Starting phenix.real_space_refine
on Tue Mar  3 16:59:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7bz2_30249/03_2026/7bz2_30249.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7bz2_30249/03_2026/7bz2_30249.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.82
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7bz2_30249/03_2026/7bz2_30249.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7bz2_30249/03_2026/7bz2_30249.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7bz2_30249/03_2026/7bz2_30249.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7bz2_30249/03_2026/7bz2_30249.map"
  }
  resolution = 3.82
  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=   0.000 sd=   0.005
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      44      5.16       5
     C    4725      2.51       5
     N    1275      2.21       5
     O    1349      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: 7393
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1561
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1561
          Classifications: {'peptide': 198}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 33}
          Link IDs: {'PTRANS': 3, 'TRANS': 194}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 123
          Unresolved non-hydrogen angles: 151
          Unresolved non-hydrogen dihedrals: 98
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ARG:plan': 6, 'ASN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 7, 'GLN:plan1': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 81
    Chain: "B"
      Number of atoms: 2453
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 331, 2453
          Classifications: {'peptide': 331}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 5, 'TRANS': 325}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 92
          Unresolved non-hydrogen angles: 113
          Unresolved non-hydrogen dihedrals: 71
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 6, 'GLN:plan1': 4, 'GLU:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 73
    Chain: "G"
      Number of atoms: 246
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 246
          Classifications: {'peptide': 37}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 1, 'TRANS': 35}
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "N"
      Number of atoms: 956
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 956
          Classifications: {'peptide': 127}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "R"
      Number of atoms: 2152
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2152
          Classifications: {'peptide': 285}
          Incomplete info: {'truncation_to_alanine': 38}
          Link IDs: {'PTRANS': 7, 'TRANS': 277}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 152
          Unresolved non-hydrogen angles: 197
          Unresolved non-hydrogen dihedrals: 134
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'TRP:plan': 3, 'GLU:plan': 7, 'PHE:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 102
    Chain: "R"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'H98': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.74, per 1000 atoms: 0.24
  Number of scatterers: 7393
  At special positions: 0
  Unit cell: (92.22, 96.46, 117.66, 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      44     16.00
     O    1349      8.00
     N    1275      7.00
     C    4725      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 184 " - pdb=" SG  CYS R 190 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.80
  Conformation dependent library (CDL) restraints added in 280.3 milliseconds
  

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1842

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 12 sheets defined
      33.8% alpha, 8.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 13
    Processing helix  chain 'A' and resid 14 through 38
      removed outlier: 3.705A  pdb=" N   ALA A  22 " --> pdb=" O   ALA A  18 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   LYS A  28 " --> pdb=" O   LYS A  24 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   GLN A  31 " --> pdb=" O   GLU A  27 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
      removed outlier: 4.655A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 279
      removed outlier: 3.628A  pdb=" N   ALA A 269 " --> pdb=" O   ARG A 265 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   SER A 275 " --> pdb=" O   ASN A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 316
      removed outlier: 3.697A  pdb=" N   PHE A 315 " --> pdb=" O   PHE A 312 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 312 through 316'
    Processing helix  chain 'A' and resid 332 through 350
      removed outlier: 4.822A  pdb=" N   ALA A 337 " --> pdb=" O   ARG A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 389
      removed outlier: 3.959A  pdb=" N   ASP A 378 " --> pdb=" O   ARG A 374 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ASP A 381 " --> pdb=" O   ASN A 377 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   ILE A 382 " --> pdb=" O   ASP A 378 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ILE A 383 " --> pdb=" O   CYS A 379 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 25
    Processing helix  chain 'G' and resid 16 through 24
    Processing helix  chain 'G' and resid 29 through 45
      removed outlier: 4.199A  pdb=" N   ALA G  35 " --> pdb=" O   SER G  31 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   CYS G  41 " --> pdb=" O   LEU G  37 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 38 through 60
      removed outlier: 3.822A  pdb=" N   ILE R  43 " --> pdb=" O   VAL R  39 " (cutoff:3.500A)
