Starting phenix.real_space_refine
on Wed Mar  4 04:07:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kau_22784/03_2026/7kau_22784.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kau_22784/03_2026/7kau_22784.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kau_22784/03_2026/7kau_22784.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kau_22784/03_2026/7kau_22784.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kau_22784/03_2026/7kau_22784.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kau_22784/03_2026/7kau_22784.map"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.008 sd=   0.063
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      39      5.16       5
     C    6981      2.51       5
     N    1810      2.21       5
     O    1881      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10711
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 440, 3358
          Classifications: {'peptide': 440}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 20, 'TRANS': 419}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 81
          Unresolved non-hydrogen angles: 101
          Unresolved non-hydrogen dihedrals: 70
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 4, 'TYR:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 64
    Chain: "C"
      Number of atoms: 435
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 435
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 2, 'TRANS': 52}
    Chain: "B"
      Number of atoms: 229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 229
          Classifications: {'peptide': 32}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 1, 'TRANS': 30}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "D"
      Number of atoms: 3809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 485, 3809
          Classifications: {'peptide': 485}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 27, 'TRANS': 457}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 99
          Unresolved non-hydrogen angles: 125
          Unresolved non-hydrogen dihedrals: 75
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 12, 'GLN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 86
    Chain: "E"
      Number of atoms: 1129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1129
          Classifications: {'peptide': 138}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 2, 'TRANS': 135}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "F"
      Number of atoms: 1471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 190, 1471
          Classifications: {'peptide': 190}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 7, 'TRANS': 182}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "G"
      Number of atoms: 280
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 280
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 56}
          Link IDs: {'TRANS': 55}
          Unresolved non-hydrogen bonds: 112
          Unresolved non-hydrogen angles: 168
          Unresolved non-hydrogen dihedrals: 56
          Planarities with less than four sites: {'UNK:plan-1': 56}
          Unresolved non-hydrogen planarities: 56
  Time building chain proxies: 2.53, per 1000 atoms: 0.24
  Number of scatterers: 10711
  At special positions: 0
  Unit cell: (109.48, 127.33, 138.04, 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      39     16.00
     O    1881      8.00
     N    1810      7.00
     C    6981      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.82
  Conformation dependent library (CDL) restraints added in 623.0 milliseconds
  

