Starting phenix.real_space_refine
on Thu Mar  5 00:13:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7w56_32315/03_2026/7w56_32315.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7w56_32315/03_2026/7w56_32315.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7w56_32315/03_2026/7w56_32315.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7w56_32315/03_2026/7w56_32315.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7w56_32315/03_2026/7w56_32315.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7w56_32315/03_2026/7w56_32315.cif"
  }
  resolution = 2.9
  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=   0.002 sd=   0.030
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      64      5.16       5
     C    5706      2.51       5
     N    1568      2.21       5
     O    1649      1.98       5
     H    8894      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 17881
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3759
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 3759
          Classifications: {'peptide': 230}
          Link IDs: {'PTRANS': 6, 'TRANS': 223}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "B"
      Number of atoms: 5136
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 5136
          Classifications: {'peptide': 341}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
    Chain: "C"
      Number of atoms: 156
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 156
          Classifications: {'peptide': 9}
          Link IDs: {'PTRANS': 1, 'TRANS': 7}
          Unresolved chain link angles: 1
          Unresolved chain link dihedrals: 2
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "E"
      Number of atoms: 3504
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 3504
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "G"
      Number of atoms: 885
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 885
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "R"
      Number of atoms: 4441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 4441
          Classifications: {'peptide': 276}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 262}
          Chain breaks: 2
  Time building chain proxies: 2.75, per 1000 atoms: 0.15
  Number of scatterers: 17881
  At special positions: 0
  Unit cell: (118.8, 130.68, 110.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      64     16.00
     O    1649      8.00
     N    1568      7.00
     C    5706      6.00
     H    8894      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 134 " - pdb=" SG  CYS R 219 " 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: 1.61
  Conformation dependent library (CDL) restraints added in 473.7 milliseconds
  

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2136

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 13 sheets defined
      39.5% alpha, 23.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 3.935A  pdb=" N   VAL A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 52
    Processing helix  chain 'A' and resid 210 through 218
      removed outlier: 4.263A  pdb=" N   ASP A 217 " --> pdb=" O   CYS A 214 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   VAL A 218 " --> pdb=" O   PHE A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 245
      removed outlier: 3.753A  pdb=" N   GLU A 235 " --> pdb=" O   ASN A 231 " (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 284
    Processing helix  chain 'A' and resid 298 through 318
      removed outlier: 3.757A  pdb=" N   ILE A 315 " --> pdb=" O   GLU A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 358
    Processing helix  chain 'B' and resid 9 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 52 through 55
      removed outlier: 3.735A  pdb=" N   GLY E  55 " --> pdb=" O   SER E  52 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 52 through 55'
    Processing helix  chain 'E' and resid 73 through 75
      No H-bonds generated for 'chain 'E' and resid 73 through 75'
    Processing helix  chain 'E' and resid 86 through 90
    Processing helix  chain 'E' and resid 220 through 224
    Processing helix  chain 'G' and resid 6 through 23
    Processing helix  chain 'G' and resid 28 through 43
    Processing helix  chain 'G' and resid 44 through 47
      removed outlier: 3.512A  pdb=" N   ASP G  47 " --> pdb=" O   ALA G  44 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 44 through 47'
    Processing helix  chain 'R' and resid 60 through 88
      removed outlier: 3.520A  pdb=" N   HIS R  88 " --> pdb=" O   VAL R  84 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 89 through 92
      removed outlier: 3.758A  pdb=" N   ARG R  92 " --> pdb=" O   LYS R  89 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 89 through 92'
    Processing helix  chain 'R' and resid 93 through 123
      removed outlier: 3.672A  pdb=" N   TYR R  97 " --> pdb=" O   THR R  93 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   TYR R  98 " --> pdb=" O   PRO R  94 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   LEU R  99 " --> pdb=" O   THR R  95 " (cutoff:3.500A)
      Proline residue:  R 115  - end of helix
    Processing helix  chain 'R' and resid 129 through 160
    Processing helix  chain 'R' and resid 161 through 163
      No H-bonds generated for 'chain 'R' and resid 161 through 163'
    Processing helix  chain 'R' and resid 164 through 165
      No H-bonds generated for 'chain 'R' and resid 164 through 165'
    Processing helix  chain 'R' and resid 166 through 172
    Processing helix  chain 'R' and resid 174 through 198
      removed outlier: 3.820A  pdb=" N   VAL R 178 " --> pdb=" O   THR R 174 " (cutoff:3.500A)
      Proline residue:  R 195  - end of helix
    Processing helix  chain 'R' and resid 224 through 240
    Processing helix  chain 'R' and resid 240 through 260
    Processing helix  chain 'R' and resid 293 through 323
      removed outlier: 3.899A  pdb=" N   PHE R 300 " --> pdb=" O   THR R 296 " (cutoff:3.500A)
      Proline residue:  R 312  - end of helix
    Processing helix  chain 'R' and resid 330 through 357
      removed outlier: 3.872A  pdb=" N   PHE R 334 " --> pdb=" O   LEU R 330 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   VAL R 339 " --> pdb=" O   GLN R 335 " (cutoff:3.500A)
      Proline residue:  R 353  - end of helix
    Processing helix  chain 'R' and resid 360 through 365
    Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191
      removed outlier: 4.159A  pdb=" N   VAL A 201 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.632A  pdb=" N   ILE A 222 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.369A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 8.359A  pdb=" N   ASP A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   PHE A 257 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 257 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   ASN A 259 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
      removed outlier: 7.363A  pdb=" N   VAL A 254 " --> pdb=" O   TYR A 327 " (cutoff:3.500A)
      removed outlier: 7.561A  pdb=" N   HIS A 329 " --> pdb=" O   VAL A 254 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   LEU A 256 " --> pdb=" O   HIS A 329 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56
      removed outlier: 5.885A  pdb=" N   THR B  52 " --> pdb=" O   ASN B 345 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   ASN B 345 " --> pdb=" O   THR B  52 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   ALA B 333 " --> pdb=" O   LEU B 323 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   LEU B 323 " --> pdb=" O   ALA B 333 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   GLY B 335 " --> pdb=" O   SER B 321 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68
      removed outlier: 3.865A  pdb=" N   ALA B  65 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LYS B  83 " --> pdb=" O   SER B  79 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   LEU B  84 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   ALA B  97 " --> pdb=" O   LEU B  84 " (cutoff:3.500A)
      removed outlier: 6.361A  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: 6.383A  pdb=" N   CYS B 126 " --> pdb=" O   GLU B 143 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   GLU B 143 " --> pdb=" O   CYS B 126 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   ILE B 128 " --> pdb=" O   SER B 141 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156
      removed outlier: 6.654A  pdb=" N   SER B 165 " --> pdb=" O   SER B 152 " (cutoff:3.500A)
      removed outlier: 4.428A  pdb=" N   CYS B 154 " --> pdb=" O   VAL B 163 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   VAL B 163 " --> pdb=" O   CYS B 154 " (cutoff:3.500A)
      removed outlier: 5.031A  pdb=" N   PHE B 156 " --> pdb=" O   GLN B 161 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   GLN B 161 " --> pdb=" O   PHE B 156 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   ASP B 175 " --> pdb=" O   GLN B 181 " (cutoff:3.500A)
      removed outlier: 6.015A  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: 3.674A  pdb=" N   GLN B 225 " --> pdb=" O   LEU B 215 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   ASP B 217 " --> pdb=" O   CYS B 223 " (cutoff:3.500A)
      removed outlier: 6.373A  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: 6.691A  pdb=" N   CYS B 255 " --> pdb=" O   THR B 268 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   THR B 268 " --> pdb=" O   CYS B 255 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   LEU B 257 " --> pdb=" O   LEU B 266 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   GLN B 264 " --> pdb=" O   ASP B 259 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 280 through 283
      removed outlier: 3.705A  pdb=" N   SER B 280 " --> pdb=" O   GLY B 293 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   CYS B 299 " --> pdb=" O   VAL B 312 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   VAL B 312 " --> pdb=" O   CYS B 299 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   VAL B 301 " --> pdb=" O   ALA B 310 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6
      removed outlier: 3.536A  pdb=" N   THR E  77 " --> pdb=" O   ASP E  72 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11
      removed outlier: 6.179A  pdb=" N   GLY E   9 " --> pdb=" O   THR E 117 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   MET E  33 " --> pdb=" O   TYR E  49 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   TYR E  49 " --> pdb=" O   MET E  33 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   TRP E  35 " --> pdb=" O   VAL E  47 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11
      removed outlier: 6.179A  pdb=" N   GLY E   9 " --> pdb=" O   THR E 117 " (cutoff:3.500A)
      removed outlier: 4.050A  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 142
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148
      removed outlier: 3.722A  pdb=" N   GLY E 225 " --> pdb=" O   LEU E 245 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   LEU E 174 " --> pdb=" O   TYR E 190 " (cutoff:3.500A)
      removed outlier: 4.852A  pdb=" N   TYR E 190 " --> pdb=" O   LEU E 174 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   ARG E 191 " --> pdb=" O   ASN E 194 " (cutoff:3.500A)