      removed outlier: 4.622A  pdb=" N   VAL R  44 " --> pdb=" O   MET R  40 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ASN R  51 " --> pdb=" O   ILE R  47 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   VAL R  52 " --> pdb=" O   VAL R  48 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   LEU R  53 " --> pdb=" O   PHE R  49 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   VAL R  54 " --> pdb=" O   GLY R  50 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   ALA R  57 " --> pdb=" O   LEU R  53 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ILE R  58 " --> pdb=" O   VAL R  54 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 85
      removed outlier: 4.070A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 4.962A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   THR R  73 " --> pdb=" O   ASN R  69 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ALA R  78 " --> pdb=" O   SER R  74 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ASP R  79 " --> pdb=" O   LEU R  75 " (cutoff:3.500A)
      removed outlier: 4.670A  pdb=" N   MET R  82 " --> pdb=" O   ALA R  78 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 86 through 97
      removed outlier: 3.579A  pdb=" N   ALA R  92 " --> pdb=" O   PRO R  88 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   ILE R  94 " --> pdb=" O   GLY R  90 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 108 through 137
      removed outlier: 3.671A  pdb=" N   VAL R 114 " --> pdb=" O   THR R 110 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   LEU R 115 " --> pdb=" O   SER R 111 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   THR R 118 " --> pdb=" O   VAL R 114 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   LEU R 124 " --> pdb=" O   SER R 120 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 137 through 142
      removed outlier: 4.698A  pdb=" N   GLN R 142 " --> pdb=" O   PRO R 138 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 153 through 161
      removed outlier: 4.246A  pdb=" N   ILE R 159 " --> pdb=" O   LEU R 155 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 161 through 166
    Processing helix  chain 'R' and resid 166 through 171
    Processing helix  chain 'R' and resid 198 through 203
      removed outlier: 3.954A  pdb=" N   ALA R 202 " --> pdb=" O   ALA R 198 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 203 through 208
    Processing helix  chain 'R' and resid 209 through 227
      removed outlier: 3.915A  pdb=" N   VAL R 213 " --> pdb=" O   TYR R 209 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   TYR R 219 " --> pdb=" O   MET R 215 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ARG R 221 " --> pdb=" O   PHE R 217 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   GLU R 225 " --> pdb=" O   ARG R 221 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 232 through 236
      removed outlier: 3.545A  pdb=" N   LYS R 235 " --> pdb=" O   LYS R 232 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 272 through 287
      removed outlier: 4.915A  pdb=" N   THR R 281 " --> pdb=" O   ILE R 277 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   ALA R 285 " --> pdb=" O   THR R 281 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 288 through 299
      removed outlier: 4.764A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 309
    Processing helix  chain 'R' and resid 310 through 315
    Processing helix  chain 'R' and resid 321 through 325
    Processing helix  chain 'R' and resid 329 through 336
    Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42
      removed outlier: 7.346A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46
      removed outlier: 3.765A  pdb=" N   LEU A  46 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   PHE A 246 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   LEU A 289 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   HIS A 362 " --> pdb=" O   LEU A 289 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.645A  pdb=" N   VAL B  71 " --> pdb=" O   HIS B  62 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105
    Processing sheet with id=AA5, first strand: chain 'B' and resid 158 through 159
      removed outlier: 3.844A  pdb=" N   THR B 159 " --> pdb=" O   ALA B 167 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 200 through 201
      removed outlier: 3.713A  pdb=" N   LYS B 209 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232
      removed outlier: 4.145A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 250 through 253
      removed outlier: 3.715A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 276 through 277
      removed outlier: 4.180A  pdb=" N   SER B 277 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 6
    Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.194A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   THR N 122 " --> pdb=" O   TYR N  94 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'N' and resid 17 through 20
      removed outlier: 3.512A  pdb=" N   LEU N  20 " --> pdb=" O   LEU N  81 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   THR N  78 " --> pdb=" O   ASP N  73 " (cutoff:3.500A)

    220 hydrogen bonds defined for protein.
    624 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: 1.01

  Time building geometry restraints manager: 1.01 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2395
        1.34 -     1.46: 1787
        1.46 -     1.58: 3294
        1.58 -     1.70: 0
        1.70 -     1.81: 62
  Bond restraints: 7538
  Sorted by residual:
  bond pdb=" C19 H98 R 401 "
       pdb=" N2  H98 R 401 "
    ideal  model  delta    sigma   weight residual
    1.349  1.391 -0.042 2.00e-02 2.50e+03 4.36e+00
  bond pdb=" C3  H98 R 401 "
       pdb=" C4  H98 R 401 "
    ideal  model  delta    sigma   weight residual
    1.503  1.480  0.023 2.00e-02 2.50e+03 1.31e+00
  bond pdb=" C13 H98 R 401 "
       pdb=" C14 H98 R 401 "
    ideal  model  delta    sigma   weight residual
    1.392  1.370  0.022 2.00e-02 2.50e+03 1.23e+00
  bond pdb=" CA  GLY A  47 "
       pdb=" C   GLY A  47 "
    ideal  model  delta    sigma   weight residual