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2638

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 6 sheets defined
      70.9% alpha, 4.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 47
      removed outlier: 3.580A  pdb=" N   LYS A  32 " --> pdb=" O   PRO A  28 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   GLY A  47 " --> pdb=" O   PHE A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 70
      removed outlier: 3.658A  pdb=" N   ARG A  67 " --> pdb=" O   LEU A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 98
    Processing helix  chain 'A' and resid 107 through 137
      removed outlier: 3.819A  pdb=" N   ARG A 111 " --> pdb=" O   SER A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 174
      removed outlier: 3.583A  pdb=" N   LEU A 157 " --> pdb=" O   LEU A 153 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   GLY A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 196
    Processing helix  chain 'A' and resid 213 through 225
      removed outlier: 3.659A  pdb=" N   ALA A 217 " --> pdb=" O   GLY A 213 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ARG A 225 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 238
      removed outlier: 3.902A  pdb=" N   VAL A 233 " --> pdb=" O   LYS A 229 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   GLU A 234 " --> pdb=" O   ARG A 230 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   TYR A 237 " --> pdb=" O   VAL A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 262
      removed outlier: 3.736A  pdb=" N   VAL A 247 " --> pdb=" O   ASN A 243 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   GLY A 262 " --> pdb=" O   LEU A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 314
      removed outlier: 4.114A  pdb=" N   ILE A 293 " --> pdb=" O   SER A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 324
    Processing helix  chain 'A' and resid 341 through 346
      removed outlier: 3.567A  pdb=" N   TYR A 345 " --> pdb=" O   GLY A 341 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ILE A 346 " --> pdb=" O   LEU A 342 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 341 through 346'
    Processing helix  chain 'A' and resid 351 through 358
    Processing helix  chain 'A' and resid 358 through 384
    Processing helix  chain 'A' and resid 387 through 399
    Processing helix  chain 'A' and resid 409 through 416
      removed outlier: 3.628A  pdb=" N   LYS A 416 " --> pdb=" O   ARG A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 440
      removed outlier: 3.630A  pdb=" N   GLY A 440 " --> pdb=" O   SER A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 466
    Processing helix  chain 'C' and resid 27 through 39
    Processing helix  chain 'C' and resid 43 through 80
      removed outlier: 4.219A  pdb=" N   LYS C  49 " --> pdb=" O   LYS C  45 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ILE C  64 " --> pdb=" O   ALA C  60 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   HIS C  72 " --> pdb=" O   ILE C  68 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   ILE C  73 " --> pdb=" O   LYS C  69 " (cutoff:3.500A)
      Proline residue:  C  74  - end of helix
      removed outlier: 3.517A  pdb=" N   VAL C  80 " --> pdb=" O   ARG C  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 82
    Processing helix  chain 'D' and resid 13 through 36
      removed outlier: 3.524A  pdb=" N   PHE D  17 " --> pdb=" O   THR D  13 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   VAL D  25 " --> pdb=" O   GLY D  21 " (cutoff:3.500A)
      Proline residue:  D  28  - end of helix
    Processing helix  chain 'D' and resid 58 through 67
      removed outlier: 4.496A  pdb=" N   LEU D  62 " --> pdb=" O   VAL D  58 " (cutoff:3.500A)
      removed outlier: 4.897A  pdb=" N   GLU D  64 " --> pdb=" O   LYS D  60 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   GLU D  65 " --> pdb=" O   ASN D  61 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   TYR D  66 " --> pdb=" O   LEU D  62 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   THR D  67 " --> pdb=" O   ASN D  63 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 68 through 78
    Processing helix  chain 'D' and resid 94 through 113
      removed outlier: 3.548A  pdb=" N   ASN D 113 " --> pdb=" O   ARG D 109 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 212 through 217
      removed outlier: 3.572A  pdb=" N   GLY D 217 " --> pdb=" O   PHE D 213 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 219 through 233
      removed outlier: 3.907A  pdb=" N   LEU D 223 " --> pdb=" O   ALA D 219 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   VAL D 224 " --> pdb=" O   SER D 220 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 234 through 249
      removed outlier: 3.618A  pdb=" N   TYR D 249 " --> pdb=" O   ARG D 245 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 255 through 268
      removed outlier: 3.819A  pdb=" N   ASN D 268 " --> pdb=" O   SER D 264 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 276 through 285
      removed outlier: 3.696A  pdb=" N   ILE D 280 " --> pdb=" O   THR D 276 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 288 through 294
      removed outlier: 3.703A  pdb=" N   GLN D 292 " --> pdb=" O   HIS D 288 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   PHE D 293 " --> pdb=" O   GLU D 289 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   PHE D 294 " --> pdb=" O   PHE D 290 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 288 through 294'
    Processing helix  chain 'D' and resid 298 through 311
    Processing helix  chain 'D' and resid 318 through 343
      removed outlier: 3.803A  pdb=" N   ARG D 324 " --> pdb=" O   ASN D 320 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   HIS D 330 " --> pdb=" O   VAL D 326 " (cutoff:3.500A)
      removed outlier: 5.618A  pdb=" N   SER D 331 " --> pdb=" O   ALA D 327 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   LEU D 332 " --> pdb=" O   LYS D 328 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 345 through 362
      removed outlier: 4.030A  pdb=" N   ALA D 349 " --> pdb=" O   ASN D 345 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 378 through 386
      removed outlier: 4.335A  pdb=" N   THR D 384 " --> pdb=" O   GLU D 380 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 391 through 397
    Processing helix  chain 'D' and resid 399 through 408
      removed outlier: 3.664A  pdb=" N   GLY D 404 " --> pdb=" O   ASP D 400 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 411 through 423
      removed outlier: 4.263A  pdb=" N   GLU D 417 " --> pdb=" O   ALA D 413 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 480 through 486
    Processing helix  chain 'D' and resid 487 through 492
      removed outlier: 4.273A  pdb=" N   MET D 491 " --> pdb=" O   PRO D 487 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 537 through 541
    Processing helix  chain 'E' and resid 72 through 86
      removed outlier: 3.749A  pdb=" N   PHE E  76 " --> pdb=" O   HIS E  72 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ASN E  84 " --> pdb=" O   GLU E  80 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LYS E  86 " --> pdb=" O   SER E  82 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 89 through 124
      removed outlier: 4.006A  pdb=" N   LYS E  93 " --> pdb=" O   GLU E  89 " (cutoff:3.500A)
      Proline residue:  E 115  - end of helix
    Processing helix  chain 'E' and resid 128 through 156
      removed outlier: 3.652A  pdb=" N   LYS E 132 " --> pdb=" O   GLU E 128 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   LYS E 139 " --> pdb=" O   GLU E 135 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   GLU E 142 " --> pdb=" O   VAL E 138 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 162 through 182
      removed outlier: 4.042A  pdb=" N   PHE E 172 " --> pdb=" O   LYS E 168 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 182 through 195
      removed outlier: 4.891A  pdb=" N   GLU E 188 " --> pdb=" O   LEU E 184 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   VAL E 189 " --> pdb=" O   LYS E 185 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   CYS E 190 " --> pdb=" O   ARG E 186 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ILE E 191 " --> pdb=" O   LYS E 187 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 199 through 203
      removed outlier: 3.962A  pdb=" N   GLY E 202 " --> pdb=" O   ASN E 199 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ARG E 203 " --> pdb=" O   ASN E 200 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 199 through 203'
    Processing helix  chain 'F' and resid 21 through 41
      removed outlier: 3.678A  pdb=" N   GLU F  25 " --> pdb=" O   ALA F  21 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 52 through 71
      removed outlier: 4.045A  pdb=" N   ASN F  68 " --> pdb=" O   SER F  64 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   LEU F  69 " --> pdb=" O   GLY F  65 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   GLN F  70 " --> pdb=" O   MET F  66 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 75 through 91
      removed outlier: 3.762A  pdb=" N   LYS F  79 " --> pdb=" O   ASN F  75 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 97 through 120
      removed outlier: 3.663A  pdb=" N   GLN F 101 " --> pdb=" O   ALA F  97 " (cutoff:3.500A)
      Proline residue:  F 103  - end of helix
    Processing helix  chain 'F' and resid 122 through 135
    Processing helix  chain 'F' and resid 139 through 153
      removed outlier: 3.719A  pdb=" N   PHE F 143 " --> pdb=" O   GLN F 139 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   VAL F 144 " --> pdb=" O   PRO F 140 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   ARG F 145 " --> pdb=" O   ASP F 141 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 156 through 168
    Processing helix  chain 'F' and resid 175 through 192
    Processing helix  chain 'G' and resid 151 through 170
      removed outlier: 3.598A  pdb=" N   UNK G 170 " --> pdb=" O   UNK G 166 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 175 through 205
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 211
      removed outlier: 3.511A  pdb=" N   GLU A 210 " --> pdb=" O   VAL A 203 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   VAL A 203 " --> pdb=" O   GLU A 210 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 278 through 284
    Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 327
    Processing sheet with id=AA4, first strand: chain 'D' and resid 430 through 434
      removed outlier: 6.842A  pdb=" N   LYS D 454 " --> pdb=" O   ILE D 431 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   ALA D 433 " --> pdb=" O   SER D 452 " (cutoff:3.500A)
      removed outlier: 7.415A  pdb=" N   SER D 452 " --> pdb=" O   ALA D 433 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 532
      removed outlier: 3.527A  pdb=" N   VAL D 590 " --> pdb=" O   ILE D 604 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ILE D 604 " --> pdb=" O   VAL D 590 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   VAL D 592 " --> pdb=" O   LEU D 602 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LEU D 602 " --> pdb=" O   VAL D 592 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 5 through 6

    678 hydrogen bonds defined for protein.
    2004 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.71

