m-30)
REVERT: B  263 ASP cc_start: 0.8051 (t70) cc_final: 0.7552 (t0)
REVERT: B  291 LEU cc_start: 0.8499 (mp) cc_final: 0.8287 (mt)
REVERT: E   16 SER cc_start: 0.8398 (p) cc_final: 0.8125 (t)
REVERT: E   42 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8649 (mtpt)
REVERT: E   68 THR cc_start: 0.8890 (OUTLIER) cc_final: 0.8639 (p)
REVERT: E  139 VAL cc_start: 0.8498 (t) cc_final: 0.8215 (p)
REVERT: E  203 PHE cc_start: 0.8536 (m-80) cc_final: 0.7823 (m-80)
REVERT: E  206 SER cc_start: 0.8581 (t) cc_final: 0.8230 (p)
REVERT: E  213 THR cc_start: 0.8440 (OUTLIER) cc_final: 0.8078 (p)
REVERT: E  237 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8103 (mt)
REVERT: R   36 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8114 (mp)
REVERT: R   52 LEU cc_start: 0.8583 (mt) cc_final: 0.8373 (mm)
REVERT: R   84 LEU cc_start: 0.8281 (mt) cc_final: 0.8066 (mp)
REVERT: R  101 VAL cc_start: 0.8567 (t) cc_final: 0.8313 (p)
REVERT: R  125 LEU cc_start: 0.8906 (mp) cc_final: 0.8698 (mt)
REVERT: R  152 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8329 (tp)
REVERT: R  250 PHE cc_start: 0.8498 (t80) cc_final: 0.8119 (t80)
REVERT: R  255 LEU cc_start: 0.8525 (mm) cc_final: 0.8268 (mm)
  outliers start: 48
  outliers final: 29
  residues processed: 288
  average time/residue: 0.5414
  time to fit residues: 166.7979
Evaluate side-chains
  299 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 262
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
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  242 SER
Chi-restraints excluded: chain A residue  243 ILE
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  165 SER
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  222 MET
Chi-restraints excluded: chain B residue  267 MET
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  154 SER
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   36 ILE
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  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 41 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 82 optimal weight:    4.9990
   chunk 91 optimal weight:    0.0870
   chunk 44 optimal weight:    0.9990
   chunk 75 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0670
   chunk 99 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 13 optimal weight:    0.4980
   overall best weight:    0.4698

-------------------------------------------------------------------------------
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 225 GLN
B 264 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.117843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.108525 restraints weight = 12601.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.3562 rms_B_bonded: 1.83
r_work: 0.3470 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3349 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.3885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8516  Z= 0.112
  Angle     :  0.525   6.127  11593  Z= 0.273
  Chirality :  0.042   0.159   1346
  Planarity :  0.004   0.058   1468
  Dihedral  :  3.876  18.665   1177
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 28.80 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.46 (0.26), residues: 1081
  helix:  2.91 (0.26), residues: 369
  sheet:  0.15 (0.31), residues: 271
  loop : -0.13 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 300 
 TYR   0.018   0.001   TYR L  17 
 PHE   0.035   0.002   PHE E  28 
 TRP   0.013   0.001   TRP B 174 
 HIS   0.003   0.001   HIS B 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 8515)
  covalent geometry    : angle       0.52515 (11591)
  SS BOND              : bond        0.00106 (    1)
  SS BOND              : angle       0.43312 (    2)
  hydrogen bonds       : bond        0.03487 (  458)
  hydrogen bonds       : angle       4.25964 ( 1275)