    1.514  1.499  0.015 1.41e-02 5.03e+03 1.19e+00
  bond pdb=" CB  TRP B  82 "
       pdb=" CG  TRP B  82 "
    ideal  model  delta    sigma   weight residual
    1.498  1.465  0.033 3.10e-02 1.04e+03 1.13e+00
  ... (remaining 7533 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 9945
        1.68 -     3.35: 251
        3.35 -     5.03: 37
        5.03 -     6.70: 9
        6.70 -     8.38: 3
  Bond angle restraints: 10245
  Sorted by residual:
  angle pdb=" N   VAL R  31 "
        pdb=" CA  VAL R  31 "
        pdb=" C   VAL R  31 "
      ideal   model   delta    sigma   weight residual
     113.53  109.98    3.55 9.80e-01 1.04e+00 1.31e+01
  angle pdb=" C   GLU B 172 "
        pdb=" N   THR B 173 "
        pdb=" CA  THR B 173 "
      ideal   model   delta    sigma   weight residual
     121.54  128.13   -6.59 1.91e+00 2.74e-01 1.19e+01
  angle pdb=" C15 H98 R 401 "
        pdb=" N2  H98 R 401 "
        pdb=" C19 H98 R 401 "
      ideal   model   delta    sigma   weight residual
     129.13  120.75    8.38 3.00e+00 1.11e-01 7.80e+00
  angle pdb=" N   GLY B 162 "
        pdb=" CA  GLY B 162 "
        pdb=" C   GLY B 162 "
      ideal   model   delta    sigma   weight residual
     113.18  107.08    6.10 2.37e+00 1.78e-01 6.62e+00
  angle pdb=" CA  LEU A 393 "
        pdb=" CB  LEU A 393 "
        pdb=" CG  LEU A 393 "
      ideal   model   delta    sigma   weight residual
     116.30  124.44   -8.14 3.50e+00 8.16e-02 5.40e+00
  ... (remaining 10240 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 3942
       17.95 -    35.90: 383
       35.90 -    53.85: 64
       53.85 -    71.81: 17
       71.81 -    89.76: 6
  Dihedral angle restraints: 4412
    sinusoidal: 1573
      harmonic: 2839
  Sorted by residual:
  dihedral pdb=" CA  PHE R 290 "
           pdb=" C   PHE R 290 "
           pdb=" N   ILE R 291 "
           pdb=" CA  ILE R 291 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.15   25.85     0      5.00e+00 4.00e-02 2.67e+01
  dihedral pdb=" CB  CYS R 184 "
           pdb=" SG  CYS R 184 "
           pdb=" SG  CYS R 190 "
           pdb=" CB  CYS R 190 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -47.65  -38.35     1      1.00e+01 1.00e-02 2.07e+01
  dihedral pdb=" CA  ASN R  69 "
           pdb=" C   ASN R  69 "
           pdb=" N   TYR R  70 "
           pdb=" CA  TYR R  70 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.62   22.38     0      5.00e+00 4.00e-02 2.00e+01
  ... (remaining 4409 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 627
       0.030 -    0.060: 364
       0.060 -    0.091: 128
       0.091 -    0.121: 64
       0.121 -    0.151: 11
  Chirality restraints: 1194
  Sorted by residual:
  chirality pdb=" CG  LEU A 291 "
            pdb=" CB  LEU A 291 "
            pdb=" CD1 LEU A 291 "
            pdb=" CD2 LEU A 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.70e-01
  chirality pdb=" CA  ILE B  58 "
            pdb=" N   ILE B  58 "
            pdb=" C   ILE B  58 "
            pdb=" CB  ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.02e-01
  chirality pdb=" CA  TYR R 219 "
            pdb=" N   TYR R 219 "
            pdb=" C   TYR R 219 "
            pdb=" CB  TYR R 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.81e-01
  ... (remaining 1191 not shown)

  Planarity restraints: 1295
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 167 "   -0.033 5.00e-02 4.00e+02   5.02e-02 4.03e+00
        pdb=" N   PRO R 168 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO R 168 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO R 168 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.032 5.00e-02 4.00e+02   4.86e-02 3.79e+00
        pdb=" N   PRO B 236 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS N  87 "    0.024 5.00e-02 4.00e+02   3.64e-02 2.12e+00
        pdb=" N   PRO N  88 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO N  88 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO N  88 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1292 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 146
        2.66 -     3.22: 7103
        3.22 -     3.78: 10470
        3.78 -     4.34: 14131
        4.34 -     4.90: 23768
  Nonbonded interactions: 55618
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.101 3.040
  nonbonded pdb=" OD2 ASP B 247 "
            pdb=" OG1 THR B 249 "
     model   vdw
     2.134 3.040
  nonbonded pdb=" OG1 THR N 104 "
            pdb=" OD1 ASP N 106 "
     model   vdw
     2.193 3.040
  nonbonded pdb=" OD1 ASP B 291 "
            pdb=" ND2 ASN B 293 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" OG  SER R 203 "
            pdb=" O2  H98 R 401 "
     model   vdw
     2.221 3.040
  ... (remaining 55613 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 group one per residue
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:             0.580
  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:             0.020
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.370
  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:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7540  Z= 0.185
  Angle     :  0.680   8.376  10249  Z= 0.376
  Chirality :  0.046   0.151   1194
  Planarity :  0.004   0.050   1295
  Dihedral  : 15.119  89.757   2564
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.21 %
    Favored  : 89.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.26 %
    Favored  : 90.74 %
  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: -6.04 (0.20), residues: 950
  helix: -3.35 (0.21), residues: 342
  sheet: -4.69 (0.26), residues: 190
  loop : -4.15 (0.21), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N 118 
 TYR   0.013   0.001   TYR B  59 
 PHE   0.014   0.002   PHE N 108 
 TRP   0.018   0.002   TRP R 109 
 HIS   0.007   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 7538)
  covalent geometry    : angle       0.67970 (10245)
