Starting phenix.real_space_refine
on Sat Aug 23 00:40:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8phe_17659/08_2025/8phe_17659.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8phe_17659/08_2025/8phe_17659.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8phe_17659/08_2025/8phe_17659.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8phe_17659/08_2025/8phe_17659.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8phe_17659/08_2025/8phe_17659.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8phe_17659/08_2025/8phe_17659.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.119
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     C    5656      2.51       5
     N    1498      2.21       5
     O    1714      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8914
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4304
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 551, 4304
          Classifications: {'peptide': 551}
          Link IDs: {'PTRANS': 15, 'TRANS': 535}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4304
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 551, 4304
          Classifications: {'peptide': 551}
          Link IDs: {'PTRANS': 15, 'TRANS': 535}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 134
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 134
          Classifications: {'peptide': 15}
          Link IDs: {'PTRANS': 2, 'TRANS': 12}
    Chain: "D"
      Number of atoms: 134
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 134
          Classifications: {'peptide': 15}
          Link IDs: {'PTRANS': 2, 'TRANS': 12}
    Chain: "A"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 19
          Classifications: {'water': 19}
          Link IDs: {None: 18}
    Chain: "B"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 19
          Classifications: {'water': 19}
          Link IDs: {None: 18}
  Time building chain proxies: 1.79, per 1000 atoms: 0.20
  Number of scatterers: 8914
  At special positions: 0
  Unit cell: (91.797, 121.569, 76.084, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      46     16.00
     O    1714      8.00
     N    1498      7.00
     C    5656      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.80
  Conformation dependent library (CDL) restraints added in 371.9 milliseconds
  
  Enol-peptide restraints added in 1.7 microseconds
  

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2088

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 5 sheets defined
      62.6% alpha, 9.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 39 through 44
      removed outlier: 3.537A  pdb=" N   PHE A  44 " --> pdb=" O   ALA A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 71
    Processing helix  chain 'A' and resid 74 through 81
    Processing helix  chain 'A' and resid 83 through 91
    Processing helix  chain 'A' and resid 94 through 105
    Processing helix  chain 'A' and resid 112 through 116
    Processing helix  chain 'A' and resid 121 through 133
      removed outlier: 3.526A  pdb=" N   SER A 126 " --> pdb=" O   ASN A 122 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ARG A 127 " --> pdb=" O   THR A 123 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LEU A 128 " --> pdb=" O   MET A 124 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLU A 130 " --> pdb=" O   SER A 126 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   ILE A 131 " --> pdb=" O   ARG A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 147
      removed outlier: 3.719A  pdb=" N   THR A 141 " --> pdb=" O   SER A 137 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ALA A 143 " --> pdb=" O   THR A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 157
    Processing helix  chain 'A' and resid 158 through 171
      removed outlier: 3.654A  pdb=" N   LYS A 164 " --> pdb=" O   GLU A 160 " (cutoff:3.500A)
      Proline residue:  A 167  - end of helix
      removed outlier: 3.508A  pdb=" N   SER A 171 " --> pdb=" O   PRO A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 252
      No H-bonds generated for 'chain 'A' and resid 250 through 252'
    Processing helix  chain 'A' and resid 292 through 303
      removed outlier: 3.820A  pdb=" N   GLY A 303 " --> pdb=" O   ILE A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 328