*********************** 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
  309 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 270
  time to evaluate  : 0.383 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.8853 (p0) cc_final: 0.8612 (p0)
REVERT: A  192 ASP cc_start: 0.7546 (m-30) cc_final: 0.7053 (m-30)
REVERT: A  205 ARG cc_start: 0.8649 (mtp-110) cc_final: 0.8235 (mtm-85)
REVERT: A  267 LYS cc_start: 0.8418 (ttmm) cc_final: 0.8084 (ptpt)
REVERT: A  297 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6731 (mm-30)
REVERT: A  314 ASP cc_start: 0.7976 (m-30) cc_final: 0.7624 (m-30)
REVERT: A  337 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7464 (mp0)
REVERT: A  340 ARG cc_start: 0.8545 (tpp-160) cc_final: 0.8119 (tpp-160)
REVERT: B   10 ASP cc_start: 0.7031 (OUTLIER) cc_final: 0.4211 (t70)
REVERT: B   18 GLN cc_start: 0.8414 (tm-30) cc_final: 0.7997 (tm-30)
REVERT: B   19 LEU cc_start: 0.8960 (mm) cc_final: 0.8395 (mm)
REVERT: B   37 GLN cc_start: 0.8354 (mt0) cc_final: 0.8146 (mt0)
REVERT: B  191 ASP cc_start: 0.7946 (m-30) cc_final: 0.7462 (m-30)
REVERT: B  263 ASP cc_start: 0.8053 (t0) cc_final: 0.7559 (t0)
REVERT: B  291 LEU cc_start: 0.8491 (mp) cc_final: 0.8234 (mt)
REVERT: E   16 SER cc_start: 0.8363 (p) cc_final: 0.8110 (t)
REVERT: E   42 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8632 (mtpt)
REVERT: E   68 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8630 (p)
REVERT: E  139 VAL cc_start: 0.8473 (t) cc_final: 0.8184 (p)
REVERT: E  174 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8238 (tm)
REVERT: E  203 PHE cc_start: 0.8534 (m-80) cc_final: 0.7783 (m-80)
REVERT: E  206 SER cc_start: 0.8572 (t) cc_final: 0.8224 (p)
REVERT: E  213 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8052 (p)
REVERT: E  237 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8201 (mt)
REVERT: R   36 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8096 (mp)
REVERT: R   84 LEU cc_start: 0.8256 (mt) cc_final: 0.8047 (mp)
REVERT: R  101 VAL cc_start: 0.8565 (t) cc_final: 0.8311 (p)
REVERT: R  125 LEU cc_start: 0.8901 (mp) cc_final: 0.8693 (mt)
REVERT: R  152 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8310 (tp)
REVERT: R  250 PHE cc_start: 0.8404 (t80) cc_final: 0.8068 (t80)
REVERT: R  255 LEU cc_start: 0.8510 (mm) cc_final: 0.8270 (mm)
  outliers start: 39
  outliers final: 28
  residues processed: 289
  average time/residue: 0.5204
  time to fit residues: 161.1086
Evaluate side-chains
  297 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 261
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
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  233 LEU
Chi-restraints excluded: chain A residue  242 SER
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  165 SER
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  222 MET
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 E residue  237 LEU
Chi-restraints excluded: chain R residue   36 ILE
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  200 ILE
Chi-restraints excluded: chain R residue  249 LEU
Chi-restraints excluded: chain R residue  258 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 64 optimal weight:    5.9990
   chunk 93 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 104 optimal weight:    0.7980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 225 GLN
B 264 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.116935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.107639 restraints weight = 12554.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 1.82
r_work: 0.3460 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3338 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.3944

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= 0.152
  Angle     :  0.562  11.261  11593  Z= 0.288
  Chirality :  0.043   0.356   1346
  Planarity :  0.004   0.059   1468
  Dihedral  :  3.969  19.316   1177
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 29.15 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.43 (0.26), residues: 1081
  helix:  2.86 (0.25), residues: 369
  sheet:  0.14 (0.31), residues: 271
  loop : -0.13 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  24 
 TYR   0.015   0.001   TYR L  17 
 PHE   0.037   0.002   PHE E  28 
 TRP   0.013   0.001   TRP A 211 
 HIS   0.005   0.001   HIS B 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 8515)
  covalent geometry    : angle       0.56226 (11591)
  SS BOND              : bond        0.00021 (    1)
  SS BOND              : angle       0.67006 (    2)
  hydrogen bonds       : bond        0.03635 (  458)
  hydrogen bonds       : angle       4.31780 ( 1275)

