Starting phenix.real_space_refine
on Thu Jun 19 00:39:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8bwc_16282/06_2025/8bwc_16282.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bwc_16282/06_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_16282/06_2025/8bwc_16282.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bwc_16282/06_2025/8bwc_16282.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bwc_16282/06_2025/8bwc_16282.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bwc_16282/06_2025/8bwc_16282.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.013 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.24, per 1000 atoms: 0.55
  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: 6.27
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  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: 2.14
  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: 9.07

  Time building geometry restraints manager: 7.62 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.720
  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:             0.460
  Extract box with map and model:          1.110
  Check model and map are aligned:         0.200
  Set scattering table:                    0.240
  Process input model:                     52.930
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   62.190
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (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
 TRP   0.012   0.001   TRP A 745 
 HIS   0.002   0.001   HIS B 165 
 PHE   0.020   0.001   PHE A 347 
 TYR   0.018   0.001   TYR A 230 
 ARG   0.006   0.001   ARG B  77 

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

*********************** 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  : 2.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.5676
  time to fit residues: 123.4420
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  : 1.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 119 optimal weight:    3.9990
   chunk 106 optimal weight:   10.0000
   chunk 59 optimal weight:   10.0000
   chunk 36 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 110 optimal weight:    2.9990
   chunk 42 optimal weight:    0.0980
   chunk 67 optimal weight:    4.9990
   chunk 82 optimal weight:    1.9990
   chunk 128 optimal weight:    1.9990
   overall best weight:    1.4188

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.171644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.108505 restraints weight = 37138.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.113565 restraints weight = 17841.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.116682 restraints weight = 11790.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.1404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  11516  Z= 0.139
  Angle     :  0.531   4.813  15654  Z= 0.290
  Chirality :  0.043   0.153   1700
  Planarity :  0.004   0.051   2062
  Dihedral  :  4.521  21.455   1580
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 2.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  5.30 %
    Favored  : 93.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.22), residues: 1428
  helix:  0.97 (0.30), residues: 306
  sheet: -0.31 (0.24), residues: 450
  loop : -0.83 (0.24), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  93 
 HIS   0.002   0.000   HIS A 196 
 PHE   0.012   0.001   PHE A 347 
 TYR   0.015   0.001   TYR D 184 
 ARG   0.004   0.000   ARG D 173 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05175 (  468)
  hydrogen bonds       : angle       5.45909 ( 1284)
  covalent geometry    : bond        0.00315 (11516)
  covalent geometry    : angle       0.53124 (15654)

*********************** 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
  134 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 124
  time to evaluate  : 1.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  266 ASN cc_start: 0.7533 (m110) cc_final: 0.7238 (m-40)
REVERT: D   30 ASN cc_start: 0.7632 (m-40) cc_final: 0.7204 (m110)
  outliers start: 10
  outliers final: 9
  residues processed: 129
  average time/residue: 0.6079
  time to fit residues: 110.5021
Evaluate side-chains
  119 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 110
  time to evaluate  : 1.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 85 optimal weight:    3.9990
   chunk 103 optimal weight:   10.0000
   chunk 82 optimal weight:    4.9990
   chunk 111 optimal weight:    2.9990
   chunk 115 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 123 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   overall best weight:    1.9786

-------------------------------------------------------------------------------
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 = 0.3936 r_free = 0.3936 target = 0.173088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.110904 restraints weight = 37292.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.115088 restraints weight = 19068.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.115913 restraints weight = 13312.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.1867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  11516  Z= 0.169
  Angle     :  0.516   5.375  15654  Z= 0.282
  Chirality :  0.043   0.151   1700
  Planarity :  0.004   0.039   2062
  Dihedral  :  4.405  21.034   1580
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  7.13 %
    Favored  : 91.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.22), residues: 1428
  helix:  1.03 (0.30), residues: 305
  sheet: -0.27 (0.24), residues: 448
  loop : -0.88 (0.24), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 745 
 HIS   0.002   0.001   HIS A 196 
 PHE   0.013   0.001   PHE A 347 
 TYR   0.014   0.001   TYR D 184 
 ARG   0.003   0.000   ARG A 421 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04607 (  468)
  hydrogen bonds       : angle       5.03768 ( 1284)
  covalent geometry    : bond        0.00397 (11516)
  covalent geometry    : angle       0.51598 (15654)

