Starting phenix.real_space_refine
on Fri Aug 22 23:27:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ia7_35297/08_2025/8ia7_35297.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ia7_35297/08_2025/8ia7_35297.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ia7_35297/08_2025/8ia7_35297.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ia7_35297/08_2025/8ia7_35297.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ia7_35297/08_2025/8ia7_35297.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ia7_35297/08_2025/8ia7_35297.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
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      59      5.16       5
     C    5489      2.51       5
     N    1473      2.21       5
     O    1565      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8586
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "R"
      Number of atoms: 2159
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2159
          Classifications: {'peptide': 276}
          Link IDs: {'PTRANS': 13, 'TRANS': 262}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2471
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 132
          Unresolved non-hydrogen angles: 162
          Unresolved non-hydrogen dihedrals: 106
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6, 'GLN:plan1': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 99
    Chain: "C"
      Number of atoms: 353
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 353
          Classifications: {'peptide': 51}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "E"
      Number of atoms: 1723
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1723
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 10, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 54
          Unresolved non-hydrogen angles: 67
          Unresolved non-hydrogen dihedrals: 41
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 37
    Chain: "A"
      Number of atoms: 1802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1802
          Classifications: {'peptide': 219}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 213}
          Chain breaks: 2
    Chain: "L"
      Number of atoms: 77
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 77
          Classifications: {'peptide': 8}
          Link IDs: {'TRANS': 7}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'TYS:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "L"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.32, per 1000 atoms: 0.27
  Number of scatterers: 8586
  At special positions: 0
  Unit cell: (114.582, 114.582, 123.708, 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      59     16.00
     O    1565      8.00
     N    1473      7.00
     C    5489      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 127 " - pdb=" SG  CYS R 205 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 147 " - pdb=" SG  CYS E 217 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.75
  Conformation dependent library (CDL) restraints added in 472.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2096

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 13 sheets defined
      36.1% alpha, 21.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'R' and resid 54 through 82
    Processing helix  chain 'R' and resid 87 through 108
      removed outlier: 3.787A  pdb=" N   ALA R  91 " --> pdb=" O   THR R  87 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   PHE R  92 " --> pdb=" O   VAL R  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 108 through 117
      Proline residue:  R 114  - end of helix
    Processing helix  chain 'R' and resid 122 through 158
      removed outlier: 4.370A  pdb=" N   ILE R 126 " --> pdb=" O   PHE R 122 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   SER R 139 " --> pdb=" O   GLY R 135 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ARG R 158 " --> pdb=" O   SER R 154 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 158 through 164
      removed outlier: 3.950A  pdb=" N   VAL R 164 " --> pdb=" O   LEU R 160 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 167 through 186
    Processing helix  chain 'R' and resid 187 through 192
    Processing helix  chain 'R' and resid 214 through 227
    Processing helix  chain 'R' and resid 227 through 248
      removed outlier: 3.920A  pdb=" N   GLY R 248 " --> pdb=" O   GLU R 244 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 325 through 360
      Proline residue:  R 348  - end of helix
    Processing helix  chain 'R' and resid 360 through 367
    Processing helix  chain 'R' and resid 370 through 391
      removed outlier: 3.523A  pdb=" N   PHE R 374 " --> pdb=" O   ALA R 370 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   SER R 382 " --> pdb=" O   LEU R 378 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   ALA R 383 " --> pdb=" O   SER R 379 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   CYS R 384 " --> pdb=" O   TYR R 380 " (cutoff:3.500A)
      Proline residue:  R 387  - end of helix
    Processing helix  chain 'R' and resid 396 through 403
      removed outlier: 3.694A  pdb=" N   ALA R 400 " --> pdb=" O   ARG R 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.665A  pdb=" N   ARG B   8 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.622A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 12 through 24
      removed outlier: 3.554A  pdb=" N   VAL C  16 " --> pdb=" O   ALA C  12 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.522A  pdb=" N   ALA C  33 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 3.901A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   GLU A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 56
      removed outlier: 3.528A  pdb=" N   ILE A  56 " --> pdb=" O   GLN A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 214
    Processing helix  chain 'A' and resid 241 through 254
    Processing helix  chain 'A' and resid 269 through 277
      removed outlier: 3.587A  pdb=" N   LEU A 273 " --> pdb=" O   LYS A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 309
    Processing helix  chain 'A' and resid 329 through 350
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.817A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.888A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.735A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.069A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.812A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.966A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.158A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.583A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.702A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.957A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.366A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.408A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.551A  pdb=" N   CYS B 250 " --> pdb=" O   TYR B 264 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.845A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.049A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.861A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12
    Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60
      removed outlier: 5.282A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
      removed outlier: 5.878A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ARG E  98 " --> pdb=" O   PHE E 110 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 134 through 136
      removed outlier: 3.501A  pdb=" N   VAL E 135 " --> pdb=" O   LYS E 232 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLU E 234 " --> pdb=" O   VAL E 135 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   LEU E 162 " --> pdb=" O   TYR E 178 " (cutoff:3.500A)
      removed outlier: 4.833A  pdb=" N   TYR E 178 " --> pdb=" O   LEU E 162 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   TRP E 164 " --> pdb=" O   LEU E 176 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 143 through 148
    Processing sheet with id=AB4, first strand: chain 'A' and resid 183 through 190
      removed outlier: 4.231A  pdb=" N   VAL A 200 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   GLY A  40 " --> pdb=" O   VAL A 200 " (cutoff:3.500A)
      removed outlier: 7.257A  pdb=" N   LYS A  35 " --> pdb=" O   SER A 219 " (cutoff:3.500A)
      removed outlier: 8.159A  pdb=" N   MET A 221 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   LEU A  37 " --> pdb=" O   MET A 221 " (cutoff:3.500A)
      removed outlier: 7.401A  pdb=" N   LEU A 223 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   LEU A  39 " --> pdb=" O   LEU A 223 " (cutoff:3.500A)
      removed outlier: 8.685A  pdb=" N   ALA A 225 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   ILE A 220 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 7.585A  pdb=" N   PHE A 266 " --> pdb=" O   ILE A 220 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   PHE A 222 " --> pdb=" O   PHE A 266 " (cutoff:3.500A)
      removed outlier: 7.093A  pdb=" N   ASN A 268 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   VAL A 224 " --> pdb=" O   ASN A 268 " (cutoff:3.500A)

