Starting phenix.real_space_refine
on Wed Mar 12 05:29:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7bz2_30249/03_2025/7bz2_30249.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7bz2_30249/03_2025/7bz2_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7bz2_30249/03_2025/7bz2_30249.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7bz2_30249/03_2025/7bz2_30249.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7bz2_30249/03_2025/7bz2_30249.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7bz2_30249/03_2025/7bz2_30249.cif"
  }
  resolution = 3.82
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 7, 'GLU:plan': 4, 'ARG:plan': 6}
          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: {'GLN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 6, '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: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 2}
          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: 4.86, per 1000 atoms: 0.66
  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: 1.90
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.81
  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: 1.79

  Time building geometry restraints manager: 2.25 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:             0.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     19.980
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.940
-------------------------------------------------------------------------------
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   7538  Z= 0.279
  Angle     :  0.680   8.376  10245  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 : 12.35
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.018   0.002   TRP R 109 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.014   0.002   PHE N 108 
 TYR   0.013   0.001   TYR B  59 
 ARG   0.003   0.000   ARG N 118 

*********************** 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  : 0.813 
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: 0.2341
  time to fit residues: 57.2172
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  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 80 optimal weight:    6.9990
   chunk 72 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    9.9990
   chunk 38 optimal weight:    0.6980
   chunk 74 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 55 optimal weight:    0.0050
   chunk 86 optimal weight:    0.8980
   overall best weight:    0.6796

-------------------------------------------------------------------------------
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 = 0.4104 r_free = 0.4104 target = 0.181624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.159817 restraints weight = 8078.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.152063 restraints weight = 12190.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.149098 restraints weight = 9653.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.1381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7538  Z= 0.173
  Angle     :  0.589   8.486  10245  Z= 0.310
  Chirality :  0.044   0.136   1194
  Planarity :  0.004   0.048   1295
  Dihedral  :  7.554  82.166   1058
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.68 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 17.30 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.92 (0.23), residues: 950
  helix: -2.37 (0.25), residues: 347
  sheet: -4.24 (0.29), residues: 187
  loop : -3.48 (0.24), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP R 313 
 HIS   0.007   0.001   HIS B 311 
 PHE   0.032   0.002   PHE R 208 
 TYR   0.014   0.001   TYR G  40 
 ARG   0.005   0.000   ARG N  72 

*********************** 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
  186 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 168
  time to evaluate  : 1.014 
Fit side-chains
REVERT: A   45 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8346 (tt)
REVERT: B  111 TYR cc_start: 0.7889 (m-80) cc_final: 0.7249 (m-80)
REVERT: B  154 ASP cc_start: 0.8075 (m-30) cc_final: 0.7365 (t0)
  outliers start: 18
  outliers final: 11
  residues processed: 178
  average time/residue: 0.2437
  time to fit residues: 59.7496
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  : 0.908 
-------------------------------------------------------------------------------
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 80 optimal weight:    5.9990
   chunk 6 optimal weight:    4.9990
   chunk 35 optimal weight:    9.9990
   chunk 74 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 69 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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 = 0.4073 r_free = 0.4073 target = 0.177857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.152381 restraints weight = 8271.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.148536 restraints weight = 13562.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.149857 restraints weight = 12794.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.1681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7538  Z= 0.247
  Angle     :  0.611   9.520  10245  Z= 0.320
  Chirality :  0.044   0.147   1194
  Planarity :  0.004   0.047   1295
  Dihedral  :  7.345  88.403   1058
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.21 %
    Favored  : 91.79 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 19.62 %
    Favored  : 75.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.54 (0.24), residues: 950
  helix: -2.14 (0.26), residues: 355
  sheet: -3.90 (0.29), residues: 202
  loop : -3.19 (0.26), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP R 109 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.021   0.002   PHE A 222 
 TYR   0.011   0.001   TYR B  59 
 ARG   0.006   0.000   ARG B 256 

