Starting phenix.real_space_refine
on Tue Mar  3 16:35:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ezk_31388/03_2026/7ezk_31388.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ezk_31388/03_2026/7ezk_31388.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ezk_31388/03_2026/7ezk_31388.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ezk_31388/03_2026/7ezk_31388.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ezk_31388/03_2026/7ezk_31388.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ezk_31388/03_2026/7ezk_31388.cif"
  }
  resolution = 3.1
  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=   0.033
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    4584      2.51       5
     N    1242      2.21       5
     O    1313      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 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: 7196
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1871
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1871
          Classifications: {'peptide': 227}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 6, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 2561
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2561
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 35
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 41
    Chain: "D"
      Number of atoms: 2298
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 294, 2298
          Classifications: {'peptide': 294}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 12, 'TRANS': 281}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 50
          Unresolved non-hydrogen angles: 60
          Unresolved non-hydrogen dihedrals: 42
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 36
    Chain: "G"
      Number of atoms: 388
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 388
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "P"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
          Unresolved chain link angles: 1
          Unresolved chain link dihedrals: 2
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYS:plan-2': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 8
  Time building chain proxies: 1.72, per 1000 atoms: 0.24
  Number of scatterers: 7196
  At special positions: 0
  Unit cell: (102.41, 113.905, 101.365, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      57     16.00
     O    1313      8.00
     N    1242      7.00
     C    4584      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS D 114 " - pdb=" SG  CYS D 196 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.73
  Conformation dependent library (CDL) restraints added in 275.5 milliseconds
  

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1752

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 10 sheets defined
      49.0% alpha, 18.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 3.726A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   LYS A  25 " --> pdb=" O   LYS A  21 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   VAL A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 49
    Processing helix  chain 'A' and resid 208 through 213
      removed outlier: 3.997A  pdb=" N   GLN A 213 " --> pdb=" O   ARG A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 216
      No H-bonds generated for 'chain 'A' and resid 214 through 216'
    Processing helix  chain 'A' and resid 229 through 246
      removed outlier: 3.974A  pdb=" N   GLN A 234 " --> pdb=" O   TYR A 230 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   GLU A 235 " --> pdb=" O   ASN A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 270
    Processing helix  chain 'A' and resid 274 through 279
      removed outlier: 3.947A  pdb=" N   TYR A 278 " --> pdb=" O   LYS A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 285
    Processing helix  chain 'A' and resid 298 through 319
      removed outlier: 3.651A  pdb=" N   SER A 319 " --> pdb=" O   ILE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 359
      removed outlier: 4.223A  pdb=" N   GLN A 357 " --> pdb=" O   MET A 353 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   TYR A 358 " --> pdb=" O   HIS A 354 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 24
      removed outlier: 5.314A  pdb=" N   GLN B   9 " --> pdb=" O   ASP B   5 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.566A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 39 through 69
      removed outlier: 4.320A  pdb=" N   VAL D  43 " --> pdb=" O   TRP D  39 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 70 through 73
    Processing helix  chain 'D' and resid 74 through 95
    Processing helix  chain 'D' and resid 95 through 105
      Proline residue:  D 101  - end of helix
    Processing helix  chain 'D' and resid 110 through 145
    Processing helix  chain 'D' and resid 145 through 150
      removed outlier: 4.279A  pdb=" N   ARG D 150 " --> pdb=" O   PRO D 146 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 151 through 153
      No H-bonds generated for 'chain 'D' and resid 151 through 153'
    Processing helix  chain 'D' and resid 154 through 173
    Processing helix  chain 'D' and resid 174 through 179
    Processing helix  chain 'D' and resid 202 through 218
    Processing helix  chain 'D' and resid 218 through 246
    Processing helix  chain 'D' and resid 302 through 339
      Proline residue:  D 328  - end of helix
    Processing helix  chain 'D' and resid 339 through 348
    Processing helix  chain 'D' and resid 349 through 371
      removed outlier: 4.281A  pdb=" N   SER D 363 " --> pdb=" O   SER D 359 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   CYS D 364 " --> pdb=" O   TYR D 360 " (cutoff:3.500A)
      Proline residue:  D 367  - end of helix
    Processing helix  chain 'D' and resid 374 through 382
      removed outlier: 4.503A  pdb=" N   GLY D 380 " --> pdb=" O   ARG D 376 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 12 through 24
      removed outlier: 4.049A  pdb=" N   VAL G  16 " --> pdb=" O   ALA G  12 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 45
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.339A  pdb=" N   HIS A  34 " --> pdb=" O   HIS A 197 " (cutoff:3.500A)
      removed outlier: 7.909A  pdb=" N   PHE A 199 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.851A  pdb=" N   ILE A 222 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.223A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 8.391A  pdb=" N   ASP A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
      removed outlier: 7.254A  pdb=" N   PHE A 257 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 257 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   ASN A 259 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.703A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.718A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.881A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.012A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.032A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.222A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.600A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.865A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.177A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.383A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 231 through 234
      removed outlier: 3.783A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.922A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 180 through 181