  Time building geometry restraints manager: 1.13 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3390
        1.34 -     1.46: 1852
        1.46 -     1.57: 5615
        1.57 -     1.69: 0
        1.69 -     1.81: 61
  Bond restraints: 10918
  Sorted by residual:
  bond pdb=" C   THR D 595 "
       pdb=" N   ASP D 596 "
    ideal  model  delta    sigma   weight residual
    1.332  1.316  0.016 1.40e-02 5.10e+03 1.34e+00
  bond pdb=" C   ILE D 425 "
       pdb=" N   PRO D 426 "
    ideal  model  delta    sigma   weight residual
    1.334  1.323  0.011 1.11e-02 8.12e+03 9.83e-01
  bond pdb=" CB  TRP D 283 "
       pdb=" CG  TRP D 283 "
    ideal  model  delta    sigma   weight residual
    1.498  1.471  0.027 3.10e-02 1.04e+03 7.78e-01
  bond pdb=" CA  GLN F 155 "
       pdb=" CB  GLN F 155 "
    ideal  model  delta    sigma   weight residual
    1.532  1.519  0.014 1.62e-02 3.81e+03 7.13e-01
  bond pdb=" CA  GLY A 176 "
       pdb=" C   GLY A 176 "
    ideal  model  delta    sigma   weight residual
    1.522  1.512  0.010 1.29e-02 6.01e+03 6.08e-01
  ... (remaining 10913 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 14637
        1.99 -     3.99: 154
        3.99 -     5.98: 15
        5.98 -     7.98: 4
        7.98 -     9.97: 1
  Bond angle restraints: 14811
  Sorted by residual:
  angle pdb=" N   ILE E 126 "
        pdb=" CA  ILE E 126 "
        pdb=" C   ILE E 126 "
      ideal   model   delta    sigma   weight residual
     113.71  109.99    3.72 9.50e-01 1.11e+00 1.53e+01
  angle pdb=" N   VAL E 205 "
        pdb=" CA  VAL E 205 "
        pdb=" C   VAL E 205 "
      ideal   model   delta    sigma   weight residual
     111.88  108.56    3.32 1.06e+00 8.90e-01 9.80e+00
  angle pdb=" CA  VAL D 215 "
        pdb=" C   VAL D 215 "
        pdb=" N   ASP D 216 "
      ideal   model   delta    sigma   weight residual
     116.60  120.55   -3.95 1.45e+00 4.76e-01 7.40e+00
  angle pdb=" C   GLU A 266 "
        pdb=" N   LEU A 267 "
        pdb=" CA  LEU A 267 "
      ideal   model   delta    sigma   weight residual
     121.95  111.98    9.97 3.74e+00 7.15e-02 7.11e+00
  angle pdb=" N   SER A 289 "
        pdb=" CA  SER A 289 "
        pdb=" C   SER A 289 "
      ideal   model   delta    sigma   weight residual
     111.11  114.24   -3.13 1.20e+00 6.94e-01 6.81e+00
  ... (remaining 14806 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.36: 6066
       17.36 -    34.72: 430
       34.72 -    52.09: 62
       52.09 -    69.45: 7
       69.45 -    86.81: 8
  Dihedral angle restraints: 6573
    sinusoidal: 2514
      harmonic: 4059
  Sorted by residual:
  dihedral pdb=" CA  VAL D 437 "
           pdb=" C   VAL D 437 "
           pdb=" N   PRO D 438 "
           pdb=" CA  PRO D 438 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.34   19.66     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CA  ILE D 425 "
           pdb=" C   ILE D 425 "
           pdb=" N   PRO D 426 "
           pdb=" CA  PRO D 426 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.11  -15.89     0      5.00e+00 4.00e-02 1.01e+01
  dihedral pdb=" CB  GLU D 473 "
           pdb=" CG  GLU D 473 "
           pdb=" CD  GLU D 473 "
           pdb=" OE1 GLU D 473 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -86.81   86.81     1      3.00e+01 1.11e-03 1.01e+01
  ... (remaining 6570 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 945
       0.025 -    0.050: 540
       0.050 -    0.076: 169
       0.076 -    0.101: 73
       0.101 -    0.126: 41
  Chirality restraints: 1768
  Sorted by residual:
  chirality pdb=" CA  ILE D 470 "
            pdb=" N   ILE D 470 "
            pdb=" C   ILE D 470 "
            pdb=" CB  ILE D 470 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.97e-01
  chirality pdb=" CA  PRO D 375 "
            pdb=" N   PRO D 375 "
            pdb=" C   PRO D 375 "
            pdb=" CB  PRO D 375 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.12 2.00e-01 2.50e+01 3.83e-01
  chirality pdb=" CA  THR A 291 "
            pdb=" N   THR A 291 "
            pdb=" C   THR A 291 "
            pdb=" CB  THR A 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.40    0.12 2.00e-01 2.50e+01 3.82e-01
  ... (remaining 1765 not shown)

  Planarity restraints: 1846
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR F  47 "    0.030 5.00e-02 4.00e+02   4.47e-02 3.20e+00
        pdb=" N   PRO F  48 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO F  48 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO F  48 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA F  93 "   -0.023 5.00e-02 4.00e+02   3.49e-02 1.95e+00
        pdb=" N   PRO F  94 "    0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO F  94 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO F  94 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL D 437 "   -0.023 5.00e-02 4.00e+02   3.46e-02 1.91e+00
        pdb=" N   PRO D 438 "    0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO D 438 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO D 438 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 1843 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2401
        2.78 -     3.31: 10631
        3.31 -     3.84: 16840
        3.84 -     4.37: 17505
        4.37 -     4.90: 31497
  Nonbonded interactions: 78874
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP D 308 "
            pdb=" NH1 ARG D 313 "
     model   vdw
     2.251 3.120
  nonbonded pdb=" OG  SER A 271 "
            pdb=" O   VAL A 274 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" NZ  LYS D 538 "
            pdb=" O   ASP D 565 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" O   PHE A 198 "
            pdb=" OH  TYR C  66 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" OE1 GLN D 370 "
            pdb=" OG1 THR D 391 "
     model   vdw
     2.283 3.040
  ... (remaining 78869 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.840
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.980
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
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      :  0.003   0.027  10918  Z= 0.151
  Angle     :  0.559   9.970  14811  Z= 0.311
  Chirality :  0.038   0.126   1768
  Planarity :  0.003   0.045   1846
  Dihedral  : 12.117  86.810   3935
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.93 (0.22), residues: 1316
  helix:  0.39 (0.17), residues: 808
  sheet: -2.21 (0.48), residues: 82
  loop : -2.18 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  75 
 TYR   0.018   0.001   TYR F 190 
 PHE   0.015   0.001   PHE A 194 
 TRP   0.013   0.001   TRP A 380 
 HIS   0.003   0.001   HIS B  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (10918)
  covalent geometry    : angle       0.55929 (14811)
  hydrogen bonds       : bond        0.12394 (  678)
  hydrogen bonds       : angle       4.49046 ( 2004)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  249 MET cc_start: 0.9095 (mmm) cc_final: 0.8823 (mmm)
REVERT: A  290 ASN cc_start: 0.8938 (m-40) cc_final: 0.8510 (p0)
REVERT: A  368 PHE cc_start: 0.9524 (t80) cc_final: 0.9241 (t80)
REVERT: D  102 LEU cc_start: 0.8862 (mm) cc_final: 0.8460 (mm)
REVERT: D  491 MET cc_start: 0.8811 (ttp) cc_final: 0.8126 (tmm)
REVERT: D  601 ASP cc_start: 0.9055 (m-30) cc_final: 0.8821 (m-30)
REVERT: E   81 MET cc_start: 0.8743 (ttm) cc_final: 0.8095 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.0898
  time to fit residues: 13.9349
Evaluate side-chains
  59 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    8.9990
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.0000
   chunk 91 optimal weight:    2.9990
   chunk 55 optimal weight:    9.9990
   overall best weight:    1.9790

