Starting phenix.real_space_refine
on Sun Aug 24 18:08:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8bwc_16282/08_2025/8bwc_16282.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bwc_16282/08_2025/8bwc_16282.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8bwc_16282/08_2025/8bwc_16282.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bwc_16282/08_2025/8bwc_16282.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bwc_16282/08_2025/8bwc_16282.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bwc_16282/08_2025/8bwc_16282.cif"
  }
  resolution = 3.5
  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=  -0.013 sd=   0.031
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: 5
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    7100      2.51       5
     N    1917      2.21       5
     O    2217      1.98       5
     H   10846      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 22112
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 10923
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 706, 10923
          Classifications: {'peptide': 706}
          Link IDs: {'PTRANS': 27, 'TRANS': 678}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 5445
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 366, 5445
          Classifications: {'peptide': 366}
          Link IDs: {'PTRANS': 11, 'TRANS': 354}
    Chain: "C"
      Number of atoms: 933
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 933
          Classifications: {'peptide': 65}
          Link IDs: {'PTRANS': 7, 'TRANS': 57}
    Chain: "D"
      Number of atoms: 3460
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 3460
          Classifications: {'peptide': 218}
          Link IDs: {'PTRANS': 12, 'TRANS': 205}
    Chain: "E"
      Number of atoms: 1351
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 1351
          Classifications: {'peptide': 87}
          Link IDs: {'PTRANS': 5, 'TRANS': 81}
  Time building chain proxies: 2.96, per 1000 atoms: 0.13
  Number of scatterers: 22112
  At special positions: 0
  Unit cell: (114.7, 126.54, 138.38, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      32     16.00
     O    2217      8.00
     N    1917      7.00
     C    7100      6.00
     H   10846      1.00
    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: 1.51
  Conformation dependent library (CDL) restraints added in 611.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2634