*********************** 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
  131 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 1.943 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8331 (mm-30)
REVERT: A  189 THR cc_start: 0.8849 (m) cc_final: 0.8454 (p)
REVERT: A  272 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7517 (mt-10)
REVERT: B  266 ASN cc_start: 0.7498 (m110) cc_final: 0.6901 (m-40)
REVERT: D   30 ASN cc_start: 0.7556 (m-40) cc_final: 0.7156 (m110)
  outliers start: 12
  outliers final: 10
  residues processed: 124
  average time/residue: 0.5715
  time to fit residues: 99.1734
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  : 1.819 
-------------------------------------------------------------------------------
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  122 VAL
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 E residue   36 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 94 optimal weight:   20.0000
   chunk 82 optimal weight:    0.9980
   chunk 84 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 124 optimal weight:    0.9980
   chunk 104 optimal weight:    8.9990
   chunk 115 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 101 optimal weight:    6.9990
   overall best weight:    2.5986

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

Flipped N/Q/H residues before XYZ refinement:
A 113 ASN
D  40 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.169704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.107815 restraints weight = 37559.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.110364 restraints weight = 19204.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.111362 restraints weight = 12720.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  11516  Z= 0.210
  Angle     :  0.536   4.796  15654  Z= 0.293
  Chirality :  0.044   0.145   1700
  Planarity :  0.004   0.043   2062
  Dihedral  :  4.493  22.055   1580
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  7.62 %
    Favored  : 91.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.22), residues: 1428
  helix:  1.00 (0.30), residues: 305
  sheet: -0.28 (0.24), residues: 443
  loop : -1.04 (0.24), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 745 
 HIS   0.006   0.001   HIS B  64 
 PHE   0.016   0.002   PHE A 791 
 TYR   0.016   0.001   TYR A 585 
 ARG   0.004   0.000   ARG B 355 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04680 (  468)
  hydrogen bonds       : angle       4.98860 ( 1284)
  covalent geometry    : bond        0.00497 (11516)
  covalent geometry    : angle       0.53569 (15654)

*********************** 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
  132 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 2.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8372 (mm-30)
REVERT: A  147 TYR cc_start: 0.8498 (m-80) cc_final: 0.8239 (m-80)
REVERT: A  189 THR cc_start: 0.8914 (m) cc_final: 0.8531 (p)
REVERT: B  266 ASN cc_start: 0.7442 (m110) cc_final: 0.6844 (t0)
REVERT: D   30 ASN cc_start: 0.7586 (m-40) cc_final: 0.7240 (m110)
  outliers start: 16
  outliers final: 14
  residues processed: 126
  average time/residue: 0.5643
  time to fit residues: 99.5359
Evaluate side-chains
  124 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 1.812 
-------------------------------------------------------------------------------
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  514 THR
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  241 ILE
Chi-restraints excluded: chain B residue  380 ILE
Chi-restraints excluded: chain C residue   49 GLU
Chi-restraints excluded: chain E residue   36 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 97 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 87 optimal weight:    5.9990
   chunk 12 optimal weight:    6.9990
   chunk 83 optimal weight:    0.6980
   chunk 127 optimal weight:    0.9990
   chunk 123 optimal weight:    2.9990
   chunk 77 optimal weight:    6.9990
   chunk 92 optimal weight:    1.9990
   chunk 79 optimal weight:    6.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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 = 0.3883 r_free = 0.3883 target = 0.169005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.105576 restraints weight = 37280.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.110621 restraints weight = 17954.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.113582 restraints weight = 11905.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11516  Z= 0.136
  Angle     :  0.478   4.275  15654  Z= 0.258
  Chirality :  0.042   0.146   1700
  Planarity :  0.003   0.038   2062
  Dihedral  :  4.206  20.956   1580
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  8.29 %
    Favored  : 90.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.22), residues: 1428
  helix:  1.29 (0.30), residues: 306
  sheet: -0.15 (0.24), residues: 443
  loop : -0.97 (0.24), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 745 
 HIS   0.003   0.001   HIS B  64 
 PHE   0.010   0.001   PHE A 791 
 TYR   0.014   0.001   TYR D 184 
 ARG   0.002   0.000   ARG A 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03978 (  468)
  hydrogen bonds       : angle       4.71952 ( 1284)
  covalent geometry    : bond        0.00314 (11516)
  covalent geometry    : angle       0.47803 (15654)