  SS BOND              : bond        0.00143 (    2)
  SS BOND              : angle       0.35880 (    4)
  hydrogen bonds       : bond        0.15042 (  220)
  hydrogen bonds       : angle       6.82933 (  624)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
REVERT: B  111 TYR cc_start: 0.7918 (m-80) cc_final: 0.7697 (m-80)
REVERT: R  227 LYS cc_start: 0.8479 (ttpt) cc_final: 0.7850 (tttt)
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 0.0944
  time to fit residues: 23.0752
Evaluate side-chains
  144 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    0.0970
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    7.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
A 220 HIS
A 371 ASN
B 176 GLN
B 230 ASN
N  39 GLN
R 142 GLN
R 148 ASN
R 312 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.179970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.156602 restraints weight = 8236.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.152980 restraints weight = 14793.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.153311 restraints weight = 14501.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.151989 restraints weight = 11485.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.152890 restraints weight = 9522.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.1338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7540  Z= 0.131
  Angle     :  0.605   9.018  10249  Z= 0.319
  Chirality :  0.044   0.136   1194
  Planarity :  0.004   0.048   1295
  Dihedral  :  7.619  82.809   1058
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.11 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 17.71 %
    Favored  : 79.84 %
  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: -4.94 (0.23), residues: 950
  helix: -2.37 (0.25), residues: 345
  sheet: -4.26 (0.29), residues: 187
  loop : -3.50 (0.24), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG N  72 
 TYR   0.013   0.001   TYR G  40 
 PHE   0.030   0.002   PHE R 208 
 TRP   0.015   0.001   TRP R 313 
 HIS   0.005   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 7538)
  covalent geometry    : angle       0.60489 (10245)
  SS BOND              : bond        0.00324 (    2)
  SS BOND              : angle       0.64706 (    4)
  hydrogen bonds       : bond        0.03786 (  220)
  hydrogen bonds       : angle       5.30987 (  624)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 161
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A   45 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8349 (tt)
REVERT: B  111 TYR cc_start: 0.7829 (m-80) cc_final: 0.7237 (m-80)
REVERT: B  154 ASP cc_start: 0.7924 (m-30) cc_final: 0.7377 (t0)
  outliers start: 18
  outliers final: 11
  residues processed: 171
  average time/residue: 0.0818
  time to fit residues: 19.0102
Evaluate side-chains
  158 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 146
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  381 ASP
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   40 MET
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  206 VAL
Chi-restraints excluded: chain R residue  312 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 82 optimal weight:    0.0170
   chunk 52 optimal weight:    7.9990
   chunk 69 optimal weight:    0.0470
   chunk 4 optimal weight:    9.9990
   chunk 50 optimal weight:    6.9990
   chunk 44 optimal weight:    0.0570
   chunk 81 optimal weight:    0.8980
   chunk 0 optimal weight:   20.0000
   chunk 45 optimal weight:    4.9990
   chunk 2 optimal weight:    0.0000
   chunk 75 optimal weight:    0.8980
   overall best weight:    0.2038

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN
B 176 GLN
B 183 HIS
B 220 GLN
R 142 GLN
R 148 ASN
R 170 GLN
R 293 ASN
R 312 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.186220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.161415 restraints weight = 8069.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.158049 restraints weight = 14229.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.157652 restraints weight = 13464.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.156611 restraints weight = 10904.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.157718 restraints weight = 9266.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.1960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7540  Z= 0.097
  Angle     :  0.553   8.103  10249  Z= 0.287
  Chirality :  0.042   0.139   1194
  Planarity :  0.003   0.047   1295
  Dihedral  :  6.879  86.016   1058
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 19.35 %
    Favored  : 76.98 %
  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: -4.20 (0.24), residues: 950
  helix: -1.83 (0.27), residues: 343
  sheet: -3.74 (0.31), residues: 185
  loop : -3.06 (0.25), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG N  72 
 TYR   0.009   0.001   TYR G  40 
 PHE   0.017   0.001   PHE A 222 
 TRP   0.023   0.001   TRP R 109 
 HIS   0.004   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00202 ( 7538)
  covalent geometry    : angle       0.55306 (10245)
  SS BOND              : bond        0.00213 (    2)
  SS BOND              : angle       0.46124 (    4)
  hydrogen bonds       : bond        0.03237 (  220)
  hydrogen bonds       : angle       4.85921 (  624)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 145
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8352 (tt)
REVERT: B  111 TYR cc_start: 0.7788 (m-80) cc_final: 0.7327 (m-80)
REVERT: B  154 ASP cc_start: 0.7886 (m-30) cc_final: 0.7348 (t0)
REVERT: B  188 MET cc_start: 0.8327 (mmp) cc_final: 0.7849 (mmm)
REVERT: R  300 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7043 (m-30)
  outliers start: 27
  outliers final: 11
  residues processed: 160
  average time/residue: 0.0707
  time to fit residues: 16.1694
Evaluate side-chains
  146 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 133