    Processing sheet with id=AB1, first strand: chain 'D' and resid 184 through 186

    400 hydrogen bonds defined for protein.
    1152 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.17

  Time building geometry restraints manager: 0.94 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1832
        1.33 -     1.46: 2104
        1.46 -     1.60: 3323
        1.60 -     1.73: 1
        1.73 -     1.86: 84
  Bond restraints: 7344
  Sorted by residual:
  bond pdb=" O3  TYS P   2 "
       pdb=" S   TYS P   2 "
    ideal  model  delta    sigma   weight residual
    1.458  1.630 -0.172 2.00e-02 2.50e+03 7.41e+01
  bond pdb=" OH  TYS P   2 "
       pdb=" S   TYS P   2 "
    ideal  model  delta    sigma   weight residual
    1.679  1.567  0.112 2.00e-02 2.50e+03 3.16e+01
  bond pdb=" O2  TYS P   2 "
       pdb=" S   TYS P   2 "
    ideal  model  delta    sigma   weight residual
    1.461  1.411  0.050 2.00e-02 2.50e+03 6.26e+00
  bond pdb=" CZ  ARG A 347 "
       pdb=" NH2 ARG A 347 "
    ideal  model  delta    sigma   weight residual
    1.330  1.300  0.030 1.30e-02 5.92e+03 5.21e+00
  bond pdb=" CZ  ARG A  31 "
       pdb=" NH1 ARG A  31 "
    ideal  model  delta    sigma   weight residual
    1.323  1.354 -0.031 1.40e-02 5.10e+03 4.85e+00
  ... (remaining 7339 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.41: 9672
        2.41 -     4.81: 264
        4.81 -     7.22: 21
        7.22 -     9.62: 3
        9.62 -    12.03: 2
  Bond angle restraints: 9962
  Sorted by residual:
  angle pdb=" O2  TYS P   2 "
        pdb=" S   TYS P   2 "
        pdb=" O3  TYS P   2 "
      ideal   model   delta    sigma   weight residual
     115.38  103.35   12.03 3.00e+00 1.11e-01 1.61e+01
  angle pdb=" OH  TYS P   2 "
        pdb=" S   TYS P   2 "
        pdb=" O3  TYS P   2 "
      ideal   model   delta    sigma   weight residual
     100.21  110.88  -10.67 3.00e+00 1.11e-01 1.27e+01
  angle pdb=" N   ARG D 310 "
        pdb=" CA  ARG D 310 "
        pdb=" C   ARG D 310 "
      ideal   model   delta    sigma   weight residual
     111.36  107.77    3.59 1.09e+00 8.42e-01 1.08e+01
  angle pdb=" CZ  TYS P   2 "
        pdb=" OH  TYS P   2 "
        pdb=" S   TYS P   2 "
      ideal   model   delta    sigma   weight residual
     116.88  126.28   -9.40 3.00e+00 1.11e-01 9.81e+00
  angle pdb=" NE  ARG B  48 "
        pdb=" CZ  ARG B  48 "
        pdb=" NH1 ARG B  48 "
      ideal   model   delta    sigma   weight residual
     121.50  118.68    2.82 1.00e+00 1.00e+00 7.93e+00
  ... (remaining 9957 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 4031
       17.82 -    35.64: 282
       35.64 -    53.46: 41
       53.46 -    71.28: 13
       71.28 -    89.10: 7
  Dihedral angle restraints: 4374
    sinusoidal: 1681
      harmonic: 2693
  Sorted by residual:
  dihedral pdb=" CA  ASP A 217 "
           pdb=" C   ASP A 217 "
           pdb=" N   VAL A 218 "
           pdb=" CA  VAL A 218 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.64   29.36     0      5.00e+00 4.00e-02 3.45e+01
  dihedral pdb=" CA  TYR B 289 "
           pdb=" C   TYR B 289 "
           pdb=" N   ASP B 290 "
           pdb=" CA  ASP B 290 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.65   29.35     0      5.00e+00 4.00e-02 3.45e+01
  dihedral pdb=" CA  LYS B  78 "
           pdb=" C   LYS B  78 "
           pdb=" N   LEU B  79 "
           pdb=" CA  LEU B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.19   27.81     0      5.00e+00 4.00e-02 3.09e+01
  ... (remaining 4371 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 698
       0.053 -    0.105: 351
       0.105 -    0.157: 81
       0.157 -    0.210: 8
       0.210 -    0.262: 4
  Chirality restraints: 1142
  Sorted by residual:
  chirality pdb=" CG  LEU D 214 "
            pdb=" CB  LEU D 214 "
            pdb=" CD1 LEU D 214 "
            pdb=" CD2 LEU D 214 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.33   -0.26 2.00e-01 2.50e+01 1.72e+00
  chirality pdb=" CB  ILE A 184 "
            pdb=" CA  ILE A 184 "
            pdb=" CG1 ILE A 184 "
            pdb=" CG2 ILE A 184 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CB  VAL D 151 "
            pdb=" CA  VAL D 151 "
            pdb=" CG1 VAL D 151 "
            pdb=" CG2 VAL D 151 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 1139 not shown)

  Planarity restraints: 1261
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 300 "    0.064 9.50e-02 1.11e+02   4.95e-02 2.07e+01
        pdb=" NE  ARG A 300 "   -0.030 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 300 "    0.077 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 300 "   -0.027 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 300 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO D 367 "    0.019 2.00e-02 2.50e+03   3.84e-02 1.48e+01
        pdb=" C   PRO D 367 "   -0.066 2.00e-02 2.50e+03
        pdb=" O   PRO D 367 "    0.024 2.00e-02 2.50e+03
        pdb=" N   ILE D 368 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU D 214 "   -0.019 2.00e-02 2.50e+03   3.74e-02 1.40e+01
        pdb=" C   LEU D 214 "    0.065 2.00e-02 2.50e+03
        pdb=" O   LEU D 214 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   LEU D 215 "   -0.022 2.00e-02 2.50e+03
  ... (remaining 1258 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 689
        2.74 -     3.28: 7507
        3.28 -     3.82: 12112
        3.82 -     4.36: 14972
        4.36 -     4.90: 25331
  Nonbonded interactions: 60611
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" OD1 ASN D  98 "
            pdb=" OH  TYR D 360 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" NZ  LYS D 115 "
            pdb=" O   PRO D 177 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" NH2 ARG A 205 "
            pdb=" OE1 GLU A 207 "
     model   vdw
     2.312 3.120
  nonbonded pdb=" NH1 ARG D 197 "
            pdb=" O1  TYS P   2 "
     model   vdw
     2.337 3.120
  ... (remaining 60606 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.370
  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:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.300
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6906
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      :  0.011   0.172   7345  Z= 0.555
  Angle     :  1.037  12.028   9964  Z= 0.616
  Chirality :  0.061   0.262   1142
  Planarity :  0.010   0.082   1261
  Dihedral  : 13.268  89.095   2619
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  2.34 %
    Favored  : 97.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.02 (0.27), residues: 905
  helix: -0.92 (0.22), residues: 399
  sheet:  0.04 (0.38), residues: 191
  loop : -0.47 (0.37), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.078   0.010   ARG A 300 
 TYR   0.028   0.008   TYR D 229 
 PHE   0.033   0.006   PHE G  61 
 TRP   0.034   0.008   TRP B  99 
 HIS   0.020   0.007   HIS A 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.01058 ( 7344)
  covalent geometry    : angle       1.03652 ( 9962)
  SS BOND              : bond        0.00628 (    1)
  SS BOND              : angle       1.84624 (    2)
  hydrogen bonds       : bond        0.13855 (  400)
  hydrogen bonds       : angle       6.54292 ( 1152)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 225
  time to evaluate  : 0.275 
Fit side-chains
REVERT: A   20 GLU cc_start: 0.6657 (mt-10) cc_final: 0.6164 (mt-10)