*********************** 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
  131 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 3.523 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8354 (mm-30)
REVERT: A  189 THR cc_start: 0.8879 (m) cc_final: 0.8492 (p)
REVERT: B   32 MET cc_start: 0.4889 (tpt) cc_final: 0.4183 (tpt)
REVERT: B  266 ASN cc_start: 0.7466 (m110) cc_final: 0.6852 (m-40)
REVERT: B  295 ARG cc_start: 0.7271 (mtp85) cc_final: 0.6930 (mtm-85)
REVERT: D   30 ASN cc_start: 0.7669 (m-40) cc_final: 0.7453 (m110)
  outliers start: 14
  outliers final: 8
  residues processed: 124
  average time/residue: 0.8135
  time to fit residues: 145.0831
Evaluate side-chains
  123 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 2.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 ASP
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 E residue   36 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 115 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0030
   chunk 125 optimal weight:    1.9990
   chunk 108 optimal weight:    4.9990
   chunk 112 optimal weight:    1.9990
   chunk 98 optimal weight:    9.9990
   chunk 126 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 119 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.9194

-------------------------------------------------------------------------------
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 = 0.3917 r_free = 0.3917 target = 0.171991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.108358 restraints weight = 37082.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.113576 restraints weight = 17913.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.116682 restraints weight = 11898.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.2578

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= 0.100
  Angle     :  0.454   4.173  15654  Z= 0.244
  Chirality :  0.042   0.147   1700
  Planarity :  0.003   0.032   2062
  Dihedral  :  3.979  19.865   1580
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  8.29 %
    Favored  : 90.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.23), residues: 1428
  helix:  1.55 (0.31), residues: 306
  sheet: -0.13 (0.25), residues: 431
  loop : -0.82 (0.24), residues: 691

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  93 
 HIS   0.002   0.000   HIS B  64 
 PHE   0.008   0.001   PHE A 354 
 TYR   0.017   0.001   TYR A 142 
 ARG   0.005   0.000   ARG B 355 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03533 (  468)
  hydrogen bonds       : angle       4.48980 ( 1284)
  covalent geometry    : bond        0.00228 (11516)
  covalent geometry    : angle       0.45385 (15654)

*********************** 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
  135 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 119
  time to evaluate  : 1.848 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 THR cc_start: 0.8827 (m) cc_final: 0.8412 (p)
REVERT: A  272 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7368 (mt-10)
REVERT: A  589 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.7994 (t70)
REVERT: B  266 ASN cc_start: 0.7445 (m110) cc_final: 0.6792 (m-40)
REVERT: B  295 ARG cc_start: 0.7255 (mtp85) cc_final: 0.6930 (mtm-85)
  outliers start: 16
  outliers final: 13
  residues processed: 130
  average time/residue: 0.8367
  time to fit residues: 158.6595
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  : 3.054 
-------------------------------------------------------------------------------
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  254 ILE
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 E residue   36 ASN
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 8 optimal weight:    6.9990
   chunk 34 optimal weight:    9.9990
   chunk 131 optimal weight:    0.4980
   chunk 1 optimal weight:    9.9990
   chunk 84 optimal weight:    6.9990
   chunk 101 optimal weight:   10.0000
   chunk 6 optimal weight:    5.9990
   chunk 91 optimal weight:    7.9990
   chunk 47 optimal weight:    1.9990
   chunk 124 optimal weight:    0.6980
   chunk 138 optimal weight:    2.9990
   overall best weight:    2.4386

-------------------------------------------------------------------------------
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 = 0.3884 r_free = 0.3884 target = 0.168855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.104753 restraints weight = 37498.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.109728 restraints weight = 18380.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.112833 restraints weight = 12332.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.2681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  11516  Z= 0.197
  Angle     :  0.508   4.434  15654  Z= 0.277
  Chirality :  0.043   0.142   1700
  Planarity :  0.004   0.039   2062
  Dihedral  :  4.212  21.110   1580
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  8.78 %
    Favored  : 89.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.22), residues: 1428
  helix:  1.28 (0.30), residues: 306
  sheet: -0.25 (0.24), residues: 428
  loop : -0.94 (0.23), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 745 
 HIS   0.004   0.001   HIS B  64 
 PHE   0.016   0.001   PHE A 791 
 TYR   0.018   0.001   TYR A 142 
 ARG   0.003   0.000   ARG D 166 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04274 (  468)
  hydrogen bonds       : angle       4.71224 ( 1284)
  covalent geometry    : bond        0.00468 (11516)
  covalent geometry    : angle       0.50840 (15654)

