Starting phenix.real_space_refine
on Thu Feb 13 01:37:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ia7_35297/02_2025/8ia7_35297.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ia7_35297/02_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_35297/02_2025/8ia7_35297.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ia7_35297/02_2025/8ia7_35297.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ia7_35297/02_2025/8ia7_35297.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ia7_35297/02_2025/8ia7_35297.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 4, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 7}
          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, 'GLU:plan': 2, 'ARG:plan': 1, '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: {'GLN:plan1': 1, 'GLU:plan': 7, '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: 5.13, per 1000 atoms: 0.60
  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: 2.49
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.95
  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: 2.79

  Time building geometry restraints manager: 2.79 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:                  0.010
  Normalize map: mean=0, sd=1:             0.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.110
  Process input model:                     22.910
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  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:3.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.100
-------------------------------------------------------------------------------
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   8766  Z= 0.265
  Angle     :  0.727  10.122  11910  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 : 7.95
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.23 (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
 TRP   0.010   0.001   TRP R 346 
 HIS   0.005   0.001   HIS B 183 
 PHE   0.012   0.001   PHE A  49 
 TYR   0.015   0.001   TYR E  94 
 ARG   0.003   0.000   ARG A  32 

*********************** 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  : 0.942 
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: 0.2211
  time to fit residues: 54.4088
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  : 0.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 82 optimal weight:    8.9990
   chunk 45 optimal weight:    0.2980
   chunk 28 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 85 optimal weight:   30.0000
   chunk 33 optimal weight:    0.0770
   chunk 51 optimal weight:    8.9990
   chunk 63 optimal weight:    0.3980
   chunk 98 optimal weight:    5.9990
   overall best weight:    1.3542

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

Flipped N/Q/H residues before XYZ refinement:
R  72 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: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.164868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.124185 restraints weight = 10168.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 2.37
r_work: 0.3362 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.1158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8766  Z= 0.218
  Angle     :  0.583   7.774  11910  Z= 0.298
  Chirality :  0.043   0.229   1376
  Planarity :  0.004   0.053   1500
  Dihedral  :  4.704  42.784   1220
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.09 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 12.49 %
    Favored  : 85.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.09 (0.25), residues: 1101
  helix:  1.39 (0.27), residues: 363
  sheet: -0.72 (0.31), residues: 270
  loop : -2.52 (0.26), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  63 
 HIS   0.005   0.001   HIS B 183 
 PHE   0.013   0.001   PHE B 253 
 TYR   0.015   0.002   TYR R 192 
 ARG   0.003   0.000   ARG E  18 

*********************** 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
  156 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 140
  time to evaluate  : 1.019 
Fit side-chains
REVERT: R  189 TYR cc_start: 0.7899 (m-80) cc_final: 0.7401 (m-80)
REVERT: R  333 ARG cc_start: 0.7252 (ttm170) cc_final: 0.6157 (ttp80)
REVERT: R  367 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6646 (pp)
REVERT: B  259 GLN cc_start: 0.8938 (pt0) cc_final: 0.8666 (pt0)
REVERT: C   29 LYS cc_start: 0.8576 (mmtt) cc_final: 0.8371 (mmtt)
REVERT: E  103 TYR cc_start: 0.8918 (t80) cc_final: 0.8595 (t80)
REVERT: L    6 MET cc_start: 0.7146 (ttt) cc_final: 0.6866 (ttp)
  outliers start: 16
  outliers final: 10
  residues processed: 144
  average time/residue: 0.2091
  time to fit residues: 42.2854
Evaluate side-chains
  140 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
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   63 THR
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 49 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 103 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 97 optimal weight:    2.9990
   chunk 61 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   chunk 105 optimal weight:    2.9990
   overall best weight:    1.5788