REVERT: A  216 ASN cc_start: 0.8316 (t0) cc_final: 0.8111 (t0)
REVERT: A  223 PHE cc_start: 0.8172 (t80) cc_final: 0.7865 (t80)
REVERT: A  276 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6866 (mt-10)
REVERT: A  348 ASP cc_start: 0.7331 (t70) cc_final: 0.6992 (t0)
REVERT: B   59 TYR cc_start: 0.7599 (OUTLIER) cc_final: 0.7101 (m-80)
REVERT: B   76 ASP cc_start: 0.6661 (t70) cc_final: 0.6347 (t0)
REVERT: B  145 TYR cc_start: 0.8301 (p90) cc_final: 0.7667 (p90)
REVERT: B  147 SER cc_start: 0.8402 (t) cc_final: 0.8053 (p)
REVERT: B  149 CYS cc_start: 0.7155 (p) cc_final: 0.6674 (p)
REVERT: B  150 ARG cc_start: 0.8148 (mmt-90) cc_final: 0.7427 (mmt-90)
REVERT: B  188 MET cc_start: 0.7168 (tpt) cc_final: 0.6900 (mmm)
REVERT: B  189 SER cc_start: 0.8346 (p) cc_final: 0.8026 (t)
REVERT: B  191 SER cc_start: 0.8118 (m) cc_final: 0.7915 (p)
REVERT: B  201 SER cc_start: 0.8254 (m) cc_final: 0.7588 (p)
REVERT: B  273 ILE cc_start: 0.7793 (mt) cc_final: 0.7363 (mt)
REVERT: B  277 SER cc_start: 0.8177 (t) cc_final: 0.7701 (m)
REVERT: B  295 ASN cc_start: 0.7992 (m-40) cc_final: 0.7720 (m110)
REVERT: B  325 MET cc_start: 0.6838 (tpp) cc_final: 0.6452 (tpp)
REVERT: B  333 ASP cc_start: 0.6664 (m-30) cc_final: 0.6419 (m-30)
REVERT: D   56 VAL cc_start: 0.6996 (t) cc_final: 0.6674 (m)
REVERT: D   86 SER cc_start: 0.8548 (t) cc_final: 0.8144 (p)
REVERT: D  117 THR cc_start: 0.7240 (m) cc_final: 0.6852 (p)
REVERT: D  382 MET cc_start: 0.5512 (mpp) cc_final: 0.5130 (mpp)
  outliers start: 2
  outliers final: 0
  residues processed: 225
  average time/residue: 0.0892
  time to fit residues: 26.8418
Evaluate side-chains
  196 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 195
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.2980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    0.4980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
B 268 ASN
D 131 ASN
** D 210 HIS ** 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 = 0.3844 r_free = 0.3844 target = 0.146150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.126561 restraints weight = 9834.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 2.16
r_work: 0.3446 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3275 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7356
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7345  Z= 0.152
  Angle     :  0.580   6.260   9964  Z= 0.308
  Chirality :  0.044   0.142   1142
  Planarity :  0.005   0.055   1261
  Dihedral  :  5.789  48.924    998
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 10.40 %
    Favored  : 87.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.62 (0.29), residues: 905
  helix:  1.05 (0.26), residues: 402
  sheet: -0.23 (0.36), residues: 197
  loop :  0.24 (0.40), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 352 
 TYR   0.012   0.002   TYR D 176 
 PHE   0.014   0.002   PHE A 189 
 TRP   0.021   0.002   TRP B 339 
 HIS   0.006   0.001   HIS A 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 7344)
  covalent geometry    : angle       0.57961 ( 9962)
  SS BOND              : bond        0.00050 (    1)
  SS BOND              : angle       1.72619 (    2)
  hydrogen bonds       : bond        0.04353 (  400)
  hydrogen bonds       : angle       5.17560 ( 1152)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 221
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ILE cc_start: 0.7822 (mm) cc_final: 0.7376 (mt)
REVERT: A   20 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6831 (mt-10)
REVERT: A   27 LYS cc_start: 0.8239 (tttt) cc_final: 0.7923 (tttm)
REVERT: A  216 ASN cc_start: 0.8418 (t0) cc_final: 0.8157 (t0)
REVERT: A  223 PHE cc_start: 0.8517 (t80) cc_final: 0.8282 (t80)
REVERT: A  237 LEU cc_start: 0.8024 (tp) cc_final: 0.7784 (mt)
REVERT: A  247 ARG cc_start: 0.7903 (mtt90) cc_final: 0.7301 (mtt90)
REVERT: A  250 ARG cc_start: 0.6679 (mtt180) cc_final: 0.6448 (mtt180)
REVERT: A  276 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7090 (mt-10)
REVERT: A  359 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7188 (mt-10)
REVERT: B   59 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.7614 (m-80)
REVERT: B   68 ARG cc_start: 0.7763 (ttt90) cc_final: 0.7476 (ttt90)
REVERT: B   98 SER cc_start: 0.7884 (m) cc_final: 0.7654 (p)
REVERT: B  145 TYR cc_start: 0.8447 (p90) cc_final: 0.7559 (p90)
REVERT: B  147 SER cc_start: 0.8532 (t) cc_final: 0.8288 (t)
REVERT: B  163 ASP cc_start: 0.7364 (p0) cc_final: 0.6967 (p0)
REVERT: B  181 THR cc_start: 0.8204 (p) cc_final: 0.7809 (m)
REVERT: B  188 MET cc_start: 0.7850 (tpt) cc_final: 0.7393 (mmm)
REVERT: B  189 SER cc_start: 0.8510 (p) cc_final: 0.8213 (t)
REVERT: B  201 SER cc_start: 0.8542 (m) cc_final: 0.8190 (p)
REVERT: B  214 ARG cc_start: 0.7575 (mpt90) cc_final: 0.7050 (mpt180)
REVERT: B  217 MET cc_start: 0.7692 (tpp) cc_final: 0.7350 (tpp)
REVERT: B  219 ARG cc_start: 0.7354 (mmt180) cc_final: 0.7114 (mmt-90)
REVERT: B  233 CYS cc_start: 0.8191 (t) cc_final: 0.7945 (t)
REVERT: B  253 PHE cc_start: 0.8145 (m-80) cc_final: 0.7814 (m-80)
REVERT: B  283 ARG cc_start: 0.8422 (tpt-90) cc_final: 0.8019 (tpt170)
REVERT: B  316 SER cc_start: 0.7837 (t) cc_final: 0.7544 (p)
REVERT: B  325 MET cc_start: 0.8128 (tpp) cc_final: 0.7810 (tpp)
REVERT: B  333 ASP cc_start: 0.7349 (m-30) cc_final: 0.6954 (m-30)
REVERT: D   56 VAL cc_start: 0.7260 (t) cc_final: 0.6909 (m)
REVERT: D   80 LEU cc_start: 0.7714 (mt) cc_final: 0.7435 (mp)
REVERT: D   86 SER cc_start: 0.8879 (t) cc_final: 0.8622 (p)
REVERT: D  104 LEU cc_start: 0.8128 (mt) cc_final: 0.7915 (mt)
REVERT: D  118 THR cc_start: 0.8620 (t) cc_final: 0.8127 (p)
REVERT: D  121 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7622 (mtt)
REVERT: D  182 LEU cc_start: 0.8205 (tp) cc_final: 0.7890 (tt)
REVERT: D  195 MET cc_start: 0.7387 (ptp) cc_final: 0.7184 (mtm)
  outliers start: 17
  outliers final: 9
  residues processed: 225
  average time/residue: 0.0955
  time to fit residues: 28.3957
Evaluate side-chains
  224 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 213
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain D residue  121 MET
Chi-restraints excluded: chain D residue  136 SER
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  316 ILE
Chi-restraints excluded: chain D residue  340 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 59 optimal weight:    0.5980
   chunk 57 optimal weight:    0.8980
   chunk 24 optimal weight:    9.9990
   chunk 1 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 62 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.141736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.120756 restraints weight = 9915.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3552 rms_B_bonded: 2.23
r_work: 0.3413 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.2599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7345  Z= 0.155
  Angle     :  0.544   7.009   9964  Z= 0.286
  Chirality :  0.043   0.138   1142
  Planarity :  0.004   0.053   1261
  Dihedral  :  5.384  48.678    998
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 13.26 %
    Favored  : 83.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.29), residues: 905
  helix:  1.52 (0.27), residues: 389
  sheet: -0.53 (0.35), residues: 204
  loop :  0.38 (0.40), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 251 
 TYR   0.012   0.001   TYR B 289 
 PHE   0.015   0.001   PHE A 189 
 TRP   0.015   0.002   TRP B 339 
 HIS   0.004   0.001   HIS D 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 7344)