    455 hydrogen bonds defined for protein.
    1266 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: 3.92

  Time building geometry restraints manager: 2.07 seconds

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

  Histogram of bond lengths:
        0.82 -     1.02: 8864
        1.02 -     1.22: 38
        1.22 -     1.41: 3812
        1.41 -     1.61: 5260
        1.61 -     1.81: 96
  Bond restraints: 18070
  Sorted by residual:
  bond pdb=" SG  CYS B 322 "
       pdb=" HG  CYS B 322 "
    ideal  model  delta    sigma   weight residual
    1.200  1.338 -0.138 2.00e-02 2.50e+03 4.77e+01
  bond pdb=" SG  CYS B 238 "
       pdb=" HG  CYS B 238 "
    ideal  model  delta    sigma   weight residual
    1.200  1.336 -0.136 2.00e-02 2.50e+03 4.60e+01
  bond pdb=" NE  ARG A 323 "
       pdb=" HE  ARG A 323 "
    ideal  model  delta    sigma   weight residual
    0.860  0.970 -0.110 2.00e-02 2.50e+03 3.04e+01
  bond pdb=" CA  GLU E 234 "
       pdb=" C   GLU E 234 "
    ideal  model  delta    sigma   weight residual
    1.522  1.459  0.063 1.21e-02 6.83e+03 2.69e+01
  bond pdb=" CA  LEU B 151 "
       pdb=" C   LEU B 151 "
    ideal  model  delta    sigma   weight residual
    1.524  1.465  0.059 1.31e-02 5.83e+03 2.01e+01
  ... (remaining 18065 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.33: 32232
        2.33 -     4.66: 220
        4.66 -     6.99: 23
        6.99 -     9.32: 8
        9.32 -    11.65: 10
  Bond angle restraints: 32493
  Sorted by residual:
  angle pdb=" N   ASP B 251 "
        pdb=" CA  ASP B 251 "
        pdb=" C   ASP B 251 "
      ideal   model   delta    sigma   weight residual
     111.28  102.85    8.43 1.09e+00 8.42e-01 5.98e+01
  angle pdb=" N   PHE B 240 "
        pdb=" CA  PHE B 240 "
        pdb=" C   PHE B 240 "
      ideal   model   delta    sigma   weight residual
     110.39   99.49   10.90 1.50e+00 4.44e-01 5.28e+01
  angle pdb=" N   GLY E 113 "
        pdb=" CA  GLY E 113 "
        pdb=" C   GLY E 113 "
      ideal   model   delta    sigma   weight residual
     111.95  118.81   -6.86 9.50e-01 1.11e+00 5.21e+01
  angle pdb=" N   TYR B 294 "
        pdb=" CA  TYR B 294 "
        pdb=" C   TYR B 294 "
      ideal   model   delta    sigma   weight residual
     114.39  124.49  -10.10 1.45e+00 4.76e-01 4.85e+01
  angle pdb=" C   TYR E 235 "
        pdb=" N   PRO E 236 "
        pdb=" CA  PRO E 236 "
      ideal   model   delta    sigma   weight residual
     119.84  111.51    8.33 1.25e+00 6.40e-01 4.44e+01
  ... (remaining 32488 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.54: 7972
       19.54 -    39.07: 367
       39.07 -    58.61: 160
       58.61 -    78.14: 29
       78.14 -    97.68: 5
  Dihedral angle restraints: 8533
    sinusoidal: 4588
      harmonic: 3945
  Sorted by residual:
  dihedral pdb=" CA  ASP B 296 "
           pdb=" C   ASP B 296 "
           pdb=" N   PHE B 297 "
           pdb=" CA  PHE B 297 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   82.32   97.68     0      5.00e+00 4.00e-02 3.82e+02
  dihedral pdb=" N   TYR E 235 "
           pdb=" C   TYR E 235 "
           pdb=" CA  TYR E 235 "
           pdb=" CB  TYR E 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  145.00  -22.20     0      2.50e+00 1.60e-01 7.88e+01
  dihedral pdb=" C   TYR E 235 "
           pdb=" N   TYR E 235 "
           pdb=" CA  TYR E 235 "
           pdb=" CB  TYR E 235 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -144.34   21.74     0      2.50e+00 1.60e-01 7.57e+01
  ... (remaining 8530 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.213: 1398
       0.213 -    0.425: 4
       0.425 -    0.638: 0
       0.638 -    0.850: 0
       0.850 -    1.063: 1
  Chirality restraints: 1403
  Sorted by residual:
  chirality pdb=" CA  TYR E 235 "
            pdb=" N   TYR E 235 "
            pdb=" C   TYR E 235 "
            pdb=" CB  TYR E 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.45    1.06 2.00e-01 2.50e+01 2.82e+01
  chirality pdb=" CA  TYR B 294 "
            pdb=" N   TYR B 294 "
            pdb=" C   TYR B 294 "
            pdb=" CB  TYR B 294 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.59e+00
  chirality pdb=" CA  TYR R 125 "
            pdb=" N   TYR R 125 "
            pdb=" C   TYR R 125 "
            pdb=" CB  TYR R 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.82   -0.31 2.00e-01 2.50e+01 2.35e+00
  ... (remaining 1400 not shown)

  Planarity restraints: 2677
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU E 233 "   -0.019 2.00e-02 2.50e+03   3.79e-02 1.43e+01
        pdb=" C   LEU E 233 "    0.066 2.00e-02 2.50e+03
        pdb=" O   LEU E 233 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   GLU E 234 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 297 "    0.016 2.00e-02 2.50e+03   3.14e-02 9.88e+00
        pdb=" N   ASN B 298 "   -0.054 2.00e-02 2.50e+03
        pdb=" CA  ASN B 298 "    0.014 2.00e-02 2.50e+03
        pdb=" H   ASN B 298 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 240 "    0.045 5.00e-02 4.00e+02   6.73e-02 7.26e+00
        pdb=" N   PRO B 241 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO B 241 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 241 "    0.038 5.00e-02 4.00e+02
  ... (remaining 2674 not shown)