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

Flipped N/Q/H residues before XYZ refinement:
D 334 HIS
D 424 HIS
D 427 ASN
D 494 GLN
D 558 HIS
E  88 HIS
E 174 GLN
F  68 ASN
F  70 GLN
F  71 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.063563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.048725 restraints weight = 59843.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.050010 restraints weight = 31688.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.050881 restraints weight = 21295.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.051430 restraints weight = 16567.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.051728 restraints weight = 14183.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.1181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10918  Z= 0.133
  Angle     :  0.540   6.864  14811  Z= 0.270
  Chirality :  0.038   0.147   1768
  Planarity :  0.004   0.044   1846
  Dihedral  :  3.477  19.952   1476
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 11.32 %
    Favored  : 87.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.69 (0.23), residues: 1316
  helix:  1.77 (0.18), residues: 811
  sheet: -1.50 (0.49), residues: 82
  loop : -1.78 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.000   ARG D 440 
 TYR   0.016   0.001   TYR F 190 
 PHE   0.011   0.001   PHE D 547 
 TRP   0.012   0.001   TRP A 380 
 HIS   0.003   0.001   HIS C  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (10918)
  covalent geometry    : angle       0.53969 (14811)
  hydrogen bonds       : bond        0.03732 (  678)
  hydrogen bonds       : angle       3.64263 ( 2004)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 ASP cc_start: 0.9038 (t70) cc_final: 0.8787 (t0)
REVERT: A  249 MET cc_start: 0.9217 (mmm) cc_final: 0.8905 (mmm)
REVERT: A  290 ASN cc_start: 0.9054 (m-40) cc_final: 0.8662 (p0)
REVERT: A  368 PHE cc_start: 0.9512 (t80) cc_final: 0.9297 (t80)
REVERT: D  102 LEU cc_start: 0.8920 (mm) cc_final: 0.8526 (mm)
REVERT: E   81 MET cc_start: 0.8780 (ttm) cc_final: 0.8187 (tmm)
REVERT: F   57 MET cc_start: 0.8939 (ptp) cc_final: 0.8718 (ptp)
  outliers start: 16
  outliers final: 8
  residues processed: 79
  average time/residue: 0.0723
  time to fit residues: 9.1023
Evaluate side-chains
  67 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   31 GLU
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain D residue  222 LEU
Chi-restraints excluded: chain D residue  341 CYS
Chi-restraints excluded: chain D residue  464 LEU
Chi-restraints excluded: chain E residue  170 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 9 optimal weight:   10.0000
   chunk 33 optimal weight:    9.9990
   chunk 38 optimal weight:    6.9990
   chunk 56 optimal weight:    8.9990
   chunk 125 optimal weight:    7.9990
   chunk 18 optimal weight:    6.9990
   chunk 11 optimal weight:    8.9990
   chunk 17 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 83 optimal weight:    5.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
D 307 GLN
** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 123 ASN
F  49 GLN
F  89 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.062309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.046547 restraints weight = 62409.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.047771 restraints weight = 34018.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.048507 restraints weight = 23402.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.049062 restraints weight = 18690.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.049295 restraints weight = 16133.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052  10918  Z= 0.269
  Angle     :  0.662   8.302  14811  Z= 0.334
  Chirality :  0.041   0.138   1768
  Planarity :  0.004   0.047   1846
  Dihedral  :  3.876  21.677   1476
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 14.82 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.24), residues: 1316
  helix:  1.99 (0.18), residues: 816
  sheet: -1.21 (0.52), residues: 80
  loop : -1.53 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  75 
 TYR   0.026   0.002   TYR F 190 
 PHE   0.015   0.001   PHE D 547 
 TRP   0.016   0.002   TRP A 380 
 HIS   0.004   0.001   HIS C  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00605 (10918)
  covalent geometry    : angle       0.66172 (14811)
  hydrogen bonds       : bond        0.04450 (  678)
  hydrogen bonds       : angle       4.07834 ( 2004)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 53
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 ASP cc_start: 0.9117 (t70) cc_final: 0.8811 (t0)
REVERT: A  249 MET cc_start: 0.9198 (mmm) cc_final: 0.8942 (mmm)
REVERT: A  290 ASN cc_start: 0.9099 (m-40) cc_final: 0.8697 (p0)
REVERT: B   72 HIS cc_start: 0.8728 (OUTLIER) cc_final: 0.7820 (m170)
REVERT: D  102 LEU cc_start: 0.9030 (mm) cc_final: 0.8652 (mm)
REVERT: D  608 MET cc_start: 0.8452 (ptt) cc_final: 0.7708 (ppp)
REVERT: E   81 MET cc_start: 0.8762 (ttm) cc_final: 0.8235 (tmm)
  outliers start: 23
  outliers final: 17
  residues processed: 71
  average time/residue: 0.0718
  time to fit residues: 8.3838
Evaluate side-chains
  69 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 51
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain C residue   31 GLU
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue   72 HIS
Chi-restraints excluded: chain D residue  222 LEU
Chi-restraints excluded: chain D residue  228 VAL
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  341 CYS
Chi-restraints excluded: chain D residue  360 VAL
Chi-restraints excluded: chain D residue  464 LEU
Chi-restraints excluded: chain D residue  516 LEU
Chi-restraints excluded: chain E residue  104 VAL
Chi-restraints excluded: chain E residue  170 ILE
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue  153 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 125 optimal weight:    3.9990
   chunk 9 optimal weight:   20.0000
   chunk 21 optimal weight:   10.0000
   chunk 128 optimal weight:    3.9990
   chunk 46 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 20 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 54 optimal weight:    9.9990
   chunk 45 optimal weight:    9.9990
   chunk 82 optimal weight:    1.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 118 GLN
A 308 GLN
** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 381 HIS
** E  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.062849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.047175 restraints weight = 62328.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.048432 restraints weight = 33668.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.049258 restraints weight = 22985.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.049801 restraints weight = 18118.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.050033 restraints weight = 15601.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.1990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  10918  Z= 0.204
  Angle     :  0.581   7.720  14811  Z= 0.292