      removed outlier: 3.785A  pdb=" N   ARG A 317 " --> pdb=" O   GLY A 313 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLU A 320 " --> pdb=" O   LYS A 316 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ALA A 323 " --> pdb=" O   ILE A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 338
    Processing helix  chain 'A' and resid 339 through 368
      removed outlier: 3.994A  pdb=" N   LYS A 345 " --> pdb=" O   LEU A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 401
      removed outlier: 3.976A  pdb=" N   ALA A 379 " --> pdb=" O   CYS A 375 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   LEU A 401 " --> pdb=" O   ALA A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 405
    Processing helix  chain 'A' and resid 412 through 419
    Processing helix  chain 'A' and resid 420 through 424
    Processing helix  chain 'A' and resid 428 through 453
      removed outlier: 3.711A  pdb=" N   MET A 434 " --> pdb=" O   GLU A 430 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   HIS A 443 " --> pdb=" O   THR A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 493
      No H-bonds generated for 'chain 'A' and resid 491 through 493'
    Processing helix  chain 'A' and resid 494 through 520
      removed outlier: 3.748A  pdb=" N   ALA A 498 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ASN A 499 " --> pdb=" O   ALA A 495 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   LYS A 500 " --> pdb=" O   ASP A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 521 through 525
    Processing helix  chain 'A' and resid 526 through 557
      removed outlier: 3.584A  pdb=" N   LEU A 530 " --> pdb=" O   GLU A 526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 585
      removed outlier: 3.918A  pdb=" N   GLU A 564 " --> pdb=" O   ASN A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 595 through 609
      removed outlier: 3.832A  pdb=" N   LYS A 600 " --> pdb=" O   GLU A 596 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 46
    Processing helix  chain 'B' and resid 60 through 81
      Proline residue:  B  73  - end of helix
    Processing helix  chain 'B' and resid 83 through 91
    Processing helix  chain 'B' and resid 94 through 105
    Processing helix  chain 'B' and resid 106 through 109
      removed outlier: 4.167A  pdb=" N   LEU B 109 " --> pdb=" O   LEU B 106 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 106 through 109'
    Processing helix  chain 'B' and resid 112 through 116
    Processing helix  chain 'B' and resid 121 through 133
      removed outlier: 3.589A  pdb=" N   LEU B 128 " --> pdb=" O   MET B 124 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLU B 130 " --> pdb=" O   SER B 126 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   ILE B 131 " --> pdb=" O   ARG B 127 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   SER B 133 " --> pdb=" O   GLY B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 147
      removed outlier: 3.570A  pdb=" N   THR B 141 " --> pdb=" O   SER B 137 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ALA B 143 " --> pdb=" O   THR B 139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 150 through 157
    Processing helix  chain 'B' and resid 158 through 171
      removed outlier: 3.510A  pdb=" N   ALA B 163 " --> pdb=" O   GLU B 159 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LYS B 164 " --> pdb=" O   GLU B 160 " (cutoff:3.500A)
      Proline residue:  B 167  - end of helix
      removed outlier: 3.502A  pdb=" N   SER B 171 " --> pdb=" O   PRO B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 252
      No H-bonds generated for 'chain 'B' and resid 250 through 252'
    Processing helix  chain 'B' and resid 291 through 302
      removed outlier: 4.274A  pdb=" N   VAL B 295 " --> pdb=" O   ASP B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 327
      removed outlier: 4.009A  pdb=" N   GLY B 308 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   SER B 309 " --> pdb=" O   PHE B 305 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ARG B 317 " --> pdb=" O   GLY B 313 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ALA B 323 " --> pdb=" O   ILE B 319 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   GLU B 324 " --> pdb=" O   GLU B 320 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 368
      removed outlier: 4.010A  pdb=" N   LYS B 345 " --> pdb=" O   LEU B 341 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 401