  Histogram of nonbonded interaction distances:
        1.48 -     2.10: 413
        2.10 -     2.73: 31740
        2.73 -     3.35: 52701
        3.35 -     3.98: 67220
        3.98 -     4.60: 105606
  Nonbonded interactions: 257680
  Sorted by model distance:
  nonbonded pdb="HH12 ARG A  15 "
            pdb=" O   VAL B  95 "
     model   vdw
     1.480 2.450
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" HH  TYR E 175 "
     model   vdw
     1.533 2.450
  nonbonded pdb=" OD1 ASP A 298 "
            pdb=" H   ARG A 300 "
     model   vdw
     1.568 2.450
  nonbonded pdb=" OD1 ASP B 210 "
            pdb=" HG  SER B 212 "
     model   vdw
     1.570 2.450
  nonbonded pdb="HH22 ARG E  66 "
            pdb=" OD2 ASP E  89 "
     model   vdw
     1.574 2.450
  ... (remaining 257675 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=0.00 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:             0.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.090
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     15.530
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7072
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      :  0.006   0.074   9177  Z= 0.321
  Angle     :  0.719  11.648  12431  Z= 0.435
  Chirality :  0.053   1.063   1403
  Planarity :  0.004   0.067   1582
  Dihedral  : 11.515  97.681   3317
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  2.86 %
    Favored  : 96.73 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.25), residues: 1124
  helix:  1.24 (0.26), residues: 393
  sheet:  0.22 (0.29), residues: 302
  loop : -0.30 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E  66 
 TYR   0.022   0.002   TYR E 190 
 PHE   0.023   0.002   PHE B 239 
 TRP   0.010   0.001   TRP B  87 
 HIS   0.010   0.001   HIS A 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00552 ( 9176)
  covalent geometry    : angle       0.71919 (12429)
  SS BOND              : bond        0.00092 (    1)
  SS BOND              : angle       0.81341 (    2)
  hydrogen bonds       : bond        0.14936 (  451)
  hydrogen bonds       : angle       6.51481 ( 1266)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  333 is missing expected H atoms. Skipping.
Residue SER  136 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Evaluate side-chains
  323 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 319
  time to evaluate  : 0.466 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  216 ASN cc_start: 0.7532 (t0) cc_final: 0.7311 (t0)
REVERT: A  217 ASP cc_start: 0.6978 (t0) cc_final: 0.6554 (t0)
REVERT: A  241 LYS cc_start: 0.7830 (tttt) cc_final: 0.7572 (tttp)
REVERT: A  314 ASP cc_start: 0.7774 (t0) cc_final: 0.7560 (t0)
REVERT: B   34 THR cc_start: 0.8373 (t) cc_final: 0.8165 (p)
REVERT: B   81 ASP cc_start: 0.6455 (t70) cc_final: 0.6201 (t0)
REVERT: B  132 LYS cc_start: 0.8692 (mttm) cc_final: 0.8416 (mptp)
REVERT: B  135 GLU cc_start: 0.7035 (mp0) cc_final: 0.6798 (mp0)
REVERT: B  169 THR cc_start: 0.7991 (m) cc_final: 0.7761 (p)
REVERT: B  177 GLU cc_start: 0.7317 (tp30) cc_final: 0.7062 (tp30)
REVERT: B  235 ASN cc_start: 0.8059 (m-40) cc_final: 0.7854 (m-40)
REVERT: B  263 ASP cc_start: 0.7307 (t70) cc_final: 0.6650 (t0)
REVERT: B  298 ASN cc_start: 0.8334 (p0) cc_final: 0.8113 (p0)
REVERT: B  300 ASN cc_start: 0.7722 (m-40) cc_final: 0.7497 (m-40)
REVERT: B  323 LEU cc_start: 0.7753 (tt) cc_final: 0.7452 (tt)
REVERT: E   38 GLN cc_start: 0.8165 (tt0) cc_final: 0.7929 (tt0)
REVERT: G   18 LEU cc_start: 0.8300 (mm) cc_final: 0.8037 (mt)
REVERT: R   91 MET cc_start: 0.7667 (mmt) cc_final: 0.7298 (mmp)
REVERT: R  232 VAL cc_start: 0.7939 (t) cc_final: 0.7713 (t)
REVERT: R  244 MET cc_start: 0.7573 (tpp) cc_final: 0.7263 (tpt)
  outliers start: 4
  outliers final: 2
  residues processed: 321
  average time/residue: 1.1023
  time to fit residues: 379.4934
Evaluate side-chains
  278 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 276
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 HIS
Chi-restraints excluded: chain B residue  239 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.4980
   chunk 106 optimal weight:    0.9980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 245 ASN
A 246 ASN
A 259 ASN
** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 124 ASN
** R 200 HIS ** 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 = 0.3756 r_free = 0.3756 target = 0.131996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.116123 restraints weight = 37988.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3537 rms_B_bonded: 2.08
r_work: 0.3432 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3289 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   9177  Z= 0.210
  Angle     :  0.611   9.039  12431  Z= 0.330
  Chirality :  0.043   0.243   1403
  Planarity :  0.005   0.055   1582
  Dihedral  :  6.034  56.435   1256
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 12.35 %
    Favored  : 85.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.25), residues: 1124
  helix:  1.51 (0.26), residues: 392
  sheet: -0.01 (0.29), residues: 274
  loop : -0.31 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 300 
 TYR   0.020   0.002   TYR E 190 
 PHE   0.022   0.002   PHE B 297 
 TRP   0.014   0.001   TRP B 174 
 HIS   0.005   0.001   HIS R 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 ( 9176)
  covalent geometry    : angle       0.61108 (12429)
  SS BOND              : bond        0.00295 (    1)
  SS BOND              : angle       0.78885 (    2)
  hydrogen bonds       : bond        0.04906 (  451)
  hydrogen bonds       : angle       5.30990 ( 1266)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  333 is missing expected H atoms. Skipping.
Residue SER  136 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Evaluate side-chains
  302 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 282
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 PHE cc_start: 0.8508 (m-80) cc_final: 0.8153 (m-80)
REVERT: A  216 ASN cc_start: 0.8135 (t0) cc_final: 0.7843 (t0)
REVERT: A  217 ASP cc_start: 0.7785 (t0) cc_final: 0.7343 (t0)
REVERT: A  241 LYS cc_start: 0.8261 (tttt) cc_final: 0.8060 (tttp)
REVERT: A  314 ASP cc_start: 0.8123 (t0) cc_final: 0.7908 (t0)
REVERT: A  359 ASN cc_start: 0.8380 (m-40) cc_final: 0.8137 (m110)
REVERT: B   34 THR cc_start: 0.8440 (t) cc_final: 0.8190 (p)
REVERT: B  132 LYS cc_start: 0.8798 (mttm) cc_final: 0.8584 (mptp)
REVERT: B  177 GLU cc_start: 0.8022 (tp30) cc_final: 0.7767 (tp30)
REVERT: B  193 MET cc_start: 0.8304 (mmm) cc_final: 0.7952 (mmm)
REVERT: B  300 ASN cc_start: 0.8072 (m-40) cc_final: 0.7828 (m-40)
REVERT: B  308 ASP cc_start: 0.8030 (m-30) cc_final: 0.7813 (m-30)
REVERT: B  323 LEU cc_start: 0.7979 (tt) cc_final: 0.7752 (tt)
REVERT: E  219 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8297 (tp)
REVERT: E  235 TYR cc_start: 0.7159 (OUTLIER) cc_final: 0.6778 (t80)
REVERT: G   18 LEU cc_start: 0.8300 (mm) cc_final: 0.8041 (mt)
REVERT: G   21 GLU cc_start: 0.8052 (tt0) cc_final: 0.7759 (tt0)
REVERT: G   29 VAL cc_start: 0.8612 (t) cc_final: 0.8400 (p)
REVERT: R   91 MET cc_start: 0.7684 (mmt) cc_final: 0.7267 (mmp)
REVERT: R  131 VAL cc_start: 0.7824 (p) cc_final: 0.7596 (t)