*********************** 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
  136 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 1.792 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 THR cc_start: 0.8924 (m) cc_final: 0.8548 (p)
REVERT: B  266 ASN cc_start: 0.7460 (m110) cc_final: 0.6788 (m-40)
REVERT: B  295 ARG cc_start: 0.7266 (mtp85) cc_final: 0.6929 (mtm-85)
  outliers start: 18
  outliers final: 14
  residues processed: 130
  average time/residue: 0.5649
  time to fit residues: 103.5400
Evaluate side-chains
  130 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 1.776 
-------------------------------------------------------------------------------
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  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  245 SER
Chi-restraints excluded: chain E residue   36 ASN
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 84 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 120 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 124 optimal weight:    0.6980
   chunk 75 optimal weight:    7.9990
   chunk 71 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 95 optimal weight:    9.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.3916 r_free = 0.3916 target = 0.172067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.107112 restraints weight = 37415.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.112417 restraints weight = 17844.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.115684 restraints weight = 11774.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  11516  Z= 0.118
  Angle     :  0.462   4.237  15654  Z= 0.248
  Chirality :  0.042   0.143   1700
  Planarity :  0.003   0.035   2062
  Dihedral  :  3.997  20.649   1580
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 2.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  9.44 %
    Favored  : 89.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.22), residues: 1428
  helix:  1.49 (0.31), residues: 306
  sheet: -0.17 (0.25), residues: 425
  loop : -0.81 (0.24), residues: 697

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  93 
 HIS   0.003   0.001   HIS B  64 
 PHE   0.009   0.001   PHE A 354 
 TYR   0.015   0.001   TYR A 142 
 ARG   0.004   0.000   ARG B 355 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03664 (  468)
  hydrogen bonds       : angle       4.50980 ( 1284)
  covalent geometry    : bond        0.00272 (11516)
  covalent geometry    : angle       0.46171 (15654)

*********************** 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
  131 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 1.693 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 THR cc_start: 0.8851 (m) cc_final: 0.8426 (p)
REVERT: B  266 ASN cc_start: 0.7476 (m110) cc_final: 0.6763 (t0)
REVERT: B  295 ARG cc_start: 0.7264 (mtp85) cc_final: 0.6932 (mtm-85)
  outliers start: 14
  outliers final: 13
  residues processed: 126
  average time/residue: 0.5770
  time to fit residues: 102.4992
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  : 1.641 
-------------------------------------------------------------------------------
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  248 THR
Chi-restraints excluded: chain A residue  254 ILE
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  161 LEU
Chi-restraints excluded: chain B residue  198 SER
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 71 optimal weight:    0.8980
   chunk 89 optimal weight:   10.0000
   chunk 130 optimal weight:    3.9990
   chunk 127 optimal weight:    0.9990
   chunk 121 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 134 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 52 optimal weight:    0.6980
   chunk 112 optimal weight:    0.7980
   chunk 31 optimal weight:    0.2980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 677 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.173137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.109849 restraints weight = 37218.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.116665 restraints weight = 18446.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.118001 restraints weight = 11407.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.2923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  11516  Z= 0.085
  Angle     :  0.440   5.634  15654  Z= 0.234
  Chirality :  0.041   0.143   1700
  Planarity :  0.003   0.035   2062
  Dihedral  :  3.743  19.117   1580
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 2.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  9.61 %
    Favored  : 89.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.23), residues: 1428
  helix:  1.79 (0.31), residues: 306
  sheet: -0.04 (0.25), residues: 425
  loop : -0.65 (0.24), residues: 697

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  93 
 HIS   0.002   0.000   HIS B  64 
 PHE   0.008   0.001   PHE A 354 
 TYR   0.014   0.001   TYR D 184 
 ARG   0.004   0.000   ARG B 355 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03200 (  468)
  hydrogen bonds       : angle       4.28168 ( 1284)
  covalent geometry    : bond        0.00192 (11516)
  covalent geometry    : angle       0.43976 (15654)