    407 hydrogen bonds defined for protein.
    1161 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: 1.48

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1742
        1.33 -     1.45: 2110
        1.45 -     1.57: 4826
        1.57 -     1.69: 1
        1.69 -     1.82: 87
  Bond restraints: 8766
  Sorted by residual:
  bond pdb=" O2  TYS L   2 "
       pdb=" S   TYS L   2 "
    ideal  model  delta    sigma   weight residual
    1.461  1.632 -0.171 2.00e-02 2.50e+03 7.35e+01
  bond pdb=" OH  TYS L   2 "
       pdb=" S   TYS L   2 "
    ideal  model  delta    sigma   weight residual
    1.679  1.534  0.145 2.00e-02 2.50e+03 5.29e+01
  bond pdb=" C   ALA R 352 "
       pdb=" O   ALA R 352 "
    ideal  model  delta    sigma   weight residual
    1.237  1.207  0.030 1.17e-02 7.31e+03 6.49e+00
  bond pdb=" CA  ASN R 353 "
       pdb=" C   ASN R 353 "
    ideal  model  delta    sigma   weight residual
    1.523  1.494  0.029 1.30e-02 5.92e+03 4.97e+00
  bond pdb=" CA  TRP R 355 "
       pdb=" C   TRP R 355 "
    ideal  model  delta    sigma   weight residual
    1.523  1.548 -0.025 1.30e-02 5.92e+03 3.76e+00
  ... (remaining 8761 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.02: 11653
        2.02 -     4.05: 211
        4.05 -     6.07: 35
        6.07 -     8.10: 8
        8.10 -    10.12: 3
  Bond angle restraints: 11910
  Sorted by residual:
  angle pdb=" N   THR R 193 "
        pdb=" CA  THR R 193 "
        pdb=" C   THR R 193 "
      ideal   model   delta    sigma   weight residual
     108.56  118.68  -10.12 1.74e+00 3.30e-01 3.38e+01
  angle pdb=" CA  TYR R 189 "
        pdb=" C   TYR R 189 "
        pdb=" N   PRO R 190 "
      ideal   model   delta    sigma   weight residual
     120.58  116.55    4.03 7.40e-01 1.83e+00 2.97e+01
  angle pdb=" N   TYR E 161 "
        pdb=" CA  TYR E 161 "
        pdb=" C   TYR E 161 "
      ideal   model   delta    sigma   weight residual
     108.52  116.46   -7.94 1.74e+00 3.30e-01 2.08e+01
  angle pdb=" C   TYR R 189 "
        pdb=" N   PRO R 190 "
        pdb=" CA  PRO R 190 "
      ideal   model   delta    sigma   weight residual
     119.05  123.92   -4.87 1.11e+00 8.12e-01 1.93e+01
  angle pdb=" N   ASP L   7 "
        pdb=" CA  ASP L   7 "
        pdb=" C   ASP L   7 "
      ideal   model   delta    sigma   weight residual
     110.80  119.96   -9.16 2.13e+00 2.20e-01 1.85e+01
  ... (remaining 11905 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.74: 4728
       17.74 -    35.49: 393
       35.49 -    53.23: 48
       53.23 -    70.97: 4
       70.97 -    88.71: 1
  Dihedral angle restraints: 5174
    sinusoidal: 1924
      harmonic: 3250
  Sorted by residual:
  dihedral pdb=" CA  TYR E 223 "
           pdb=" C   TYR E 223 "
           pdb=" N   PRO E 224 "
           pdb=" CA  PRO E 224 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  137.63   42.37     0      5.00e+00 4.00e-02 7.18e+01
  dihedral pdb=" CA  LEU R 203 "
           pdb=" C   LEU R 203 "
           pdb=" N   GLN R 204 "
           pdb=" CA  GLN R 204 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.25   26.75     0      5.00e+00 4.00e-02 2.86e+01
  dihedral pdb=" CA  ASP A 313 "
           pdb=" C   ASP A 313 "
           pdb=" N   SER A 314 "
           pdb=" CA  SER A 314 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.55   20.45     0      5.00e+00 4.00e-02 1.67e+01
  ... (remaining 5171 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1227
       0.070 -    0.139: 141
       0.139 -    0.209: 5
       0.209 -    0.278: 2
       0.278 -    0.348: 1
  Chirality restraints: 1376
  Sorted by residual:
  chirality pdb=" CA  ASP L   7 "
            pdb=" N   ASP L   7 "
            pdb=" C   ASP L   7 "
            pdb=" CB  ASP L   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.03e+00
  chirality pdb=" CA  THR R 193 "
            pdb=" N   THR R 193 "
            pdb=" C   THR R 193 "
            pdb=" CB  THR R 193 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.26    0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" CA  PHE L   8 "
            pdb=" N   PHE L   8 "
            pdb=" C   PHE L   8 "
            pdb=" CB  PHE L   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.52e+00
  ... (remaining 1373 not shown)