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 17 sheets defined
      24.6% alpha, 28.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 106 through 117
      removed outlier: 3.618A  pdb=" N   SER A 117 " --> pdb=" O   ASN A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 128
      No H-bonds generated for 'chain 'A' and resid 126 through 128'
    Processing helix  chain 'A' and resid 129 through 141
      removed outlier: 3.705A  pdb=" N   TYR A 141 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 144
      No H-bonds generated for 'chain 'A' and resid 142 through 144'
    Processing helix  chain 'A' and resid 189 through 196
      removed outlier: 3.887A  pdb=" N   HIS A 196 " --> pdb=" O   GLU A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 232
      removed outlier: 3.796A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A 216 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLY A 221 " --> pdb=" O   GLN A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 288
    Processing helix  chain 'A' and resid 297 through 315
      removed outlier: 3.851A  pdb=" N   TYR A 315 " --> pdb=" O   LEU A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 367
    Processing helix  chain 'A' and resid 378 through 393
      removed outlier: 3.503A  pdb=" N   LYS A 386 " --> pdb=" O   VAL A 382 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   GLY A 393 " --> pdb=" O   LEU A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 452
    Processing helix  chain 'A' and resid 542 through 552
      removed outlier: 4.077A  pdb=" N   TYR A 548 " --> pdb=" O   ALA A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 651
    Processing helix  chain 'A' and resid 726 through 731
      removed outlier: 3.613A  pdb=" N   ALA A 730 " --> pdb=" O   ASP A 727 " (cutoff:3.500A)
      removed outlier: 5.566A  pdb=" N   ASN A 731 " --> pdb=" O   LYS A 728 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 39 through 44
      removed outlier: 3.569A  pdb=" N   ALA C  44 " --> pdb=" O   TYR C  41 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 59 through 63
      removed outlier: 3.743A  pdb=" N   GLY C  63 " --> pdb=" O   VAL C  60 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 80
    Processing helix  chain 'D' and resid 31 through 46
      removed outlier: 3.608A  pdb=" N   ILE D  35 " --> pdb=" O   PRO D  31 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 47 through 62
    Processing helix  chain 'D' and resid 65 through 68
    Processing helix  chain 'D' and resid 69 through 82
    Processing helix  chain 'D' and resid 84 through 99
    Processing helix  chain 'D' and resid 104 through 119
      removed outlier: 3.672A  pdb=" N   VAL D 108 " --> pdb=" O   ASN D 104 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 123 through 128
    Processing helix  chain 'D' and resid 131 through 135
      removed outlier: 4.405A  pdb=" N   ASP D 134 " --> pdb=" O   ASP D 131 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 137 through 154
    Processing helix  chain 'D' and resid 159 through 188
      removed outlier: 3.875A  pdb=" N   ASP D 172 " --> pdb=" O   VAL D 168 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LYS D 176 " --> pdb=" O   ASP D 172 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   TYR D 177 " --> pdb=" O   ARG D 173 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 190 through 205
    Processing helix  chain 'D' and resid 208 through 225
      removed outlier: 3.630A  pdb=" N   ARG D 212 " --> pdb=" O   THR D 208 " (cutoff:3.500A)
      Proline residue:  D 216  - end of helix
      removed outlier: 3.515A  pdb=" N   GLU D 219 " --> pdb=" O   LEU D 215 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   MET D 225 " --> pdb=" O   ALA D 221 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 227 through 241
      removed outlier: 4.398A  pdb=" N   LYS D 233 " --> pdb=" O   ALA D 229 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   VAL D 234 " --> pdb=" O   GLN D 230 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 41 through 46
      removed outlier: 3.768A  pdb=" N   ILE E  46 " --> pdb=" O   ASP E  42 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 60
    Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 100
      removed outlier: 4.511A  pdb=" N   ILE A  94 " --> pdb=" O   VAL A 163 " (cutoff:3.500A)
      removed outlier: 7.207A  pdb=" N   LEU A 165 " --> pdb=" O   ILE A  94 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   SER A  96 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 8.054A  pdb=" N   LEU A 167 " --> pdb=" O   SER A  96 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   THR A  98 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.977A  pdb=" N   PHE A 169 " --> pdb=" O   THR A  98 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   SER A 100 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 176 through 183
      removed outlier: 6.304A  pdb=" N   GLU A 176 " --> pdb=" O   ILE A 254 " (cutoff:3.500A)
      removed outlier: 7.957A  pdb=" N   VAL A 256 " --> pdb=" O   GLU A 176 " (cutoff:3.500A)
      removed outlier: 8.305A  pdb=" N   GLN A 178 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 12.788A  pdb=" N   VAL A 258 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
      removed outlier: 9.991A  pdb=" N   ILE A 180 " --> pdb=" O   VAL A 258 " (cutoff:3.500A)
      removed outlier: 12.008A  pdb=" N   ILE A 260 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 9.607A  pdb=" N   ILE A 182 " --> pdb=" O   ILE A 260 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   SER A 242 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   THR A 261 " --> pdb=" O   ILE A 240 " (cutoff:3.500A)
      removed outlier: 5.765A  pdb=" N   ILE A 240 " --> pdb=" O   THR A 261 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   SER B 193 " --> pdb=" O   VAL A 245 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 276
      removed outlier: 6.055A  pdb=" N   LYS A 267 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 7.492A  pdb=" N   LEU A 337 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
      removed outlier: 8.401A  pdb=" N   SER A 269 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 12.297A  pdb=" N   VAL A 339 " --> pdb=" O   SER A 269 " (cutoff:3.500A)
      removed outlier: 9.397A  pdb=" N   VAL A 271 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 11.406A  pdb=" N   VAL A 341 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      removed outlier: 9.192A  pdb=" N   VAL A 273 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ARG A 338 " --> pdb=" O   MET A 325 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 349 through 355
      removed outlier: 7.565A  pdb=" N   VAL A 414 " --> pdb=" O   ARG A 350 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   ILE A 352 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   TYR A 416 " --> pdb=" O   ILE A 352 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   PHE A 354 " --> pdb=" O   TYR A 416 " (cutoff:3.500A)
      removed outlier: 7.299A  pdb=" N   VAL A 418 " --> pdb=" O   PHE A 354 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   VAL A 415 " --> pdb=" O   THR A 400 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   THR A 400 " --> pdb=" O   VAL A 415 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   LYS A 417 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   VAL A 398 " --> pdb=" O   LYS A 417 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   LYS A 419 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 425 through 426
      removed outlier: 3.507A  pdb=" N   GLN A 441 " --> pdb=" O   GLY A 429 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 426
      removed outlier: 3.513A  pdb=" N   PHE A 440 " --> pdb=" O   LYS A 462 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   PHE A 490 " --> pdb=" O   GLY A 510 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ARG A 526 " --> pdb=" O   GLY A 575 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   GLY A 575 " --> pdb=" O   ARG A 526 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   TYR A 574 " --> pdb=" O   GLY A 597 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLY A 597 " --> pdb=" O   TYR A 574 " (cutoff:3.500A)
      removed outlier: 5.608A  pdb=" N   TYR A 608 " --> pdb=" O   THR A 600 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   THR A 633 " --> pdb=" O   THR A 615 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   THR A 735 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   MET A 768 " --> pdb=" O   PHE A 791 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   PHE A 791 " --> pdb=" O   MET A 768 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 48 through 51
      removed outlier: 5.171A  pdb=" N   TRP B  48 " --> pdb=" O   SER B 389 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   SER B 389 " --> pdb=" O   TRP B  48 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   LEU B 378 " --> pdb=" O   ILE B 390 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 68
      removed outlier: 3.628A  pdb=" N   TRP B  93 " --> pdb=" O   ALA B  83 " (cutoff:3.500A)
      removed outlier: 5.526A  pdb=" N   ASN B  85 " --> pdb=" O   GLU B  91 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   GLU B  91 " --> pdb=" O   ASN B  85 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 99 through 100
      removed outlier: 3.511A  pdb=" N   GLU B  99 " --> pdb=" O   GLU B 107 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 116 through 118
      removed outlier: 6.660A  pdb=" N   VAL B 131 " --> pdb=" O   GLN B 144 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   GLN B 144 " --> pdb=" O   VAL B 131 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   ALA B 133 " --> pdb=" O   ALA B 142 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 157
      removed outlier: 4.045A  pdb=" N   TRP B 183 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 203
      removed outlier: 3.936A  pdb=" N   TRP B 228 " --> pdb=" O   ALA B 218 " (cutoff:3.500A)
      removed outlier: 5.754A  pdb=" N   LEU B 220 " --> pdb=" O   MET B 226 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   MET B 226 " --> pdb=" O   LEU B 220 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 254
      removed outlier: 6.566A  pdb=" N   LEU B 267 " --> pdb=" O   LYS B 280 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   LYS B 280 " --> pdb=" O   LEU B 267 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   ALA B 269 " --> pdb=" O   MET B 278 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 290 through 292
      removed outlier: 3.744A  pdb=" N   TRP B 317 " --> pdb=" O   ALA B 307 " (cutoff:3.500A)
      removed outlier: 6.115A  pdb=" N   THR B 309 " --> pdb=" O   THR B 315 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   THR B 315 " --> pdb=" O   THR B 309 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 333
      removed outlier: 6.580A  pdb=" N   LEU B 346 " --> pdb=" O   GLN B 359 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   GLN B 359 " --> pdb=" O   LEU B 346 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   TRP B 348 " --> pdb=" O   VAL B 357 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 32 through 35
      removed outlier: 4.176A  pdb=" N   MET E  64 " --> pdb=" O   PHE E  74 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 35