*********************** 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
  136 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 124
  time to evaluate  : 1.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 THR cc_start: 0.8781 (m) cc_final: 0.8334 (p)
REVERT: A  566 LYS cc_start: 0.8430 (ttmt) cc_final: 0.7787 (tttm)
REVERT: B  215 ARG cc_start: 0.7861 (mmt90) cc_final: 0.7518 (mmm160)
REVERT: B  266 ASN cc_start: 0.7390 (m110) cc_final: 0.6609 (t0)
REVERT: B  278 MET cc_start: 0.5931 (mtt) cc_final: 0.5571 (mmm)
REVERT: B  295 ARG cc_start: 0.7295 (mtp85) cc_final: 0.7026 (mtm-85)
  outliers start: 12
  outliers final: 10
  residues processed: 130
  average time/residue: 0.6145
  time to fit residues: 113.4406
Evaluate side-chains
  127 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 117
  time to evaluate  : 1.743 
-------------------------------------------------------------------------------
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  230 TYR
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  161 LEU
Chi-restraints excluded: chain B residue  198 SER
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 10 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 55 optimal weight:    3.9990
   chunk 97 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 89 optimal weight:    9.9990
   chunk 51 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9980
   chunk 109 optimal weight:    3.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
B 266 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 = 0.171676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.110840 restraints weight = 37327.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.113453 restraints weight = 24049.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.113982 restraints weight = 14553.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.3001

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= 0.109
  Angle     :  0.452   4.588  15654  Z= 0.241
  Chirality :  0.042   0.142   1700
  Planarity :  0.003   0.064   2062
  Dihedral  :  3.775  19.338   1580
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  9.78 %
    Favored  : 89.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.23), residues: 1428
  helix:  1.81 (0.31), residues: 306
  sheet: -0.04 (0.25), residues: 433
  loop : -0.64 (0.24), residues: 689

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  93 
 HIS   0.003   0.000   HIS B  64 
 PHE   0.009   0.001   PHE A 791 
 TYR   0.013   0.001   TYR D 184 
 ARG   0.008   0.000   ARG D 152 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03404 (  468)
  hydrogen bonds       : angle       4.30691 ( 1284)
  covalent geometry    : bond        0.00254 (11516)
  covalent geometry    : angle       0.45229 (15654)

********************** 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
  128 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 1.948 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 THR cc_start: 0.8822 (m) cc_final: 0.8394 (p)
REVERT: A  566 LYS cc_start: 0.8416 (ttmt) cc_final: 0.7787 (ttpp)
REVERT: B  215 ARG cc_start: 0.8063 (mmt90) cc_final: 0.7691 (mmm160)
REVERT: B  266 ASN cc_start: 0.7408 (m-40) cc_final: 0.6882 (t0)
REVERT: B  295 ARG cc_start: 0.7271 (mtp85) cc_final: 0.7060 (mtm-85)
  outliers start: 10
  outliers final: 10
  residues processed: 123
  average time/residue: 0.6495
  time to fit residues: 111.1736
Evaluate side-chains
  128 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 1.915 
-------------------------------------------------------------------------------
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  230 TYR
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  161 LEU
Chi-restraints excluded: chain B residue  198 SER
Chi-restraints excluded: chain E residue   36 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 59 optimal weight:    7.9990
   chunk 32 optimal weight:    1.9990
   chunk 139 optimal weight:    0.0070
   chunk 112 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9990
   chunk 107 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 129 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   overall best weight:    0.9404

-------------------------------------------------------------------------------
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 = 0.3954 r_free = 0.3954 target = 0.175080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.110324 restraints weight = 37444.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.115694 restraints weight = 18167.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.118969 restraints weight = 11976.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.3063

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     :  0.441   4.016  15654  Z= 0.234
  Chirality :  0.041   0.145   1700
  Planarity :  0.003   0.055   2062
  Dihedral  :  3.693  19.099   1580
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 2.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  9.78 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.23), residues: 1428
  helix:  1.90 (0.31), residues: 306
  sheet:  0.01 (0.25), residues: 430
  loop : -0.59 (0.24), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  93 
 HIS   0.003   0.000   HIS B  64 
 PHE   0.007   0.001   PHE E  77 
 TYR   0.013   0.001   TYR D 184 
 ARG   0.009   0.000   ARG D 152 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03245 (  468)
  hydrogen bonds       : angle       4.22845 ( 1284)
  covalent geometry    : bond        0.00219 (11516)
  covalent geometry    : angle       0.44052 (15654)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8904.97 seconds
wall clock time: 159 minutes 12.47 seconds (9552.47 seconds total)