  Planarity restraints: 1500
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR E 223 "   -0.041 5.00e-02 4.00e+02   6.24e-02 6.23e+00
        pdb=" N   PRO E 224 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO E 224 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO E 224 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO R 188 "   -0.008 2.00e-02 2.50e+03   1.64e-02 2.68e+00
        pdb=" C   PRO R 188 "    0.028 2.00e-02 2.50e+03
        pdb=" O   PRO R 188 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   TYR R 189 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG E 179 "    0.007 2.00e-02 2.50e+03   1.42e-02 2.00e+00
        pdb=" C   ARG E 179 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   ARG E 179 "    0.009 2.00e-02 2.50e+03
        pdb=" N   MET E 180 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1497 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 797
        2.74 -     3.28: 8289
        3.28 -     3.82: 13600
        3.82 -     4.36: 16186
        4.36 -     4.90: 28937
  Nonbonded interactions: 67809
  Sorted by model distance:
  nonbonded pdb=" O   SER E 194 "
            pdb=" OG1 THR E 201 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" O   ARG B  68 "
            pdb=" OG  SER B  84 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   SER E 106 "
            pdb=" OG  SER E 106 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" OH  TYR R 189 "
            pdb=" OD2 ASP L   7 "
     model   vdw
     2.286 3.040
  ... (remaining 67804 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     9.850
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
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   0.171   8769  Z= 0.241
  Angle     :  0.727  10.122  11914  Z= 0.434
  Chirality :  0.045   0.348   1376
  Planarity :  0.004   0.062   1500
  Dihedral  : 12.552  88.713   3072
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.00 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.23 (0.23), residues: 1101
  helix:  0.12 (0.26), residues: 357
  sheet: -1.07 (0.31), residues: 251
  loop : -2.99 (0.24), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  32 
 TYR   0.015   0.001   TYR E  94 
 PHE   0.012   0.001   PHE A  49 
 TRP   0.010   0.001   TRP R 346 
 HIS   0.005   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 8766)
  covalent geometry    : angle       0.72711 (11910)
  SS BOND              : bond        0.00327 (    2)
  SS BOND              : angle       0.91957 (    4)
  hydrogen bonds       : bond        0.11931 (  407)
  hydrogen bonds       : angle       5.93184 ( 1161)
  Misc. bond           : bond        0.10205 (    1)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.332 
Fit side-chains
REVERT: R  189 TYR cc_start: 0.7404 (m-80) cc_final: 0.7051 (m-80)
REVERT: R  244 GLU cc_start: 0.6481 (mp0) cc_final: 0.5780 (mp0)
REVERT: B  215 GLU cc_start: 0.7815 (tt0) cc_final: 0.7457 (tt0)
REVERT: B  304 ARG cc_start: 0.8241 (ttm170) cc_final: 0.7867 (ttp-170)
REVERT: C   29 LYS cc_start: 0.8675 (mmtt) cc_final: 0.8459 (mmtt)
REVERT: C   48 ASP cc_start: 0.8917 (t0) cc_final: 0.8705 (t0)
REVERT: E  103 TYR cc_start: 0.8681 (t80) cc_final: 0.8357 (t80)
REVERT: A  230 ASP cc_start: 0.8047 (m-30) cc_final: 0.7838 (m-30)
REVERT: L    6 MET cc_start: 0.7200 (ttt) cc_final: 0.6797 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 181
  average time/residue: 0.0999
  time to fit residues: 24.7579
Evaluate side-chains
  143 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    0.0770
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9980
   overall best weight:    0.9942