    474 hydrogen bonds defined for protein.
    1284 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: 4.64

  Time building geometry restraints manager: 2.12 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 10843
        1.03 -     1.23: 29
        1.23 -     1.42: 4962
        1.42 -     1.62: 6467
        1.62 -     1.81: 61
  Bond restraints: 22362
  Sorted by residual:
  bond pdb=" N   TYR E  28 "
       pdb=" CA  TYR E  28 "
    ideal  model  delta    sigma   weight residual
    1.458  1.498 -0.041 1.16e-02 7.43e+03 1.24e+01
  bond pdb=" N   VAL B 357 "
       pdb=" CA  VAL B 357 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.23e-02 6.61e+03 9.43e+00
  bond pdb=" N   VAL B 362 "
       pdb=" CA  VAL B 362 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.25e-02 6.40e+03 8.85e+00
  bond pdb=" N   VAL B 147 "
       pdb=" CA  VAL B 147 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.86e+00
  bond pdb=" N   PHE B 356 "
       pdb=" CA  PHE B 356 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.034 1.23e-02 6.61e+03 7.86e+00
  ... (remaining 22357 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 37020
        2.05 -     4.10: 3044
        4.10 -     6.16: 140
        6.16 -     8.21: 8
        8.21 -    10.26: 1
  Bond angle restraints: 40213
  Sorted by residual:
  angle pdb=" N   ASP C  38 "
        pdb=" CA  ASP C  38 "
        pdb=" C   ASP C  38 "
      ideal   model   delta    sigma   weight residual
     108.00  116.00   -8.00 1.48e+00 4.57e-01 2.92e+01
  angle pdb=" N   ARG A 370 "
        pdb=" CA  ARG A 370 "
        pdb=" C   ARG A 370 "
      ideal   model   delta    sigma   weight residual
     113.97  107.57    6.40 1.28e+00 6.10e-01 2.50e+01
  angle pdb=" N   ARG D 173 "
        pdb=" CA  ARG D 173 "
        pdb=" C   ARG D 173 "
      ideal   model   delta    sigma   weight residual
     113.23  107.15    6.08 1.24e+00 6.50e-01 2.40e+01
  angle pdb=" N   ARG B  77 "
        pdb=" CA  ARG B  77 "
        pdb=" C   ARG B  77 "
      ideal   model   delta    sigma   weight residual
     112.86  106.91    5.95 1.22e+00 6.72e-01 2.38e+01
  angle pdb=" N   LYS B 361 "
        pdb=" CA  LYS B 361 "
        pdb=" C   LYS B 361 "
      ideal   model   delta    sigma   weight residual
     110.44  104.90    5.54 1.20e+00 6.94e-01 2.13e+01
  ... (remaining 40208 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 9741
       17.95 -    35.89: 592
       35.89 -    53.84: 213
       53.84 -    71.78: 62
       71.78 -    89.73: 15
  Dihedral angle restraints: 10623
    sinusoidal: 5712
      harmonic: 4911
  Sorted by residual:
  dihedral pdb=" CD  ARG A 346 "
           pdb=" NE  ARG A 346 "
           pdb=" CZ  ARG A 346 "
           pdb=" NH1 ARG A 346 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -56.24   56.24     1      1.00e+01 1.00e-02 4.27e+01
  dihedral pdb=" CA  GLN A 446 "
           pdb=" C   GLN A 446 "
           pdb=" N   ASP A 447 "
           pdb=" CA  ASP A 447 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.63   22.37     0      5.00e+00 4.00e-02 2.00e+01
  dihedral pdb=" CA  VAL E  26 "
           pdb=" C   VAL E  26 "
           pdb=" N   VAL E  27 "
           pdb=" CA  VAL E  27 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.63  -19.37     0      5.00e+00 4.00e-02 1.50e+01
  ... (remaining 10620 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1140
       0.035 -    0.070: 356
       0.070 -    0.105: 115
       0.105 -    0.141: 80
       0.141 -    0.176: 9
  Chirality restraints: 1700
  Sorted by residual:
  chirality pdb=" CA  MET B  32 "
            pdb=" N   MET B  32 "
            pdb=" C   MET B  32 "
            pdb=" CB  MET B  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 7.73e-01
  chirality pdb=" CA  VAL B 147 "
            pdb=" N   VAL B 147 "
            pdb=" C   VAL B 147 "
            pdb=" CB  VAL B 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.38e-01
  chirality pdb=" CA  LEU B 192 "
            pdb=" N   LEU B 192 "
            pdb=" C   LEU B 192 "
            pdb=" CB  LEU B 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.75e-01
  ... (remaining 1697 not shown)