  Chirality :  0.039   0.134   1768
  Planarity :  0.004   0.050   1846
  Dihedral  :  3.754  21.714   1476
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.44 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.49 (0.24), residues: 1316
  helix:  2.26 (0.18), residues: 820
  sheet: -0.89 (0.55), residues: 82
  loop : -1.30 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 238 
 TYR   0.020   0.002   TYR F 190 
 PHE   0.013   0.001   PHE D 547 
 TRP   0.013   0.002   TRP A 380 
 HIS   0.002   0.001   HIS B  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 (10918)
  covalent geometry    : angle       0.58115 (14811)
  hydrogen bonds       : bond        0.03909 (  678)
  hydrogen bonds       : angle       3.84643 ( 2004)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 54
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7789 (tp40)
REVERT: A  237 TYR cc_start: 0.6053 (OUTLIER) cc_final: 0.5441 (m-10)
REVERT: A  249 MET cc_start: 0.9176 (mmm) cc_final: 0.8909 (mmm)
REVERT: A  290 ASN cc_start: 0.9068 (m-40) cc_final: 0.8713 (p0)
REVERT: B   72 HIS cc_start: 0.8746 (OUTLIER) cc_final: 0.7881 (m170)
REVERT: D  102 LEU cc_start: 0.9011 (mm) cc_final: 0.8609 (mm)
REVERT: D  370 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8808 (mt0)
REVERT: D  608 MET cc_start: 0.8390 (ptt) cc_final: 0.7733 (ppp)
REVERT: E   81 MET cc_start: 0.8747 (ttm) cc_final: 0.8256 (tmm)
  outliers start: 32
  outliers final: 18
  residues processed: 78
  average time/residue: 0.0652
  time to fit residues: 8.4879
Evaluate side-chains
  69 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 47
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue  118 GLN
Chi-restraints excluded: chain A residue  165 MET
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  237 TYR
Chi-restraints excluded: chain C residue   31 GLU
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue   72 HIS
Chi-restraints excluded: chain D residue  228 VAL
Chi-restraints excluded: chain D residue  239 VAL
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  341 CYS
Chi-restraints excluded: chain D residue  355 THR
Chi-restraints excluded: chain D residue  360 VAL
Chi-restraints excluded: chain D residue  370 GLN
Chi-restraints excluded: chain D residue  377 VAL
Chi-restraints excluded: chain D residue  464 LEU
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain E residue  170 ILE
Chi-restraints excluded: chain F residue   87 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 10 optimal weight:    9.9990
   chunk 35 optimal weight:    0.9980
   chunk 5 optimal weight:   10.0000
   chunk 113 optimal weight:    7.9990
   chunk 129 optimal weight:    2.9990
   chunk 43 optimal weight:    9.9990
   chunk 17 optimal weight:    0.9990
   chunk 38 optimal weight:    9.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
D 334 HIS
** E  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 123 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.063161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.047756 restraints weight = 61195.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.049019 restraints weight = 32691.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.049864 restraints weight = 22075.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.050389 restraints weight = 17308.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.050646 restraints weight = 14905.516|
|-----------------------------------------------------------------------------|
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.2079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10918  Z= 0.136
  Angle     :  0.529   7.353  14811  Z= 0.263
  Chirality :  0.038   0.128   1768
  Planarity :  0.003   0.049   1846
  Dihedral  :  3.565  21.809   1476
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 17.52 %
    Favored  : 79.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.83 (0.24), residues: 1316
  helix:  2.48 (0.19), residues: 824
  sheet: -0.62 (0.57), residues: 82
  loop : -1.12 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  99 
 TYR   0.017   0.001   TYR F 190 
 PHE   0.009   0.001   PHE D 547 
 TRP   0.012   0.001   TRP A 380 
 HIS   0.003   0.001   HIS D 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (10918)
  covalent geometry    : angle       0.52938 (14811)
  hydrogen bonds       : bond        0.03581 (  678)
  hydrogen bonds       : angle       3.58650 ( 2004)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 58
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  237 TYR cc_start: 0.5961 (OUTLIER) cc_final: 0.5334 (m-10)
REVERT: A  249 MET cc_start: 0.9279 (mmm) cc_final: 0.8969 (mmm)
REVERT: A  290 ASN cc_start: 0.9098 (m-40) cc_final: 0.8743 (p0)
REVERT: B   72 HIS cc_start: 0.8656 (OUTLIER) cc_final: 0.7979 (m170)
REVERT: D  102 LEU cc_start: 0.8976 (mm) cc_final: 0.8591 (mm)
REVERT: D  608 MET cc_start: 0.8476 (ptt) cc_final: 0.7673 (ppp)
REVERT: E   81 MET cc_start: 0.8966 (ttm) cc_final: 0.8388 (tmm)
  outliers start: 29
  outliers final: 19
  residues processed: 80
  average time/residue: 0.0629
  time to fit residues: 8.3110
Evaluate side-chains
  72 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 51
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  237 TYR
Chi-restraints excluded: chain C residue   31 GLU
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue   72 HIS
Chi-restraints excluded: chain D residue  222 LEU
Chi-restraints excluded: chain D residue  228 VAL
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  341 CYS
Chi-restraints excluded: chain D residue  343 PHE
Chi-restraints excluded: chain D residue  377 VAL
Chi-restraints excluded: chain D residue  464 LEU
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain E residue  170 ILE
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   87 MET
Chi-restraints excluded: chain F residue  183 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 58 optimal weight:    0.2980
   chunk 13 optimal weight:    6.9990
   chunk 17 optimal weight:    5.9990
   chunk 71 optimal weight:   10.0000
   chunk 72 optimal weight:    2.9990
   chunk 93 optimal weight:    0.8980
   chunk 89 optimal weight:    2.9990
   chunk 37 optimal weight:   20.0000
   chunk 128 optimal weight:    6.9990
   chunk 124 optimal weight:    9.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    2.2386

