Starting phenix.real_space_refine
on Wed Feb 12 05:33:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7bz2_30249/02_2025/7bz2_30249.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7bz2_30249/02_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_30249/02_2025/7bz2_30249.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7bz2_30249/02_2025/7bz2_30249.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7bz2_30249/02_2025/7bz2_30249.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7bz2_30249/02_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-5592/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: 4.29, per 1000 atoms: 0.58
  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: 1.93
  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: 0.75
  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: 1.80

  Time building geometry restraints manager: 2.12 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:             0.250
  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:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     18.990
  Find NCS groups from input model:        0.080
  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:             0.010
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.550
-------------------------------------------------------------------------------
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: 0.2083
  time to fit residues: 50.5292
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  : 0.844 
-------------------------------------------------------------------------------
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:    0.5980
   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:    0.6396

-------------------------------------------------------------------------------
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 = 0.4105 r_free = 0.4105 target = 0.181740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.159461 restraints weight = 8078.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.155661 restraints weight = 13176.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.155874 restraints weight = 12231.713|
|-----------------------------------------------------------------------------|
r_work (final): 0.3838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.1392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7538  Z= 0.171
  Angle     :  0.587   8.282  10245  Z= 0.309
  Chirality :  0.044   0.137   1194
  Planarity :  0.004   0.048   1295
  Dihedral  :  7.534  82.044   1058
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 17.71 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.91 (0.23), residues: 950
  helix: -2.38 (0.25), residues: 342
  sheet: -4.24 (0.29), residues: 187
  loop : -3.44 (0.24), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 313 
 HIS   0.005   0.001   HIS B 311 
 PHE   0.030   0.002   PHE R 208 
 TYR   0.013   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
  185 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 168
  time to evaluate  : 0.819 
Fit side-chains
REVERT: A   45 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8347 (tt)
REVERT: B  111 TYR cc_start: 0.7803 (m-80) cc_final: 0.7234 (m-80)
REVERT: B  154 ASP cc_start: 0.7902 (m-30) cc_final: 0.7372 (t0)
  outliers start: 17
  outliers final: 10
  residues processed: 178
  average time/residue: 0.1886
  time to fit residues: 45.3877
Evaluate side-chains
  160 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 149
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
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:    6.9990
   chunk 6 optimal weight:    4.9990
   chunk 35 optimal weight:    8.9990
   chunk 74 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 69 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   chunk 70 optimal weight:    0.8980
   overall best weight:    1.2986

-------------------------------------------------------------------------------
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 = 0.4087 r_free = 0.4087 target = 0.179370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.156387 restraints weight = 8257.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.153293 restraints weight = 13540.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.153132 restraints weight = 12829.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.1715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7538  Z= 0.218
  Angle     :  0.599   9.126  10245  Z= 0.313
  Chirality :  0.044   0.135   1194
  Planarity :  0.004   0.047   1295
  Dihedral  :  7.250  87.630   1058
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.58 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 19.62 %
    Favored  : 76.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.46 (0.24), residues: 950
  helix: -2.09 (0.26), residues: 350
  sheet: -3.89 (0.30), residues: 197
  loop : -3.11 (0.26), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP R 109 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.020   0.002   PHE A 222 
 TYR   0.010   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
  186 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 154
  time to evaluate  : 0.828 
Fit side-chains
REVERT: A   45 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8453 (tt)
REVERT: B   88 ASN cc_start: 0.8728 (m-40) cc_final: 0.8299 (m110)
REVERT: B  111 TYR cc_start: 0.7795 (m-80) cc_final: 0.7310 (m-80)
REVERT: B  154 ASP cc_start: 0.7872 (m-30) cc_final: 0.7405 (t0)
REVERT: R   64 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.7035 (mt)
REVERT: R  300 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7103 (m-30)
  outliers start: 32
  outliers final: 16
  residues processed: 173
  average time/residue: 0.1692
  time to fit residues: 40.8066
Evaluate side-chains
  161 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 142
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
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  218 VAL
Chi-restraints excluded: chain R residue  300 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0770
   chunk 52 optimal weight:    5.9990
   chunk 71 optimal weight:    0.7980
   chunk 6 optimal weight:    0.2980
   chunk 72 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 76 optimal weight:    0.5980
   chunk 78 optimal weight:    0.2980
   chunk 26 optimal weight:    0.7980
   chunk 0 optimal weight:   20.0000
   overall best weight:    0.4138