-------------------------------------------------------------------------------
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 = 0.3953 r_free = 0.3953 target = 0.164338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.123548 restraints weight = 10301.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 2.37
r_work: 0.3345 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.1396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8766  Z= 0.232
  Angle     :  0.574   7.636  11910  Z= 0.292
  Chirality :  0.043   0.174   1376
  Planarity :  0.004   0.053   1500
  Dihedral  :  4.620  42.870   1220
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.00 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 14.83 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.26), residues: 1101
  helix:  1.86 (0.28), residues: 365
  sheet: -0.51 (0.31), residues: 268
  loop : -2.25 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  63 
 HIS   0.005   0.001   HIS B 183 
 PHE   0.013   0.001   PHE B 253 
 TYR   0.035   0.002   TYR R 192 
 ARG   0.003   0.000   ARG E  18 

*********************** 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: 24
    poor density    : 130
  time to evaluate  : 0.912 
Fit side-chains
REVERT: R  204 GLN cc_start: 0.6901 (OUTLIER) cc_final: 0.6625 (tt0)
REVERT: R  244 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6280 (mp0)
REVERT: R  333 ARG cc_start: 0.7244 (ttm170) cc_final: 0.6127 (ttp80)
REVERT: R  367 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6698 (pp)
REVERT: B  259 GLN cc_start: 0.8834 (pt0) cc_final: 0.8485 (pt0)
REVERT: E  103 TYR cc_start: 0.8924 (t80) cc_final: 0.8623 (t80)
REVERT: L    6 MET cc_start: 0.7123 (ttt) cc_final: 0.6853 (ttp)
  outliers start: 24
  outliers final: 19
  residues processed: 140
  average time/residue: 0.1992
  time to fit residues: 39.7420
Evaluate side-chains
  147 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 125
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
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  326 LEU
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  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 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  226 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 77 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9990
   chunk 97 optimal weight:    2.9990
   chunk 29 optimal weight:    6.9990
   chunk 88 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.3955 r_free = 0.3955 target = 0.164571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.128616 restraints weight = 10122.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 2.32
r_work: 0.3343 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3210 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.1540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8766  Z= 0.207
  Angle     :  0.560   7.570  11910  Z= 0.284
  Chirality :  0.042   0.162   1376
  Planarity :  0.003   0.051   1500
  Dihedral  :  4.538  41.668   1220
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.90 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 16.28 %
    Favored  : 80.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.26), residues: 1101
  helix:  2.10 (0.28), residues: 366
  sheet: -0.37 (0.32), residues: 268
  loop : -2.12 (0.27), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  63 
 HIS   0.004   0.001   HIS A 212 
 PHE   0.012   0.001   PHE B 253 
 TYR   0.017   0.001   TYR R 192 
 ARG   0.002   0.000   ARG E  38 

*********************** 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
  156 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 131
  time to evaluate  : 0.943 
Fit side-chains
REVERT: R  204 GLN cc_start: 0.6813 (OUTLIER) cc_final: 0.5898 (tp40)
REVERT: R  244 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6181 (mp0)
REVERT: R  333 ARG cc_start: 0.7123 (ttm170) cc_final: 0.6009 (ttp80)
REVERT: R  367 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6636 (pp)
REVERT: B  101 MET cc_start: 0.9078 (mtp) cc_final: 0.8718 (mmm)
REVERT: B  226 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8127 (pt0)
REVERT: C   47 GLU cc_start: 0.7573 (pm20) cc_final: 0.7040 (pt0)
REVERT: E  103 TYR cc_start: 0.8921 (t80) cc_final: 0.8580 (t80)
REVERT: A   52 GLN cc_start: 0.8054 (tp-100) cc_final: 0.7750 (tp-100)
REVERT: L    6 MET cc_start: 0.7131 (ttt) cc_final: 0.6885 (ttp)
  outliers start: 25
  outliers final: 19
  residues processed: 143
  average time/residue: 0.1850
  time to fit residues: 37.9757
Evaluate side-chains
  146 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  167 THR
Chi-restraints excluded: chain R residue  204 GLN
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  388 LEU
Chi-restraints excluded: chain B residue   29 THR
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 B residue  322 ASP
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   63 THR
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  203 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 50 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 19 optimal weight:    7.9990
   chunk 15 optimal weight:    9.9990
   chunk 20 optimal weight:    0.6980
   chunk 91 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 71 optimal weight:    7.9990
   overall best weight:    1.1388