*********************** 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
  299 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 257
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.8897 (p0) cc_final: 0.8646 (p0)
REVERT: A  192 ASP cc_start: 0.7546 (m-30) cc_final: 0.7113 (m-30)
REVERT: A  205 ARG cc_start: 0.8664 (mtp-110) cc_final: 0.8349 (mtm-85)
REVERT: A  267 LYS cc_start: 0.8441 (ttmm) cc_final: 0.8178 (ptmt)
REVERT: A  297 GLU cc_start: 0.7317 (mm-30) cc_final: 0.6771 (mm-30)
REVERT: A  314 ASP cc_start: 0.7995 (m-30) cc_final: 0.7622 (m-30)
REVERT: A  337 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7474 (mp0)
REVERT: B   10 ASP cc_start: 0.6991 (OUTLIER) cc_final: 0.4020 (t70)
REVERT: B   18 GLN cc_start: 0.8413 (tm-30) cc_final: 0.7982 (tm-30)
REVERT: B   19 LEU cc_start: 0.8981 (mm) cc_final: 0.8406 (mm)
REVERT: B   37 GLN cc_start: 0.8366 (mt0) cc_final: 0.8149 (mt0)
REVERT: B  191 ASP cc_start: 0.7935 (m-30) cc_final: 0.7497 (m-30)
REVERT: B  263 ASP cc_start: 0.8053 (t0) cc_final: 0.7553 (t0)
REVERT: B  291 LEU cc_start: 0.8494 (mp) cc_final: 0.8271 (mt)
REVERT: E   16 SER cc_start: 0.8382 (p) cc_final: 0.8135 (t)
REVERT: E   42 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8629 (mtpt)
REVERT: E   68 THR cc_start: 0.8898 (OUTLIER) cc_final: 0.8649 (p)
REVERT: E  139 VAL cc_start: 0.8488 (t) cc_final: 0.8207 (p)
REVERT: E  174 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8262 (tm)
REVERT: E  206 SER cc_start: 0.8562 (t) cc_final: 0.8245 (p)
REVERT: E  213 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8072 (p)
REVERT: R   36 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8121 (mp)
REVERT: R   84 LEU cc_start: 0.8309 (mt) cc_final: 0.8101 (mp)
REVERT: R  101 VAL cc_start: 0.8582 (t) cc_final: 0.8333 (p)
REVERT: R  152 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8324 (tp)
REVERT: R  250 PHE cc_start: 0.8386 (t80) cc_final: 0.8067 (t80)
REVERT: R  255 LEU cc_start: 0.8512 (mm) cc_final: 0.8276 (mm)
  outliers start: 42
  outliers final: 29
  residues processed: 277
  average time/residue: 0.5384
  time to fit residues: 159.5043
Evaluate side-chains
  285 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 249
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
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  233 LEU
Chi-restraints excluded: chain A residue  242 SER
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  165 SER
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  222 MET
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  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   36 ILE
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  200 ILE
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:    0.9980
   chunk 75 optimal weight:    6.9990
   chunk 55 optimal weight:    3.9990
   chunk 64 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 56 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   chunk 79 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.3683 r_free = 0.3683 target = 0.116680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.107372 restraints weight = 12530.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 1.81
r_work: 0.3453 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3331 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.3963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8516  Z= 0.162
  Angle     :  0.565  10.218  11593  Z= 0.291
  Chirality :  0.044   0.345   1346
  Planarity :  0.004   0.047   1468
  Dihedral  :  4.018  20.063   1177
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 30.20 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.40 (0.26), residues: 1081
  helix:  2.84 (0.25), residues: 370
  sheet:  0.12 (0.31), residues: 271
  loop : -0.15 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 300 
 TYR   0.013   0.001   TYR E 190 
 PHE   0.037   0.002   PHE E  28 
 TRP   0.013   0.001   TRP A 211 
 HIS   0.005   0.001   HIS B 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 8515)
  covalent geometry    : angle       0.56481 (11591)
  SS BOND              : bond        0.00047 (    1)
  SS BOND              : angle       0.56369 (    2)
  hydrogen bonds       : bond        0.03683 (  458)
  hydrogen bonds       : angle       4.35125 ( 1275)