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

Flipped N/Q/H residues before XYZ refinement:
D 334 HIS
** E  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.059146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.043810 restraints weight = 59797.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.045033 restraints weight = 33024.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.045833 restraints weight = 22674.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.046355 restraints weight = 17890.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.046613 restraints weight = 15435.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.2235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10918  Z= 0.136
  Angle     :  0.540   8.681  14811  Z= 0.265
  Chirality :  0.038   0.142   1768
  Planarity :  0.003   0.048   1846
  Dihedral  :  3.480  21.257   1476
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 17.25 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.98 (0.24), residues: 1316
  helix:  2.57 (0.18), residues: 823
  sheet: -0.28 (0.62), residues: 72
  loop : -1.03 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  99 
 TYR   0.017   0.001   TYR F 190 
 PHE   0.009   0.001   PHE D 547 
 TRP   0.014   0.001   TRP D  14 
 HIS   0.004   0.001   HIS D 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (10918)
  covalent geometry    : angle       0.53984 (14811)
  hydrogen bonds       : bond        0.03465 (  678)
  hydrogen bonds       : angle       3.52160 ( 2004)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 56
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  237 TYR cc_start: 0.5912 (OUTLIER) cc_final: 0.5299 (m-10)
REVERT: A  249 MET cc_start: 0.9199 (mmm) cc_final: 0.8917 (mmm)
REVERT: A  290 ASN cc_start: 0.9050 (m-40) cc_final: 0.8697 (p0)
REVERT: B   72 HIS cc_start: 0.8705 (OUTLIER) cc_final: 0.7956 (m170)
REVERT: D  102 LEU cc_start: 0.9003 (mm) cc_final: 0.8612 (mm)
REVERT: D  526 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8396 (pp)
REVERT: D  608 MET cc_start: 0.8383 (ptt) cc_final: 0.7684 (ppp)
REVERT: E   81 MET cc_start: 0.8818 (ttm) cc_final: 0.8313 (tmm)
  outliers start: 36
  outliers final: 23
  residues processed: 86
  average time/residue: 0.0629
  time to fit residues: 9.1324
Evaluate side-chains
  76 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 50
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  237 TYR
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain C residue   31 GLU
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue   72 HIS
Chi-restraints excluded: chain D residue   61 ASN
Chi-restraints excluded: chain D residue  228 VAL
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  341 CYS
Chi-restraints excluded: chain D residue  343 PHE
Chi-restraints excluded: chain D residue  355 THR
Chi-restraints excluded: chain D residue  360 VAL
Chi-restraints excluded: chain D residue  377 VAL
Chi-restraints excluded: chain D residue  464 LEU
Chi-restraints excluded: chain D residue  516 LEU
Chi-restraints excluded: chain D residue  526 LEU
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain E residue  170 ILE
Chi-restraints excluded: chain F residue  153 LEU
Chi-restraints excluded: chain F residue  183 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0870
   chunk 85 optimal weight:    0.9980
   chunk 39 optimal weight:    7.9990
   chunk 69 optimal weight:    0.0570
   chunk 91 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 118 optimal weight:    7.9990
   chunk 104 optimal weight:    0.9980
   chunk 84 optimal weight:    7.9990
   chunk 129 optimal weight:    5.9990
   overall best weight:    0.8278

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

Flipped N/Q/H residues before XYZ refinement:
D 282 HIS
D 334 HIS
D 539 ASN
E  88 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.060402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.045078 restraints weight = 58703.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.046348 restraints weight = 31896.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.047187 restraints weight = 21714.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.047711 restraints weight = 17025.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.047963 restraints weight = 14666.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.2342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  10918  Z= 0.094
  Angle     :  0.510   8.717  14811  Z= 0.247
  Chirality :  0.037   0.129   1768
  Planarity :  0.003   0.048   1846
  Dihedral  :  3.308  20.564   1476
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 18.42 %
    Favored  : 79.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.15 (0.24), residues: 1316
  helix:  2.67 (0.19), residues: 824
  sheet: -0.00 (0.63), residues: 72
  loop : -0.95 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 238 
 TYR   0.014   0.001   TYR F 190 
 PHE   0.008   0.001   PHE A 114 
 TRP   0.012   0.001   TRP D  14 
 HIS   0.005   0.001   HIS D 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00200 (10918)
  covalent geometry    : angle       0.51045 (14811)
  hydrogen bonds       : bond        0.03048 (  678)
  hydrogen bonds       : angle       3.30437 ( 2004)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 71
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  249 MET cc_start: 0.9146 (mmm) cc_final: 0.8820 (mmm)
REVERT: A  290 ASN cc_start: 0.9054 (m-40) cc_final: 0.8706 (p0)
REVERT: B   72 HIS cc_start: 0.8655 (OUTLIER) cc_final: 0.7967 (m170)
REVERT: D  102 LEU cc_start: 0.8972 (mm) cc_final: 0.8575 (mm)
REVERT: D  526 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8451 (pp)
REVERT: D  608 MET cc_start: 0.8305 (ptt) cc_final: 0.7655 (ppp)
REVERT: E   81 MET cc_start: 0.8769 (ttm) cc_final: 0.8261 (tmm)
  outliers start: 22
  outliers final: 15
  residues processed: 88
  average time/residue: 0.0652
  time to fit residues: 9.6282
Evaluate side-chains
  74 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 57
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain C residue   31 GLU
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   72 HIS
Chi-restraints excluded: chain D residue  228 VAL
Chi-restraints excluded: chain D residue  341 CYS
Chi-restraints excluded: chain D residue  355 THR
Chi-restraints excluded: chain D residue  377 VAL
Chi-restraints excluded: chain D residue  464 LEU
Chi-restraints excluded: chain D residue  516 LEU
Chi-restraints excluded: chain D residue  526 LEU
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain E residue  170 ILE
Chi-restraints excluded: chain F residue  153 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 134 optimal weight:   50.0000
   chunk 131 optimal weight:    3.9990
   chunk 82 optimal weight:    6.9990
   chunk 37 optimal weight:   20.0000
   chunk 102 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0870
   chunk 44 optimal weight:   20.0000
   chunk 97 optimal weight:    6.9990
   chunk 115 optimal weight:    5.9990
   overall best weight:    3.2166