  Planarity restraints: 3435
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 346 "    0.948 9.50e-02 1.11e+02   3.17e-01 1.06e+02
        pdb=" NE  ARG A 346 "   -0.041 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 346 "   -0.020 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 346 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 346 "    0.002 2.00e-02 2.50e+03
        pdb="HH11 ARG A 346 "   -0.007 2.00e-02 2.50e+03
        pdb="HH12 ARG A 346 "    0.010 2.00e-02 2.50e+03
        pdb="HH21 ARG A 346 "    0.002 2.00e-02 2.50e+03
        pdb="HH22 ARG A 346 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  77 "   -0.338 9.50e-02 1.11e+02   1.13e-01 1.43e+01
        pdb=" NE  ARG B  77 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  77 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  77 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  77 "   -0.001 2.00e-02 2.50e+03
        pdb="HH11 ARG B  77 "    0.016 2.00e-02 2.50e+03
        pdb="HH12 ARG B  77 "   -0.007 2.00e-02 2.50e+03
        pdb="HH21 ARG B  77 "    0.011 2.00e-02 2.50e+03
        pdb="HH22 ARG B  77 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 212 "   -0.338 9.50e-02 1.11e+02   1.13e-01 1.39e+01
        pdb=" NE  ARG A 212 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 212 "    0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 212 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 212 "   -0.001 2.00e-02 2.50e+03
        pdb="HH11 ARG A 212 "   -0.002 2.00e-02 2.50e+03
        pdb="HH12 ARG A 212 "   -0.001 2.00e-02 2.50e+03
        pdb="HH21 ARG A 212 "   -0.007 2.00e-02 2.50e+03
        pdb="HH22 ARG A 212 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 3432 not shown)

  Histogram of nonbonded interaction distances:
        1.39 -     2.03: 311
        2.03 -     2.67: 31681
        2.67 -     3.32: 61427
        3.32 -     3.96: 78771
        3.96 -     4.60: 124421
  Nonbonded interactions: 296611
  Sorted by model distance:
  nonbonded pdb=" H   GLY B  55 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     1.391 2.450
  nonbonded pdb=" OD2 ASP B 300 "
            pdb="HD22 ASN B 302 "
     model   vdw
     1.469 2.450
  nonbonded pdb=" HG  SER B 112 "
            pdb=" OE2 GLU B 127 "
     model   vdw
     1.508 2.450
  nonbonded pdb=" O   TYR A 548 "
            pdb=" HG  SER A 551 "
     model   vdw
     1.539 2.450
  nonbonded pdb=" OD2 ASP B 303 "
            pdb=" H   LEU B 326 "
     model   vdw
     1.544 2.450
  ... (remaining 296606 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=0.00 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.080
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     17.190
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
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   0.041  11516  Z= 0.223
  Angle     :  0.686   7.999  15654  Z= 0.434
  Chirality :  0.045   0.176   1700
  Planarity :  0.012   0.412   2062
  Dihedral  : 13.350  89.727   4165
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  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 aren not related in a simple way.
  whole: -0.72 (0.22), residues: 1428
  helix:  0.61 (0.30), residues: 304
  sheet: -0.57 (0.24), residues: 443
  loop : -0.82 (0.24), residues: 681

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  77 
 TYR   0.018   0.001   TYR A 230 
 PHE   0.020   0.001   PHE A 347 
 TRP   0.012   0.001   TRP A 745 
 HIS   0.002   0.001   HIS B 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (11516)
  covalent geometry    : angle       0.68603 (15654)
  hydrogen bonds       : bond        0.21240 (  468)
  hydrogen bonds       : angle       8.00184 ( 1284)

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.546 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  306 MET cc_start: 0.7140 (ptp) cc_final: 0.6940 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.2125
  time to fit residues: 46.2810
Evaluate side-chains
  116 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    0.5980
   chunk 103 optimal weight:    7.9990
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    9.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    2.4786

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

Flipped N/Q/H residues before XYZ refinement:
A 753 GLN
B 266 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.170909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 87)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.106528 restraints weight = 37630.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.111602 restraints weight = 18171.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.114727 restraints weight = 12073.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.116486 restraints weight = 9616.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 55)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.117514 restraints weight = 8478.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.1479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  11516  Z= 0.212
  Angle     :  0.575   4.920  15654  Z= 0.316
  Chirality :  0.044   0.147   1700
  Planarity :  0.004   0.053   2062
  Dihedral  :  4.695  22.323   1580
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  5.80 %
    Favored  : 93.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.68 (0.22), residues: 1428
  helix:  0.77 (0.30), residues: 305
  sheet: -0.44 (0.24), residues: 450
  loop : -0.96 (0.24), residues: 673

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 346 
 TYR   0.017   0.002   TYR A 585 
 PHE   0.015   0.002   PHE A 347 
 TRP   0.012   0.001   TRP A 745 
 HIS   0.002   0.001   HIS A 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 (11516)
  covalent geometry    : angle       0.57460 (15654)
  hydrogen bonds       : bond        0.05412 (  468)
  hydrogen bonds       : angle       5.53076 ( 1284)