REVERT: R  135 TYR cc_start: 0.7244 (m-80) cc_final: 0.6833 (m-80)
REVERT: R  164 VAL cc_start: 0.7133 (t) cc_final: 0.5629 (p)
REVERT: R  232 VAL cc_start: 0.8110 (t) cc_final: 0.7904 (t)
REVERT: R  244 MET cc_start: 0.7830 (tpp) cc_final: 0.7601 (tpt)
  outliers start: 20
  outliers final: 9
  residues processed: 293
  average time/residue: 1.1059
  time to fit residues: 346.7574
Evaluate side-chains
  276 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 265
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  324 HIS
Chi-restraints excluded: chain B residue   18 GLN
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain E residue   29 SER
Chi-restraints excluded: chain E residue  219 LEU
Chi-restraints excluded: chain E residue  235 TYR
Chi-restraints excluded: chain R residue  323 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    0.9980
   chunk 90 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 104 optimal weight:    1.9990
   chunk 80 optimal weight:    0.5980
   chunk 53 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 100 optimal weight:    0.0970
   chunk 93 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
A 245 ASN
A 259 ASN
** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  17 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.132364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.116681 restraints weight = 38077.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 2.10
r_work: 0.3441 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3293 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.2416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9177  Z= 0.166
  Angle     :  0.556   6.335  12431  Z= 0.298
  Chirality :  0.042   0.203   1403
  Planarity :  0.004   0.050   1582
  Dihedral  :  5.692  57.248   1256
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 14.18 %
    Favored  : 83.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.25), residues: 1124
  helix:  1.76 (0.26), residues: 392
  sheet: -0.29 (0.29), residues: 266
  loop : -0.37 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 300 
 TYR   0.018   0.001   TYR E 190 
 PHE   0.011   0.001   PHE B 246 
 TRP   0.013   0.001   TRP B 174 
 HIS   0.004   0.001   HIS R 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 9176)
  covalent geometry    : angle       0.55592 (12429)
  SS BOND              : bond        0.00307 (    1)
  SS BOND              : angle       0.63031 (    2)
  hydrogen bonds       : bond        0.04430 (  451)
  hydrogen bonds       : angle       5.03706 ( 1266)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  333 is missing expected H atoms. Skipping.
Residue SER  136 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Evaluate side-chains
  289 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 270
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 PHE cc_start: 0.8485 (m-80) cc_final: 0.8278 (m-80)
REVERT: A  216 ASN cc_start: 0.8174 (t0) cc_final: 0.7858 (t0)
REVERT: A  217 ASP cc_start: 0.7783 (t0) cc_final: 0.7325 (t0)
REVERT: A  241 LYS cc_start: 0.8234 (tttt) cc_final: 0.7974 (tttp)
REVERT: A  314 ASP cc_start: 0.8099 (t0) cc_final: 0.7883 (t0)
REVERT: A  359 ASN cc_start: 0.8395 (m-40) cc_final: 0.8139 (m110)
REVERT: B   34 THR cc_start: 0.8451 (t) cc_final: 0.8224 (p)
REVERT: B  132 LYS cc_start: 0.8758 (mttm) cc_final: 0.8528 (mptp)
REVERT: B  177 GLU cc_start: 0.8019 (tp30) cc_final: 0.7772 (tp30)
REVERT: B  193 MET cc_start: 0.8263 (mmm) cc_final: 0.7996 (mmm)
REVERT: B  194 SER cc_start: 0.8390 (m) cc_final: 0.8147 (p)
REVERT: B  202 ARG cc_start: 0.7875 (mtm180) cc_final: 0.7521 (mtm180)
REVERT: B  232 SER cc_start: 0.8476 (m) cc_final: 0.8222 (m)
REVERT: B  300 ASN cc_start: 0.8119 (m-40) cc_final: 0.7843 (m-40)
REVERT: B  323 LEU cc_start: 0.7886 (tt) cc_final: 0.7637 (tt)
REVERT: E   38 GLN cc_start: 0.8425 (tt0) cc_final: 0.8163 (tt0)
REVERT: E   82 MET cc_start: 0.8096 (mtt) cc_final: 0.7763 (mtm)
REVERT: E  158 SER cc_start: 0.8682 (m) cc_final: 0.8259 (t)
REVERT: E  219 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8345 (mt)
REVERT: G   18 LEU cc_start: 0.8305 (mm) cc_final: 0.8054 (mt)
REVERT: G   29 VAL cc_start: 0.8597 (t) cc_final: 0.8360 (p)
REVERT: R   91 MET cc_start: 0.7628 (mmt) cc_final: 0.7279 (mmp)
REVERT: R  131 VAL cc_start: 0.7835 (p) cc_final: 0.7628 (t)
REVERT: R  135 TYR cc_start: 0.7187 (m-80) cc_final: 0.6804 (m-80)
REVERT: R  164 VAL cc_start: 0.6973 (t) cc_final: 0.5421 (p)
REVERT: R  232 VAL cc_start: 0.8113 (t) cc_final: 0.7908 (t)
REVERT: R  244 MET cc_start: 0.7756 (tpp) cc_final: 0.7536 (tpt)
  outliers start: 19
  outliers final: 7
  residues processed: 277
  average time/residue: 1.2138
  time to fit residues: 358.7124
Evaluate side-chains
  275 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 267
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  324 HIS
Chi-restraints excluded: chain B residue   18 GLN
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  330 MET
Chi-restraints excluded: chain E residue  219 LEU
Chi-restraints excluded: chain R residue  156 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 44 optimal weight:    0.8980
   chunk 93 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 109 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 245 ASN
** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.129148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.113943 restraints weight = 38375.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 2.07
r_work: 0.3415 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3268 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.2688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   9177  Z= 0.293
  Angle     :  0.608   6.029  12431  Z= 0.328
  Chirality :  0.044   0.218   1403
  Planarity :  0.005   0.051   1582
  Dihedral  :  5.762  58.171   1256
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 15.10 %
    Favored  : 82.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.28 (0.25), residues: 1124
  helix:  1.58 (0.26), residues: 393
  sheet: -0.49 (0.30), residues: 265
  loop : -0.51 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 300 
 TYR   0.025   0.002   TYR E 190 
 PHE   0.015   0.002   PHE B 204 
 TRP   0.016   0.002   TRP B 174 
 HIS   0.006   0.001   HIS B 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00650 ( 9176)
  covalent geometry    : angle       0.60811 (12429)
  SS BOND              : bond        0.00427 (    1)
  SS BOND              : angle       0.26154 (    2)
  hydrogen bonds       : bond        0.04562 (  451)
  hydrogen bonds       : angle       5.12126 ( 1266)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  333 is missing expected H atoms. Skipping.
Residue SER  136 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Evaluate side-chains
  304 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 276
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.7551 (tt0) cc_final: 0.7264 (tm-30)
REVERT: A  199 PHE cc_start: 0.8334 (m-80) cc_final: 0.8038 (m-80)
REVERT: A  216 ASN cc_start: 0.8175 (t0) cc_final: 0.7875 (t0)
REVERT: A  217 ASP cc_start: 0.7856 (t0) cc_final: 0.7378 (t0)