  covalent geometry    : angle       0.54361 ( 9962)
  SS BOND              : bond        0.00202 (    1)
  SS BOND              : angle       1.28583 (    2)
  hydrogen bonds       : bond        0.04121 (  400)
  hydrogen bonds       : angle       4.97381 ( 1152)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 224
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.7747 (mmtt) cc_final: 0.7259 (mmtt)
REVERT: A   20 GLU cc_start: 0.7597 (mt-10) cc_final: 0.6929 (mt-10)
REVERT: A  186 GLU cc_start: 0.7500 (tt0) cc_final: 0.7236 (tt0)
REVERT: A  192 ASP cc_start: 0.7753 (m-30) cc_final: 0.7547 (m-30)
REVERT: A  216 ASN cc_start: 0.8322 (t0) cc_final: 0.8077 (t0)
REVERT: A  267 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8186 (mttp)
REVERT: A  276 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7060 (mt-10)
REVERT: A  309 ARG cc_start: 0.7867 (ttp-170) cc_final: 0.7487 (ttp-170)
REVERT: A  341 ARG cc_start: 0.8601 (mtt90) cc_final: 0.8166 (mtt180)
REVERT: B   59 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.7663 (m-80)
REVERT: B   68 ARG cc_start: 0.7812 (ttt90) cc_final: 0.7528 (ttt90)
REVERT: B   83 ASP cc_start: 0.8118 (t0) cc_final: 0.7575 (t0)
REVERT: B   98 SER cc_start: 0.7963 (m) cc_final: 0.7753 (p)
REVERT: B  137 ARG cc_start: 0.8086 (mmt-90) cc_final: 0.7744 (mmt-90)
REVERT: B  145 TYR cc_start: 0.8464 (p90) cc_final: 0.7560 (p90)
REVERT: B  147 SER cc_start: 0.8527 (t) cc_final: 0.8205 (p)
REVERT: B  201 SER cc_start: 0.8569 (m) cc_final: 0.8331 (p)
REVERT: B  214 ARG cc_start: 0.7733 (mpt90) cc_final: 0.7102 (mpt180)
REVERT: B  217 MET cc_start: 0.7849 (tpp) cc_final: 0.7558 (tpp)
REVERT: B  219 ARG cc_start: 0.7405 (mmt180) cc_final: 0.6973 (mmt-90)
REVERT: B  233 CYS cc_start: 0.8485 (t) cc_final: 0.8154 (t)
REVERT: B  268 ASN cc_start: 0.7062 (m-40) cc_final: 0.6789 (m-40)
REVERT: B  277 SER cc_start: 0.8251 (t) cc_final: 0.7665 (m)
REVERT: B  304 ARG cc_start: 0.8058 (ttm170) cc_final: 0.7695 (ttm170)
REVERT: B  325 MET cc_start: 0.8094 (tpp) cc_final: 0.7718 (tpp)
REVERT: D   56 VAL cc_start: 0.7408 (t) cc_final: 0.7051 (m)
REVERT: D   86 SER cc_start: 0.8822 (t) cc_final: 0.8598 (p)
REVERT: D   98 ASN cc_start: 0.8304 (m-40) cc_final: 0.7790 (m110)
REVERT: D  104 LEU cc_start: 0.8136 (mt) cc_final: 0.7895 (mt)
REVERT: D  121 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7752 (mtm)
REVERT: D  123 THR cc_start: 0.8188 (m) cc_final: 0.7949 (p)
REVERT: D  136 SER cc_start: 0.8450 (t) cc_final: 0.7875 (p)
REVERT: D  182 LEU cc_start: 0.8152 (tp) cc_final: 0.7898 (tt)
REVERT: D  195 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7014 (mtm)
  outliers start: 23
  outliers final: 13
  residues processed: 231
  average time/residue: 0.1174
  time to fit residues: 34.1667
Evaluate side-chains
  224 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 207
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain D residue  121 MET
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  195 MET
Chi-restraints excluded: chain D residue  226 MET
Chi-restraints excluded: chain D residue  331 SER
Chi-restraints excluded: chain D residue  340 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0020
   chunk 83 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.8992

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.142734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.121444 restraints weight = 9896.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3525 rms_B_bonded: 2.25
r_work: 0.3385 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3209 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.3054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7345  Z= 0.166
  Angle     :  0.554   7.615   9964  Z= 0.289
  Chirality :  0.044   0.140   1142
  Planarity :  0.004   0.052   1261
  Dihedral  :  5.216  47.779    998
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 14.43 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.88 (0.29), residues: 905
  helix:  1.64 (0.27), residues: 390
  sheet: -0.64 (0.36), residues: 196
  loop :  0.25 (0.39), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  35 
 TYR   0.013   0.001   TYR B 289 
 PHE   0.016   0.001   PHE A 189 
 TRP   0.013   0.002   TRP B 339 
 HIS   0.004   0.001   HIS A 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 7344)
  covalent geometry    : angle       0.55344 ( 9962)
  SS BOND              : bond        0.00259 (    1)
  SS BOND              : angle       1.57741 (    2)
  hydrogen bonds       : bond        0.04103 (  400)
  hydrogen bonds       : angle       4.94700 ( 1152)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 211
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.7805 (mmtt) cc_final: 0.7411 (mmtt)
REVERT: A   20 GLU cc_start: 0.7622 (mt-10) cc_final: 0.6990 (mt-10)
REVERT: A  186 GLU cc_start: 0.7543 (tt0) cc_final: 0.7303 (tt0)
REVERT: A  216 ASN cc_start: 0.8295 (t0) cc_final: 0.8077 (t0)
REVERT: A  247 ARG cc_start: 0.8017 (mtt90) cc_final: 0.7201 (mtt90)
REVERT: A  250 ARG cc_start: 0.7080 (mtt180) cc_final: 0.6675 (mtt180)
REVERT: A  267 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8195 (mttp)
REVERT: A  276 GLU cc_start: 0.7356 (mt-10) cc_final: 0.7082 (mt-10)
REVERT: A  311 GLU cc_start: 0.6821 (mm-30) cc_final: 0.6219 (mm-30)
REVERT: A  314 ARG cc_start: 0.7742 (ttm170) cc_final: 0.7365 (ttm170)
REVERT: A  335 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7572 (m-30)
REVERT: B   68 ARG cc_start: 0.7956 (ttt90) cc_final: 0.7501 (ttt90)
REVERT: B   98 SER cc_start: 0.8050 (m) cc_final: 0.7761 (p)
REVERT: B  147 SER cc_start: 0.8526 (t) cc_final: 0.8244 (p)
REVERT: B  214 ARG cc_start: 0.7784 (mpt90) cc_final: 0.7070 (mpt180)
REVERT: B  217 MET cc_start: 0.7946 (tpp) cc_final: 0.7272 (tpp)
REVERT: B  219 ARG cc_start: 0.7409 (mmt180) cc_final: 0.6927 (mmt-90)
REVERT: B  233 CYS cc_start: 0.8534 (t) cc_final: 0.8185 (t)
REVERT: B  268 ASN cc_start: 0.7086 (m-40) cc_final: 0.6802 (m-40)
REVERT: B  277 SER cc_start: 0.8243 (t) cc_final: 0.7681 (m)
REVERT: B  304 ARG cc_start: 0.8109 (ttm170) cc_final: 0.7711 (ttm170)
REVERT: B  322 ASP cc_start: 0.6939 (t0) cc_final: 0.6677 (t0)
REVERT: B  325 MET cc_start: 0.8052 (tpp) cc_final: 0.7724 (tpp)
REVERT: D   56 VAL cc_start: 0.7458 (t) cc_final: 0.7082 (m)
REVERT: D   86 SER cc_start: 0.8823 (t) cc_final: 0.8592 (p)
REVERT: D  104 LEU cc_start: 0.8140 (mt) cc_final: 0.7916 (mt)
REVERT: D  121 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7759 (mtt)
REVERT: D  123 THR cc_start: 0.8142 (m) cc_final: 0.7874 (p)
REVERT: D  136 SER cc_start: 0.8404 (t) cc_final: 0.7825 (p)
REVERT: D  137 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7816 (mt)
REVERT: D  139 ARG cc_start: 0.8378 (mtt180) cc_final: 0.8136 (mtt-85)
REVERT: D  182 LEU cc_start: 0.8199 (tp) cc_final: 0.7952 (tt)
REVERT: D  195 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.7177 (mtm)
REVERT: D  225 MET cc_start: 0.8410 (ttm) cc_final: 0.8176 (ttm)
REVERT: D  321 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6944 (tp)
REVERT: P    6 MET cc_start: 0.8140 (mtp) cc_final: 0.7914 (mtm)
  outliers start: 28
  outliers final: 13
  residues processed: 220
  average time/residue: 0.1130
  time to fit residues: 31.6806
Evaluate side-chains
  226 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 207
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  335 ASP
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain D residue  121 MET