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

Flipped N/Q/H residues before XYZ refinement:
R  72 ASN
R 115 ASN
R 204 GLN
R 353 ASN
B  32 GLN
E 167 GLN
E 174 GLN
A 293 GLN
A 311 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.166106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.125470 restraints weight = 10233.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 2.38
r_work: 0.3375 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3242 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.1154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8769  Z= 0.123
  Angle     :  0.570   7.668  11914  Z= 0.291
  Chirality :  0.043   0.246   1376
  Planarity :  0.004   0.052   1500
  Dihedral  :  4.623  42.029   1220
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.72 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 12.26 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.04 (0.25), residues: 1101
  helix:  1.44 (0.27), residues: 363
  sheet: -0.69 (0.31), residues: 270
  loop : -2.50 (0.26), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  18 
 TYR   0.015   0.001   TYR E 178 
 PHE   0.013   0.001   PHE B 253 
 TRP   0.010   0.001   TRP R 346 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 8766)
  covalent geometry    : angle       0.57031 (11910)
  SS BOND              : bond        0.00283 (    2)
  SS BOND              : angle       0.82507 (    4)
  hydrogen bonds       : bond        0.03722 (  407)
  hydrogen bonds       : angle       4.65960 ( 1161)
  Misc. bond           : bond        0.00019 (    1)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 143
  time to evaluate  : 0.308 
Fit side-chains
REVERT: R  189 TYR cc_start: 0.7910 (m-80) cc_final: 0.7413 (m-80)
REVERT: R  333 ARG cc_start: 0.7274 (ttm170) cc_final: 0.6166 (ttp80)
REVERT: R  367 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6567 (pp)
REVERT: B  215 GLU cc_start: 0.8333 (tt0) cc_final: 0.8029 (tt0)
REVERT: B  259 GLN cc_start: 0.8948 (pt0) cc_final: 0.8673 (pt0)
REVERT: C   29 LYS cc_start: 0.8591 (mmtt) cc_final: 0.8388 (mmtt)
REVERT: E   90 ASP cc_start: 0.8341 (m-30) cc_final: 0.8068 (m-30)
REVERT: E  103 TYR cc_start: 0.8903 (t80) cc_final: 0.8594 (t80)
REVERT: L    6 MET cc_start: 0.7164 (ttt) cc_final: 0.6885 (ttp)
  outliers start: 16
  outliers final: 9
  residues processed: 147
  average time/residue: 0.0848
  time to fit residues: 17.7288
Evaluate side-chains
  140 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 130
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  337 VAL
Chi-restraints excluded: chain R residue  367 LEU
Chi-restraints excluded: chain R residue  388 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  198 THR
Chi-restraints excluded: chain E residue  226 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 67 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9980
   chunk 97 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 91 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 61 optimal weight:    9.9990
   chunk 19 optimal weight:    7.9990
   chunk 26 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
R 161 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.162354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.121462 restraints weight = 10198.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 2.36
r_work: 0.3322 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3191 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.1405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8769  Z= 0.184
  Angle     :  0.602   7.868  11914  Z= 0.307
  Chirality :  0.044   0.182   1376
  Planarity :  0.004   0.055   1500
  Dihedral  :  4.752  44.169   1220
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.45 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 15.16 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.71 (0.26), residues: 1101
  helix:  1.75 (0.28), residues: 365
  sheet: -0.60 (0.31), residues: 270
  loop : -2.29 (0.27), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  18 
 TYR   0.032   0.002   TYR R 192 
 PHE   0.013   0.001   PHE B 253 
 TRP   0.013   0.001   TRP B  63 
 HIS   0.006   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 8766)
  covalent geometry    : angle       0.60170 (11910)
  SS BOND              : bond        0.00485 (    2)
  SS BOND              : angle       1.10625 (    4)
  hydrogen bonds       : bond        0.04146 (  407)
  hydrogen bonds       : angle       4.65515 ( 1161)
  Misc. bond           : bond        0.00024 (    1)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 131
  time to evaluate  : 0.288 
Fit side-chains
REVERT: R  204 GLN cc_start: 0.7068 (OUTLIER) cc_final: 0.6779 (tt0)
REVERT: R  244 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6254 (mp0)
REVERT: R  333 ARG cc_start: 0.7287 (ttm170) cc_final: 0.6160 (ttp80)
REVERT: R  367 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.6777 (pp)
REVERT: B  215 GLU cc_start: 0.8338 (tt0) cc_final: 0.8130 (tt0)
REVERT: B  259 GLN cc_start: 0.8901 (pt0) cc_final: 0.8564 (pt0)
REVERT: B  291 ASP cc_start: 0.8288 (m-30) cc_final: 0.7808 (m-30)
REVERT: E   38 ARG cc_start: 0.8374 (ptt180) cc_final: 0.8143 (ptt180)
REVERT: E  103 TYR cc_start: 0.8952 (t80) cc_final: 0.8633 (t80)
REVERT: L    6 MET cc_start: 0.7141 (ttt) cc_final: 0.6896 (ttp)
  outliers start: 23
  outliers final: 18
  residues processed: 142
  average time/residue: 0.0789
  time to fit residues: 15.9824
Evaluate side-chains
  148 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  204 GLN
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  244 GLU
Chi-restraints excluded: chain R residue  337 VAL
Chi-restraints excluded: chain R residue  344 LEU
Chi-restraints excluded: chain R residue  358 PHE
Chi-restraints excluded: chain R residue  367 LEU
Chi-restraints excluded: chain R residue  388 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain E residue  198 THR
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain E residue  226 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 81 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0670
   chunk 60 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 30 optimal weight:    7.9990
   chunk 39 optimal weight:    0.0030
   chunk 48 optimal weight:   10.0000
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.5328