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.183902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.159768 restraints weight = 8001.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.157511 restraints weight = 12891.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.157704 restraints weight = 10980.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.2130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7538  Z= 0.134
  Angle     :  0.535   7.912  10245  Z= 0.279
  Chirality :  0.042   0.138   1194
  Planarity :  0.003   0.046   1295
  Dihedral  :  6.597  86.055   1058
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 22.07 %
    Favored  : 74.66 %
  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: -3.80 (0.25), residues: 950
  helix: -1.57 (0.27), residues: 348
  sheet: -3.52 (0.31), residues: 199
  loop : -2.70 (0.28), 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   0.014   0.001   PHE R 193 
 TYR   0.008   0.001   TYR B 145 
 ARG   0.005   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
  170 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 146
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7766 (mp0)
REVERT: A   45 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8396 (tt)
REVERT: B  111 TYR cc_start: 0.7727 (m-80) cc_final: 0.7247 (m-80)
REVERT: B  154 ASP cc_start: 0.7834 (m-30) cc_final: 0.7375 (t0)
REVERT: N   60 TYR cc_start: 0.8754 (m-80) cc_final: 0.8387 (m-80)
REVERT: R   36 MET cc_start: 0.6864 (mmt) cc_final: 0.6608 (mmm)
REVERT: R  300 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.6736 (m-30)
  outliers start: 24
  outliers final: 13
  residues processed: 159
  average time/residue: 0.1770
  time to fit residues: 38.6875
Evaluate side-chains
  145 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain G residue   44 HIS
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  218 VAL
Chi-restraints excluded: chain R residue  300 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 94 optimal weight:    0.5980
   chunk 0 optimal weight:   20.0000
   chunk 68 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 60 optimal weight:    6.9990
   chunk 57 optimal weight:    1.9990
   chunk 59 optimal weight:    0.5980
   chunk 6 optimal weight:    0.0570
   chunk 93 optimal weight:    0.9990
   chunk 20 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.8502

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN
B 183 HIS
B 220 GLN
N  39 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.184812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.162185 restraints weight = 8026.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.159989 restraints weight = 13759.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.160133 restraints weight = 13298.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.2314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7538  Z= 0.168
  Angle     :  0.552   8.967  10245  Z= 0.285
  Chirality :  0.043   0.191   1194
  Planarity :  0.003   0.045   1295
  Dihedral  :  6.461  84.243   1058
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 24.52 %
    Favored  : 72.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.56 (0.25), residues: 950
  helix: -1.35 (0.27), residues: 348
  sheet: -3.41 (0.31), residues: 201
  loop : -2.57 (0.28), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP R 313 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.012   0.001   PHE A 222 
 TYR   0.009   0.001   TYR G  40 
 ARG   0.006   0.000   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
  156 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 132
  time to evaluate  : 0.856 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8416 (tt)
REVERT: B  154 ASP cc_start: 0.7803 (m-30) cc_final: 0.7596 (m-30)
REVERT: N   60 TYR cc_start: 0.8728 (m-80) cc_final: 0.8362 (m-80)
REVERT: R   64 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6890 (mt)
REVERT: R  300 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.6717 (m-30)
  outliers start: 24
  outliers final: 13
  residues processed: 144
  average time/residue: 0.1766
  time to fit residues: 35.5753
Evaluate side-chains
  143 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 127
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
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  243 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  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  300 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0570
   chunk 1 optimal weight:    0.9990
   chunk 80 optimal weight:   20.0000
   chunk 44 optimal weight:    9.9990
   chunk 83 optimal weight:    4.9990
   chunk 76 optimal weight:    0.6980
   overall best weight:    0.6900