      removed outlier: 3.646A  pdb=" N   LEU B 401 " --> pdb=" O   ALA B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 402 through 405
    Processing helix  chain 'B' and resid 412 through 419
    Processing helix  chain 'B' and resid 420 through 424
    Processing helix  chain 'B' and resid 428 through 453
      removed outlier: 3.867A  pdb=" N   MET B 434 " --> pdb=" O   GLU B 430 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 491 through 493
      No H-bonds generated for 'chain 'B' and resid 491 through 493'
    Processing helix  chain 'B' and resid 494 through 519
      removed outlier: 3.730A  pdb=" N   ALA B 498 " --> pdb=" O   LEU B 494 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ASN B 499 " --> pdb=" O   ALA B 495 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   LYS B 500 " --> pdb=" O   ASP B 496 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 520 through 525
      removed outlier: 3.854A  pdb=" N   MET B 524 " --> pdb=" O   LYS B 521 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 526 through 557
      removed outlier: 3.567A  pdb=" N   ARG B 532 " --> pdb=" O   LEU B 528 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   LEU B 547 " --> pdb=" O   MET B 543 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 585
      removed outlier: 3.820A  pdb=" N   GLU B 564 " --> pdb=" O   ASN B 560 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   PHE B 571 " --> pdb=" O   LEU B 567 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLU B 574 " --> pdb=" O   THR B 570 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   GLN B 585 " --> pdb=" O   PHE B 581 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 595 through 609
    Processing helix  chain 'C' and resid 321 through 327
    Processing helix  chain 'D' and resid 323 through 327
    Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 179
      removed outlier: 6.952A  pdb=" N   ALA A 177 " --> pdb=" O   THR A 224 " (cutoff:3.500A)
      removed outlier: 8.201A  pdb=" N   PHE A 226 " --> pdb=" O   ALA A 177 " (cutoff:3.500A)
      removed outlier: 7.611A  pdb=" N   CYS A 179 " --> pdb=" O   PHE A 226 " (cutoff:3.500A)
      removed outlier: 9.375A  pdb=" N   LYS A 228 " --> pdb=" O   CYS A 179 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 195 through 198
      removed outlier: 6.415A  pdb=" N   TYR A 205 " --> pdb=" O   LYS A 279 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   LYS A 279 " --> pdb=" O   TYR A 205 " (cutoff:3.500A)
      removed outlier: 5.585A  pdb=" N   LEU A 207 " --> pdb=" O   ASN A 277 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   TRP A 213 " --> pdb=" O   CYS A 271 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   CYS A 271 " --> pdb=" O   TRP A 213 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 176 through 179
      removed outlier: 7.038A  pdb=" N   ALA B 177 " --> pdb=" O   THR B 224 " (cutoff:3.500A)
      removed outlier: 8.254A  pdb=" N   PHE B 226 " --> pdb=" O   ALA B 177 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   CYS B 179 " --> pdb=" O   PHE B 226 " (cutoff:3.500A)
      removed outlier: 9.389A  pdb=" N   LYS B 228 " --> pdb=" O   CYS B 179 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   GLU B 230 " --> pdb=" O   ALA B 196 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   LEU B 198 " --> pdb=" O   GLU B 230 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   TYR B 205 " --> pdb=" O   LYS B 279 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   LYS B 279 " --> pdb=" O   TYR B 205 " (cutoff:3.500A)
      removed outlier: 5.577A  pdb=" N   LEU B 207 " --> pdb=" O   ASN B 277 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   TRP B 213 " --> pdb=" O   CYS B 271 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   CYS B 271 " --> pdb=" O   TRP B 213 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 176 through 179
      removed outlier: 7.038A  pdb=" N   ALA B 177 " --> pdb=" O   THR B 224 " (cutoff:3.500A)
      removed outlier: 8.254A  pdb=" N   PHE B 226 " --> pdb=" O   ALA B 177 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   CYS B 179 " --> pdb=" O   PHE B 226 " (cutoff:3.500A)
      removed outlier: 9.389A  pdb=" N   LYS B 228 " --> pdb=" O   CYS B 179 " (cutoff:3.500A)
      removed outlier: 4.827A  pdb=" N   ALA B 244 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 330 through 331

    493 hydrogen bonds defined for protein.