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   40 MET
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  125 VAL
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  300 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 84 optimal weight:    0.0470
   chunk 21 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 15 optimal weight:    0.6980
   chunk 73 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 70 optimal weight:    0.0570
   chunk 16 optimal weight:    3.9990
   chunk 81 optimal weight:    8.9990
   chunk 67 optimal weight:    0.0870
   overall best weight:    0.3374

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN
B 183 HIS
N  39 GLN
R 142 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.186977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.156677 restraints weight = 8091.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.153889 restraints weight = 10155.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.155964 restraints weight = 9698.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.156833 restraints weight = 7438.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.156918 restraints weight = 6380.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.2320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7540  Z= 0.089
  Angle     :  0.518   6.610  10249  Z= 0.271
  Chirality :  0.041   0.136   1194
  Planarity :  0.003   0.045   1295
  Dihedral  :  6.482  85.922   1058
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 21.53 %
    Favored  : 74.52 %
  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: -3.70 (0.25), residues: 950
  helix: -1.46 (0.27), residues: 349
  sheet: -3.45 (0.32), residues: 194
  loop : -2.70 (0.27), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 304 
 TYR   0.009   0.001   TYR G  40 
 PHE   0.014   0.001   PHE R 193 
 TRP   0.023   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00191 ( 7538)
  covalent geometry    : angle       0.51788 (10245)
  SS BOND              : bond        0.00201 (    2)
  SS BOND              : angle       0.43689 (    4)
  hydrogen bonds       : bond        0.02858 (  220)
  hydrogen bonds       : angle       4.60798 (  624)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 136
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7731 (mp0)
REVERT: A   45 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8334 (tt)
REVERT: B  111 TYR cc_start: 0.7757 (m-80) cc_final: 0.7189 (m-80)
REVERT: B  154 ASP cc_start: 0.7801 (m-30) cc_final: 0.7295 (t0)
REVERT: N   60 TYR cc_start: 0.8746 (m-80) cc_final: 0.8395 (m-80)
REVERT: R   64 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6753 (mt)
REVERT: R  300 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.6750 (m-30)
REVERT: R  309 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8444 (tt)
  outliers start: 29
  outliers final: 13
  residues processed: 153
  average time/residue: 0.0722
  time to fit residues: 15.5457
Evaluate side-chains
  141 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   40 MET
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  125 VAL
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  300 ASP
Chi-restraints excluded: chain R residue  309 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 31 optimal weight:    8.9990
   chunk 88 optimal weight:    0.7980
   chunk 82 optimal weight:   10.0000
   chunk 85 optimal weight:    2.9990
   chunk 41 optimal weight:    7.9990
   chunk 50 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 36 optimal weight:    8.9990
   chunk 92 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN
B 183 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.184774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.160169 restraints weight = 8201.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.157536 restraints weight = 14269.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.158376 restraints weight = 12696.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.157436 restraints weight = 10162.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.157557 restraints weight = 8857.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.2368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7540  Z= 0.120
  Angle     :  0.549   8.685  10249  Z= 0.285
  Chirality :  0.043   0.177   1194
  Planarity :  0.003   0.044   1295
  Dihedral  :  6.464  83.931   1058
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 22.21 %
    Favored  : 73.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.47 (0.25), residues: 950
  helix: -1.22 (0.28), residues: 345
  sheet: -3.34 (0.32), residues: 194
  loop : -2.62 (0.27), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 256 
 TYR   0.011   0.001   TYR A 339 
 PHE   0.013   0.001   PHE A 222 
 TRP   0.031   0.002   TRP R 313 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7538)
  covalent geometry    : angle       0.54860 (10245)
  SS BOND              : bond        0.00219 (    2)
  SS BOND              : angle       0.52114 (    4)
  hydrogen bonds       : bond        0.03090 (  220)
  hydrogen bonds       : angle       4.67245 (  624)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 132
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8378 (tt)
REVERT: B   88 ASN cc_start: 0.8665 (m-40) cc_final: 0.8136 (m110)
REVERT: B  154 ASP cc_start: 0.7882 (m-30) cc_final: 0.7644 (m-30)
REVERT: B  256 ARG cc_start: 0.7078 (mmm160) cc_final: 0.6704 (mtm180)
REVERT: R   64 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6871 (mt)
REVERT: R  300 ASP cc_start: 0.7368 (OUTLIER) cc_final: 0.6734 (m-30)
  outliers start: 31
  outliers final: 18
  residues processed: 150
  average time/residue: 0.0724
  time to fit residues: 15.3261
Evaluate side-chains
  147 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  381 ASP
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   45 LEU
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue  125 VAL