REVERT: A  241 LYS cc_start: 0.8220 (tttt) cc_final: 0.7932 (tttp)
REVERT: A  314 ASP cc_start: 0.8100 (t0) cc_final: 0.7892 (t0)
REVERT: B   34 THR cc_start: 0.8459 (t) cc_final: 0.8224 (p)
REVERT: B  177 GLU cc_start: 0.8033 (tp30) cc_final: 0.7785 (tp30)
REVERT: B  193 MET cc_start: 0.8296 (mmm) cc_final: 0.8057 (mmm)
REVERT: B  232 SER cc_start: 0.8516 (m) cc_final: 0.8251 (m)
REVERT: B  300 ASN cc_start: 0.8145 (m-40) cc_final: 0.7917 (m-40)
REVERT: C    6 ARG cc_start: 0.8978 (mtm110) cc_final: 0.8735 (mtm110)
REVERT: E   38 GLN cc_start: 0.8446 (tt0) cc_final: 0.8194 (tt0)
REVERT: E   82 MET cc_start: 0.8111 (mtt) cc_final: 0.7875 (mtm)
REVERT: E  158 SER cc_start: 0.8800 (m) cc_final: 0.8418 (t)
REVERT: E  169 ASN cc_start: 0.7300 (m-40) cc_final: 0.7043 (m-40)
REVERT: E  219 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8394 (mt)
REVERT: E  235 TYR cc_start: 0.7371 (OUTLIER) cc_final: 0.6558 (t80)
REVERT: G   18 LEU cc_start: 0.8344 (mm) cc_final: 0.8083 (mt)
REVERT: G   29 VAL cc_start: 0.8662 (t) cc_final: 0.8416 (p)
REVERT: R   91 MET cc_start: 0.7610 (mmt) cc_final: 0.7179 (mmp)
REVERT: R   96 ASN cc_start: 0.8388 (m-40) cc_final: 0.8164 (m110)
REVERT: R  135 TYR cc_start: 0.7129 (m-80) cc_final: 0.6741 (m-80)
REVERT: R  164 VAL cc_start: 0.7164 (t) cc_final: 0.5566 (p)
REVERT: R  237 LEU cc_start: 0.8479 (tp) cc_final: 0.8214 (tm)
REVERT: R  362 ARG cc_start: 0.8421 (mtm-85) cc_final: 0.8077 (mtp180)
  outliers start: 28
  outliers final: 17
  residues processed: 288
  average time/residue: 1.2370
  time to fit residues: 379.9570
Evaluate side-chains
  285 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 266
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 SER
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  324 HIS
Chi-restraints excluded: chain B residue   18 GLN
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  223 CYS
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  308 ASP
Chi-restraints excluded: chain B residue  330 MET
Chi-restraints excluded: chain E residue   29 SER
Chi-restraints excluded: chain E residue  219 LEU
Chi-restraints excluded: chain E residue  233 LEU
Chi-restraints excluded: chain E residue  235 TYR
Chi-restraints excluded: chain R residue  114 LEU
Chi-restraints excluded: chain R residue  122 TRP
Chi-restraints excluded: chain R residue  156 SER
Chi-restraints excluded: chain R residue  357 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 47 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 16 optimal weight:    0.3980
   chunk 75 optimal weight:    4.9990
   chunk 110 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 245 ASN
A 259 ASN
** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.132292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.117070 restraints weight = 38337.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3542 rms_B_bonded: 2.07
r_work: 0.3437 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3293 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          0.2988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9177  Z= 0.149
  Angle     :  0.549   5.940  12431  Z= 0.291
  Chirality :  0.042   0.183   1403
  Planarity :  0.004   0.052   1582
  Dihedral  :  5.469  58.995   1256
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 18.16 %
    Favored  : 79.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.25), residues: 1124
  helix:  1.83 (0.26), residues: 392
  sheet: -0.59 (0.30), residues: 265
  loop : -0.45 (0.29), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 300 
 TYR   0.026   0.001   TYR E 235 
 PHE   0.012   0.001   PHE R 313 
 TRP   0.012   0.001   TRP B 174 
 HIS   0.004   0.001   HIS R 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 9176)
  covalent geometry    : angle       0.54887 (12429)
  SS BOND              : bond        0.00172 (    1)
  SS BOND              : angle       0.16393 (    2)
  hydrogen bonds       : bond        0.04181 (  451)
  hydrogen bonds       : angle       4.94112 ( 1266)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  333 is missing expected H atoms. Skipping.
Residue SER  136 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Evaluate side-chains
  291 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 269
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.7514 (tt0) cc_final: 0.7231 (tm-30)
REVERT: A  216 ASN cc_start: 0.8141 (t0) cc_final: 0.7843 (t0)
REVERT: A  217 ASP cc_start: 0.7842 (t0) cc_final: 0.7390 (t0)
REVERT: A  228 SER cc_start: 0.6524 (t) cc_final: 0.6219 (m)
REVERT: A  241 LYS cc_start: 0.8181 (tttt) cc_final: 0.7918 (tttm)
REVERT: A  250 ARG cc_start: 0.7877 (ttp-170) cc_final: 0.7594 (ptp-110)
REVERT: A  273 SER cc_start: 0.8472 (t) cc_final: 0.8079 (p)
REVERT: A  314 ASP cc_start: 0.8073 (t0) cc_final: 0.7865 (t0)
REVERT: A  316 SER cc_start: 0.8046 (t) cc_final: 0.7599 (p)
REVERT: B   34 THR cc_start: 0.8434 (t) cc_final: 0.8229 (p)
REVERT: B  177 GLU cc_start: 0.7966 (tp30) cc_final: 0.7737 (tp30)
REVERT: B  193 MET cc_start: 0.8291 (mmm) cc_final: 0.8069 (mmm)
REVERT: B  194 SER cc_start: 0.8454 (m) cc_final: 0.8179 (p)
REVERT: B  232 SER cc_start: 0.8500 (m) cc_final: 0.8257 (m)
REVERT: B  300 ASN cc_start: 0.8084 (m-40) cc_final: 0.7824 (m-40)
REVERT: C    6 ARG cc_start: 0.8948 (mtm110) cc_final: 0.8716 (mtm110)
REVERT: E   38 GLN cc_start: 0.8408 (tt0) cc_final: 0.8162 (tt0)
REVERT: E   82 MET cc_start: 0.8095 (mtt) cc_final: 0.7767 (mtm)
REVERT: E  158 SER cc_start: 0.8688 (m) cc_final: 0.8295 (t)
REVERT: E  169 ASN cc_start: 0.7293 (m-40) cc_final: 0.7074 (m-40)
REVERT: E  219 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8393 (mt)
REVERT: E  235 TYR cc_start: 0.7247 (OUTLIER) cc_final: 0.6520 (t80)
REVERT: G   18 LEU cc_start: 0.8294 (mm) cc_final: 0.8040 (mt)
REVERT: G   29 VAL cc_start: 0.8652 (t) cc_final: 0.8402 (p)
REVERT: R   91 MET cc_start: 0.7604 (mmt) cc_final: 0.7100 (mmp)
REVERT: R  129 LEU cc_start: 0.7984 (mp) cc_final: 0.7776 (mm)
REVERT: R  135 TYR cc_start: 0.7088 (m-80) cc_final: 0.6765 (m-80)
REVERT: R  164 VAL cc_start: 0.6983 (t) cc_final: 0.5381 (p)
REVERT: R  237 LEU cc_start: 0.8440 (tp) cc_final: 0.8167 (tm)
  outliers start: 22
  outliers final: 10
  residues processed: 278
  average time/residue: 1.1839
  time to fit residues: 352.1553
Evaluate side-chains
  279 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 267
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 SER
Chi-restraints excluded: chain B residue   18 GLN
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  223 CYS
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  330 MET
Chi-restraints excluded: chain E residue   29 SER
Chi-restraints excluded: chain E residue  219 LEU
Chi-restraints excluded: chain E residue  235 TYR
Chi-restraints excluded: chain R residue  114 LEU
Chi-restraints excluded: chain R residue  156 SER
Chi-restraints excluded: chain R residue  357 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 102 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 74 optimal weight:    0.4980
   chunk 46 optimal weight:    0.9990
   chunk 111 optimal weight:    2.9990
   chunk 110 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    1.2988