*********************** 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
  184 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 151
  time to evaluate  : 1.215 
Fit side-chains
REVERT: A   45 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8453 (tt)
REVERT: B   88 ASN cc_start: 0.8629 (m-40) cc_final: 0.8186 (m110)
REVERT: B  111 TYR cc_start: 0.7836 (m-80) cc_final: 0.7309 (m-80)
REVERT: B  154 ASP cc_start: 0.7922 (m-30) cc_final: 0.7417 (t0)
REVERT: R   64 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7064 (mt)
REVERT: R  300 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7121 (m-30)
REVERT: R  312 ASN cc_start: 0.6576 (OUTLIER) cc_final: 0.5985 (t0)
  outliers start: 33
  outliers final: 17
  residues processed: 170
  average time/residue: 0.2406
  time to fit residues: 58.0190
Evaluate side-chains
  161 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 140
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
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   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 B residue  255 LEU
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   73 ASP
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  205 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
Chi-restraints excluded: chain R residue  312 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 52 optimal weight:    5.9990
   chunk 71 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 72 optimal weight:    0.0670
   chunk 25 optimal weight:    0.9990
   chunk 76 optimal weight:    0.6980
   chunk 78 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.7322

-------------------------------------------------------------------------------
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 312 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.182920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.158949 restraints weight = 8123.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.156270 restraints weight = 13861.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.154607 restraints weight = 12646.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.1945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7538  Z= 0.163
  Angle     :  0.552   8.679  10245  Z= 0.289
  Chirality :  0.042   0.137   1194
  Planarity :  0.003   0.047   1295
  Dihedral  :  6.952  88.066   1058
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 22.34 %
    Favored  : 74.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.01 (0.25), residues: 950
  helix: -1.76 (0.27), residues: 350
  sheet: -3.61 (0.31), residues: 197
  loop : -2.82 (0.27), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP R 109 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.015   0.001   PHE R 193 
 TYR   0.007   0.001   TYR A 360 
 ARG   0.006   0.000   ARG B 256 

*********************** 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
  176 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 150
  time to evaluate  : 0.810 
Fit side-chains
REVERT: A   45 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8398 (tt)
REVERT: B   88 ASN cc_start: 0.8687 (m-40) cc_final: 0.8207 (m110)
REVERT: B  111 TYR cc_start: 0.7755 (m-80) cc_final: 0.7292 (m-80)
REVERT: B  154 ASP cc_start: 0.7872 (m-30) cc_final: 0.7374 (t0)
REVERT: R   36 MET cc_start: 0.7060 (mmt) cc_final: 0.6751 (mmm)
REVERT: R  300 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.6971 (m-30)
REVERT: R  312 ASN cc_start: 0.6504 (OUTLIER) cc_final: 0.6258 (t0)
  outliers start: 26
  outliers final: 15
  residues processed: 163
  average time/residue: 0.1760
  time to fit residues: 39.9441
Evaluate side-chains
  152 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
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   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   73 ASP
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  205 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  300 ASP
Chi-restraints excluded: chain R residue  312 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 68 optimal weight:    3.9990
   chunk 28 optimal weight:    7.9990
   chunk 60 optimal weight:    4.9990
   chunk 57 optimal weight:    3.9990
   chunk 59 optimal weight:    7.9990
   chunk 6 optimal weight:    0.8980
   chunk 93 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 52 optimal weight:    8.9990
   overall best weight:    3.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 ASN
A 390 GLN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN
B 220 GLN
N  39 GLN
R 312 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.171992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.138490 restraints weight = 8298.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.137927 restraints weight = 8395.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.138149 restraints weight = 8313.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.088   7538  Z= 0.456
  Angle     :  0.726  11.047  10245  Z= 0.383
  Chirality :  0.049   0.233   1194
  Planarity :  0.005   0.046   1295
  Dihedral  :  7.603  83.423   1058
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 24.66 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.30 (0.24), residues: 950
  helix: -2.04 (0.26), residues: 352
  sheet: -3.81 (0.30), residues: 206
  loop : -2.88 (0.27), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.003   TRP R 313 
 HIS   0.005   0.002   HIS A 362 
 PHE   0.019   0.002   PHE A 222 
 TYR   0.021   0.002   TYR B  59 
 ARG   0.008   0.001   ARG B 256 