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.165695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.124734 restraints weight = 10164.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 2.38
r_work: 0.3365 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3233 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.1698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8766  Z= 0.185
  Angle     :  0.549   7.376  11910  Z= 0.279
  Chirality :  0.042   0.156   1376
  Planarity :  0.003   0.047   1500
  Dihedral  :  4.416  40.070   1220
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.09 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 16.28 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.26), residues: 1101
  helix:  2.29 (0.28), residues: 365
  sheet: -0.25 (0.32), residues: 266
  loop : -1.99 (0.27), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 346 
 HIS   0.003   0.001   HIS A 212 
 PHE   0.012   0.001   PHE B 253 
 TYR   0.014   0.001   TYR R 192 
 ARG   0.002   0.000   ARG E  18 

*********************** 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
  160 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 132
  time to evaluate  : 0.967 
Fit side-chains
REVERT: R  244 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6199 (mp0)
REVERT: R  333 ARG cc_start: 0.7160 (ttm170) cc_final: 0.6068 (ttp80)
REVERT: R  367 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6669 (pp)
REVERT: B   70 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8519 (pt)
REVERT: B  101 MET cc_start: 0.9056 (mtp) cc_final: 0.8758 (mmm)
REVERT: B  226 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8121 (pt0)
REVERT: B  325 MET cc_start: 0.8643 (mmm) cc_final: 0.8421 (mmm)
REVERT: C   47 GLU cc_start: 0.7560 (pm20) cc_final: 0.6969 (pt0)
REVERT: E  103 TYR cc_start: 0.8887 (t80) cc_final: 0.8569 (t80)
REVERT: A   52 GLN cc_start: 0.8080 (tp-100) cc_final: 0.7785 (tp-100)
REVERT: L    6 MET cc_start: 0.7162 (ttt) cc_final: 0.6928 (ttp)
  outliers start: 28
  outliers final: 22
  residues processed: 146
  average time/residue: 0.1933
  time to fit residues: 39.7482
Evaluate side-chains
  150 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 125
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
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  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 B residue  322 ASP
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 82 optimal weight:    0.0470
   chunk 64 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   chunk 78 optimal weight:    9.9990
   chunk 56 optimal weight:    3.9990
   chunk 72 optimal weight:    8.9990
   chunk 85 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.7884

-------------------------------------------------------------------------------
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 = 0.3927 r_free = 0.3927 target = 0.162655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.126364 restraints weight = 10248.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3539 rms_B_bonded: 2.35
r_work: 0.3327 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3193 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.1753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8766  Z= 0.246
  Angle     :  0.575   7.583  11910  Z= 0.292
  Chirality :  0.043   0.160   1376
  Planarity :  0.003   0.048   1500
  Dihedral  :  4.514  40.984   1220
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.00 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 16.83 %
    Favored  : 79.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.26), residues: 1101
  helix:  2.25 (0.27), residues: 365
  sheet: -0.20 (0.32), residues: 263
  loop : -2.01 (0.27), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  63 
 HIS   0.003   0.001   HIS A 212 
 PHE   0.012   0.001   PHE B 253 
 TYR   0.012   0.001   TYR A 289 
 ARG   0.002   0.000   ARG E  18 