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

Flipped N/Q/H residues before XYZ refinement:
A 245 ASN
A 259 ASN
A 324 HIS
** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.131275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.116114 restraints weight = 38074.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.3541 rms_B_bonded: 2.06
r_work: 0.3433 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3288 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.3153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   9177  Z= 0.208
  Angle     :  0.565   5.921  12431  Z= 0.300
  Chirality :  0.042   0.199   1403
  Planarity :  0.004   0.052   1582
  Dihedral  :  5.380  59.437   1254
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 18.16 %
    Favored  : 79.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.25), residues: 1124
  helix:  1.83 (0.26), residues: 392
  sheet: -0.66 (0.30), residues: 265
  loop : -0.44 (0.29), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 300 
 TYR   0.026   0.002   TYR E 235 
 PHE   0.016   0.002   PHE E  67 
 TRP   0.012   0.001   TRP B 174 
 HIS   0.006   0.001   HIS A 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 9176)
  covalent geometry    : angle       0.56469 (12429)
  SS BOND              : bond        0.00051 (    1)
  SS BOND              : angle       0.28451 (    2)
  hydrogen bonds       : bond        0.04223 (  451)
  hydrogen bonds       : angle       4.90950 ( 1266)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  333 is missing expected H atoms. Skipping.
Residue SER  136 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Evaluate side-chains
  298 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 271
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.7522 (tt0) cc_final: 0.7206 (tm-30)
REVERT: A  216 ASN cc_start: 0.8172 (t0) cc_final: 0.7877 (t0)
REVERT: A  217 ASP cc_start: 0.7848 (t0) cc_final: 0.7375 (t0)
REVERT: A  228 SER cc_start: 0.6234 (t) cc_final: 0.5989 (m)
REVERT: A  241 LYS cc_start: 0.8196 (tttt) cc_final: 0.7914 (tttp)
REVERT: A  250 ARG cc_start: 0.7878 (ttp-170) cc_final: 0.7576 (ptp-110)
REVERT: A  273 SER cc_start: 0.8486 (t) cc_final: 0.8084 (p)
REVERT: A  309 ARG cc_start: 0.7952 (ttt-90) cc_final: 0.7702 (tmm-80)
REVERT: A  314 ASP cc_start: 0.8084 (t0) cc_final: 0.7875 (t0)
REVERT: A  316 SER cc_start: 0.8064 (t) cc_final: 0.7614 (p)
REVERT: B   34 THR cc_start: 0.8440 (t) cc_final: 0.8238 (p)
REVERT: B  193 MET cc_start: 0.8308 (mmm) cc_final: 0.8087 (mmm)
REVERT: B  194 SER cc_start: 0.8438 (m) cc_final: 0.8133 (p)
REVERT: B  232 SER cc_start: 0.8522 (m) cc_final: 0.8279 (m)
REVERT: B  300 ASN cc_start: 0.8107 (m-40) cc_final: 0.7858 (m-40)
REVERT: C    6 ARG cc_start: 0.8949 (mtm110) cc_final: 0.8715 (mtm110)
REVERT: E   38 GLN cc_start: 0.8420 (tt0) cc_final: 0.8178 (tt0)
REVERT: E  158 SER cc_start: 0.8727 (m) cc_final: 0.8342 (t)
REVERT: E  219 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8417 (mt)
REVERT: E  235 TYR cc_start: 0.7228 (OUTLIER) cc_final: 0.6512 (t80)
REVERT: G   18 LEU cc_start: 0.8334 (mm) cc_final: 0.8078 (mt)
REVERT: G   29 VAL cc_start: 0.8688 (t) cc_final: 0.8441 (p)
REVERT: R   91 MET cc_start: 0.7397 (mmt) cc_final: 0.7103 (mmp)
REVERT: R  129 LEU cc_start: 0.8008 (mp) cc_final: 0.7791 (mm)
REVERT: R  135 TYR cc_start: 0.7120 (m-80) cc_final: 0.6745 (m-80)
REVERT: R  164 VAL cc_start: 0.6959 (t) cc_final: 0.5292 (p)
REVERT: R  223 ARG cc_start: 0.7807 (mmt180) cc_final: 0.7485 (mmm160)
REVERT: R  237 LEU cc_start: 0.8476 (tp) cc_final: 0.8199 (tm)
  outliers start: 27
  outliers final: 15
  residues processed: 285
  average time/residue: 1.1451
  time to fit residues: 349.8697
Evaluate side-chains
  286 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 269
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 SER
Chi-restraints excluded: chain B residue   18 GLN
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  223 CYS
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  330 MET
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain E residue   16 SER
Chi-restraints excluded: chain E residue   29 SER
Chi-restraints excluded: chain E residue  219 LEU
Chi-restraints excluded: chain E residue  233 LEU
Chi-restraints excluded: chain E residue  235 TYR
Chi-restraints excluded: chain R residue  114 LEU
Chi-restraints excluded: chain R residue  122 TRP
Chi-restraints excluded: chain R residue  156 SER
Chi-restraints excluded: chain R residue  357 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 111 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
A 245 ASN
A 259 ASN
** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 147 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.129833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.114581 restraints weight = 38432.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 2.07
r_work: 0.3423 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3278 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.3285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   9177  Z= 0.242
  Angle     :  0.573   6.378  12431  Z= 0.307
  Chirality :  0.043   0.193   1403
  Planarity :  0.004   0.052   1582
  Dihedral  :  5.401  59.902   1254
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 18.16 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.25), residues: 1124
  helix:  1.77 (0.26), residues: 393
  sheet: -0.76 (0.30), residues: 267
  loop : -0.44 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 300 
 TYR   0.030   0.002   TYR E 235 
 PHE   0.016   0.002   PHE R 313 
 TRP   0.012   0.002   TRP B 174 
 HIS   0.011   0.001   HIS A 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00536 ( 9176)
  covalent geometry    : angle       0.57265 (12429)
  SS BOND              : bond        0.00071 (    1)
  SS BOND              : angle       0.30672 (    2)
  hydrogen bonds       : bond        0.04276 (  451)
  hydrogen bonds       : angle       4.94424 ( 1266)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  333 is missing expected H atoms. Skipping.
Residue SER  136 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Evaluate side-chains
  299 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 269
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.7510 (tt0) cc_final: 0.7193 (tm-30)
REVERT: A  216 ASN cc_start: 0.8174 (t0) cc_final: 0.7872 (t0)
REVERT: A  217 ASP cc_start: 0.7817 (t0) cc_final: 0.7371 (t0)
REVERT: A  228 SER cc_start: 0.6027 (t) cc_final: 0.5688 (m)
REVERT: A  241 LYS cc_start: 0.8185 (tttt) cc_final: 0.7916 (tttp)
REVERT: A  250 ARG cc_start: 0.7910 (ttp-170) cc_final: 0.7572 (ptp-110)
REVERT: A  273 SER cc_start: 0.8491 (t) cc_final: 0.8105 (p)
REVERT: B   34 THR cc_start: 0.8454 (t) cc_final: 0.8252 (p)
REVERT: B  102 SER cc_start: 0.8332 (OUTLIER) cc_final: 0.7984 (p)
REVERT: B  147 HIS cc_start: 0.8800 (OUTLIER) cc_final: 0.8551 (m-70)
REVERT: B  232 SER cc_start: 0.8530 (m) cc_final: 0.8296 (m)
REVERT: B  300 ASN cc_start: 0.8112 (m-40) cc_final: 0.7862 (m-40)
REVERT: E   17 ARG cc_start: 0.7930 (tpt90) cc_final: 0.7395 (mmt180)
REVERT: E   38 GLN cc_start: 0.8431 (tt0) cc_final: 0.8181 (tt0)
REVERT: E   44 LEU cc_start: 0.8823 (mt) cc_final: 0.8599 (mt)
REVERT: E   63 VAL cc_start: 0.8320 (t) cc_final: 0.7993 (p)
REVERT: E   85 LEU cc_start: 0.8939 (mt) cc_final: 0.8736 (mp)
REVERT: E  158 SER cc_start: 0.8735 (m) cc_final: 0.8360 (t)
REVERT: E  212 PHE cc_start: 0.8277 (m-80) cc_final: 0.8074 (m-80)
REVERT: E  219 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8343 (tp)
REVERT: G   18 LEU cc_start: 0.8321 (mm) cc_final: 0.8066 (mt)
REVERT: G   29 VAL cc_start: 0.8727 (t) cc_final: 0.8473 (p)
REVERT: R  129 LEU cc_start: 0.8029 (mp) cc_final: 0.7796 (mm)
REVERT: R  135 TYR cc_start: 0.7123 (m-80) cc_final: 0.6732 (m-80)
REVERT: R  164 VAL cc_start: 0.6965 (t) cc_final: 0.5264 (p)
REVERT: R  223 ARG cc_start: 0.7882 (mmt180) cc_final: 0.7653 (mmm160)
REVERT: R  229 ASN cc_start: 0.8169 (OUTLIER) cc_final: 0.7929 (t0)
REVERT: R  237 LEU cc_start: 0.8515 (tp) cc_final: 0.8217 (tm)
  outliers start: 30
  outliers final: 19
  residues processed: 287
  average time/residue: 1.1288
  time to fit residues: 347.1464
Evaluate side-chains
  288 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 265
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 SER
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain B residue   18 GLN
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain B residue  147 HIS
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  223 CYS
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  252 ASP
Chi-restraints excluded: chain B residue  322 CYS
Chi-restraints excluded: chain B residue  330 MET
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain E residue   16 SER
Chi-restraints excluded: chain E residue   29 SER
Chi-restraints excluded: chain E residue  219 LEU
Chi-restraints excluded: chain E residue  233 LEU
Chi-restraints excluded: chain E residue  235 TYR
Chi-restraints excluded: chain R residue  114 LEU
Chi-restraints excluded: chain R residue  122 TRP
Chi-restraints excluded: chain R residue  156 SER
Chi-restraints excluded: chain R residue  229 ASN
Chi-restraints excluded: chain R residue  357 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 59 optimal weight:    2.9990
   chunk 106 optimal weight:    0.7980
   chunk 44 optimal weight:    0.7980
   chunk 107 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 31 optimal weight:    0.2980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 245 ASN
** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.131628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.116493 restraints weight = 38074.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 2.07
r_work: 0.3450 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3307 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.3374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9177  Z= 0.138
  Angle     :  0.541   7.446  12431  Z= 0.286
  Chirality :  0.041   0.168   1403
  Planarity :  0.004   0.051   1582
  Dihedral  :  5.282  59.598   1254
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 19.18 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.46 (0.25), residues: 1124
  helix:  1.98 (0.26), residues: 392
  sheet: -0.73 (0.30), residues: 265
  loop : -0.42 (0.29), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 300 
 TYR   0.025   0.001   TYR E 235 
 PHE   0.015   0.001   PHE R 313 
 TRP   0.011   0.001   TRP B 174 
 HIS   0.011   0.001   HIS B 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 9176)
  covalent geometry    : angle       0.54149 (12429)
  SS BOND              : bond        0.00134 (    1)
  SS BOND              : angle       0.31958 (    2)
  hydrogen bonds       : bond        0.04028 (  451)
  hydrogen bonds       : angle       4.82184 ( 1266)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  333 is missing expected H atoms. Skipping.
Residue SER  136 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Evaluate side-chains
  288 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 266
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.7488 (tt0) cc_final: 0.7180 (tm-30)
REVERT: A  216 ASN cc_start: 0.8162 (t0) cc_final: 0.7872 (t0)
REVERT: A  217 ASP cc_start: 0.7800 (t0) cc_final: 0.7361 (t0)
REVERT: A  241 LYS cc_start: 0.8138 (tttt) cc_final: 0.7899 (tttp)
REVERT: A  250 ARG cc_start: 0.7908 (ttp-170) cc_final: 0.7580 (ptp-110)
REVERT: A  263 LEU cc_start: 0.8335 (mm) cc_final: 0.8073 (mt)
REVERT: A  273 SER cc_start: 0.8509 (t) cc_final: 0.8141 (p)
REVERT: A  316 SER cc_start: 0.8030 (t) cc_final: 0.7590 (p)
REVERT: B   34 THR cc_start: 0.8449 (t) cc_final: 0.8247 (p)
REVERT: B  232 SER cc_start: 0.8513 (m) cc_final: 0.8279 (m)
REVERT: B  300 ASN cc_start: 0.8044 (m-40) cc_final: 0.7800 (m-40)
REVERT: E   17 ARG cc_start: 0.7915 (tpt90) cc_final: 0.7384 (mmt180)
REVERT: E   38 GLN cc_start: 0.8414 (tt0) cc_final: 0.8167 (tt0)
REVERT: E   44 LEU cc_start: 0.8814 (mt) cc_final: 0.8590 (mp)
REVERT: E   63 VAL cc_start: 0.8301 (t) cc_final: 0.7954 (p)
REVERT: E  158 SER cc_start: 0.8683 (m) cc_final: 0.8338 (t)
REVERT: E  194 ASN cc_start: 0.8141 (m110) cc_final: 0.7918 (m110)
REVERT: E  219 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8351 (tp)
REVERT: G   18 LEU cc_start: 0.8334 (mm) cc_final: 0.8073 (mt)
REVERT: G   29 VAL cc_start: 0.8674 (t) cc_final: 0.8403 (p)
REVERT: R  129 LEU cc_start: 0.8050 (mp) cc_final: 0.7822 (mm)
REVERT: R  135 TYR cc_start: 0.7059 (m-80) cc_final: 0.6700 (m-80)
REVERT: R  164 VAL cc_start: 0.6935 (t) cc_final: 0.5233 (p)
REVERT: R  223 ARG cc_start: 0.7839 (mmt180) cc_final: 0.7606 (mmm160)
REVERT: R  229 ASN cc_start: 0.8157 (OUTLIER) cc_final: 0.7908 (t0)
REVERT: R  237 LEU cc_start: 0.8530 (tp) cc_final: 0.8233 (tm)
  outliers start: 22
  outliers final: 17
  residues processed: 278
  average time/residue: 1.1842
  time to fit residues: 353.3648
Evaluate side-chains
  285 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 266
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 SER
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain B residue   18 GLN
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  223 CYS
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  252 ASP
Chi-restraints excluded: chain B residue  322 CYS
Chi-restraints excluded: chain B residue  330 MET
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain E residue   29 SER
Chi-restraints excluded: chain E residue  219 LEU
Chi-restraints excluded: chain E residue  235 TYR
Chi-restraints excluded: chain R residue  114 LEU
Chi-restraints excluded: chain R residue  122 TRP
Chi-restraints excluded: chain R residue  156 SER
Chi-restraints excluded: chain R residue  229 ASN
Chi-restraints excluded: chain R residue  357 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   chunk 82 optimal weight:    0.0870
   chunk 34 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 47 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.7358