*********************** 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
  178 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 140
  time to evaluate  : 1.344 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8562 (tt)
REVERT: B  111 TYR cc_start: 0.7836 (m-80) cc_final: 0.7347 (m-80)
REVERT: B  154 ASP cc_start: 0.8041 (m-30) cc_final: 0.7523 (t0)
REVERT: R  312 ASN cc_start: 0.7269 (OUTLIER) cc_final: 0.6953 (t0)
  outliers start: 38
  outliers final: 29
  residues processed: 164
  average time/residue: 0.2180
  time to fit residues: 49.2794
Evaluate side-chains
  165 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 134
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  242 THR
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  186 ASP
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  258 ASP
Chi-restraints excluded: chain B residue  321 THR
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   20 LEU
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue   87 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  312 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 55 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 81 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 83 optimal weight:    8.9990
   chunk 76 optimal weight:    0.7980
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 ASN
R 312 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.176098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.151946 restraints weight = 8253.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.145213 restraints weight = 14154.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.141546 restraints weight = 9968.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.2014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7538  Z= 0.268
  Angle     :  0.624  10.111  10245  Z= 0.327
  Chirality :  0.045   0.158   1194
  Planarity :  0.004   0.047   1295
  Dihedral  :  7.273  78.567   1058
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 25.89 %
    Favored  : 69.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.00 (0.25), residues: 950
  helix: -1.84 (0.26), residues: 346
  sheet: -3.62 (0.30), residues: 206
  loop : -2.68 (0.28), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.054   0.002   TRP R 313 
 HIS   0.003   0.001   HIS B 311 
 PHE   0.014   0.002   PHE A 222 
 TYR   0.018   0.001   TYR R 308 
 ARG   0.007   0.000   ARG B 256 

*********************** 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
  174 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 138
  time to evaluate  : 0.828 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7882 (mp0)
REVERT: A  388 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8694 (mp)
REVERT: B  111 TYR cc_start: 0.7826 (m-80) cc_final: 0.7256 (m-80)
REVERT: B  154 ASP cc_start: 0.8044 (m-30) cc_final: 0.7413 (t0)
REVERT: R   36 MET cc_start: 0.7142 (mmt) cc_final: 0.6912 (mmm)
REVERT: R   64 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7091 (mt)
REVERT: R  312 ASN cc_start: 0.7449 (OUTLIER) cc_final: 0.7090 (t0)
  outliers start: 36
  outliers final: 24
  residues processed: 163
  average time/residue: 0.2115
  time to fit residues: 49.3395
Evaluate side-chains
  161 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 133
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  381 ASP
Chi-restraints excluded: chain A residue  388 LEU
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  200 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  321 THR
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   73 ASP
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  206 VAL
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  312 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 81 optimal weight:    7.9990
   chunk 38 optimal weight:    0.0770
   chunk 51 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 59 optimal weight:    7.9990
   chunk 52 optimal weight:    1.9990
   chunk 40 optimal weight:    7.9990
   overall best weight:    1.4144

-------------------------------------------------------------------------------
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
B 183 HIS
R 312 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.177761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.151895 restraints weight = 8179.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.148775 restraints weight = 12765.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.148339 restraints weight = 13659.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.2088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7538  Z= 0.232
  Angle     :  0.600   9.713  10245  Z= 0.313
  Chirality :  0.044   0.148   1194
  Planarity :  0.004   0.047   1295
  Dihedral  :  7.067  77.651   1058
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.32 %
    Favored  : 91.68 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 26.16 %
    Favored  : 68.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.84 (0.25), residues: 950
  helix: -1.69 (0.26), residues: 355
  sheet: -3.46 (0.31), residues: 204
  loop : -2.67 (0.28), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.059   0.002   TRP R 313 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.013   0.002   PHE A 222 
 TYR   0.014   0.001   TYR B  59 
 ARG   0.005   0.000   ARG B 256 