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN
B 176 GLN
N  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.186195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.164650 restraints weight = 8180.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.161992 restraints weight = 14784.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.161566 restraints weight = 14355.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.2471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7538  Z= 0.151
  Angle     :  0.537   7.570  10245  Z= 0.277
  Chirality :  0.042   0.151   1194
  Planarity :  0.003   0.045   1295
  Dihedral  :  6.343  81.431   1058
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 24.80 %
    Favored  : 71.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.30 (0.26), residues: 950
  helix: -1.12 (0.28), residues: 351
  sheet: -3.18 (0.33), residues: 199
  loop : -2.50 (0.29), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP R 313 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.011   0.001   PHE A 222 
 TYR   0.016   0.001   TYR B 111 
 ARG   0.009   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
  160 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 131
  time to evaluate  : 0.839 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7778 (mp0)
REVERT: A   45 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8404 (tt)
REVERT: A  212 PHE cc_start: 0.7147 (p90) cc_final: 0.6891 (p90)
REVERT: B  111 TYR cc_start: 0.7530 (m-80) cc_final: 0.6971 (m-80)
REVERT: B  154 ASP cc_start: 0.7898 (m-30) cc_final: 0.7499 (t0)
REVERT: B  188 MET cc_start: 0.8330 (mmp) cc_final: 0.8082 (mmm)
REVERT: N   35 ASN cc_start: 0.8348 (p0) cc_final: 0.7924 (p0)
REVERT: N   60 TYR cc_start: 0.8686 (m-80) cc_final: 0.8347 (m-80)
REVERT: R   64 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6828 (mt)
REVERT: R   82 MET cc_start: 0.7208 (tpp) cc_final: 0.6857 (ttm)
REVERT: R  300 ASP cc_start: 0.7278 (OUTLIER) cc_final: 0.6626 (m-30)
  outliers start: 29
  outliers final: 19
  residues processed: 148
  average time/residue: 0.1831
  time to fit residues: 37.5505
Evaluate side-chains
  149 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 126
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLU
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  381 ASP
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   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  243 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   45 LEU
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue  159 ILE
Chi-restraints excluded: chain R residue  206 VAL
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  281 THR
Chi-restraints excluded: chain R residue  300 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 81 optimal weight:   10.0000
   chunk 38 optimal weight:    6.9990
   chunk 51 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 68 optimal weight:    0.8980
   chunk 33 optimal weight:    0.2980
   chunk 14 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.7180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.187216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.162951 restraints weight = 8003.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.159585 restraints weight = 15459.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.160869 restraints weight = 14508.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.2595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7538  Z= 0.154
  Angle     :  0.546   8.316  10245  Z= 0.277
  Chirality :  0.042   0.139   1194
  Planarity :  0.003   0.045   1295
  Dihedral  :  6.198  78.104   1058
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 25.34 %
    Favored  : 70.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.98 (0.26), residues: 950
  helix: -0.81 (0.29), residues: 344
  sheet: -2.96 (0.33), residues: 205
  loop : -2.35 (0.29), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP R 313 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.011   0.001   PHE A 222 
 TYR   0.012   0.001   TYR B 111 
 ARG   0.006   0.000   ARG R 304 

*********************** 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
  161 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 131
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7817 (mp0)
REVERT: A   45 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8400 (tt)
REVERT: A  212 PHE cc_start: 0.7151 (p90) cc_final: 0.6921 (p90)
REVERT: A  390 GLN cc_start: 0.8344 (tp-100) cc_final: 0.8133 (tp-100)
REVERT: B  154 ASP cc_start: 0.7955 (m-30) cc_final: 0.7457 (t0)
REVERT: N   60 TYR cc_start: 0.8668 (m-80) cc_final: 0.8402 (m-80)
REVERT: R   64 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6857 (mt)
REVERT: R  270 LYS cc_start: 0.8076 (tptt) cc_final: 0.7870 (tptt)
REVERT: R  300 ASP cc_start: 0.7250 (OUTLIER) cc_final: 0.6650 (m-30)
  outliers start: 30
  outliers final: 20
  residues processed: 148
  average time/residue: 0.1636
  time to fit residues: 33.9097
Evaluate side-chains
  151 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 127
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
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 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  243 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   45 LEU
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue  159 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  281 THR
Chi-restraints excluded: chain R residue  300 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 75 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 72 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 12 optimal weight:   10.0000
   chunk 35 optimal weight:    9.9990
   chunk 55 optimal weight:    6.9990
   chunk 85 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9990
   chunk 81 optimal weight:    6.9990
   overall best weight:    1.4786