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

Flipped N/Q/H residues before XYZ refinement:
R  90 ASN
R 161 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.167593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.131790 restraints weight = 10198.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 2.35
r_work: 0.3378 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.1621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8769  Z= 0.102
  Angle     :  0.537   7.371  11914  Z= 0.273
  Chirality :  0.041   0.152   1376
  Planarity :  0.003   0.048   1500
  Dihedral  :  4.382  39.352   1220
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 16.50 %
    Favored  : 81.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.17 (0.26), residues: 1101
  helix:  2.24 (0.28), residues: 366
  sheet: -0.23 (0.32), residues: 262
  loop : -2.04 (0.27), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  18 
 TYR   0.011   0.001   TYR E 178 
 PHE   0.012   0.001   PHE B 253 
 TRP   0.011   0.001   TRP R 346 
 HIS   0.004   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 8766)
  covalent geometry    : angle       0.53710 (11910)
  SS BOND              : bond        0.00259 (    2)
  SS BOND              : angle       0.88316 (    4)
  hydrogen bonds       : bond        0.03258 (  407)
  hydrogen bonds       : angle       4.31452 ( 1161)
  Misc. bond           : bond        0.00005 (    1)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 139
  time to evaluate  : 0.316 
Fit side-chains
REVERT: R  204 GLN cc_start: 0.6616 (OUTLIER) cc_final: 0.5784 (tp40)
REVERT: R  244 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6074 (mp0)
REVERT: R  333 ARG cc_start: 0.7061 (ttm170) cc_final: 0.5974 (ttp80)
REVERT: R  367 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6614 (pp)
REVERT: B  101 MET cc_start: 0.8967 (mtp) cc_final: 0.8607 (mmm)
REVERT: B  325 MET cc_start: 0.8641 (mmm) cc_final: 0.8389 (mmm)
REVERT: E   90 ASP cc_start: 0.8376 (m-30) cc_final: 0.8110 (m-30)
REVERT: E  103 TYR cc_start: 0.8852 (t80) cc_final: 0.8516 (t80)
REVERT: A   52 GLN cc_start: 0.8037 (tp-100) cc_final: 0.7736 (tp-100)
  outliers start: 18
  outliers final: 12
  residues processed: 147
  average time/residue: 0.0801
  time to fit residues: 16.6614
Evaluate side-chains
  141 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  204 GLN
Chi-restraints excluded: chain R residue  244 GLU
Chi-restraints excluded: chain R residue  326 LEU
Chi-restraints excluded: chain R residue  358 PHE
Chi-restraints excluded: chain R residue  367 LEU
Chi-restraints excluded: chain R residue  388 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain E residue  198 THR
Chi-restraints excluded: chain E residue  226 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 106 optimal weight:    1.9990
   chunk 59 optimal weight:   10.0000
   chunk 97 optimal weight:    1.9990
   chunk 27 optimal weight:   20.0000
   chunk 74 optimal weight:    8.9990
   chunk 79 optimal weight:    4.9990
   chunk 29 optimal weight:    8.9990
   chunk 91 optimal weight:    1.9990
   chunk 107 optimal weight:    0.0020
   overall best weight:    1.3996

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

Flipped N/Q/H residues before XYZ refinement:
R 161 GLN
R 204 GLN
R 353 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.165018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.124209 restraints weight = 10282.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 2.39
r_work: 0.3359 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3228 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.1690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8769  Z= 0.136
  Angle     :  0.556   7.443  11914  Z= 0.283
  Chirality :  0.042   0.140   1376
  Planarity :  0.003   0.047   1500
  Dihedral  :  4.441  40.217   1220
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.18 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 16.28 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.26), residues: 1101
  helix:  2.27 (0.28), residues: 366
  sheet: -0.22 (0.32), residues: 264
  loop : -2.05 (0.27), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  18 
 TYR   0.011   0.001   TYR A 289 
 PHE   0.013   0.001   PHE L   8 
 TRP   0.010   0.001   TRP B  63 
 HIS   0.003   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8766)
  covalent geometry    : angle       0.55574 (11910)
  SS BOND              : bond        0.00353 (    2)
  SS BOND              : angle       0.91555 (    4)
  hydrogen bonds       : bond        0.03563 (  407)
  hydrogen bonds       : angle       4.31037 ( 1161)
  Misc. bond           : bond        0.00003 (    1)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 131
  time to evaluate  : 0.219 
Fit side-chains
REVERT: R  189 TYR cc_start: 0.7630 (m-80) cc_final: 0.7217 (m-80)
REVERT: R  244 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6219 (mp0)
REVERT: R  333 ARG cc_start: 0.7195 (ttm170) cc_final: 0.6107 (ttp80)
REVERT: R  367 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6706 (pp)
REVERT: B  101 MET cc_start: 0.9058 (mtp) cc_final: 0.8724 (mmm)
REVERT: C   47 GLU cc_start: 0.7540 (pm20) cc_final: 0.7045 (pt0)
REVERT: E   90 ASP cc_start: 0.8438 (m-30) cc_final: 0.8192 (m-30)
REVERT: E  103 TYR cc_start: 0.8925 (t80) cc_final: 0.8587 (t80)
REVERT: A   52 GLN cc_start: 0.8092 (tp-100) cc_final: 0.7797 (tp-100)
REVERT: L    7 ASP cc_start: 0.7648 (t0) cc_final: 0.7124 (t0)
  outliers start: 22
  outliers final: 19
  residues processed: 140
  average time/residue: 0.0757
  time to fit residues: 14.5459
Evaluate side-chains
  149 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 128
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  167 THR
Chi-restraints excluded: chain R residue  214 VAL
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  244 GLU
Chi-restraints excluded: chain R residue  337 VAL
Chi-restraints excluded: chain R residue  358 PHE
Chi-restraints excluded: chain R residue  367 LEU
Chi-restraints excluded: chain R residue  368 SER
Chi-restraints excluded: chain R residue  388 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain E residue  198 THR
Chi-restraints excluded: chain E residue  226 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   chunk 79 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0030
   chunk 3 optimal weight:    6.9990
   chunk 35 optimal weight:    0.4980
   chunk 76 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    0.9980
   chunk 43 optimal weight:    5.9990
   overall best weight:    0.8992