Chi-restraints excluded: chain D residue  137 LEU
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  195 MET
Chi-restraints excluded: chain D residue  226 MET
Chi-restraints excluded: chain D residue  321 LEU
Chi-restraints excluded: chain D residue  327 MET
Chi-restraints excluded: chain D residue  331 SER
Chi-restraints excluded: chain D residue  340 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 87 optimal weight:    2.9990
   chunk 16 optimal weight:    0.4980
   chunk 35 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B 295 ASN
D  44 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.139998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.118644 restraints weight = 9898.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 2.26
r_work: 0.3376 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3201 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.3381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7345  Z= 0.158
  Angle     :  0.551   7.825   9964  Z= 0.285
  Chirality :  0.043   0.134   1142
  Planarity :  0.004   0.056   1261
  Dihedral  :  4.876  31.442    996
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 16.51 %
    Favored  : 80.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.85 (0.29), residues: 905
  helix:  1.70 (0.27), residues: 388
  sheet: -0.76 (0.35), residues: 196
  loop :  0.20 (0.38), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 251 
 TYR   0.011   0.001   TYR B 289 
 PHE   0.016   0.001   PHE A 189 
 TRP   0.013   0.002   TRP B 339 
 HIS   0.003   0.001   HIS G  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 7344)
  covalent geometry    : angle       0.55025 ( 9962)
  SS BOND              : bond        0.00256 (    1)
  SS BOND              : angle       1.67216 (    2)
  hydrogen bonds       : bond        0.03964 (  400)
  hydrogen bonds       : angle       4.93427 ( 1152)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 222
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.7855 (mmtt) cc_final: 0.7465 (mmtt)
REVERT: A   20 GLU cc_start: 0.7614 (mt-10) cc_final: 0.6977 (mt-10)
REVERT: A   26 ASP cc_start: 0.7444 (m-30) cc_final: 0.6978 (m-30)
REVERT: A  186 GLU cc_start: 0.7529 (tt0) cc_final: 0.7292 (tt0)
REVERT: A  216 ASN cc_start: 0.8172 (t0) cc_final: 0.7950 (t0)
REVERT: A  247 ARG cc_start: 0.8063 (mtt90) cc_final: 0.7250 (mtt90)
REVERT: A  250 ARG cc_start: 0.7296 (mtt180) cc_final: 0.6922 (mtt180)
REVERT: A  257 PHE cc_start: 0.8241 (m-80) cc_final: 0.8033 (m-80)
REVERT: A  267 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8204 (mttp)
REVERT: A  276 GLU cc_start: 0.7341 (mt-10) cc_final: 0.7067 (mt-10)
REVERT: A  311 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6388 (mm-30)
REVERT: A  314 ARG cc_start: 0.7783 (ttm170) cc_final: 0.7416 (ttm170)
REVERT: B   68 ARG cc_start: 0.7974 (ttt90) cc_final: 0.7479 (ttt90)
REVERT: B   98 SER cc_start: 0.8090 (m) cc_final: 0.7777 (p)
REVERT: B  101 MET cc_start: 0.8402 (mtp) cc_final: 0.8103 (mtp)
REVERT: B  147 SER cc_start: 0.8499 (t) cc_final: 0.8180 (p)
REVERT: B  214 ARG cc_start: 0.7826 (mpt90) cc_final: 0.7111 (mpt180)
REVERT: B  217 MET cc_start: 0.8017 (tpp) cc_final: 0.7540 (tpp)
REVERT: B  219 ARG cc_start: 0.7345 (mmt180) cc_final: 0.6946 (mmt180)
REVERT: B  233 CYS cc_start: 0.8441 (t) cc_final: 0.8126 (t)
REVERT: B  268 ASN cc_start: 0.7094 (m-40) cc_final: 0.6822 (m-40)
REVERT: B  277 SER cc_start: 0.8241 (t) cc_final: 0.7645 (m)
REVERT: B  295 ASN cc_start: 0.8254 (m-40) cc_final: 0.8020 (m110)
REVERT: B  322 ASP cc_start: 0.7069 (t0) cc_final: 0.6763 (t0)
REVERT: B  323 ASP cc_start: 0.7870 (p0) cc_final: 0.7613 (p0)
REVERT: D   56 VAL cc_start: 0.7461 (t) cc_final: 0.7077 (m)
REVERT: D   61 LEU cc_start: 0.7471 (mp) cc_final: 0.7240 (mt)
REVERT: D   72 MET cc_start: 0.6628 (ttm) cc_final: 0.6359 (ttm)
REVERT: D   86 SER cc_start: 0.8823 (t) cc_final: 0.8593 (p)
REVERT: D  104 LEU cc_start: 0.8146 (mt) cc_final: 0.7935 (mt)
REVERT: D  121 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7745 (mtm)
REVERT: D  136 SER cc_start: 0.8395 (t) cc_final: 0.8121 (t)
REVERT: D  137 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7861 (mt)
REVERT: D  139 ARG cc_start: 0.8402 (mtt180) cc_final: 0.8144 (mtt180)
REVERT: D  195 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.7157 (mtm)
REVERT: D  321 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.7050 (tp)
  outliers start: 23
  outliers final: 13
  residues processed: 231
  average time/residue: 0.1133
  time to fit residues: 33.3922
Evaluate side-chains
  233 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 215
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain D residue  121 MET
Chi-restraints excluded: chain D residue  137 LEU
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  195 MET
Chi-restraints excluded: chain D residue  226 MET
Chi-restraints excluded: chain D residue  321 LEU
Chi-restraints excluded: chain D residue  327 MET
Chi-restraints excluded: chain D residue  331 SER
Chi-restraints excluded: chain D residue  340 THR
Chi-restraints excluded: chain P residue    3 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 83 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 82 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 77 optimal weight:    0.8980
   chunk 50 optimal weight:    0.7980
   chunk 4 optimal weight:    0.0470
   overall best weight:    0.7080

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.144152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.123107 restraints weight = 9590.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 2.19
r_work: 0.3393 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3217 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.3581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7345  Z= 0.143
  Angle     :  0.537   8.282   9964  Z= 0.279
  Chirality :  0.043   0.142   1142
  Planarity :  0.004   0.056   1261
  Dihedral  :  4.776  30.547    996
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 17.30 %
    Favored  : 79.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.94 (0.29), residues: 905
  helix:  1.80 (0.27), residues: 388
  sheet: -0.78 (0.35), residues: 194
  loop :  0.26 (0.38), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  49 
 TYR   0.009   0.001   TYR B 289 
 PHE   0.015   0.001   PHE A 189 
 TRP   0.012   0.001   TRP B 339 
 HIS   0.004   0.001   HIS A 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 7344)
  covalent geometry    : angle       0.53623 ( 9962)
  SS BOND              : bond        0.00257 (    1)
  SS BOND              : angle       2.22284 (    2)
  hydrogen bonds       : bond        0.03838 (  400)
  hydrogen bonds       : angle       4.89834 ( 1152)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 213
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.7870 (mmtt) cc_final: 0.7490 (mmtt)
REVERT: A   20 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7057 (mt-10)
REVERT: A   26 ASP cc_start: 0.7451 (m-30) cc_final: 0.6975 (m-30)
REVERT: A  186 GLU cc_start: 0.7526 (tt0) cc_final: 0.7294 (tt0)
REVERT: A  247 ARG cc_start: 0.8053 (mtt90) cc_final: 0.7241 (mtt90)
REVERT: A  250 ARG cc_start: 0.7399 (mtt180) cc_final: 0.7026 (mtt180)
REVERT: A  267 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8221 (mttp)
REVERT: A  276 GLU cc_start: 0.7316 (mt-10) cc_final: 0.7059 (mt-10)
REVERT: A  311 GLU cc_start: 0.6946 (mm-30) cc_final: 0.6443 (mm-30)