*********************** 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
  178 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 140
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7883 (mp0)
REVERT: B  111 TYR cc_start: 0.7767 (m-80) cc_final: 0.7273 (m-80)
REVERT: B  154 ASP cc_start: 0.7942 (m-30) cc_final: 0.7395 (t0)
REVERT: R   64 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.7056 (mt)
  outliers start: 38
  outliers final: 26
  residues processed: 167
  average time/residue: 0.1692
  time to fit residues: 39.4128
Evaluate side-chains
  160 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 132
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
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  242 THR
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  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  321 THR
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   73 ASP
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue   66 THR
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  312 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 75 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 72 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9980
   chunk 12 optimal weight:    7.9990
   chunk 35 optimal weight:    8.9990
   chunk 55 optimal weight:   10.0000
   chunk 85 optimal weight:    0.2980
   chunk 38 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9990
   chunk 81 optimal weight:    0.4980
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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
R 312 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.182004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.157356 restraints weight = 8144.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.151540 restraints weight = 13640.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.150093 restraints weight = 9394.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.2354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   7538  Z= 0.162
  Angle     :  0.585   9.547  10245  Z= 0.297
  Chirality :  0.043   0.140   1194
  Planarity :  0.003   0.047   1295
  Dihedral  :  6.630  80.140   1058
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 26.84 %
    Favored  : 68.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.44 (0.26), residues: 950
  helix: -1.35 (0.27), residues: 355
  sheet: -3.23 (0.33), residues: 202
  loop : -2.47 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP R 109 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.014   0.001   PHE A 222 
 TYR   0.010   0.001   TYR G  40 
 ARG   0.008   0.000   ARG B 256 

*********************** 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
  162 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 130
  time to evaluate  : 0.784 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7890 (mp0)
REVERT: A  212 PHE cc_start: 0.7298 (p90) cc_final: 0.7032 (p90)
REVERT: B   88 ASN cc_start: 0.8586 (m-40) cc_final: 0.8228 (m110)
REVERT: B  111 TYR cc_start: 0.7832 (m-80) cc_final: 0.7327 (m-80)
REVERT: B  147 SER cc_start: 0.8721 (t) cc_final: 0.8505 (t)
REVERT: B  154 ASP cc_start: 0.8001 (m-30) cc_final: 0.7342 (t0)
REVERT: R   64 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6932 (mt)
REVERT: R   82 MET cc_start: 0.7024 (tpp) cc_final: 0.6779 (ttm)
REVERT: R  312 ASN cc_start: 0.6618 (OUTLIER) cc_final: 0.5903 (t0)
  outliers start: 32
  outliers final: 20
  residues processed: 153
  average time/residue: 0.1700
  time to fit residues: 36.6195
Evaluate side-chains
  148 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 125
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
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  242 THR
Chi-restraints excluded: chain A residue  372 ILE
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  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  277 SER
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  312 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 64 optimal weight:    5.9990
   chunk 40 optimal weight:    8.9990
   chunk 10 optimal weight:    2.9990
   chunk 20 optimal weight:    7.9990
   chunk 2 optimal weight:    0.8980
   chunk 93 optimal weight:    0.0870
   chunk 63 optimal weight:    4.9990
   chunk 51 optimal weight:    0.0000
   chunk 65 optimal weight:    0.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.9966

-------------------------------------------------------------------------------
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
B 183 HIS
N  39 GLN
R 312 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.171519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.143224 restraints weight = 8445.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.140563 restraints weight = 12526.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.143248 restraints weight = 11261.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.2449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7538  Z= 0.185
  Angle     :  0.587  10.475  10245  Z= 0.299
  Chirality :  0.043   0.137   1194
  Planarity :  0.003   0.047   1295
  Dihedral  :  6.556  82.580   1058
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 27.38 %
    Favored  : 68.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.27 (0.26), residues: 950
  helix: -1.16 (0.28), residues: 352
  sheet: -3.12 (0.33), residues: 204
  loop : -2.44 (0.29), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP R 109 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.014   0.001   PHE A 222 
 TYR   0.011   0.001   TYR B  59 
 ARG   0.006   0.000   ARG B 256 