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

Flipped N/Q/H residues before XYZ refinement:
R  90 ASN
R 161 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.167119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.131142 restraints weight = 10114.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3577 rms_B_bonded: 2.38
r_work: 0.3369 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.1855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8769  Z= 0.109
  Angle     :  0.530   7.218  11914  Z= 0.269
  Chirality :  0.041   0.140   1376
  Planarity :  0.003   0.043   1500
  Dihedral  :  4.296  37.860   1220
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 16.39 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.09 (0.26), residues: 1101
  helix:  2.43 (0.28), residues: 367
  sheet: -0.14 (0.32), residues: 264
  loop : -1.85 (0.27), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  38 
 TYR   0.010   0.001   TYR A 289 
 PHE   0.012   0.001   PHE A  49 
 TRP   0.010   0.001   TRP R 346 
 HIS   0.003   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 8766)
  covalent geometry    : angle       0.52973 (11910)
  SS BOND              : bond        0.00252 (    2)
  SS BOND              : angle       0.90634 (    4)
  hydrogen bonds       : bond        0.03252 (  407)
  hydrogen bonds       : angle       4.16303 ( 1161)
  Misc. bond           : bond        0.00023 (    1)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 137
  time to evaluate  : 0.191 
Fit side-chains
REVERT: R  244 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.5838 (mp0)
REVERT: R  333 ARG cc_start: 0.7001 (ttm170) cc_final: 0.5982 (ttp80)
REVERT: R  367 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6457 (pp)
REVERT: B   70 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8500 (pt)
REVERT: B  101 MET cc_start: 0.9014 (mtp) cc_final: 0.8644 (mmm)
REVERT: B  325 MET cc_start: 0.8633 (mmm) cc_final: 0.8361 (mmm)
REVERT: C   47 GLU cc_start: 0.7394 (pm20) cc_final: 0.6970 (pt0)
REVERT: E  103 TYR cc_start: 0.8768 (t80) cc_final: 0.8360 (t80)
REVERT: L    7 ASP cc_start: 0.7359 (t0) cc_final: 0.6925 (t0)
  outliers start: 26
  outliers final: 18
  residues processed: 151
  average time/residue: 0.0779
  time to fit residues: 16.3251
Evaluate side-chains
  148 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  167 THR
Chi-restraints excluded: chain R residue  214 VAL
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  244 GLU
Chi-restraints excluded: chain R residue  344 LEU
Chi-restraints excluded: chain R residue  358 PHE
Chi-restraints excluded: chain R residue  367 LEU
Chi-restraints excluded: chain R residue  368 SER
Chi-restraints excluded: chain R residue  388 LEU
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain E residue  198 THR
Chi-restraints excluded: chain E residue  226 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 99 optimal weight:    1.9990
   chunk 66 optimal weight:    7.9990
   chunk 59 optimal weight:    5.9990
   chunk 72 optimal weight:    6.9990
   chunk 105 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   chunk 85 optimal weight:    8.9990
   chunk 25 optimal weight:    7.9990
   chunk 95 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
R 161 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.163347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.121391 restraints weight = 10453.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 2.46
r_work: 0.3350 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3214 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.1873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8769  Z= 0.152
  Angle     :  0.565   7.512  11914  Z= 0.288
  Chirality :  0.042   0.180   1376
  Planarity :  0.003   0.044   1500
  Dihedral  :  4.461  40.047   1220
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 16.61 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.01 (0.26), residues: 1101
  helix:  2.35 (0.27), residues: 365
  sheet: -0.18 (0.32), residues: 274
  loop : -1.93 (0.27), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 208 
 TYR   0.017   0.001   TYR A 229 
 PHE   0.015   0.001   PHE L   8 
 TRP   0.011   0.001   TRP B  63 
 HIS   0.003   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 8766)
  covalent geometry    : angle       0.56429 (11910)
  SS BOND              : bond        0.00401 (    2)
  SS BOND              : angle       1.08583 (    4)
  hydrogen bonds       : bond        0.03692 (  407)
  hydrogen bonds       : angle       4.31107 ( 1161)
  Misc. bond           : bond        0.00030 (    1)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 129
  time to evaluate  : 0.238 
Fit side-chains
REVERT: R  244 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6268 (mp0)
REVERT: R  333 ARG cc_start: 0.7177 (ttm170) cc_final: 0.6121 (ttp80)
REVERT: R  367 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7089 (pp)
REVERT: B   70 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8525 (pt)
REVERT: B  215 GLU cc_start: 0.8162 (tt0) cc_final: 0.7559 (tt0)
REVERT: B  291 ASP cc_start: 0.8300 (m-30) cc_final: 0.7964 (m-30)
REVERT: C   47 GLU cc_start: 0.7696 (pm20) cc_final: 0.7096 (pt0)
REVERT: E  103 TYR cc_start: 0.8924 (t80) cc_final: 0.8559 (t80)
REVERT: L    7 ASP cc_start: 0.7350 (t0) cc_final: 0.7103 (t0)
  outliers start: 31
  outliers final: 24
  residues processed: 145
  average time/residue: 0.0684
  time to fit residues: 13.9023
Evaluate side-chains
  152 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 125
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  167 THR
Chi-restraints excluded: chain R residue  187 VAL
Chi-restraints excluded: chain R residue  214 VAL
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  244 GLU
Chi-restraints excluded: chain R residue  337 VAL
Chi-restraints excluded: chain R residue  344 LEU
Chi-restraints excluded: chain R residue  358 PHE
Chi-restraints excluded: chain R residue  367 LEU
Chi-restraints excluded: chain R residue  368 SER
Chi-restraints excluded: chain R residue  388 LEU
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain E residue  198 THR
Chi-restraints excluded: chain E residue  226 THR
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  272 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 91 optimal weight:    0.9990
   chunk 64 optimal weight:    7.9990
   chunk 77 optimal weight:    0.0570
   chunk 1 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 48 optimal weight:    7.9990
   chunk 93 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    1.4106