REVERT: A  314 ARG cc_start: 0.7841 (ttm170) cc_final: 0.7473 (ttm170)
REVERT: B   68 ARG cc_start: 0.7996 (ttt90) cc_final: 0.7496 (ttt90)
REVERT: B   98 SER cc_start: 0.8077 (m) cc_final: 0.7780 (p)
REVERT: B  139 LEU cc_start: 0.8663 (mt) cc_final: 0.8460 (mt)
REVERT: B  147 SER cc_start: 0.8491 (t) cc_final: 0.8231 (p)
REVERT: B  214 ARG cc_start: 0.7902 (mpt90) cc_final: 0.7180 (mpt180)
REVERT: B  217 MET cc_start: 0.8045 (tpp) cc_final: 0.7603 (tpp)
REVERT: B  219 ARG cc_start: 0.7317 (mmt180) cc_final: 0.6810 (mmt-90)
REVERT: B  233 CYS cc_start: 0.8507 (t) cc_final: 0.8161 (t)
REVERT: B  268 ASN cc_start: 0.7056 (m-40) cc_final: 0.6811 (m-40)
REVERT: B  277 SER cc_start: 0.8257 (t) cc_final: 0.7644 (m)
REVERT: B  295 ASN cc_start: 0.8189 (m-40) cc_final: 0.7908 (m110)
REVERT: B  304 ARG cc_start: 0.8116 (mmm-85) cc_final: 0.7793 (mmm-85)
REVERT: B  322 ASP cc_start: 0.7122 (t0) cc_final: 0.6827 (t0)
REVERT: D   56 VAL cc_start: 0.7502 (t) cc_final: 0.7095 (m)
REVERT: D   72 MET cc_start: 0.6630 (ttm) cc_final: 0.6367 (ttm)
REVERT: D   86 SER cc_start: 0.8816 (t) cc_final: 0.8605 (p)
REVERT: D   98 ASN cc_start: 0.8356 (m-40) cc_final: 0.7817 (m110)
REVERT: D  121 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7729 (mtm)
REVERT: D  136 SER cc_start: 0.8398 (t) cc_final: 0.8125 (t)
REVERT: D  137 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7869 (mt)
REVERT: D  195 MET cc_start: 0.7282 (ptp) cc_final: 0.7029 (ptm)
REVERT: D  321 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7073 (tp)
REVERT: P    6 MET cc_start: 0.8032 (mtp) cc_final: 0.7645 (mtm)
  outliers start: 23
  outliers final: 13
  residues processed: 223
  average time/residue: 0.1005
  time to fit residues: 29.0292
Evaluate side-chains
  224 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 207
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  279 SER
Chi-restraints excluded: chain D residue  107 PHE
Chi-restraints excluded: chain D residue  121 MET
Chi-restraints excluded: chain D residue  137 LEU
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  226 MET
Chi-restraints excluded: chain D residue  321 LEU
Chi-restraints excluded: chain D residue  327 MET
Chi-restraints excluded: chain D residue  340 THR
Chi-restraints excluded: chain P residue    3 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 68 optimal weight:    0.6980
   chunk 45 optimal weight:    0.0670
   chunk 42 optimal weight:    0.9990
   chunk 63 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9980
   chunk 60 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 72 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
A 216 ASN
B 230 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.141367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.120173 restraints weight = 9792.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 2.27
r_work: 0.3378 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.3723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7345  Z= 0.133
  Angle     :  0.539   8.277   9964  Z= 0.282
  Chirality :  0.043   0.197   1142
  Planarity :  0.004   0.057   1261
  Dihedral  :  4.700  31.215    996
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 17.56 %
    Favored  : 79.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.97 (0.29), residues: 905
  helix:  1.80 (0.27), residues: 394
  sheet: -0.79 (0.35), residues: 193
  loop :  0.30 (0.38), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  49 
 TYR   0.010   0.001   TYR B 289 
 PHE   0.014   0.001   PHE A 189 
 TRP   0.013   0.001   TRP B 339 
 HIS   0.003   0.001   HIS A 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 7344)
  covalent geometry    : angle       0.53798 ( 9962)
  SS BOND              : bond        0.00865 (    1)
  SS BOND              : angle       2.33606 (    2)
  hydrogen bonds       : bond        0.03783 (  400)
  hydrogen bonds       : angle       4.87083 ( 1152)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 206
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.7863 (mmtt) cc_final: 0.7493 (mmtt)
REVERT: A   20 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7000 (mt-10)
REVERT: A   26 ASP cc_start: 0.7418 (m-30) cc_final: 0.6947 (m-30)
REVERT: A  186 GLU cc_start: 0.7555 (tt0) cc_final: 0.7323 (tt0)
REVERT: A  247 ARG cc_start: 0.8062 (mtt90) cc_final: 0.7291 (mtt90)
REVERT: A  250 ARG cc_start: 0.7493 (mtt180) cc_final: 0.7141 (mtt180)
REVERT: A  267 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8187 (mttp)
REVERT: A  276 GLU cc_start: 0.7266 (mt-10) cc_final: 0.7030 (mt-10)
REVERT: A  311 GLU cc_start: 0.6954 (mm-30) cc_final: 0.6487 (mm-30)
REVERT: A  314 ARG cc_start: 0.7781 (ttm170) cc_final: 0.7492 (ttm170)
REVERT: A  323 ARG cc_start: 0.7757 (mtm180) cc_final: 0.7480 (mtm180)
REVERT: A  329 HIS cc_start: 0.8544 (m170) cc_final: 0.8141 (m170)
REVERT: B   68 ARG cc_start: 0.7942 (ttt90) cc_final: 0.7459 (ttt90)
REVERT: B   98 SER cc_start: 0.8048 (m) cc_final: 0.7745 (p)
REVERT: B  101 MET cc_start: 0.8423 (mtp) cc_final: 0.8193 (mtp)
REVERT: B  214 ARG cc_start: 0.7965 (mpt90) cc_final: 0.7284 (mpt180)
REVERT: B  217 MET cc_start: 0.8016 (tpp) cc_final: 0.7624 (tpp)
REVERT: B  219 ARG cc_start: 0.7317 (mmt180) cc_final: 0.6919 (mmt180)
REVERT: B  233 CYS cc_start: 0.8407 (t) cc_final: 0.8092 (t)
REVERT: B  254 ASP cc_start: 0.7090 (t70) cc_final: 0.6591 (t0)
REVERT: B  268 ASN cc_start: 0.7020 (m-40) cc_final: 0.6778 (m-40)
REVERT: B  277 SER cc_start: 0.8284 (t) cc_final: 0.7652 (m)
REVERT: B  295 ASN cc_start: 0.8212 (m-40) cc_final: 0.7931 (m110)
REVERT: B  304 ARG cc_start: 0.8079 (mmm-85) cc_final: 0.7794 (mmm-85)
REVERT: B  322 ASP cc_start: 0.7126 (t0) cc_final: 0.6831 (t0)
REVERT: D   56 VAL cc_start: 0.7463 (t) cc_final: 0.7038 (m)
REVERT: D   72 MET cc_start: 0.6543 (ttm) cc_final: 0.6311 (ttm)
REVERT: D   86 SER cc_start: 0.8802 (t) cc_final: 0.8594 (p)
REVERT: D   98 ASN cc_start: 0.8343 (m-40) cc_final: 0.7798 (m110)
REVERT: D  118 THR cc_start: 0.8694 (t) cc_final: 0.8465 (m)
REVERT: D  136 SER cc_start: 0.8388 (t) cc_final: 0.8126 (t)
REVERT: D  137 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7830 (mt)
REVERT: D  170 PHE cc_start: 0.6957 (m-10) cc_final: 0.5844 (m-80)
REVERT: D  192 THR cc_start: 0.8105 (m) cc_final: 0.7865 (t)
REVERT: D  321 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.7054 (tp)
  outliers start: 23
  outliers final: 13
  residues processed: 216
  average time/residue: 0.1026
  time to fit residues: 28.5772
Evaluate side-chains
  218 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 202
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  279 SER
Chi-restraints excluded: chain D residue  107 PHE
Chi-restraints excluded: chain D residue  137 LEU
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  226 MET
Chi-restraints excluded: chain D residue  321 LEU
Chi-restraints excluded: chain D residue  327 MET
Chi-restraints excluded: chain D residue  340 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 23 optimal weight:    9.9990
   chunk 12 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 49 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.8382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.143872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.122761 restraints weight = 9682.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 2.20
r_work: 0.3380 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.3855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7345  Z= 0.158