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

Flipped N/Q/H residues before XYZ refinement:
A 245 ASN
A 259 ASN
** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.131961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.116608 restraints weight = 37791.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 2.07
r_work: 0.3459 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3314 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.3507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9177  Z= 0.142
  Angle     :  0.531   6.024  12431  Z= 0.281
  Chirality :  0.041   0.162   1403
  Planarity :  0.004   0.051   1582
  Dihedral  :  5.122  59.104   1254
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 19.90 %
    Favored  : 78.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.25), residues: 1124
  helix:  2.08 (0.26), residues: 392
  sheet: -0.72 (0.30), residues: 265
  loop : -0.38 (0.30), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 300 
 TYR   0.025   0.001   TYR E 235 
 PHE   0.014   0.001   PHE R 313 
 TRP   0.010   0.001   TRP B 174 
 HIS   0.006   0.001   HIS B 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 9176)
  covalent geometry    : angle       0.53065 (12429)
  SS BOND              : bond        0.00116 (    1)
  SS BOND              : angle       0.24447 (    2)
  hydrogen bonds       : bond        0.03926 (  451)
  hydrogen bonds       : angle       4.72267 ( 1266)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  333 is missing expected H atoms. Skipping.
Residue SER  136 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Evaluate side-chains
  293 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 274
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.7491 (tt0) cc_final: 0.7176 (tm-30)
REVERT: A  214 CYS cc_start: 0.8296 (m) cc_final: 0.8040 (m)
REVERT: A  216 ASN cc_start: 0.8151 (t0) cc_final: 0.7871 (t0)
REVERT: A  217 ASP cc_start: 0.7790 (t0) cc_final: 0.7346 (t0)
REVERT: A  241 LYS cc_start: 0.8109 (tttt) cc_final: 0.7858 (tttp)
REVERT: A  250 ARG cc_start: 0.7904 (ttp-170) cc_final: 0.7570 (ptp-110)
REVERT: A  263 LEU cc_start: 0.8299 (mm) cc_final: 0.8087 (mt)
REVERT: A  273 SER cc_start: 0.8530 (t) cc_final: 0.8139 (p)
REVERT: A  311 GLU cc_start: 0.7687 (tp30) cc_final: 0.7416 (tp30)
REVERT: A  316 SER cc_start: 0.8032 (t) cc_final: 0.7602 (p)
REVERT: A  347 LYS cc_start: 0.8040 (mttt) cc_final: 0.7769 (mmmm)
REVERT: B  194 SER cc_start: 0.8447 (m) cc_final: 0.8131 (p)
REVERT: B  196 SER cc_start: 0.8550 (t) cc_final: 0.8025 (p)
REVERT: B  232 SER cc_start: 0.8507 (m) cc_final: 0.8265 (m)
REVERT: B  300 ASN cc_start: 0.8035 (m-40) cc_final: 0.7772 (m-40)
REVERT: E   17 ARG cc_start: 0.7910 (tpt90) cc_final: 0.7586 (mmt90)
REVERT: E   38 GLN cc_start: 0.8416 (tt0) cc_final: 0.8168 (tt0)
REVERT: E   44 LEU cc_start: 0.8815 (mt) cc_final: 0.8592 (mp)
REVERT: E   64 LYS cc_start: 0.8354 (ttmm) cc_final: 0.8132 (ttmm)
REVERT: E   92 MET cc_start: 0.8297 (ttm) cc_final: 0.8040 (ttt)
REVERT: E  158 SER cc_start: 0.8677 (m) cc_final: 0.8332 (t)
REVERT: E  194 ASN cc_start: 0.8098 (m110) cc_final: 0.7857 (m110)
REVERT: E  219 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8352 (tp)
REVERT: G   18 LEU cc_start: 0.8332 (mm) cc_final: 0.8078 (mt)
REVERT: G   29 VAL cc_start: 0.8654 (t) cc_final: 0.8382 (p)
REVERT: R  109 VAL cc_start: 0.7479 (t) cc_final: 0.7172 (t)
REVERT: R  129 LEU cc_start: 0.8070 (mp) cc_final: 0.7841 (mm)
REVERT: R  135 TYR cc_start: 0.7066 (m-80) cc_final: 0.6720 (m-80)
REVERT: R  164 VAL cc_start: 0.6918 (t) cc_final: 0.5236 (p)
REVERT: R  223 ARG cc_start: 0.7842 (mmt180) cc_final: 0.7616 (mmm160)
REVERT: R  229 ASN cc_start: 0.8148 (OUTLIER) cc_final: 0.7892 (t0)
REVERT: R  237 LEU cc_start: 0.8516 (tp) cc_final: 0.8228 (tm)
REVERT: R  317 ARG cc_start: 0.8298 (mtm180) cc_final: 0.8039 (mtm180)
  outliers start: 19
  outliers final: 15
  residues processed: 285
  average time/residue: 1.0997
  time to fit residues: 336.9260
Evaluate side-chains
  286 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 269
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 SER
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain B residue   18 GLN
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  223 CYS
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  252 ASP
Chi-restraints excluded: chain B residue  322 CYS
Chi-restraints excluded: chain B residue  330 MET
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain E residue  219 LEU
Chi-restraints excluded: chain E residue  235 TYR
Chi-restraints excluded: chain R residue  114 LEU
Chi-restraints excluded: chain R residue  122 TRP
Chi-restraints excluded: chain R residue  156 SER
Chi-restraints excluded: chain R residue  229 ASN
Chi-restraints excluded: chain R residue  357 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 83 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 109 optimal weight:    0.9980
   chunk 2 optimal weight:    0.0040
   chunk 42 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.6992