*********************** 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
  162 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 130
  time to evaluate  : 1.003 
Fit side-chains
REVERT: R  244 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6180 (mp0)
REVERT: R  333 ARG cc_start: 0.7129 (ttm170) cc_final: 0.6029 (ttp80)
REVERT: R  367 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.6990 (pp)
REVERT: B   70 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8519 (pt)
REVERT: B  101 MET cc_start: 0.9099 (mtp) cc_final: 0.8796 (mmm)
REVERT: B  226 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8102 (pt0)
REVERT: B  291 ASP cc_start: 0.8291 (m-30) cc_final: 0.7838 (m-30)
REVERT: E  103 TYR cc_start: 0.8939 (t80) cc_final: 0.8616 (t80)
REVERT: A   52 GLN cc_start: 0.7982 (tp-100) cc_final: 0.7680 (tp-100)
REVERT: L    5 TRP cc_start: 0.8310 (t60) cc_final: 0.8101 (t60)
REVERT: L    6 MET cc_start: 0.7181 (ttt) cc_final: 0.6928 (ttp)
  outliers start: 32
  outliers final: 24
  residues processed: 150
  average time/residue: 0.2163
  time to fit residues: 44.6362
Evaluate side-chains
  153 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 126
  time to evaluate  : 1.235 
-------------------------------------------------------------------------------
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  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  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  203 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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 104 optimal weight:    2.9990
   chunk 14 optimal weight:   10.0000
   chunk 62 optimal weight:    2.9990
   chunk 73 optimal weight:    0.5980
   chunk 106 optimal weight:    4.9990
   chunk 47 optimal weight:    0.5980
   chunk 87 optimal weight:    6.9990
   chunk 82 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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 = 0.3975 r_free = 0.3975 target = 0.166640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.130763 restraints weight = 10055.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 2.34
r_work: 0.3367 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3235 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.1894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8766  Z= 0.156
  Angle     :  0.533   7.251  11910  Z= 0.270
  Chirality :  0.041   0.153   1376
  Planarity :  0.003   0.044   1500
  Dihedral  :  4.270  38.154   1220
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 17.61 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.26), residues: 1101
  helix:  2.48 (0.28), residues: 367
  sheet: -0.10 (0.32), residues: 263
  loop : -1.85 (0.27), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 346 
 HIS   0.003   0.001   HIS R 207 
 PHE   0.014   0.001   PHE A  49 
 TYR   0.009   0.001   TYR E 178 
 ARG   0.001   0.000   ARG B 137 

*********************** 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
  156 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 130
  time to evaluate  : 1.014 
Fit side-chains
REVERT: R  189 TYR cc_start: 0.7430 (m-80) cc_final: 0.7207 (m-80)
REVERT: R  244 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6062 (mp0)
REVERT: R  333 ARG cc_start: 0.7042 (ttm170) cc_final: 0.5995 (ttp80)
REVERT: R  367 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6613 (pp)
REVERT: B   98 SER cc_start: 0.8915 (p) cc_final: 0.8689 (p)
REVERT: B  101 MET cc_start: 0.9056 (mtp) cc_final: 0.8733 (mmm)
REVERT: B  226 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8097 (pt0)
REVERT: C   47 GLU cc_start: 0.7469 (pm20) cc_final: 0.7061 (pt0)
REVERT: E   67 ARG cc_start: 0.7441 (ptt90) cc_final: 0.7060 (ptt-90)
REVERT: E  103 TYR cc_start: 0.8857 (t80) cc_final: 0.8527 (t80)
REVERT: L    6 MET cc_start: 0.7175 (ttt) cc_final: 0.6884 (ttp)
  outliers start: 26
  outliers final: 20
  residues processed: 140
  average time/residue: 0.2068
  time to fit residues: 40.3697
Evaluate side-chains
  146 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
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  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  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  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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 95 optimal weight:    8.9990
   chunk 64 optimal weight:    0.0370
   chunk 9 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 82 optimal weight:    7.9990
   chunk 6 optimal weight:    4.9990
   chunk 80 optimal weight:    0.9980
   chunk 87 optimal weight:    0.2980
   overall best weight:    0.5858