Chi-restraints excluded: chain R residue  159 ILE
Chi-restraints excluded: chain R residue  206 VAL
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  300 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 85 optimal weight:    0.6980
   chunk 87 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 59 optimal weight:    5.9990
   chunk 50 optimal weight:    0.0270
   chunk 83 optimal weight:   10.0000
   chunk 90 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9980
   chunk 49 optimal weight:    5.9990
   chunk 40 optimal weight:    8.9990
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.7240

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.187079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.154826 restraints weight = 8145.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.153099 restraints weight = 8409.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.153667 restraints weight = 7986.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.153751 restraints weight = 7054.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.153752 restraints weight = 6841.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.2482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7540  Z= 0.102
  Angle     :  0.530   7.477  10249  Z= 0.275
  Chirality :  0.042   0.135   1194
  Planarity :  0.003   0.045   1295
  Dihedral  :  6.294  81.705   1058
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 23.84 %
    Favored  : 72.21 %
  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: -3.15 (0.26), residues: 950
  helix: -1.00 (0.28), residues: 352
  sheet: -3.05 (0.33), residues: 199
  loop : -2.45 (0.29), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 304 
 TYR   0.017   0.001   TYR B 111 
 PHE   0.012   0.001   PHE A 222 
 TRP   0.037   0.002   TRP R 313 
 HIS   0.003   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 7538)
  covalent geometry    : angle       0.52992 (10245)
  SS BOND              : bond        0.00206 (    2)
  SS BOND              : angle       0.45872 (    4)
  hydrogen bonds       : bond        0.02907 (  220)
  hydrogen bonds       : angle       4.53976 (  624)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 131
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7711 (mp0)
REVERT: A   45 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8415 (tt)
REVERT: A  212 PHE cc_start: 0.7215 (p90) cc_final: 0.6969 (p90)
REVERT: B  111 TYR cc_start: 0.7608 (m-80) cc_final: 0.6983 (m-80)
REVERT: B  154 ASP cc_start: 0.7945 (m-30) cc_final: 0.7445 (t0)
REVERT: N   35 ASN cc_start: 0.8329 (p0) cc_final: 0.7788 (p0)
REVERT: N   60 TYR cc_start: 0.8703 (m-80) cc_final: 0.8388 (m-80)
REVERT: R   64 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6884 (mt)
REVERT: R  300 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.6792 (m-30)
  outliers start: 29
  outliers final: 19
  residues processed: 149
  average time/residue: 0.0704
  time to fit residues: 14.7398
Evaluate side-chains
  147 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  381 ASP
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue  159 ILE
Chi-restraints excluded: chain R residue  206 VAL
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  281 THR
Chi-restraints excluded: chain R residue  300 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 89 optimal weight:    0.6980
   chunk 28 optimal weight:    7.9990
   chunk 67 optimal weight:   10.0000
   chunk 62 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   chunk 87 optimal weight:    0.4980
   chunk 64 optimal weight:    3.9990
   chunk 78 optimal weight:    0.0470
   chunk 94 optimal weight:    0.9990
   chunk 82 optimal weight:   10.0000
   chunk 4 optimal weight:    0.0070
   overall best weight:    0.4498

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.178175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.143998 restraints weight = 8271.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.144587 restraints weight = 7027.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.144814 restraints weight = 6302.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.145339 restraints weight = 6001.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.145891 restraints weight = 5855.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.2716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7540  Z= 0.093
  Angle     :  0.546   8.226  10249  Z= 0.277
  Chirality :  0.041   0.133   1194
  Planarity :  0.003   0.044   1295
  Dihedral  :  6.109  78.833   1058
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 24.80 %
    Favored  : 71.25 %
  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: -2.81 (0.27), residues: 950
  helix: -0.66 (0.29), residues: 344
  sheet: -2.86 (0.33), residues: 204
  loop : -2.27 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 256 
 TYR   0.012   0.001   TYR B 111 
 PHE   0.010   0.001   PHE A 222 
 TRP   0.035   0.002   TRP R 313 
 HIS   0.003   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 ( 7538)
  covalent geometry    : angle       0.54565 (10245)
  SS BOND              : bond        0.00175 (    2)
  SS BOND              : angle       0.43634 (    4)
  hydrogen bonds       : bond        0.02770 (  220)
  hydrogen bonds       : angle       4.42582 (  624)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 130
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7592 (mp0)
REVERT: A   45 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8383 (tt)
REVERT: A  212 PHE cc_start: 0.7169 (p90) cc_final: 0.6959 (p90)
REVERT: A  390 GLN cc_start: 0.8406 (tp-100) cc_final: 0.8175 (tp-100)
REVERT: B  111 TYR cc_start: 0.7646 (m-80) cc_final: 0.7286 (m-80)
REVERT: B  154 ASP cc_start: 0.8009 (m-30) cc_final: 0.7414 (t0)
REVERT: N   35 ASN cc_start: 0.8083 (p0) cc_final: 0.7729 (p0)
REVERT: N   60 TYR cc_start: 0.8719 (m-80) cc_final: 0.8446 (m-80)
REVERT: R   64 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6778 (mt)