*********************** 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
  289 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 252
  time to evaluate  : 0.405 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.8580 (ttmm) cc_final: 0.8359 (ttmm)
REVERT: A   43 ASN cc_start: 0.8915 (p0) cc_final: 0.8657 (p0)
REVERT: A  192 ASP cc_start: 0.7508 (m-30) cc_final: 0.7122 (m-30)
REVERT: A  205 ARG cc_start: 0.8689 (mtp-110) cc_final: 0.8328 (mtm-85)
REVERT: A  267 LYS cc_start: 0.8426 (ttmm) cc_final: 0.8155 (ptmt)
REVERT: A  297 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6778 (mm-30)
REVERT: A  314 ASP cc_start: 0.8037 (m-30) cc_final: 0.7658 (m-30)
REVERT: A  337 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7467 (mp0)
REVERT: B   10 ASP cc_start: 0.7047 (OUTLIER) cc_final: 0.3951 (t70)
REVERT: B   18 GLN cc_start: 0.8421 (tm-30) cc_final: 0.7987 (tm-30)
REVERT: B   19 LEU cc_start: 0.8991 (mm) cc_final: 0.8413 (mm)
REVERT: B   37 GLN cc_start: 0.8370 (mt0) cc_final: 0.8154 (mt0)
REVERT: B  191 ASP cc_start: 0.7953 (m-30) cc_final: 0.7445 (m-30)
REVERT: B  263 ASP cc_start: 0.8032 (t0) cc_final: 0.7539 (t0)
REVERT: B  291 LEU cc_start: 0.8542 (mp) cc_final: 0.8320 (mt)
REVERT: E   16 SER cc_start: 0.8408 (p) cc_final: 0.8145 (t)
REVERT: E   42 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8638 (mtpt)
REVERT: E   68 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8663 (p)
REVERT: E  139 VAL cc_start: 0.8488 (t) cc_final: 0.8205 (p)
REVERT: E  174 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8251 (tm)
REVERT: E  213 THR cc_start: 0.8459 (OUTLIER) cc_final: 0.8170 (p)
REVERT: R   36 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8121 (mp)
REVERT: R   84 LEU cc_start: 0.8331 (mt) cc_final: 0.8125 (mp)
REVERT: R  101 VAL cc_start: 0.8579 (t) cc_final: 0.8334 (p)
REVERT: R  152 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8327 (tp)
REVERT: R  250 PHE cc_start: 0.8353 (t80) cc_final: 0.8046 (t80)
REVERT: R  255 LEU cc_start: 0.8537 (mm) cc_final: 0.8313 (mm)
  outliers start: 37
  outliers final: 25
  residues processed: 273
  average time/residue: 0.5438
  time to fit residues: 158.8064
Evaluate side-chains
  282 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 250
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
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  222 MET
Chi-restraints excluded: chain B residue  267 MET
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  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   36 ILE
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  218 ILE
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 76 optimal weight:    0.0570
   chunk 63 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 60 optimal weight:    0.0970
   chunk 106 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9990
   chunk 74 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.6096

-------------------------------------------------------------------------------
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
** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.117612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.108384 restraints weight = 12559.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 1.82
r_work: 0.3472 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3348 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.4065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8516  Z= 0.128
  Angle     :  0.565   9.825  11593  Z= 0.290
  Chirality :  0.043   0.330   1346
  Planarity :  0.004   0.043   1468
  Dihedral  :  3.982  20.285   1177
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 30.43 %
    Favored  : 65.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.46 (0.26), residues: 1081
  helix:  2.88 (0.25), residues: 370
  sheet:  0.18 (0.32), residues: 271
  loop : -0.13 (0.31), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  24 
 TYR   0.012   0.001   TYR E 190 
 PHE   0.039   0.002   PHE E  28 
 TRP   0.013   0.001   TRP A 211 
 HIS   0.004   0.001   HIS B 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 8515)
  covalent geometry    : angle       0.56524 (11591)
  SS BOND              : bond        0.00042 (    1)
  SS BOND              : angle       0.35667 (    2)
  hydrogen bonds       : bond        0.03548 (  458)
  hydrogen bonds       : angle       4.31963 ( 1275)