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

Flipped N/Q/H residues before XYZ refinement:
R 161 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.165244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.124483 restraints weight = 10143.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 2.37
r_work: 0.3357 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3224 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8769  Z= 0.135
  Angle     :  0.559   7.459  11914  Z= 0.285
  Chirality :  0.042   0.173   1376
  Planarity :  0.003   0.044   1500
  Dihedral  :  4.440  39.742   1220
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 17.28 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (0.26), residues: 1101
  helix:  2.39 (0.27), residues: 365
  sheet: -0.11 (0.32), residues: 264
  loop : -1.94 (0.27), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 137 
 TYR   0.010   0.001   TYR A 289 
 PHE   0.013   0.001   PHE L   8 
 TRP   0.010   0.001   TRP B  63 
 HIS   0.003   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 8766)
  covalent geometry    : angle       0.55913 (11910)
  SS BOND              : bond        0.00345 (    2)
  SS BOND              : angle       1.13063 (    4)
  hydrogen bonds       : bond        0.03565 (  407)
  hydrogen bonds       : angle       4.30762 ( 1161)
  Misc. bond           : bond        0.00040 (    1)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 128
  time to evaluate  : 0.200 
Fit side-chains
REVERT: R  244 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6175 (mp0)
REVERT: R  333 ARG cc_start: 0.7168 (ttm170) cc_final: 0.6124 (ttp80)
REVERT: R  367 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7027 (pp)
REVERT: B   70 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8509 (pt)
REVERT: B  101 MET cc_start: 0.9066 (mtp) cc_final: 0.8829 (mmm)
REVERT: B  219 ARG cc_start: 0.8550 (ttm-80) cc_final: 0.8270 (mmt-90)
REVERT: B  291 ASP cc_start: 0.8273 (m-30) cc_final: 0.7928 (m-30)
REVERT: B  325 MET cc_start: 0.8829 (mmm) cc_final: 0.8604 (mmm)
REVERT: C   47 GLU cc_start: 0.7590 (pm20) cc_final: 0.7013 (pt0)
REVERT: E  103 TYR cc_start: 0.8893 (t80) cc_final: 0.8526 (t80)
  outliers start: 29
  outliers final: 24
  residues processed: 144
  average time/residue: 0.0739
  time to fit residues: 14.5390
Evaluate side-chains
  154 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 127
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  167 THR
Chi-restraints excluded: chain R residue  187 VAL
Chi-restraints excluded: chain R residue  214 VAL
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  244 GLU
Chi-restraints excluded: chain R residue  337 VAL
Chi-restraints excluded: chain R residue  358 PHE
Chi-restraints excluded: chain R residue  367 LEU
Chi-restraints excluded: chain R residue  368 SER
Chi-restraints excluded: chain R residue  388 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain E residue  198 THR
Chi-restraints excluded: chain E residue  226 THR
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  272 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 60 optimal weight:   10.0000
   chunk 94 optimal weight:    0.4980
   chunk 19 optimal weight:    6.9990
   chunk 96 optimal weight:    0.6980
   chunk 23 optimal weight:    5.9990
   chunk 18 optimal weight:    0.7980
   chunk 29 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    1.7984