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 124
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   30 ASN cc_start: 0.7654 (m-40) cc_final: 0.7207 (m110)
REVERT: E   64 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8739 (mtp)
  outliers start: 13
  outliers final: 11
  residues processed: 131
  average time/residue: 0.2231
  time to fit residues: 40.2588
Evaluate side-chains
  124 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  568 ASP
Chi-restraints excluded: chain A residue  591 SER
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  266 ASN
Chi-restraints excluded: chain B residue  353 ASP
Chi-restraints excluded: chain C residue   38 ASP
Chi-restraints excluded: chain E residue   36 ASN
Chi-restraints excluded: chain E residue   64 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 14 optimal weight:    0.1980
   chunk 63 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 97 optimal weight:    9.9990
   chunk 98 optimal weight:    3.9990
   chunk 120 optimal weight:    2.9990
   chunk 46 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    1.8388

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

Flipped N/Q/H residues before XYZ refinement:
B  64 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.173108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.113283 restraints weight = 37419.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.114999 restraints weight = 18631.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.115533 restraints weight = 12756.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.116516 restraints weight = 12447.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.116742 restraints weight = 11144.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  11516  Z= 0.159
  Angle     :  0.516   5.240  15654  Z= 0.281
  Chirality :  0.043   0.151   1700
  Planarity :  0.004   0.040   2062
  Dihedral  :  4.448  21.384   1580
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.22 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  6.71 %
    Favored  : 92.13 %
  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 aren not related in a simple way.
  whole: -0.50 (0.22), residues: 1428
  helix:  1.02 (0.30), residues: 305
  sheet: -0.30 (0.24), residues: 440
  loop : -0.92 (0.24), residues: 683

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 421 
 TYR   0.015   0.001   TYR D 184 
 PHE   0.011   0.001   PHE A 791 
 TRP   0.010   0.001   TRP A 745 
 HIS   0.002   0.001   HIS A 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (11516)
  covalent geometry    : angle       0.51647 (15654)
  hydrogen bonds       : bond        0.04611 (  468)
  hydrogen bonds       : angle       5.12138 ( 1284)

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8327 (mm-30)
REVERT: A  189 THR cc_start: 0.8847 (m) cc_final: 0.8439 (p)
REVERT: B  353 ASP cc_start: 0.4056 (OUTLIER) cc_final: 0.3835 (m-30)
REVERT: D   30 ASN cc_start: 0.7621 (m-40) cc_final: 0.7193 (m110)
REVERT: E   64 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8693 (mtp)
  outliers start: 14
  outliers final: 11
  residues processed: 127
  average time/residue: 0.2189
  time to fit residues: 38.9951
Evaluate side-chains
  124 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 111
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  286 GLN
Chi-restraints excluded: chain A residue  463 ASN
Chi-restraints excluded: chain A residue  569 ASP
Chi-restraints excluded: chain A residue  591 SER
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  353 ASP
Chi-restraints excluded: chain E residue   36 ASN
Chi-restraints excluded: chain E residue   64 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 122 optimal weight:    0.5980
   chunk 80 optimal weight:    6.9990
   chunk 78 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 130 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 89 optimal weight:    9.9990
   chunk 55 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 17 optimal weight:    5.9990
   chunk 129 optimal weight:    0.5980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 244 GLN
B 168 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.173030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.108756 restraints weight = 37166.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.113958 restraints weight = 17919.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.117187 restraints weight = 11863.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.118998 restraints weight = 9399.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.120126 restraints weight = 8261.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.2192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11516  Z= 0.121
  Angle     :  0.476   4.445  15654  Z= 0.257
  Chirality :  0.042   0.148   1700
  Planarity :  0.003   0.038   2062
  Dihedral  :  4.185  20.474   1580
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.01 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  7.54 %
    Favored  : 91.47 %
  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 aren not related in a simple way.
  whole: -0.31 (0.22), residues: 1428
  helix:  1.28 (0.30), residues: 307
  sheet: -0.12 (0.24), residues: 435
  loop : -0.91 (0.24), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 355 
 TYR   0.014   0.001   TYR D 184 
 PHE   0.009   0.001   PHE A 718 
 TRP   0.009   0.001   TRP B  93 
 HIS   0.003   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (11516)
  covalent geometry    : angle       0.47561 (15654)
  hydrogen bonds       : bond        0.03934 (  468)
  hydrogen bonds       : angle       4.77006 ( 1284)