********************** 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
  298 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 260
  time to evaluate  : 0.373 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8522 (mptm) cc_final: 0.8266 (mptm)
REVERT: A   21 LYS cc_start: 0.8566 (ttmm) cc_final: 0.8334 (ttmm)
REVERT: A   43 ASN cc_start: 0.8895 (p0) cc_final: 0.8636 (p0)
REVERT: A  192 ASP cc_start: 0.7502 (m-30) cc_final: 0.6781 (m-30)
REVERT: A  267 LYS cc_start: 0.8396 (ttmm) cc_final: 0.8142 (ptmt)
REVERT: A  297 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6737 (mm-30)
REVERT: A  314 ASP cc_start: 0.8006 (m-30) cc_final: 0.7638 (m-30)
REVERT: A  337 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7455 (mp0)
REVERT: A  340 ARG cc_start: 0.8537 (tpp-160) cc_final: 0.7677 (tpt170)
REVERT: B   10 ASP cc_start: 0.6730 (OUTLIER) cc_final: 0.3633 (t70)
REVERT: B   18 GLN cc_start: 0.8411 (tm-30) cc_final: 0.7990 (tm-30)
REVERT: B   19 LEU cc_start: 0.8991 (mm) cc_final: 0.8419 (mm)
REVERT: B   37 GLN cc_start: 0.8369 (mt0) cc_final: 0.8164 (mt0)
REVERT: B  191 ASP cc_start: 0.7946 (m-30) cc_final: 0.7554 (m-30)
REVERT: B  263 ASP cc_start: 0.7993 (t0) cc_final: 0.7474 (t0)
REVERT: B  291 LEU cc_start: 0.8493 (mp) cc_final: 0.8281 (mt)
REVERT: E   16 SER cc_start: 0.8359 (p) cc_final: 0.8119 (t)
REVERT: E   20 SER cc_start: 0.8178 (m) cc_final: 0.7854 (t)
REVERT: E   42 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8654 (mtpt)
REVERT: E   68 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8647 (p)
REVERT: E  139 VAL cc_start: 0.8448 (t) cc_final: 0.8163 (p)
REVERT: E  174 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8181 (tm)
REVERT: E  206 SER cc_start: 0.8573 (t) cc_final: 0.8246 (p)
REVERT: E  213 THR cc_start: 0.8450 (OUTLIER) cc_final: 0.8060 (p)
REVERT: R   36 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8101 (mp)
REVERT: R   84 LEU cc_start: 0.8310 (mt) cc_final: 0.8096 (mp)
REVERT: R  101 VAL cc_start: 0.8554 (t) cc_final: 0.8314 (p)
REVERT: R  152 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8301 (tp)
REVERT: R  250 PHE cc_start: 0.8221 (t80) cc_final: 0.7966 (t80)
REVERT: R  255 LEU cc_start: 0.8526 (mm) cc_final: 0.8314 (mm)
  outliers start: 38
  outliers final: 24
  residues processed: 279
  average time/residue: 0.5394
  time to fit residues: 161.1802
Evaluate side-chains
  286 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 255
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
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  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  154 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   36 ILE
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  218 ILE
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 71 optimal weight:    3.9990
   chunk 89 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 84 optimal weight:    0.0000
   chunk 58 optimal weight:    0.9980
   chunk 101 optimal weight:    0.0060
   chunk 48 optimal weight:    3.9990
   chunk 28 optimal weight:    6.9990
   chunk 97 optimal weight:    1.9990
   overall best weight:    0.8002

-------------------------------------------------------------------------------
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 = 0.3693 r_free = 0.3693 target = 0.117384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.108096 restraints weight = 12501.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 1.81
r_work: 0.3465 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3343 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.4102

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= 0.145
  Angle     :  0.570   9.218  11593  Z= 0.292
  Chirality :  0.043   0.321   1346
  Planarity :  0.004   0.044   1468
  Dihedral  :  4.000  19.817   1177
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 30.66 %
    Favored  : 65.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.26), residues: 1081
  helix:  2.85 (0.25), residues: 370
  sheet:  0.17 (0.31), residues: 282
  loop : -0.12 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG R  79 
 TYR   0.013   0.001   TYR E 190 
 PHE   0.039   0.002   PHE E  28 
 TRP   0.013   0.001   TRP A 211 
 HIS   0.003   0.001   HIS B 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 8515)
  covalent geometry    : angle       0.56959 (11591)
  SS BOND              : bond        0.00020 (    1)
  SS BOND              : angle       0.47189 (    2)
  hydrogen bonds       : bond        0.03599 (  458)
  hydrogen bonds       : angle       4.33567 ( 1275)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4038.86 seconds
wall clock time: 69 minutes 41.34 seconds (4181.34 seconds total)