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.171909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.137240 restraints weight = 8401.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.137037 restraints weight = 7712.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.137554 restraints weight = 6801.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.2543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7538  Z= 0.234
  Angle     :  0.599   9.303  10245  Z= 0.306
  Chirality :  0.044   0.150   1194
  Planarity :  0.004   0.044   1295
  Dihedral  :  6.380  75.618   1058
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 25.07 %
    Favored  : 70.30 %
  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: -3.06 (0.26), residues: 950
  helix: -0.98 (0.28), residues: 351
  sheet: -2.96 (0.34), residues: 201
  loop : -2.35 (0.29), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP R 313 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.015   0.001   PHE A 222 
 TYR   0.020   0.001   TYR B 111 
 ARG   0.005   0.000   ARG R 304 

*********************** 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
  166 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 132
  time to evaluate  : 0.903 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7826 (mp0)
REVERT: A   45 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8422 (tt)
REVERT: A  239 ASN cc_start: 0.8626 (p0) cc_final: 0.8330 (p0)
REVERT: B   88 ASN cc_start: 0.8570 (m-40) cc_final: 0.8131 (m110)
REVERT: B  154 ASP cc_start: 0.8072 (m-30) cc_final: 0.7463 (t0)
REVERT: B  258 ASP cc_start: 0.4841 (OUTLIER) cc_final: 0.4494 (t0)
REVERT: B  336 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8137 (mp)
REVERT: R   36 MET cc_start: 0.6761 (mmm) cc_final: 0.6449 (tpp)
REVERT: R   64 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6978 (mt)
REVERT: R  300 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.6835 (m-30)
  outliers start: 34
  outliers final: 21
  residues processed: 155
  average time/residue: 0.1651
  time to fit residues: 35.7056
Evaluate side-chains
  155 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 128
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
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  243 THR
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  258 ASP
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  336 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  159 ILE
Chi-restraints excluded: chain R residue  206 VAL
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  281 THR
Chi-restraints excluded: chain R residue  300 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 40 optimal weight:    7.9990
   chunk 10 optimal weight:    0.7980
   chunk 20 optimal weight:    7.9990
   chunk 2 optimal weight:    1.9990
   chunk 93 optimal weight:    6.9990
   chunk 63 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0270
   chunk 65 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   overall best weight:    1.1242

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 371 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.174294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.143045 restraints weight = 8417.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.141125 restraints weight = 8840.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.141219 restraints weight = 7948.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.2644

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= 0.195
  Angle     :  0.596  10.217  10245  Z= 0.298
  Chirality :  0.043   0.150   1194
  Planarity :  0.003   0.045   1295
  Dihedral  :  6.243  75.366   1058
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 26.16 %
    Favored  : 69.62 %
  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: -2.95 (0.27), residues: 950
  helix: -0.89 (0.28), residues: 355
  sheet: -2.84 (0.34), residues: 201
  loop : -2.35 (0.29), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP R 109 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.013   0.001   PHE A 222 
 TYR   0.015   0.001   TYR B 111 
 ARG   0.005   0.000   ARG R 304 