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8317 (mm-30)
REVERT: A  147 TYR cc_start: 0.8445 (m-80) cc_final: 0.8228 (m-80)
REVERT: A  189 THR cc_start: 0.8772 (m) cc_final: 0.8325 (p)
REVERT: B  266 ASN cc_start: 0.6772 (m-40) cc_final: 0.6494 (t0)
REVERT: D   30 ASN cc_start: 0.7615 (m-40) cc_final: 0.7372 (m110)
REVERT: E   64 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8651 (mtp)
  outliers start: 12
  outliers final: 9
  residues processed: 122
  average time/residue: 0.2199
  time to fit residues: 37.4469
Evaluate side-chains
  120 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  286 GLN
Chi-restraints excluded: chain A residue  591 SER
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  353 ASP
Chi-restraints excluded: chain E residue   36 ASN
Chi-restraints excluded: chain E residue   64 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 77 optimal weight:   10.0000
   chunk 16 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 105 optimal weight:    6.9990
   chunk 21 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 117 optimal weight:    3.9990
   chunk 91 optimal weight:    7.9990
   chunk 40 optimal weight:    3.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
B 168 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.167363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.103929 restraints weight = 37320.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.108745 restraints weight = 18696.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.111660 restraints weight = 12666.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.113246 restraints weight = 10221.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.114332 restraints weight = 9063.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.2382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047  11516  Z= 0.238
  Angle     :  0.548   4.935  15654  Z= 0.300
  Chirality :  0.045   0.144   1700
  Planarity :  0.004   0.050   2062
  Dihedral  :  4.502  21.965   1580
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.62 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  7.87 %
    Favored  : 90.64 %
  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 aren not related in a simple way.
  whole: -0.54 (0.22), residues: 1428
  helix:  1.01 (0.30), residues: 305
  sheet: -0.22 (0.24), residues: 434
  loop : -1.04 (0.23), residues: 689

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 166 
 TYR   0.016   0.002   TYR A 585 
 PHE   0.019   0.002   PHE A 791 
 TRP   0.014   0.001   TRP A 745 
 HIS   0.005   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00569 (11516)
  covalent geometry    : angle       0.54850 (15654)
  hydrogen bonds       : bond        0.04808 (  468)
  hydrogen bonds       : angle       4.98121 ( 1284)

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 THR cc_start: 0.8935 (m) cc_final: 0.8559 (p)
REVERT: D   30 ASN cc_start: 0.7705 (m-40) cc_final: 0.7453 (m110)
REVERT: E   64 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8771 (mtp)
  outliers start: 18
  outliers final: 14
  residues processed: 127
  average time/residue: 0.2387
  time to fit residues: 42.2538
Evaluate side-chains
  127 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  463 ASN
Chi-restraints excluded: chain A residue  569 ASP
Chi-restraints excluded: chain A residue  591 SER
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  198 SER
Chi-restraints excluded: chain B residue  353 ASP
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain C residue   38 ASP
Chi-restraints excluded: chain C residue   49 GLU
Chi-restraints excluded: chain E residue   36 ASN
Chi-restraints excluded: chain E residue   64 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 123 optimal weight:    0.0670
   chunk 122 optimal weight:    1.9990
   chunk 81 optimal weight:    9.9990
   chunk 102 optimal weight:   10.0000
   chunk 101 optimal weight:    4.9990
   chunk 106 optimal weight:   10.0000
   chunk 27 optimal weight:    0.8980
   chunk 75 optimal weight:    8.9990
   chunk 120 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 121 optimal weight:    0.9990
   overall best weight:    0.9522

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

Flipped N/Q/H residues before XYZ refinement:
A 113 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.171709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.108892 restraints weight = 37083.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.114084 restraints weight = 17338.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.117245 restraints weight = 11327.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.119104 restraints weight = 8940.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.120073 restraints weight = 7816.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.2543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  11516  Z= 0.103
  Angle     :  0.464   4.140  15654  Z= 0.250
  Chirality :  0.042   0.168   1700
  Planarity :  0.003   0.056   2062
  Dihedral  :  4.113  20.741   1580
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.45 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  8.86 %
    Favored  : 90.06 %
  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 aren not related in a simple way.
  whole: -0.26 (0.22), residues: 1428
  helix:  1.36 (0.31), residues: 306
  sheet: -0.06 (0.25), residues: 435
  loop : -0.91 (0.24), residues: 687

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 355 
 TYR   0.014   0.001   TYR D 184 
 PHE   0.010   0.001   PHE A 354 
 TRP   0.009   0.001   TRP B  93 
 HIS   0.002   0.000   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (11516)
  covalent geometry    : angle       0.46408 (15654)
  hydrogen bonds       : bond        0.03696 (  468)
  hydrogen bonds       : angle       4.60527 ( 1284)

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.629 
Fit side-chains
   revert: symmetry clash
REVERT: A  138 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8453 (mm-30)
REVERT: A  189 THR cc_start: 0.8826 (m) cc_final: 0.8409 (p)
REVERT: B   32 MET cc_start: 0.5002 (tpt) cc_final: 0.4231 (tpt)
REVERT: B  306 MET cc_start: 0.6464 (ptp) cc_final: 0.6022 (ptp)
REVERT: E   64 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8683 (mtp)
  outliers start: 13
  outliers final: 11
  residues processed: 121
  average time/residue: 0.2940
  time to fit residues: 49.1435
Evaluate side-chains
  125 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain A residue  569 ASP
Chi-restraints excluded: chain A residue  591 SER
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  198 SER
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  353 ASP
Chi-restraints excluded: chain E residue   36 ASN
Chi-restraints excluded: chain E residue   64 MET
Chi-restraints excluded: chain E residue   90 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 131 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9990
   chunk 95 optimal weight:   10.0000
   chunk 91 optimal weight:    5.9990
   chunk 138 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 3 optimal weight:    9.9990
   chunk 139 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.0986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.171198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.110857 restraints weight = 37334.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.113626 restraints weight = 19010.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.117183 restraints weight = 12116.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.118023 restraints weight = 10066.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.117885 restraints weight = 8818.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.2670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  11516  Z= 0.111
  Angle     :  0.457   4.148  15654  Z= 0.246
  Chirality :  0.042   0.146   1700
  Planarity :  0.003   0.033   2062
  Dihedral  :  3.970  20.085   1580
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.15 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  8.95 %
    Favored  : 89.81 %
  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 aren not related in a simple way.
  whole: -0.20 (0.23), residues: 1428
  helix:  1.51 (0.31), residues: 306
  sheet: -0.17 (0.25), residues: 434
  loop : -0.81 (0.24), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 355 
 TYR   0.014   0.001   TYR D 184 
 PHE   0.008   0.001   PHE A 791 
 TRP   0.009   0.001   TRP B  93 
 HIS   0.003   0.000   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (11516)
  covalent geometry    : angle       0.45662 (15654)
  hydrogen bonds       : bond        0.03599 (  468)
  hydrogen bonds       : angle       4.49489 ( 1284)