REVERT: R  300 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.6820 (m-30)
  outliers start: 29
  outliers final: 19
  residues processed: 147
  average time/residue: 0.0742
  time to fit residues: 15.3080
Evaluate side-chains
  145 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 122
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  381 ASP
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue  159 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  281 THR
Chi-restraints excluded: chain R residue  300 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 60 optimal weight:    0.0970
   chunk 76 optimal weight:    0.9990
   chunk 59 optimal weight:    6.9990
   chunk 34 optimal weight:    6.9990
   chunk 86 optimal weight:    0.4980
   chunk 42 optimal weight:    5.9990
   chunk 74 optimal weight:    9.9990
   chunk 82 optimal weight:    0.9980
   chunk 90 optimal weight:    2.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN
B 183 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.175374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.142185 restraints weight = 8422.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.140842 restraints weight = 7706.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.141462 restraints weight = 7031.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.141530 restraints weight = 6571.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.141790 restraints weight = 6448.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.2722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7540  Z= 0.125
  Angle     :  0.585   9.787  10249  Z= 0.294
  Chirality :  0.043   0.141   1194
  Planarity :  0.003   0.044   1295
  Dihedral  :  6.199  76.363   1058
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 25.48 %
    Favored  : 70.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.81 (0.27), residues: 950
  helix: -0.72 (0.29), residues: 351
  sheet: -2.83 (0.34), residues: 203
  loop : -2.25 (0.29), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 304 
 TYR   0.010   0.001   TYR B 111 
 PHE   0.013   0.001   PHE N  29 
 TRP   0.034   0.002   TRP R 313 
 HIS   0.003   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 7538)
  covalent geometry    : angle       0.58501 (10245)
  SS BOND              : bond        0.00212 (    2)
  SS BOND              : angle       0.48106 (    4)
  hydrogen bonds       : bond        0.02924 (  220)
  hydrogen bonds       : angle       4.47784 (  624)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 127
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7744 (mp0)
REVERT: A   45 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8399 (tt)
REVERT: A  212 PHE cc_start: 0.7221 (p90) cc_final: 0.6993 (p90)
REVERT: B   88 ASN cc_start: 0.8608 (m-40) cc_final: 0.8136 (m110)
REVERT: B  111 TYR cc_start: 0.7707 (m-80) cc_final: 0.7353 (m-80)
REVERT: B  154 ASP cc_start: 0.8089 (m-30) cc_final: 0.7491 (t0)
REVERT: N   60 TYR cc_start: 0.8738 (m-80) cc_final: 0.8462 (m-80)
REVERT: R   64 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6899 (mt)
REVERT: R  300 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.6835 (m-30)
  outliers start: 30
  outliers final: 20
  residues processed: 145
  average time/residue: 0.0708
  time to fit residues: 14.4495
Evaluate side-chains
  144 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 120
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  381 ASP
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue  159 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  281 THR
Chi-restraints excluded: chain R residue  300 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 76 optimal weight:    0.6980
   chunk 83 optimal weight:    5.9990
   chunk 44 optimal weight:    4.9990
   chunk 4 optimal weight:    0.4980
   chunk 73 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0570
   chunk 79 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 28 optimal weight:    0.1980
   overall best weight:    0.6900

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.177597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.150390 restraints weight = 8257.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.147059 restraints weight = 13618.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.149067 restraints weight = 12724.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.149015 restraints weight = 8597.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.149298 restraints weight = 8175.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.2882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7540  Z= 0.102
  Angle     :  0.556   8.676  10249  Z= 0.282
  Chirality :  0.042   0.159   1194
  Planarity :  0.003   0.044   1295
  Dihedral  :  6.105  76.957   1058
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 26.43 %
    Favored  : 70.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.71 (0.27), residues: 950
  helix: -0.64 (0.29), residues: 355
  sheet: -2.73 (0.34), residues: 205
  loop : -2.24 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 256 
 TYR   0.009   0.001   TYR G  40 
 PHE   0.011   0.001   PHE N  29 
 TRP   0.032   0.002   TRP R 313 
 HIS   0.003   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 7538)
  covalent geometry    : angle       0.55585 (10245)
  SS BOND              : bond        0.00206 (    2)
  SS BOND              : angle       0.48809 (    4)
  hydrogen bonds       : bond        0.02810 (  220)
  hydrogen bonds       : angle       4.41793 (  624)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 122
  time to evaluate  : 0.281 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7745 (mp0)
REVERT: A   45 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8400 (tt)
REVERT: B   88 ASN cc_start: 0.8596 (m-40) cc_final: 0.8143 (m110)
REVERT: B  111 TYR cc_start: 0.7630 (m-80) cc_final: 0.7247 (m-80)