    1401 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.18

  Time building geometry restraints manager: 1.10 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2917
        1.34 -     1.46: 1777
        1.46 -     1.58: 4262
        1.58 -     1.69: 0
        1.69 -     1.81: 74
  Bond restraints: 9030
  Sorted by residual:
  bond pdb=" C   GLU B 182 "
       pdb=" N   PRO B 183 "
    ideal  model  delta    sigma   weight residual
    1.333  1.345 -0.012 1.17e-02 7.31e+03 1.14e+00
  bond pdb=" CA  GLY B 287 "
       pdb=" C   GLY B 287 "
    ideal  model  delta    sigma   weight residual
    1.514  1.529 -0.015 1.41e-02 5.03e+03 1.13e+00
  bond pdb=" N   ILE B 265 "
       pdb=" CA  ILE B 265 "
    ideal  model  delta    sigma   weight residual
    1.474  1.458  0.017 1.57e-02 4.06e+03 1.11e+00
  bond pdb=" N   GLY B 287 "
       pdb=" CA  GLY B 287 "
    ideal  model  delta    sigma   weight residual
    1.449  1.464 -0.015 1.45e-02 4.76e+03 1.02e+00
  bond pdb=" CB  MET A 381 "
       pdb=" CG  MET A 381 "
    ideal  model  delta    sigma   weight residual
    1.520  1.491  0.029 3.00e-02 1.11e+03 9.40e-01
  ... (remaining 9025 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 11915
        1.41 -     2.82: 204
        2.82 -     4.23: 43
        4.23 -     5.64: 10
        5.64 -     7.06: 2
  Bond angle restraints: 12174
  Sorted by residual:
  angle pdb=" N   ILE B 265 "
        pdb=" CA  ILE B 265 "
        pdb=" C   ILE B 265 "
      ideal   model   delta    sigma   weight residual
     106.21  109.98   -3.77 1.07e+00 8.73e-01 1.24e+01
  angle pdb=" N   ILE B 148 "
        pdb=" CA  ILE B 148 "
        pdb=" C   ILE B 148 "
      ideal   model   delta    sigma   weight residual
     113.53  110.28    3.25 9.80e-01 1.04e+00 1.10e+01
  angle pdb=" C   LYS B  50 "
        pdb=" N   LYS B  51 "
        pdb=" CA  LYS B  51 "
      ideal   model   delta    sigma   weight residual
     121.54  126.58   -5.04 1.91e+00 2.74e-01 6.95e+00
  angle pdb=" C   GLY B 303 "
        pdb=" N   ARG B 304 "
        pdb=" CA  ARG B 304 "
      ideal   model   delta    sigma   weight residual
     121.54  126.51   -4.97 1.91e+00 2.74e-01 6.78e+00
  angle pdb=" CA  LYS B  51 "
        pdb=" CB  LYS B  51 "
        pdb=" CG  LYS B  51 "
      ideal   model   delta    sigma   weight residual
     114.10  119.17   -5.07 2.00e+00 2.50e-01 6.41e+00
  ... (remaining 12169 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.10: 4882
       17.10 -    34.21: 449
       34.21 -    51.31: 89
       51.31 -    68.42: 21
       68.42 -    85.52: 17
  Dihedral angle restraints: 5458
    sinusoidal: 2208
      harmonic: 3250
  Sorted by residual:
  dihedral pdb=" CB  GLU B 592 "
           pdb=" CG  GLU B 592 "
           pdb=" CD  GLU B 592 "
           pdb=" OE1 GLU B 592 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   85.52  -85.52     1      3.00e+01 1.11e-03 9.83e+00
  dihedral pdb=" CB  GLU A  58 "
           pdb=" CG  GLU A  58 "
           pdb=" CD  GLU A  58 "
           pdb=" OE1 GLU A  58 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -85.10   85.10     1      3.00e+01 1.11e-03 9.76e+00
  dihedral pdb=" CB  MET B 434 "
           pdb=" CG  MET B 434 "
           pdb=" SD  MET B 434 "
           pdb=" CE  MET B 434 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  116.47  -56.47     3      1.50e+01 4.44e-03 9.40e+00
  ... (remaining 5455 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 822
       0.028 -    0.056: 385
       0.056 -    0.084: 109
       0.084 -    0.112: 39
       0.112 -    0.140: 25
  Chirality restraints: 1380
  Sorted by residual:
  chirality pdb=" CA  VAL A 111 "
            pdb=" N   VAL A 111 "
            pdb=" C   VAL A 111 "
            pdb=" CB  VAL A 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.91e-01
  chirality pdb=" CA  ILE A 280 "
            pdb=" N   ILE A 280 "
            pdb=" C   ILE A 280 "