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

Flipped N/Q/H residues before XYZ refinement:
A 245 ASN
A 259 ASN
A 324 HIS
** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 147 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.132642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.117274 restraints weight = 37547.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 2.07
r_work: 0.3463 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3318 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.3640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9177  Z= 0.136
  Angle     :  0.532   7.771  12431  Z= 0.280
  Chirality :  0.041   0.172   1403
  Planarity :  0.004   0.052   1582
  Dihedral  :  5.040  58.346   1254
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 20.51 %
    Favored  : 77.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.26), residues: 1124
  helix:  2.20 (0.26), residues: 392
  sheet: -0.69 (0.31), residues: 265
  loop : -0.38 (0.30), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 219 
 TYR   0.023   0.001   TYR E 235 
 PHE   0.012   0.001   PHE R 313 
 TRP   0.010   0.001   TRP B 174 
 HIS   0.004   0.001   HIS R 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 9176)
  covalent geometry    : angle       0.53211 (12429)
  SS BOND              : bond        0.00092 (    1)
  SS BOND              : angle       0.33530 (    2)
  hydrogen bonds       : bond        0.03882 (  451)
  hydrogen bonds       : angle       4.68401 ( 1266)

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  241 is missing expected H atoms. Skipping.
Residue SER  333 is missing expected H atoms. Skipping.
Residue SER  136 is missing expected H atoms. Skipping.
Residue LEU  221 is missing expected H atoms. Skipping.
Residue VAL  222 is missing expected H atoms. Skipping.
Evaluate side-chains
  291 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 273
  time to evaluate  : 0.527 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.7476 (tt0) cc_final: 0.7163 (tm-30)
REVERT: A  214 CYS cc_start: 0.8290 (m) cc_final: 0.8022 (m)
REVERT: A  216 ASN cc_start: 0.8175 (t0) cc_final: 0.7899 (t0)
REVERT: A  217 ASP cc_start: 0.7782 (t0) cc_final: 0.7353 (t0)
REVERT: A  241 LYS cc_start: 0.8088 (tttt) cc_final: 0.7850 (tttp)
REVERT: A  250 ARG cc_start: 0.7864 (ttp-170) cc_final: 0.7509 (ptp-110)
REVERT: A  263 LEU cc_start: 0.8278 (mm) cc_final: 0.8030 (mt)
REVERT: A  273 SER cc_start: 0.8529 (t) cc_final: 0.8144 (p)
REVERT: A  311 GLU cc_start: 0.7660 (tp30) cc_final: 0.7401 (tp30)
REVERT: A  313 VAL cc_start: 0.7565 (t) cc_final: 0.7249 (t)
REVERT: A  316 SER cc_start: 0.8015 (t) cc_final: 0.7601 (p)
REVERT: A  347 LYS cc_start: 0.8047 (mttt) cc_final: 0.7769 (mmmm)
REVERT: B  196 SER cc_start: 0.8548 (t) cc_final: 0.8020 (p)
REVERT: B  232 SER cc_start: 0.8491 (m) cc_final: 0.8239 (m)
REVERT: E   17 ARG cc_start: 0.7908 (tpt90) cc_final: 0.7586 (mmt90)
REVERT: E   38 GLN cc_start: 0.8427 (tt0) cc_final: 0.8185 (tt0)
REVERT: E   44 LEU cc_start: 0.8806 (mt) cc_final: 0.8591 (mp)
REVERT: E   58 TYR cc_start: 0.7798 (m-10) cc_final: 0.7566 (m-10)
REVERT: E   64 LYS cc_start: 0.8343 (ttmm) cc_final: 0.8118 (ttmm)
REVERT: E   92 MET cc_start: 0.8278 (ttm) cc_final: 0.8029 (ttt)
REVERT: E  158 SER cc_start: 0.8656 (m) cc_final: 0.8308 (t)
REVERT: E  194 ASN cc_start: 0.8081 (m110) cc_final: 0.7837 (m110)
REVERT: E  219 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8357 (tp)
REVERT: G   18 LEU cc_start: 0.8280 (mm) cc_final: 0.8022 (mt)
REVERT: G   29 VAL cc_start: 0.8634 (t) cc_final: 0.8360 (p)
REVERT: R  109 VAL cc_start: 0.7467 (t) cc_final: 0.7172 (t)
REVERT: R  129 LEU cc_start: 0.8082 (mp) cc_final: 0.7848 (mm)
REVERT: R  135 TYR cc_start: 0.7077 (m-80) cc_final: 0.6743 (m-80)
REVERT: R  164 VAL cc_start: 0.7040 (t) cc_final: 0.5370 (p)
REVERT: R  223 ARG cc_start: 0.7847 (mmt180) cc_final: 0.7606 (mmm160)
REVERT: R  229 ASN cc_start: 0.8150 (OUTLIER) cc_final: 0.7894 (t0)
REVERT: R  237 LEU cc_start: 0.8449 (tp) cc_final: 0.8174 (tm)
  outliers start: 18
  outliers final: 15
  residues processed: 283
  average time/residue: 1.0737
  time to fit residues: 326.0738
Evaluate side-chains
  289 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 272
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 SER
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain B residue   18 GLN
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  223 CYS
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  322 CYS
Chi-restraints excluded: chain B residue  330 MET
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain E residue  219 LEU
Chi-restraints excluded: chain E residue  235 TYR
Chi-restraints excluded: chain R residue  114 LEU
Chi-restraints excluded: chain R residue  156 SER
Chi-restraints excluded: chain R residue  229 ASN
Chi-restraints excluded: chain R residue  343 ILE
Chi-restraints excluded: chain R residue  357 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 12 optimal weight:    0.4980
   chunk 45 optimal weight:    4.9990
   chunk 94 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 67 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 64 optimal weight:    0.7980
   chunk 42 optimal weight:    0.2980
   chunk 6 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 245 ASN
A 259 ASN
** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.132659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.117522 restraints weight = 37833.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.3572 rms_B_bonded: 2.07
r_work: 0.3467 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3324 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.3687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9177  Z= 0.133
  Angle     :  0.534   7.228  12431  Z= 0.281
  Chirality :  0.041   0.158   1403
  Planarity :  0.004   0.052   1582
  Dihedral  :  4.997  58.298   1254
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 20.41 %
    Favored  : 77.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.26), residues: 1124
  helix:  2.23 (0.26), residues: 392
  sheet: -0.69 (0.30), residues: 265
  loop : -0.36 (0.30), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 300 
 TYR   0.022   0.001   TYR E 235 
 PHE   0.013   0.001   PHE R 313 
 TRP   0.011   0.001   TRP B 174 
 HIS   0.005   0.001   HIS A 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 9176)
  covalent geometry    : angle       0.53388 (12429)
  SS BOND              : bond        0.00097 (    1)
  SS BOND              : angle       0.24060 (    2)
  hydrogen bonds       : bond        0.03830 (  451)
  hydrogen bonds       : angle       4.67831 ( 1266)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7967.47 seconds
wall clock time: 135 minutes 14.97 seconds (8114.97 seconds total)