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

Flipped N/Q/H residues before XYZ refinement:
R 161 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.162752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.126714 restraints weight = 10280.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 2.34
r_work: 0.3331 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3198 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.2002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8769  Z= 0.158
  Angle     :  0.576   7.610  11914  Z= 0.294
  Chirality :  0.043   0.166   1376
  Planarity :  0.003   0.044   1500
  Dihedral  :  4.513  40.885   1220
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 17.84 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (0.26), residues: 1101
  helix:  2.32 (0.27), residues: 365
  sheet: -0.11 (0.32), residues: 269
  loop : -1.96 (0.27), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 137 
 TYR   0.011   0.001   TYR A 289 
 PHE   0.016   0.001   PHE L   8 
 TRP   0.011   0.001   TRP B  63 
 HIS   0.003   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 8766)
  covalent geometry    : angle       0.57584 (11910)
  SS BOND              : bond        0.00451 (    2)
  SS BOND              : angle       0.71778 (    4)
  hydrogen bonds       : bond        0.03768 (  407)
  hydrogen bonds       : angle       4.36103 ( 1161)
  Misc. bond           : bond        0.00033 (    1)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 129
  time to evaluate  : 0.441 
Fit side-chains
REVERT: R  244 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6141 (mp0)
REVERT: R  333 ARG cc_start: 0.7122 (ttm170) cc_final: 0.6073 (ttp80)
REVERT: R  367 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6981 (pp)
REVERT: B   70 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8535 (pt)
REVERT: B  101 MET cc_start: 0.9094 (mtp) cc_final: 0.8853 (mmm)
REVERT: B  219 ARG cc_start: 0.8558 (ttm-80) cc_final: 0.8244 (mmt-90)
REVERT: B  291 ASP cc_start: 0.8266 (m-30) cc_final: 0.7815 (m-30)
REVERT: B  325 MET cc_start: 0.8782 (mmm) cc_final: 0.8548 (mmm)
REVERT: C   47 GLU cc_start: 0.7634 (pm20) cc_final: 0.7040 (pt0)
REVERT: E  103 TYR cc_start: 0.8935 (t80) cc_final: 0.8552 (t80)
  outliers start: 31
  outliers final: 26
  residues processed: 147
  average time/residue: 0.0712
  time to fit residues: 14.8696
Evaluate side-chains
  155 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 126
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  167 THR
Chi-restraints excluded: chain R residue  187 VAL
Chi-restraints excluded: chain R residue  214 VAL
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  244 GLU
Chi-restraints excluded: chain R residue  337 VAL
Chi-restraints excluded: chain R residue  344 LEU
Chi-restraints excluded: chain R residue  358 PHE
Chi-restraints excluded: chain R residue  367 LEU
Chi-restraints excluded: chain R residue  368 SER
Chi-restraints excluded: chain R residue  388 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain E residue  198 THR
Chi-restraints excluded: chain E residue  226 THR
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  272 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 94 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 49 optimal weight:    7.9990
   chunk 95 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 87 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 27 optimal weight:   20.0000
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
R  90 ASN
R 161 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.165716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.129505 restraints weight = 10246.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 2.35
r_work: 0.3379 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3246 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.2101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8769  Z= 0.110
  Angle     :  0.544   7.250  11914  Z= 0.277
  Chirality :  0.042   0.164   1376
  Planarity :  0.003   0.042   1500
  Dihedral  :  4.309  38.153   1220
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 18.73 %
    Favored  : 78.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.20 (0.26), residues: 1101
  helix:  2.48 (0.27), residues: 367
  sheet: -0.04 (0.32), residues: 270
  loop : -1.78 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 137 
 TYR   0.010   0.001   TYR A 289 
 PHE   0.017   0.001   PHE A  49 
 TRP   0.012   0.001   TRP R 346 
 HIS   0.002   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 8766)
  covalent geometry    : angle       0.54394 (11910)
  SS BOND              : bond        0.00261 (    2)
  SS BOND              : angle       0.98984 (    4)
  hydrogen bonds       : bond        0.03297 (  407)
  hydrogen bonds       : angle       4.20546 ( 1161)
  Misc. bond           : bond        0.00016 (    1)

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 130
  time to evaluate  : 0.255 
Fit side-chains
REVERT: R  244 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6050 (mp0)
REVERT: R  333 ARG cc_start: 0.7051 (ttm170) cc_final: 0.6004 (ttp80)
REVERT: R  367 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6875 (pp)
REVERT: B   70 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8590 (pt)
REVERT: B  101 MET cc_start: 0.9027 (mtp) cc_final: 0.8766 (mmm)
REVERT: B  127 LYS cc_start: 0.8876 (mttm) cc_final: 0.8116 (mptt)
REVERT: B  325 MET cc_start: 0.8825 (mmm) cc_final: 0.8574 (mmm)
REVERT: C   47 GLU cc_start: 0.7601 (pm20) cc_final: 0.7027 (pt0)
REVERT: E  103 TYR cc_start: 0.8870 (t80) cc_final: 0.8484 (t80)
REVERT: L    6 MET cc_start: 0.7483 (ttt) cc_final: 0.7248 (ptm)
  outliers start: 27
  outliers final: 22
  residues processed: 145
  average time/residue: 0.0665
  time to fit residues: 13.8793
Evaluate side-chains
  154 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 129
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  167 THR
Chi-restraints excluded: chain R residue  180 LEU
Chi-restraints excluded: chain R residue  187 VAL
Chi-restraints excluded: chain R residue  214 VAL
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  244 GLU
Chi-restraints excluded: chain R residue  344 LEU
Chi-restraints excluded: chain R residue  358 PHE
Chi-restraints excluded: chain R residue  367 LEU
Chi-restraints excluded: chain R residue  368 SER
Chi-restraints excluded: chain R residue  388 LEU
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain E residue  226 THR
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  272 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 75 optimal weight:    2.9990
   chunk 38 optimal weight:    6.9990
   chunk 28 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 72 optimal weight:    6.9990
   chunk 102 optimal weight:    0.9990
   chunk 44 optimal weight:    8.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
R 161 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.164426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.128459 restraints weight = 10321.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 2.41
r_work: 0.3342 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.2118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8769  Z= 0.133
  Angle     :  0.558   7.375  11914  Z= 0.285
  Chirality :  0.042   0.161   1376
  Planarity :  0.003   0.043   1500
  Dihedral  :  4.344  39.079   1220
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 19.06 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.14 (0.26), residues: 1101
  helix:  2.44 (0.27), residues: 366
  sheet: -0.03 (0.32), residues: 269
  loop : -1.85 (0.27), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 137 
 TYR   0.011   0.001   TYR A 289 
 PHE   0.016   0.001   PHE A  49 
 TRP   0.023   0.001   TRP R 346 
 HIS   0.002   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8766)
  covalent geometry    : angle       0.55792 (11910)
  SS BOND              : bond        0.00369 (    2)
  SS BOND              : angle       0.74243 (    4)
  hydrogen bonds       : bond        0.03504 (  407)
  hydrogen bonds       : angle       4.24783 ( 1161)
  Misc. bond           : bond        0.00023 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2223.33 seconds
wall clock time: 38 minutes 41.57 seconds (2321.57 seconds total)