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

Flipped N/Q/H residues before XYZ refinement:
D 334 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.059074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.043651 restraints weight = 59204.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.044866 restraints weight = 32819.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.045659 restraints weight = 22612.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.046192 restraints weight = 17924.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.046475 restraints weight = 15458.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.2453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  10918  Z= 0.179
  Angle     :  0.577   9.621  14811  Z= 0.282
  Chirality :  0.039   0.153   1768
  Planarity :  0.003   0.047   1846
  Dihedral  :  3.472  20.911   1476
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 18.24 %
    Favored  : 78.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.05 (0.24), residues: 1316
  helix:  2.57 (0.18), residues: 825
  sheet: -0.15 (0.62), residues: 72
  loop : -0.90 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 238 
 TYR   0.020   0.001   TYR F 190 
 PHE   0.011   0.001   PHE B  64 
 TRP   0.011   0.001   TRP A 380 
 HIS   0.003   0.001   HIS C  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 (10918)
  covalent geometry    : angle       0.57694 (14811)
  hydrogen bonds       : bond        0.03590 (  678)
  hydrogen bonds       : angle       3.55319 ( 2004)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 57
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  237 TYR cc_start: 0.6105 (OUTLIER) cc_final: 0.5592 (m-10)
REVERT: A  249 MET cc_start: 0.9183 (mmm) cc_final: 0.8884 (mmm)
REVERT: A  290 ASN cc_start: 0.9091 (m-40) cc_final: 0.8750 (p0)
REVERT: B   72 HIS cc_start: 0.8751 (OUTLIER) cc_final: 0.8070 (m170)
REVERT: D  102 LEU cc_start: 0.9007 (mm) cc_final: 0.8615 (mm)
REVERT: D  526 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8513 (pp)
REVERT: D  608 MET cc_start: 0.8368 (ptt) cc_final: 0.7678 (ppp)
REVERT: E   81 MET cc_start: 0.8847 (ttm) cc_final: 0.8382 (tmm)
  outliers start: 33
  outliers final: 27
  residues processed: 85
  average time/residue: 0.0582
  time to fit residues: 8.4101
Evaluate side-chains
  83 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 53
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  237 TYR
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain C residue   31 GLU
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue   72 HIS
Chi-restraints excluded: chain D residue   61 ASN
Chi-restraints excluded: chain D residue  222 LEU
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  297 LEU
Chi-restraints excluded: chain D residue  341 CYS
Chi-restraints excluded: chain D residue  355 THR
Chi-restraints excluded: chain D residue  360 VAL
Chi-restraints excluded: chain D residue  377 VAL
Chi-restraints excluded: chain D residue  464 LEU
Chi-restraints excluded: chain D residue  516 LEU
Chi-restraints excluded: chain D residue  517 VAL
Chi-restraints excluded: chain D residue  526 LEU
Chi-restraints excluded: chain D residue  590 VAL
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain E residue  170 ILE
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue  153 LEU
Chi-restraints excluded: chain F residue  163 CYS
Chi-restraints excluded: chain F residue  183 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 129 optimal weight:    3.9990
   chunk 99 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 8 optimal weight:   20.0000
   chunk 94 optimal weight:    0.0770
   chunk 6 optimal weight:    0.9980
   chunk 107 optimal weight:    8.9990
   chunk 117 optimal weight:    3.9990
   overall best weight:    1.8144

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

Flipped N/Q/H residues before XYZ refinement:
D 334 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.059858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.044501 restraints weight = 58656.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.045750 restraints weight = 32120.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.046567 restraints weight = 21988.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.047111 restraints weight = 17322.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.047293 restraints weight = 14946.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.2529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10918  Z= 0.118
  Angle     :  0.542  10.862  14811  Z= 0.262
  Chirality :  0.038   0.148   1768
  Planarity :  0.003   0.047   1846
  Dihedral  :  3.379  20.253   1476
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 18.78 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.13 (0.24), residues: 1316
  helix:  2.61 (0.18), residues: 825
  sheet: -0.02 (0.62), residues: 72
  loop : -0.83 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 238 
 TYR   0.016   0.001   TYR F 190 
 PHE   0.008   0.001   PHE D 547 
 TRP   0.010   0.001   TRP A 380 
 HIS   0.004   0.001   HIS D 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (10918)
  covalent geometry    : angle       0.54196 (14811)
  hydrogen bonds       : bond        0.03293 (  678)
  hydrogen bonds       : angle       3.39132 ( 2004)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 55
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  237 TYR cc_start: 0.6034 (OUTLIER) cc_final: 0.5505 (m-10)
REVERT: A  249 MET cc_start: 0.9177 (mmm) cc_final: 0.8848 (mmm)
REVERT: A  290 ASN cc_start: 0.9071 (m-40) cc_final: 0.8735 (p0)
REVERT: B   72 HIS cc_start: 0.8789 (OUTLIER) cc_final: 0.8095 (m170)
REVERT: D  102 LEU cc_start: 0.8997 (mm) cc_final: 0.8620 (mm)
REVERT: D  526 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8499 (pp)
REVERT: D  608 MET cc_start: 0.8362 (ptt) cc_final: 0.7660 (ppp)
REVERT: E   81 MET cc_start: 0.8845 (ttm) cc_final: 0.8369 (tmm)
  outliers start: 28
  outliers final: 23
  residues processed: 78
  average time/residue: 0.0698
  time to fit residues: 8.9909
Evaluate side-chains
  81 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 55
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  237 TYR
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain C residue   31 GLU
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   72 HIS
Chi-restraints excluded: chain D residue  258 THR
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  297 LEU
Chi-restraints excluded: chain D residue  341 CYS
Chi-restraints excluded: chain D residue  355 THR
Chi-restraints excluded: chain D residue  360 VAL
Chi-restraints excluded: chain D residue  377 VAL
Chi-restraints excluded: chain D residue  464 LEU
Chi-restraints excluded: chain D residue  516 LEU
Chi-restraints excluded: chain D residue  526 LEU
Chi-restraints excluded: chain D residue  590 VAL
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain E residue  170 ILE
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   87 MET
Chi-restraints excluded: chain F residue  153 LEU
Chi-restraints excluded: chain F residue  183 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 122 optimal weight:    8.9990
   chunk 80 optimal weight:    8.9990
   chunk 34 optimal weight:   10.0000
   chunk 1 optimal weight:    6.9990
   chunk 46 optimal weight:    2.9990
   chunk 95 optimal weight:    6.9990
   chunk 8 optimal weight:   20.0000
   chunk 120 optimal weight:    0.6980
   chunk 70 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 36 optimal weight:    6.9990
   overall best weight:    3.9388