  Angle     :  0.559   8.569   9964  Z= 0.287
  Chirality :  0.043   0.187   1142
  Planarity :  0.004   0.052   1261
  Dihedral  :  4.720  31.519    996
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 18.86 %
    Favored  : 78.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.29), residues: 905
  helix:  1.88 (0.27), residues: 389
  sheet: -0.84 (0.36), residues: 186
  loop :  0.36 (0.38), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  49 
 TYR   0.009   0.001   TYR D 176 
 PHE   0.022   0.002   PHE A 257 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 7344)
  covalent geometry    : angle       0.55708 ( 9962)
  SS BOND              : bond        0.00291 (    1)
  SS BOND              : angle       2.94892 (    2)
  hydrogen bonds       : bond        0.03867 (  400)
  hydrogen bonds       : angle       4.87601 ( 1152)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 214
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.7859 (mmtt) cc_final: 0.7523 (mmtt)
REVERT: A   20 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7022 (mt-10)
REVERT: A   31 ARG cc_start: 0.8246 (mmm-85) cc_final: 0.7875 (mmm-85)
REVERT: A  186 GLU cc_start: 0.7517 (tt0) cc_final: 0.7284 (tt0)
REVERT: A  247 ARG cc_start: 0.8025 (mtt90) cc_final: 0.7237 (mtt90)
REVERT: A  250 ARG cc_start: 0.7474 (mtt180) cc_final: 0.7185 (mtt180)
REVERT: A  276 GLU cc_start: 0.7265 (mt-10) cc_final: 0.7039 (mt-10)
REVERT: A  311 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6513 (mm-30)
REVERT: A  314 ARG cc_start: 0.7890 (ttm170) cc_final: 0.7582 (ttm170)
REVERT: A  323 ARG cc_start: 0.7763 (mtm180) cc_final: 0.7497 (mtm180)
REVERT: A  359 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7233 (mt-10)
REVERT: B   68 ARG cc_start: 0.7973 (ttt90) cc_final: 0.7640 (ttt90)
REVERT: B   83 ASP cc_start: 0.7941 (t0) cc_final: 0.7532 (t70)
REVERT: B   98 SER cc_start: 0.8075 (m) cc_final: 0.7764 (p)
REVERT: B  101 MET cc_start: 0.8396 (mtp) cc_final: 0.8114 (mtp)
REVERT: B  147 SER cc_start: 0.8546 (t) cc_final: 0.8256 (p)
REVERT: B  214 ARG cc_start: 0.7989 (mpt90) cc_final: 0.7325 (mpt180)
REVERT: B  217 MET cc_start: 0.8096 (tpp) cc_final: 0.7599 (tpp)
REVERT: B  219 ARG cc_start: 0.7309 (mmt180) cc_final: 0.6812 (mmt-90)
REVERT: B  230 ASN cc_start: 0.7947 (t0) cc_final: 0.7604 (m-40)
REVERT: B  233 CYS cc_start: 0.8502 (t) cc_final: 0.8148 (t)
REVERT: B  254 ASP cc_start: 0.7127 (t70) cc_final: 0.6643 (t0)
REVERT: B  268 ASN cc_start: 0.6998 (m-40) cc_final: 0.6773 (m-40)
REVERT: B  277 SER cc_start: 0.8331 (t) cc_final: 0.7718 (m)
REVERT: B  295 ASN cc_start: 0.8214 (m-40) cc_final: 0.7943 (m-40)
REVERT: B  304 ARG cc_start: 0.8109 (mmm-85) cc_final: 0.7861 (mmm-85)
REVERT: B  322 ASP cc_start: 0.7195 (t0) cc_final: 0.6895 (t0)
REVERT: D   56 VAL cc_start: 0.7517 (t) cc_final: 0.7043 (m)
REVERT: D   72 MET cc_start: 0.6638 (ttm) cc_final: 0.6385 (ttm)
REVERT: D   86 SER cc_start: 0.8814 (t) cc_final: 0.8610 (p)
REVERT: D   98 ASN cc_start: 0.8443 (m-40) cc_final: 0.7870 (m110)
REVERT: D  105 LYS cc_start: 0.8264 (mttt) cc_final: 0.8035 (mmmm)
REVERT: D  136 SER cc_start: 0.8385 (t) cc_final: 0.8106 (t)
REVERT: D  137 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7964 (mt)
REVERT: D  154 THR cc_start: 0.8167 (t) cc_final: 0.7838 (p)
REVERT: D  170 PHE cc_start: 0.7336 (m-10) cc_final: 0.6911 (m-10)
REVERT: D  192 THR cc_start: 0.8151 (m) cc_final: 0.7939 (t)
REVERT: D  309 LYS cc_start: 0.8087 (mtmt) cc_final: 0.7878 (mmmm)
REVERT: D  321 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7117 (tp)
  outliers start: 22
  outliers final: 14
  residues processed: 224
  average time/residue: 0.1103
  time to fit residues: 31.4720
Evaluate side-chains
  230 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 214
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  279 SER
Chi-restraints excluded: chain D residue  107 PHE
Chi-restraints excluded: chain D residue  137 LEU
Chi-restraints excluded: chain D residue  183 VAL
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  226 MET
Chi-restraints excluded: chain D residue  321 LEU
Chi-restraints excluded: chain D residue  340 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 85 optimal weight:    8.9990
   chunk 34 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.1980
   chunk 84 optimal weight:    5.9990
   chunk 43 optimal weight:    0.2980
   chunk 49 optimal weight:    0.0030
   chunk 65 optimal weight:    0.0670
   overall best weight:    0.2528

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

Flipped N/Q/H residues before XYZ refinement:
A 216 ASN
G  11 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.146551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.125640 restraints weight = 9669.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3552 rms_B_bonded: 2.21
r_work: 0.3417 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3247 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.3993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   7345  Z= 0.110
  Angle     :  0.534   8.815   9964  Z= 0.276
  Chirality :  0.042   0.157   1142
  Planarity :  0.004   0.051   1261
  Dihedral  :  4.517  29.645    996
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 19.38 %
    Favored  : 78.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.15 (0.29), residues: 905
  helix:  1.92 (0.27), residues: 393
  sheet: -0.73 (0.36), residues: 187
  loop :  0.43 (0.38), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  49 
 TYR   0.010   0.001   TYR B 289 
 PHE   0.020   0.001   PHE D 198 
 TRP   0.019   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 7344)
  covalent geometry    : angle       0.53304 ( 9962)
  SS BOND              : bond        0.00253 (    1)
  SS BOND              : angle       2.07316 (    2)
  hydrogen bonds       : bond        0.03564 (  400)
  hydrogen bonds       : angle       4.82335 ( 1152)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 208
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.7825 (mmtt) cc_final: 0.7520 (mmtt)
REVERT: A   20 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7054 (mt-10)
REVERT: A   26 ASP cc_start: 0.7388 (m-30) cc_final: 0.6924 (m-30)
REVERT: A  186 GLU cc_start: 0.7495 (tt0) cc_final: 0.7263 (tt0)
REVERT: A  247 ARG cc_start: 0.8025 (mtt90) cc_final: 0.7257 (mtt90)
REVERT: A  250 ARG cc_start: 0.7418 (mtt180) cc_final: 0.7178 (mtt180)
REVERT: A  276 GLU cc_start: 0.7239 (mt-10) cc_final: 0.7034 (mt-10)
REVERT: A  323 ARG cc_start: 0.7750 (mtm180) cc_final: 0.7485 (mtm180)
REVERT: A  329 HIS cc_start: 0.8508 (m170) cc_final: 0.8208 (m170)
REVERT: A  359 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7201 (mt-10)
REVERT: B   68 ARG cc_start: 0.7906 (ttt90) cc_final: 0.7452 (ttt90)
REVERT: B   98 SER cc_start: 0.7983 (m) cc_final: 0.7731 (p)
REVERT: B  101 MET cc_start: 0.8342 (mtp) cc_final: 0.8099 (mtp)
REVERT: B  139 LEU cc_start: 0.8586 (mt) cc_final: 0.8322 (mt)
REVERT: B  214 ARG cc_start: 0.8033 (mpt90) cc_final: 0.7287 (mpt180)
REVERT: B  217 MET cc_start: 0.7982 (tpp) cc_final: 0.7600 (tpp)
REVERT: B  219 ARG cc_start: 0.7303 (mmt180) cc_final: 0.6894 (mmt180)
REVERT: B  233 CYS cc_start: 0.8504 (t) cc_final: 0.8153 (t)
REVERT: B  254 ASP cc_start: 0.7048 (t70) cc_final: 0.6587 (t0)
REVERT: B  268 ASN cc_start: 0.6992 (m-40) cc_final: 0.6758 (m-40)
REVERT: B  277 SER cc_start: 0.8255 (t) cc_final: 0.7672 (m)
REVERT: B  295 ASN cc_start: 0.8176 (m-40) cc_final: 0.7900 (m110)