REVERT: B  154 ASP cc_start: 0.8020 (m-30) cc_final: 0.7469 (t0)
REVERT: N   60 TYR cc_start: 0.8688 (m-80) cc_final: 0.8414 (m-80)
REVERT: R   64 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6845 (mt)
REVERT: R  140 LYS cc_start: 0.7779 (mtpp) cc_final: 0.7433 (mttt)
REVERT: R  300 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.6824 (m-30)
  outliers start: 25
  outliers final: 19
  residues processed: 136
  average time/residue: 0.0786
  time to fit residues: 14.8884
Evaluate side-chains
  142 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 119
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  381 ASP
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue  159 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  281 THR
Chi-restraints excluded: chain R residue  300 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 23 optimal weight:    8.9990
   chunk 1 optimal weight:    0.4980
   chunk 89 optimal weight:    0.8980
   chunk 74 optimal weight:   10.0000
   chunk 13 optimal weight:    9.9990
   chunk 62 optimal weight:    0.6980
   chunk 80 optimal weight:    0.7980
   chunk 17 optimal weight:    0.0470
   chunk 59 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 91 optimal weight:    5.9990
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.178044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.144988 restraints weight = 8197.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.143828 restraints weight = 8368.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.144391 restraints weight = 7624.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.144553 restraints weight = 7070.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.144817 restraints weight = 6631.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.3022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7540  Z= 0.097
  Angle     :  0.555   8.385  10249  Z= 0.279
  Chirality :  0.042   0.152   1194
  Planarity :  0.003   0.045   1295
  Dihedral  :  6.011  82.890   1058
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 26.57 %
    Favored  : 69.75 %
  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: -2.55 (0.27), residues: 950
  helix: -0.49 (0.29), residues: 354
  sheet: -2.63 (0.34), residues: 205
  loop : -2.16 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 304 
 TYR   0.009   0.001   TYR G  40 
 PHE   0.016   0.001   PHE A 212 
 TRP   0.030   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 7538)
  covalent geometry    : angle       0.55536 (10245)
  SS BOND              : bond        0.00183 (    2)
  SS BOND              : angle       0.47275 (    4)
  hydrogen bonds       : bond        0.02752 (  220)
  hydrogen bonds       : angle       4.37095 (  624)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 125
  time to evaluate  : 0.302 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7640 (mp0)
REVERT: A   45 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8394 (tt)
REVERT: B   88 ASN cc_start: 0.8582 (m-40) cc_final: 0.8132 (m110)
REVERT: B  111 TYR cc_start: 0.7655 (m-80) cc_final: 0.7249 (m-80)
REVERT: B  154 ASP cc_start: 0.8096 (m-30) cc_final: 0.7483 (t0)
REVERT: N   60 TYR cc_start: 0.8639 (m-80) cc_final: 0.8364 (m-80)
REVERT: R   64 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6760 (mt)
REVERT: R  140 LYS cc_start: 0.7795 (mtpp) cc_final: 0.7447 (mttt)
REVERT: R  300 ASP cc_start: 0.7227 (OUTLIER) cc_final: 0.6725 (m-30)
  outliers start: 27
  outliers final: 17
  residues processed: 143
  average time/residue: 0.0771
  time to fit residues: 15.3279
Evaluate side-chains
  138 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  381 ASP
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain R residue   40 MET
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue  159 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  281 THR
Chi-restraints excluded: chain R residue  300 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 8 optimal weight:    0.2980
   chunk 17 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   chunk 77 optimal weight:    0.0670
   chunk 40 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   chunk 81 optimal weight:    7.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.6720

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.178164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.149416 restraints weight = 8188.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.146419 restraints weight = 13623.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.148547 restraints weight = 12031.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.148783 restraints weight = 7936.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.149376 restraints weight = 6784.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.3078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7540  Z= 0.102
  Angle     :  0.573   8.161  10249  Z= 0.288
  Chirality :  0.043   0.162   1194
  Planarity :  0.004   0.044   1295
  Dihedral  :  6.020  86.679   1058
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 27.38 %
    Favored  : 69.75 %
  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: -2.44 (0.27), residues: 950
  helix: -0.41 (0.29), residues: 354
  sheet: -2.51 (0.33), residues: 217
  loop : -2.09 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG R 304 
 TYR   0.009   0.001   TYR G  40 
 PHE   0.017   0.001   PHE N  29 
 TRP   0.056   0.002   TRP B  82 
 HIS   0.003   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 7538)
  covalent geometry    : angle       0.57282 (10245)
  SS BOND              : bond        0.00188 (    2)
  SS BOND              : angle       0.48889 (    4)
  hydrogen bonds       : bond        0.02792 (  220)
  hydrogen bonds       : angle       4.35754 (  624)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1169.83 seconds
wall clock time: 20 minutes 53.02 seconds (1253.02 seconds total)