-------------------------------------------------------------------------------
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 = 0.3975 r_free = 0.3975 target = 0.167095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.125414 restraints weight = 10348.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 2.45
r_work: 0.3401 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3266 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.2028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8766  Z= 0.143
  Angle     :  0.532   7.072  11910  Z= 0.268
  Chirality :  0.041   0.194   1376
  Planarity :  0.003   0.041   1500
  Dihedral  :  4.121  36.808   1220
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 18.28 %
    Favored  : 78.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.26), residues: 1101
  helix:  2.62 (0.28), residues: 367
  sheet: -0.15 (0.32), residues: 270
  loop : -1.78 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 346 
 HIS   0.002   0.001   HIS R 207 
 PHE   0.015   0.001   PHE A  49 
 TYR   0.015   0.001   TYR A 229 
 ARG   0.001   0.000   ARG B 137 

*********************** 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
  158 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 133
  time to evaluate  : 0.973 
Fit side-chains
REVERT: R  244 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6112 (mp0)
REVERT: R  333 ARG cc_start: 0.7106 (ttm170) cc_final: 0.6096 (ttp80)
REVERT: B   70 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8571 (pt)
REVERT: B  101 MET cc_start: 0.9024 (mtp) cc_final: 0.8652 (mmm)
REVERT: B  127 LYS cc_start: 0.8890 (mttm) cc_final: 0.8163 (mptt)
REVERT: B  226 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8134 (pt0)
REVERT: C   47 GLU cc_start: 0.7536 (pm20) cc_final: 0.7012 (pt0)
REVERT: E   67 ARG cc_start: 0.7532 (ptt90) cc_final: 0.7155 (ptt-90)
REVERT: E   90 ASP cc_start: 0.8320 (m-30) cc_final: 0.8069 (m-30)
REVERT: E  103 TYR cc_start: 0.8863 (t80) cc_final: 0.8528 (t80)
REVERT: L    6 MET cc_start: 0.7217 (ttt) cc_final: 0.6958 (ttp)
  outliers start: 25
  outliers final: 19
  residues processed: 146
  average time/residue: 0.2041
  time to fit residues: 41.7727
Evaluate side-chains
  146 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  187 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  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  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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 14 optimal weight:    0.0060
   chunk 25 optimal weight:    6.9990
   chunk 43 optimal weight:    7.9990
   chunk 46 optimal weight:    5.9990
   chunk 73 optimal weight:    0.0070
   chunk 10 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9990
   chunk 63 optimal weight:    0.0980
   chunk 34 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 67 optimal weight:    5.9990
   overall best weight:    0.3014

-------------------------------------------------------------------------------
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 = 0.3994 r_free = 0.3994 target = 0.169466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.133174 restraints weight = 10090.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 2.48
r_work: 0.3380 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8766  Z= 0.131
  Angle     :  0.538   9.383  11910  Z= 0.270
  Chirality :  0.041   0.186   1376
  Planarity :  0.003   0.039   1500
  Dihedral  :  3.977  34.810   1220
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 19.06 %
    Favored  : 78.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.26), residues: 1101
  helix:  2.71 (0.28), residues: 367
  sheet: -0.13 (0.32), residues: 273
  loop : -1.69 (0.28), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 346 
 HIS   0.003   0.000   HIS R 207 
 PHE   0.016   0.001   PHE A  49 
 TYR   0.009   0.001   TYR E 178 
 ARG   0.003   0.000   ARG R 356 