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

Flipped N/Q/H residues before XYZ refinement:
** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 539 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.059890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.044505 restraints weight = 57788.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.045753 restraints weight = 31886.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.046582 restraints weight = 21838.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.047129 restraints weight = 17214.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.047427 restraints weight = 14814.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.2645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  10918  Z= 0.211
  Angle     :  0.626  11.847  14811  Z= 0.306
  Chirality :  0.040   0.140   1768
  Planarity :  0.003   0.046   1846
  Dihedral  :  3.644  21.037   1476
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 18.60 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.95 (0.24), residues: 1316
  helix:  2.42 (0.18), residues: 827
  sheet: -0.21 (0.61), residues: 72
  loop : -0.80 (0.31), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 238 
 TYR   0.020   0.002   TYR F 190 
 PHE   0.012   0.001   PHE D 547 
 TRP   0.015   0.001   TRP F 156 
 HIS   0.004   0.001   HIS C  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 (10918)
  covalent geometry    : angle       0.62581 (14811)
  hydrogen bonds       : bond        0.03927 (  678)
  hydrogen bonds       : angle       3.70824 ( 2004)

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

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

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2632 Ramachandran restraints generated.
    1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 53
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  237 TYR cc_start: 0.6055 (OUTLIER) cc_final: 0.5597 (m-10)
REVERT: A  249 MET cc_start: 0.9185 (mmm) cc_final: 0.8887 (mmm)
REVERT: A  290 ASN cc_start: 0.9071 (m-40) cc_final: 0.8735 (p0)
REVERT: B   72 HIS cc_start: 0.8798 (OUTLIER) cc_final: 0.8075 (m170)
REVERT: D  102 LEU cc_start: 0.9046 (mm) cc_final: 0.8690 (mm)
REVERT: D  526 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8500 (pp)
REVERT: D  608 MET cc_start: 0.8292 (ptt) cc_final: 0.7609 (ppp)
REVERT: E   81 MET cc_start: 0.8884 (ttm) cc_final: 0.8343 (tmm)
  outliers start: 32
  outliers final: 26
  residues processed: 80
  average time/residue: 0.0640
  time to fit residues: 8.5650
Evaluate side-chains
  81 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 52
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  237 TYR
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain C residue   31 GLU
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue   72 HIS
Chi-restraints excluded: chain D residue   61 ASN
Chi-restraints excluded: chain D residue  246 THR
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  297 LEU
Chi-restraints excluded: chain D residue  341 CYS
Chi-restraints excluded: chain D residue  355 THR
Chi-restraints excluded: chain D residue  360 VAL
Chi-restraints excluded: chain D residue  377 VAL
Chi-restraints excluded: chain D residue  464 LEU
Chi-restraints excluded: chain D residue  516 LEU
Chi-restraints excluded: chain D residue  517 VAL
Chi-restraints excluded: chain D residue  526 LEU
Chi-restraints excluded: chain D residue  590 VAL
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain E residue  170 ILE
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue  153 LEU
Chi-restraints excluded: chain F residue  163 CYS
Chi-restraints excluded: chain F residue  183 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 133 optimal weight:   40.0000
   chunk 93 optimal weight:    1.9990
   chunk 57 optimal weight:    9.9990
   chunk 22 optimal weight:    2.9990
   chunk 125 optimal weight:    2.9990
   chunk 111 optimal weight:    6.9990
   chunk 99 optimal weight:    0.9980
   chunk 95 optimal weight:    1.9990
   chunk 109 optimal weight:    5.9990
   chunk 78 optimal weight:    4.9990
   chunk 77 optimal weight:    0.7980
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
D 334 HIS
D 370 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.059605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.044317 restraints weight = 58110.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.045565 restraints weight = 31946.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.046377 restraints weight = 21892.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.046852 restraints weight = 17239.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.047247 restraints weight = 14946.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.2692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10918  Z= 0.120
  Angle     :  0.564  12.052  14811  Z= 0.272
  Chirality :  0.038   0.187   1768
  Planarity :  0.003   0.047   1846
  Dihedral  :  3.445  20.430   1476
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 19.32 %
    Favored  : 78.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.14 (0.24), residues: 1316
  helix:  2.58 (0.18), residues: 826
  sheet: -0.05 (0.61), residues: 72
  loop : -0.76 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  99 
 TYR   0.017   0.001   TYR F 190 
 PHE   0.008   0.001   PHE D 547 
 TRP   0.011   0.001   TRP D  14 
 HIS   0.004   0.001   HIS D 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (10918)
  covalent geometry    : angle       0.56412 (14811)
  hydrogen bonds       : bond        0.03377 (  678)
  hydrogen bonds       : angle       3.44467 ( 2004)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1556.76 seconds
wall clock time: 27 minutes 41.58 seconds (1661.58 seconds total)