REVERT: B  297 TRP cc_start: 0.8767 (m100) cc_final: 0.8383 (m100)
REVERT: B  322 ASP cc_start: 0.7141 (t0) cc_final: 0.6843 (t0)
REVERT: D   72 MET cc_start: 0.6451 (ttm) cc_final: 0.6234 (ttm)
REVERT: D   98 ASN cc_start: 0.8314 (m-40) cc_final: 0.7759 (m110)
REVERT: D  136 SER cc_start: 0.8374 (t) cc_final: 0.8119 (t)
REVERT: D  137 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7776 (mt)
REVERT: D  170 PHE cc_start: 0.7397 (m-10) cc_final: 0.7026 (m-10)
REVERT: D  321 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7075 (tp)
  outliers start: 17
  outliers final: 13
  residues processed: 215
  average time/residue: 0.1131
  time to fit residues: 30.6070
Evaluate side-chains
  215 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 200
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 ASN
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  279 SER
Chi-restraints excluded: chain D residue  107 PHE
Chi-restraints excluded: chain D residue  137 LEU
Chi-restraints excluded: chain D residue  183 VAL
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  226 MET
Chi-restraints excluded: chain D residue  321 LEU
Chi-restraints excluded: chain D residue  340 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 1 optimal weight:    0.0770
   chunk 76 optimal weight:    0.6980
   chunk 75 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0980
   chunk 71 optimal weight:    0.0980
   chunk 68 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0270
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.1996

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

Flipped N/Q/H residues before XYZ refinement:
A 216 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.146832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.125812 restraints weight = 9660.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 2.22
r_work: 0.3423 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
moved from start:          0.4058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7345  Z= 0.108
  Angle     :  0.537   8.895   9964  Z= 0.274
  Chirality :  0.042   0.154   1142
  Planarity :  0.004   0.052   1261
  Dihedral  :  4.428  29.569    996
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 20.16 %
    Favored  : 77.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.12 (0.29), residues: 905
  helix:  1.94 (0.27), residues: 395
  sheet: -0.70 (0.36), residues: 181
  loop :  0.29 (0.37), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 251 
 TYR   0.010   0.001   TYR A 306 
 PHE   0.025   0.001   PHE D 198 
 TRP   0.022   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 7344)
  covalent geometry    : angle       0.53587 ( 9962)
  SS BOND              : bond        0.00139 (    1)
  SS BOND              : angle       2.00502 (    2)
  hydrogen bonds       : bond        0.03505 (  400)
  hydrogen bonds       : angle       4.74892 ( 1152)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 192
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7169 (mt-10)
REVERT: A   26 ASP cc_start: 0.7372 (m-30) cc_final: 0.6910 (m-30)
REVERT: A  186 GLU cc_start: 0.7468 (tt0) cc_final: 0.7240 (tt0)
REVERT: A  247 ARG cc_start: 0.8059 (mtt90) cc_final: 0.7273 (mtt90)
REVERT: A  250 ARG cc_start: 0.7498 (mtt180) cc_final: 0.7243 (mtt180)
REVERT: A  323 ARG cc_start: 0.7763 (mtm180) cc_final: 0.7501 (mtm180)
REVERT: A  329 HIS cc_start: 0.8537 (m170) cc_final: 0.8187 (m170)
REVERT: A  341 ARG cc_start: 0.8464 (mtt180) cc_final: 0.8261 (mtm180)
REVERT: A  359 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7210 (mt-10)
REVERT: B   68 ARG cc_start: 0.7814 (ttt90) cc_final: 0.7379 (ttt90)
REVERT: B   83 ASP cc_start: 0.7991 (t0) cc_final: 0.7410 (t70)
REVERT: B   98 SER cc_start: 0.7979 (m) cc_final: 0.7742 (p)
REVERT: B  101 MET cc_start: 0.8349 (mtp) cc_final: 0.8135 (mtp)
REVERT: B  139 LEU cc_start: 0.8584 (mt) cc_final: 0.8331 (mt)
REVERT: B  191 SER cc_start: 0.8511 (p) cc_final: 0.8259 (p)
REVERT: B  214 ARG cc_start: 0.8051 (mpt90) cc_final: 0.7277 (mpt180)
REVERT: B  217 MET cc_start: 0.7964 (tpp) cc_final: 0.7583 (tpp)
REVERT: B  219 ARG cc_start: 0.7314 (mmt180) cc_final: 0.6916 (mmt180)
REVERT: B  230 ASN cc_start: 0.8054 (m-40) cc_final: 0.7672 (m-40)
REVERT: B  233 CYS cc_start: 0.8585 (t) cc_final: 0.8209 (t)
REVERT: B  254 ASP cc_start: 0.7048 (t70) cc_final: 0.6564 (t0)
REVERT: B  268 ASN cc_start: 0.6997 (m-40) cc_final: 0.6749 (m-40)
REVERT: B  277 SER cc_start: 0.8292 (t) cc_final: 0.7713 (m)
REVERT: B  295 ASN cc_start: 0.8167 (m-40) cc_final: 0.7956 (m110)
REVERT: B  297 TRP cc_start: 0.8739 (m100) cc_final: 0.8375 (m100)
REVERT: B  322 ASP cc_start: 0.7257 (t0) cc_final: 0.6962 (t0)
REVERT: D   98 ASN cc_start: 0.8416 (m-40) cc_final: 0.7820 (m110)
REVERT: D  136 SER cc_start: 0.8408 (t) cc_final: 0.8175 (t)
REVERT: D  137 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7788 (mt)
REVERT: D  170 PHE cc_start: 0.7321 (m-10) cc_final: 0.6908 (m-10)
REVERT: D  321 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7082 (tp)
  outliers start: 18
  outliers final: 14
  residues processed: 198
  average time/residue: 0.1050
  time to fit residues: 26.4487
Evaluate side-chains
  200 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 184
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 ASN
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  279 SER
Chi-restraints excluded: chain D residue  107 PHE
Chi-restraints excluded: chain D residue  137 LEU
Chi-restraints excluded: chain D residue  183 VAL
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  226 MET
Chi-restraints excluded: chain D residue  321 LEU
Chi-restraints excluded: chain D residue  327 MET
Chi-restraints excluded: chain D residue  340 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 80 optimal weight:    0.7980
   chunk 52 optimal weight:    0.8980
   chunk 23 optimal weight:    9.9990
   chunk 30 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9980
   overall best weight:    1.0782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.143771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.122482 restraints weight = 9555.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 2.20
r_work: 0.3365 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3194 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7449
moved from start:          0.4115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7345  Z= 0.187
  Angle     :  0.586   8.903   9964  Z= 0.300
  Chirality :  0.044   0.160   1142
  Planarity :  0.004   0.052   1261
  Dihedral  :  4.617  31.040    996
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 21.07 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.96 (0.29), residues: 905
  helix:  1.81 (0.27), residues: 395
  sheet: -0.83 (0.35), residues: 186
  loop :  0.24 (0.37), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  49 
 TYR   0.013   0.001   TYR D 176 
 PHE   0.031   0.002   PHE A 257 
 TRP   0.015   0.002   TRP B  82 
 HIS   0.004   0.001   HIS A 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 7344)
  covalent geometry    : angle       0.58536 ( 9962)
  SS BOND              : bond        0.00284 (    1)
  SS BOND              : angle       2.50170 (    2)
  hydrogen bonds       : bond        0.03952 (  400)
  hydrogen bonds       : angle       4.84966 ( 1152)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2263.42 seconds
wall clock time: 39 minutes 22.82 seconds (2362.82 seconds total)