*********************** 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
  159 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.877 
Fit side-chains
REVERT: R  244 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.5671 (mp0)
REVERT: R  333 ARG cc_start: 0.6841 (ttm170) cc_final: 0.5859 (ttp80)
REVERT: R  367 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6236 (pp)
REVERT: B  127 LYS cc_start: 0.8840 (mttm) cc_final: 0.8045 (mptt)
REVERT: B  226 GLU cc_start: 0.8275 (mt-10) cc_final: 0.8052 (pt0)
REVERT: C   47 GLU cc_start: 0.7390 (pm20) cc_final: 0.6895 (pt0)
REVERT: E   67 ARG cc_start: 0.7380 (ptt90) cc_final: 0.7027 (ptt-90)
REVERT: E   90 ASP cc_start: 0.8108 (m-30) cc_final: 0.7849 (m-30)
REVERT: E  103 TYR cc_start: 0.8755 (t80) cc_final: 0.8342 (t80)
  outliers start: 25
  outliers final: 17
  residues processed: 148
  average time/residue: 0.1954
  time to fit residues: 41.1163
Evaluate side-chains
  146 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 127
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
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  244 GLU
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   32 GLN
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  160 THR
Chi-restraints excluded: chain E residue  226 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 36 optimal weight:    0.2980
   chunk 11 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 73 optimal weight:    0.0270
   chunk 88 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9980
   chunk 6 optimal weight:    7.9990
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.8640

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.169914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.133619 restraints weight = 9971.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 2.44
r_work: 0.3302 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8766  Z= 0.162
  Angle     :  0.553   9.482  11910  Z= 0.277
  Chirality :  0.042   0.175   1376
  Planarity :  0.003   0.039   1500
  Dihedral  :  4.017  35.554   1220
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 19.06 %
    Favored  : 78.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.26), residues: 1101
  helix:  2.68 (0.28), residues: 368
  sheet: -0.11 (0.31), residues: 275
  loop : -1.61 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 346 
 HIS   0.003   0.001   HIS R 207 
 PHE   0.016   0.001   PHE A  49 
 TYR   0.015   0.001   TYR A 229 
 ARG   0.001   0.000   ARG B 137 

********************** 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
  150 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 129
  time to evaluate  : 0.885 
Fit side-chains
REVERT: R  244 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.5670 (mp0)
REVERT: R  333 ARG cc_start: 0.6868 (ttm170) cc_final: 0.5887 (ttp80)
REVERT: R  367 LEU cc_start: 0.6733 (OUTLIER) cc_final: 0.6112 (pp)
REVERT: B  127 LYS cc_start: 0.8818 (mttm) cc_final: 0.8018 (mptt)
REVERT: B  226 GLU cc_start: 0.8298 (mt-10) cc_final: 0.8067 (pt0)
REVERT: C   47 GLU cc_start: 0.7373 (pm20) cc_final: 0.6936 (pt0)
REVERT: E  103 TYR cc_start: 0.8723 (t80) cc_final: 0.8347 (t80)
  outliers start: 21
  outliers final: 17
  residues processed: 141
  average time/residue: 0.1985
  time to fit residues: 39.2479
Evaluate side-chains
  144 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
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  244 GLU
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   32 GLN
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  160 THR
Chi-restraints excluded: chain E residue  226 THR
Chi-restraints excluded: chain A residue   50 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 25 optimal weight:    5.9990
   chunk 71 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 30 optimal weight:    0.5980
   chunk 96 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 57 optimal weight:    8.9990
   chunk 1 optimal weight:    2.9990
   chunk 68 optimal weight:    6.9990
   chunk 102 optimal weight:    9.9990
   chunk 97 optimal weight:    2.9990
   overall best weight:    1.6784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.165251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.129366 restraints weight = 10215.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 2.34
r_work: 0.3259 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3127 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.2177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8766  Z= 0.238
  Angle     :  0.588   8.067  11910  Z= 0.298
  Chirality :  0.043   0.174   1376
  Planarity :  0.003   0.042   1500
  Dihedral  :  4.312  39.070   1220
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 19.29 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.26), residues: 1101
  helix:  2.51 (0.27), residues: 367
  sheet: -0.20 (0.31), residues: 282
  loop : -1.69 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  63 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.014   0.001   PHE A  49 
 TYR   0.011   0.001   TYR A 289 
 ARG   0.002   0.000   ARG B 137 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4923.62 seconds
wall clock time: 87 minutes 54.61 seconds (5274.61 seconds total)