            pdb=" CB  ILE A 280 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.52e-01
  chirality pdb=" CA  ILE B 280 "
            pdb=" N   ILE B 280 "
            pdb=" C   ILE B 280 "
            pdb=" CB  ILE B 280 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.41e-01
  ... (remaining 1377 not shown)

  Planarity restraints: 1562
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 491 "    0.041 5.00e-02 4.00e+02   6.28e-02 6.31e+00
        pdb=" N   PRO B 492 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO B 492 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 492 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D 320 "    0.029 5.00e-02 4.00e+02   4.32e-02 2.99e+00
        pdb=" N   PRO D 321 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO D 321 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO D 321 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 304 "    0.008 2.00e-02 2.50e+03   1.52e-02 2.31e+00
        pdb=" C   ARG B 304 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   ARG B 304 "    0.010 2.00e-02 2.50e+03
        pdb=" N   PHE B 305 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1559 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 170
        2.70 -     3.25: 8802
        3.25 -     3.80: 13747
        3.80 -     4.35: 19172
        4.35 -     4.90: 32373
  Nonbonded interactions: 74264
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A 193 "
            pdb=" O   HOH A 701 "
     model   vdw
     2.148 3.120
  nonbonded pdb=" OG1 THR A 363 "
            pdb=" OH  TYR A 541 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" OD2 ASP B  88 "
            pdb=" NH2 ARG B 417 "
     model   vdw
     2.268 3.120
  nonbonded pdb=" OD2 ASP A  88 "
            pdb=" NH2 ARG A 417 "
     model   vdw
     2.285 3.120
  nonbonded pdb=" O   ASP A 188 "
            pdb=" O   HOH A 701 "
     model   vdw
     2.286 3.040
  ... (remaining 74259 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.940
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
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   0.030   9030  Z= 0.122
  Angle     :  0.501   7.056  12174  Z= 0.282
  Chirality :  0.039   0.140   1380
  Planarity :  0.004   0.063   1562
  Dihedral  : 14.633  85.519   3370
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.27 (0.26), residues: 1120
  helix:  0.33 (0.21), residues: 644
  sheet: -0.69 (0.50), residues: 76
  loop :  0.41 (0.36), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 408 
 TYR   0.016   0.001   TYR B 506 
 PHE   0.008   0.001   PHE A  54 
 TRP   0.005   0.001   TRP A 391 
 HIS   0.003   0.001   HIS A 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 9030)
  covalent geometry    : angle       0.50142 (12174)
  hydrogen bonds       : bond        0.19152 (  493)
  hydrogen bonds       : angle       6.91868 ( 1401)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.226 
Fit side-chains
REVERT: A   47 LYS cc_start: 0.7592 (mmtm) cc_final: 0.7291 (ptmt)
REVERT: A  521 LYS cc_start: 0.8577 (mppt) cc_final: 0.8310 (mptt)
REVERT: A  555 ARG cc_start: 0.7612 (ttp-110) cc_final: 0.7076 (ttp-110)
REVERT: B   65 ASN cc_start: 0.7728 (m-40) cc_final: 0.7403 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.1157
  time to fit residues: 21.0433
Evaluate side-chains
  111 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0870
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.0570
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    0.0020
   chunk 106 optimal weight:    0.9980
   overall best weight:    0.4286

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

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 146 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.158113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.125355 restraints weight = 8864.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 1.92