*********************** 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
  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 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7778 (mp0)
REVERT: A   45 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8424 (tt)
REVERT: A  212 PHE cc_start: 0.7257 (p90) cc_final: 0.7018 (p90)
REVERT: A  239 ASN cc_start: 0.8622 (p0) cc_final: 0.8326 (p0)
REVERT: B   88 ASN cc_start: 0.8546 (m-40) cc_final: 0.8072 (m110)
REVERT: B  154 ASP cc_start: 0.8026 (m-30) cc_final: 0.7489 (t0)
REVERT: R   64 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6885 (mt)
REVERT: R  140 LYS cc_start: 0.7499 (mtpp) cc_final: 0.7085 (mtmm)
REVERT: R  300 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.6831 (m-30)
  outliers start: 31
  outliers final: 21
  residues processed: 154
  average time/residue: 0.1708
  time to fit residues: 36.4945
Evaluate side-chains
  154 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 129
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
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  220 HIS
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  243 THR
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   40 MET
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue  159 ILE
Chi-restraints excluded: chain R residue  206 VAL
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  281 THR
Chi-restraints excluded: chain R residue  300 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 80 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0170
   chunk 33 optimal weight:    0.0770
   chunk 44 optimal weight:   10.0000
   chunk 76 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9990
   chunk 62 optimal weight:    9.9990
   chunk 93 optimal weight:    6.9990
   chunk 48 optimal weight:    4.9990
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 371 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.176197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.143303 restraints weight = 8353.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.142557 restraints weight = 8023.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.142891 restraints weight = 8487.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.2812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7538  Z= 0.150
  Angle     :  0.582   8.949  10245  Z= 0.292
  Chirality :  0.043   0.146   1194
  Planarity :  0.003   0.045   1295
  Dihedral  :  6.097  81.497   1058
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 26.70 %
    Favored  : 69.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.68 (0.27), residues: 950
  helix: -0.58 (0.29), residues: 348
  sheet: -2.70 (0.35), residues: 201
  loop : -2.25 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP R 109 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.023   0.001   PHE A 222 
 TYR   0.013   0.001   TYR B 111 
 ARG   0.006   0.000   ARG R 304 

********************** 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
  151 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 125
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7730 (mp0)
REVERT: A   45 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8426 (tt)
REVERT: A  212 PHE cc_start: 0.7299 (p90) cc_final: 0.7035 (p90)
REVERT: B   88 ASN cc_start: 0.8503 (m-40) cc_final: 0.8082 (m110)
REVERT: B  154 ASP cc_start: 0.8070 (m-30) cc_final: 0.7494 (t0)
REVERT: N   60 TYR cc_start: 0.8686 (m-80) cc_final: 0.8416 (m-80)
REVERT: R   36 MET cc_start: 0.7103 (tpp) cc_final: 0.6714 (tpp)
REVERT: R   40 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7284 (mpp)
REVERT: R   64 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6800 (mt)
REVERT: R  140 LYS cc_start: 0.7527 (mtpp) cc_final: 0.7123 (mtmm)
REVERT: R  300 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.6953 (m-30)
  outliers start: 26
  outliers final: 19
  residues processed: 141
  average time/residue: 0.1697
  time to fit residues: 33.3512
Evaluate side-chains
  147 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
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  220 HIS
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  243 THR
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   44 HIS
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   40 MET
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue  159 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  281 THR
Chi-restraints excluded: chain R residue  300 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 55 optimal weight:    8.9990
   chunk 14 optimal weight:    0.8980
   chunk 76 optimal weight:    0.7980
   chunk 56 optimal weight:    4.9990
   chunk 84 optimal weight:    3.9990
   chunk 74 optimal weight:    8.9990
   chunk 22 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   chunk 80 optimal weight:    2.9990
   overall best weight:    1.4784

-------------------------------------------------------------------------------
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
B 183 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.172778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.145077 restraints weight = 8431.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.142411 restraints weight = 13894.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.144453 restraints weight = 12864.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.2720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7538  Z= 0.234
  Angle     :  0.610   8.967  10245  Z= 0.310
  Chirality :  0.044   0.139   1194
  Planarity :  0.003   0.046   1295
  Dihedral  :  6.221  82.216   1058
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 26.70 %
    Favored  : 69.48 %
  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: -2.79 (0.27), residues: 950
  helix: -0.81 (0.28), residues: 360
  sheet: -2.71 (0.35), residues: 201
  loop : -2.22 (0.30), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP R 313 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.012   0.001   PHE A 222 
 TYR   0.014   0.001   TYR R 308 
 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: 2233.98 seconds
wall clock time: 40 minutes 52.17 seconds (2452.17 seconds total)