*********************** 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
  161 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 131
  time to evaluate  : 0.749 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7879 (mp0)
REVERT: A  212 PHE cc_start: 0.7292 (p90) cc_final: 0.7023 (p90)
REVERT: B   88 ASN cc_start: 0.8687 (m-40) cc_final: 0.8237 (m110)
REVERT: B   95 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7209 (mp)
REVERT: B  111 TYR cc_start: 0.7836 (m-80) cc_final: 0.7279 (m-80)
REVERT: B  147 SER cc_start: 0.8755 (t) cc_final: 0.8542 (t)
REVERT: B  154 ASP cc_start: 0.7951 (m-30) cc_final: 0.7486 (t0)
REVERT: R   64 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6945 (mt)
REVERT: R  312 ASN cc_start: 0.6901 (OUTLIER) cc_final: 0.6178 (t0)
  outliers start: 30
  outliers final: 21
  residues processed: 153
  average time/residue: 0.1664
  time to fit residues: 35.7060
Evaluate side-chains
  150 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 125
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
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  242 THR
Chi-restraints excluded: chain A residue  276 ILE
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   95 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  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  277 SER
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  312 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 46 optimal weight:    0.4980
   chunk 33 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 76 optimal weight:    0.0170
   chunk 84 optimal weight:    0.7980
   chunk 62 optimal weight:    0.3980
   chunk 93 optimal weight:    1.9990
   chunk 48 optimal weight:   10.0000
   overall best weight:    0.5420

-------------------------------------------------------------------------------
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
R 312 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.173501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.145244 restraints weight = 8348.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.142280 restraints weight = 12031.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.144143 restraints weight = 11258.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.2616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7538  Z= 0.146
  Angle     :  0.570   9.207  10245  Z= 0.291
  Chirality :  0.042   0.142   1194
  Planarity :  0.003   0.048   1295
  Dihedral  :  6.332  83.091   1058
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 28.47 %
    Favored  : 68.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.02 (0.26), residues: 950
  helix: -0.95 (0.28), residues: 352
  sheet: -2.95 (0.34), residues: 201
  loop : -2.33 (0.30), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP R 109 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.014   0.001   PHE A 222 
 TYR   0.010   0.001   TYR G  40 
 ARG   0.009   0.000   ARG B 256 

********************** 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
  158 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 136
  time to evaluate  : 0.872 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7717 (mp0)
REVERT: B   88 ASN cc_start: 0.8696 (m-40) cc_final: 0.8207 (m110)
REVERT: B  111 TYR cc_start: 0.7875 (m-80) cc_final: 0.7368 (m-80)
REVERT: B  147 SER cc_start: 0.8688 (t) cc_final: 0.8469 (t)
REVERT: B  154 ASP cc_start: 0.8014 (m-30) cc_final: 0.7433 (t0)
REVERT: R   64 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6866 (mt)
REVERT: R  140 LYS cc_start: 0.7485 (mtpp) cc_final: 0.7052 (mtmm)
REVERT: R  268 GLU cc_start: 0.7239 (tm-30) cc_final: 0.6732 (mt-10)
REVERT: R  312 ASN cc_start: 0.6513 (OUTLIER) cc_final: 0.5783 (t0)
  outliers start: 22
  outliers final: 17
  residues processed: 152
  average time/residue: 0.1685
  time to fit residues: 35.3357
Evaluate side-chains
  148 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 128
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
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   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  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   44 HIS
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  312 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 76 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 22 optimal weight:    9.9990
   chunk 11 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 279 ASN
A 371 ASN
B 239 ASN
R 312 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.173985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.146141 restraints weight = 8399.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.143086 restraints weight = 12975.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.144751 restraints weight = 11688.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.2737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7538  Z= 0.175
  Angle     :  0.587   8.600  10245  Z= 0.299
  Chirality :  0.043   0.166   1194
  Planarity :  0.003   0.048   1295
  Dihedral  :  6.351  84.784   1058
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 28.34 %
    Favored  : 68.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.91 (0.27), residues: 950
  helix: -0.84 (0.28), residues: 352
  sheet: -2.86 (0.34), residues: 207
  loop : -2.27 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.065   0.003   TRP B  82 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.016   0.001   PHE A 222 
 TYR   0.010   0.001   TYR G  40 
 ARG   0.006   0.000   ARG R 304 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2586.97 seconds
wall clock time: 47 minutes 42.80 seconds (2862.80 seconds total)