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.623 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 THR cc_start: 0.8800 (m) cc_final: 0.8371 (p)
REVERT: B   32 MET cc_start: 0.4967 (tpt) cc_final: 0.4211 (tpt)
REVERT: B  306 MET cc_start: 0.6376 (ptp) cc_final: 0.5904 (ptp)
REVERT: B  353 ASP cc_start: 0.4109 (OUTLIER) cc_final: 0.3877 (m-30)
REVERT: E   64 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8685 (mtp)
  outliers start: 15
  outliers final: 11
  residues processed: 122
  average time/residue: 0.2965
  time to fit residues: 50.2290
Evaluate side-chains
  125 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 GLN
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  569 ASP
Chi-restraints excluded: chain A residue  591 SER
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  198 SER
Chi-restraints excluded: chain B residue  353 ASP
Chi-restraints excluded: chain E residue   36 ASN
Chi-restraints excluded: chain E residue   64 MET
Chi-restraints excluded: chain E residue   90 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   chunk 105 optimal weight:    6.9990
   chunk 110 optimal weight:    0.4980
   chunk 70 optimal weight:   10.0000
   chunk 85 optimal weight:   10.0000
   chunk 8 optimal weight:    5.9990
   chunk 65 optimal weight:    5.9990
   chunk 92 optimal weight:    5.9990
   chunk 87 optimal weight:    5.9990
   chunk 95 optimal weight:   10.0000
   overall best weight:    4.0988

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

Flipped N/Q/H residues before XYZ refinement:
D  70 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.165242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.101468 restraints weight = 37510.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.106315 restraints weight = 18649.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.109255 restraints weight = 12585.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.110990 restraints weight = 10113.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.111843 restraints weight = 8952.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.2795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.059  11516  Z= 0.320
  Angle     :  0.603   5.645  15654  Z= 0.333
  Chirality :  0.047   0.153   1700
  Planarity :  0.005   0.062   2062
  Dihedral  :  4.655  22.817   1580
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  :  8.70 %
    Favored  : 89.31 %
  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 aren not related in a simple way.
  whole: -0.83 (0.22), residues: 1428
  helix:  0.86 (0.30), residues: 305
  sheet: -0.46 (0.24), residues: 446
  loop : -1.23 (0.23), residues: 677

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 166 
 TYR   0.020   0.002   TYR A 585 
 PHE   0.025   0.002   PHE A 791 
 TRP   0.015   0.001   TRP A 745 
 HIS   0.006   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00765 (11516)
  covalent geometry    : angle       0.60299 (15654)
  hydrogen bonds       : bond        0.05189 (  468)
  hydrogen bonds       : angle       5.04651 ( 1284)

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 119
  time to evaluate  : 0.666 
Fit side-chains
   revert: symmetry clash
REVERT: A  138 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8511 (mm-30)
REVERT: A  189 THR cc_start: 0.9027 (m) cc_final: 0.8689 (p)
REVERT: A  230 TYR cc_start: 0.8867 (OUTLIER) cc_final: 0.8354 (m-80)
REVERT: B   32 MET cc_start: 0.5082 (tpt) cc_final: 0.4290 (tpt)
REVERT: B  306 MET cc_start: 0.6741 (ptp) cc_final: 0.6463 (ptp)
  outliers start: 24
  outliers final: 19
  residues processed: 134
  average time/residue: 0.2661
  time to fit residues: 50.7489
Evaluate side-chains
  136 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain A residue  463 ASN
Chi-restraints excluded: chain A residue  569 ASP
Chi-restraints excluded: chain A residue  589 ASP
Chi-restraints excluded: chain A residue  591 SER
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  198 SER
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  353 ASP
Chi-restraints excluded: chain C residue   38 ASP
Chi-restraints excluded: chain C residue   49 GLU
Chi-restraints excluded: chain E residue   36 ASN
Chi-restraints excluded: chain E residue   90 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 132 optimal weight:    0.9980
   chunk 31 optimal weight:    0.4980
   chunk 15 optimal weight:    2.9990
   chunk 89 optimal weight:    8.9990
   chunk 16 optimal weight:    0.9990
   chunk 98 optimal weight:    9.9990
   chunk 124 optimal weight:    1.9990
   chunk 133 optimal weight:    0.8980
   chunk 108 optimal weight:    3.9990
   chunk 139 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B  70 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.170105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.107734 restraints weight = 37051.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.112745 restraints weight = 17838.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.115778 restraints weight = 11842.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.117593 restraints weight = 9421.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.118574 restraints weight = 8268.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.2870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  11516  Z= 0.100
  Angle     :  0.469   6.270  15654  Z= 0.252
  Chirality :  0.042   0.144   1700
  Planarity :  0.003   0.036   2062
  Dihedral  :  4.103  21.215   1580
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  9.94 %
    Favored  : 88.73 %
  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 aren not related in a simple way.
  whole: -0.38 (0.22), residues: 1428
  helix:  1.32 (0.31), residues: 306
  sheet: -0.24 (0.25), residues: 429
  loop : -0.95 (0.23), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 355 
 TYR   0.014   0.001   TYR D 184 
 PHE   0.011   0.001   PHE A 354 
 TRP   0.010   0.001   TRP B  93 
 HIS   0.002   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 (11516)
  covalent geometry    : angle       0.46904 (15654)
  hydrogen bonds       : bond        0.03684 (  468)
  hydrogen bonds       : angle       4.56658 ( 1284)

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.626 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8468 (mm-30)
REVERT: A  189 THR cc_start: 0.8881 (m) cc_final: 0.8467 (p)
REVERT: B   32 MET cc_start: 0.5053 (tpt) cc_final: 0.4334 (tpt)
REVERT: B  306 MET cc_start: 0.6616 (ptp) cc_final: 0.6372 (ptp)
  outliers start: 16
  outliers final: 14
  residues processed: 125
  average time/residue: 0.2784
  time to fit residues: 48.3642
Evaluate side-chains
  128 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 GLN
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  569 ASP
Chi-restraints excluded: chain A residue  591 SER
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue   70 ASN
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  198 SER
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  353 ASP
Chi-restraints excluded: chain E residue   36 ASN
Chi-restraints excluded: chain E residue   90 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 100 optimal weight:    0.8980
   chunk 134 optimal weight:    3.9990
   chunk 84 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 80 optimal weight:    5.9990
   chunk 137 optimal weight:    0.9990
   chunk 6 optimal weight:    6.9990
   chunk 64 optimal weight:    2.9990
   chunk 46 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    2.5788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.167762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.104535 restraints weight = 37576.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.109326 restraints weight = 18848.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.112288 restraints weight = 12745.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.113954 restraints weight = 10258.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.114697 restraints weight = 9077.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.2914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  11516  Z= 0.207
  Angle     :  0.515   5.639  15654  Z= 0.280
  Chirality :  0.044   0.141   1700
  Planarity :  0.004   0.037   2062
  Dihedral  :  4.243  21.375   1580
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 10.19 %
    Favored  : 88.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.52 (0.22), residues: 1428
  helix:  1.20 (0.31), residues: 305
  sheet: -0.34 (0.25), residues: 430
  loop : -1.02 (0.23), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 295 
 TYR   0.015   0.001   TYR A 585 
 PHE   0.015   0.001   PHE A 791 
 TRP   0.011   0.001   TRP A 745 
 HIS   0.004   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 (11516)
  covalent geometry    : angle       0.51496 (15654)
  hydrogen bonds       : bond        0.04272 (  468)
  hydrogen bonds       : angle       4.71322 ( 1284)

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

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

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2856 Ramachandran restraints generated.
    1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.631 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8499 (mm-30)
REVERT: A  189 THR cc_start: 0.8949 (m) cc_final: 0.8586 (p)
REVERT: A  599 VAL cc_start: 0.8946 (OUTLIER) cc_final: 0.8701 (p)
REVERT: B  306 MET cc_start: 0.6748 (ptp) cc_final: 0.6497 (ptp)
  outliers start: 16
  outliers final: 15
  residues processed: 124
  average time/residue: 0.2581
  time to fit residues: 45.4304
Evaluate side-chains
  130 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 GLN
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  463 ASN
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain A residue  569 ASP
Chi-restraints excluded: chain A residue  591 SER
Chi-restraints excluded: chain A residue  599 VAL
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  198 SER
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  353 ASP
Chi-restraints excluded: chain E residue   36 ASN
Chi-restraints excluded: chain E residue   90 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 119 optimal weight:    0.4980
   chunk 53 optimal weight:    0.9990
   chunk 108 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 107 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 138 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.170465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.108048 restraints weight = 36778.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.112983 restraints weight = 17835.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.116053 restraints weight = 11851.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.117810 restraints weight = 9413.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.118911 restraints weight = 8267.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.2988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  11516  Z= 0.096
  Angle     :  0.453   4.598  15654  Z= 0.242
  Chirality :  0.042   0.143   1700
  Planarity :  0.003   0.037   2062
  Dihedral  :  3.926  20.002   1580
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 2.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 10.36 %
    Favored  : 88.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.23 (0.23), residues: 1428
  helix:  1.52 (0.31), residues: 306
  sheet: -0.22 (0.25), residues: 436
  loop : -0.83 (0.24), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 355 
 TYR   0.014   0.001   TYR D 184 
 PHE   0.010   0.001   PHE A 354 
 TRP   0.010   0.001   TRP B  93 
 HIS   0.003   0.000   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 (11516)
  covalent geometry    : angle       0.45308 (15654)
  hydrogen bonds       : bond        0.03468 (  468)
  hydrogen bonds       : angle       4.42872 ( 1284)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3781.29 seconds
wall clock time: 65 minutes 1.83 seconds (3901.83 seconds total)