r_work: 0.3309 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3139 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.1200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9030  Z= 0.109
  Angle     :  0.473   8.265  12174  Z= 0.252
  Chirality :  0.039   0.133   1380
  Planarity :  0.004   0.058   1562
  Dihedral  :  3.713  15.407   1214
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  :  8.12 %
    Favored  : 91.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.26), residues: 1120
  helix:  1.25 (0.21), residues: 636
  sheet: -0.13 (0.52), residues: 76
  loop :  0.22 (0.34), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 408 
 TYR   0.014   0.001   TYR B 361 
 PHE   0.008   0.001   PHE B 425 
 TRP   0.004   0.001   TRP B 213 
 HIS   0.003   0.001   HIS A 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 9030)
  covalent geometry    : angle       0.47332 (12174)
  hydrogen bonds       : bond        0.04652 (  493)
  hydrogen bonds       : angle       4.18343 ( 1401)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 120
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 LYS cc_start: 0.7575 (mmtm) cc_final: 0.6964 (ptmt)
REVERT: A  272 GLU cc_start: 0.8630 (pt0) cc_final: 0.8429 (tt0)
REVERT: A  506 TYR cc_start: 0.8657 (t80) cc_final: 0.8449 (t80)
REVERT: A  521 LYS cc_start: 0.8546 (mppt) cc_final: 0.7802 (mtmm)
REVERT: A  596 GLU cc_start: 0.7368 (mp0) cc_final: 0.7011 (mp0)
REVERT: A  599 LYS cc_start: 0.7709 (mtmt) cc_final: 0.7326 (mttm)
REVERT: B   50 LYS cc_start: 0.7181 (pttp) cc_final: 0.6864 (mmtt)
REVERT: B  272 GLU cc_start: 0.8711 (pt0) cc_final: 0.8508 (tt0)
REVERT: B  522 THR cc_start: 0.8662 (t) cc_final: 0.8191 (p)
REVERT: B  551 SER cc_start: 0.8690 (t) cc_final: 0.8304 (m)
REVERT: B  599 LYS cc_start: 0.7799 (mttp) cc_final: 0.7499 (mttp)
  outliers start: 6
  outliers final: 4
  residues processed: 124
  average time/residue: 0.0933
  time to fit residues: 15.0473
Evaluate side-chains
  116 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 112
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 GLN
Chi-restraints excluded: chain A residue  100 LYS
Chi-restraints excluded: chain B residue  182 GLU
Chi-restraints excluded: chain B residue  490 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 62 optimal weight:    0.7980
   chunk 27 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0370
   chunk 11 optimal weight:    5.9990
   chunk 13 optimal weight:    6.9990
   chunk 33 optimal weight:    7.9990
   chunk 59 optimal weight:    5.9990
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.6658

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

Flipped N/Q/H residues before XYZ refinement:
** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.163983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.132327 restraints weight = 8686.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.3400 rms_B_bonded: 1.82
r_work: 0.3253 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3096 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.1468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9030  Z= 0.112
  Angle     :  0.455   8.185  12174  Z= 0.240
  Chirality :  0.039   0.131   1380
  Planarity :  0.004   0.059   1562
  Dihedral  :  3.634  15.302   1214
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 10.83 %
    Favored  : 88.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.42 (0.26), residues: 1120
  helix:  1.53 (0.21), residues: 638
  sheet: -0.06 (0.53), residues: 76
  loop :  0.37 (0.35), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 446 
 TYR   0.014   0.001   TYR B 361 
 PHE   0.009   0.001   PHE A 571 
 TRP   0.003   0.001   TRP B 213 
 HIS   0.002   0.001   HIS A 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 9030)
  covalent geometry    : angle       0.45538 (12174)
  hydrogen bonds       : bond        0.04458 (  493)
  hydrogen bonds       : angle       3.90311 ( 1401)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 LYS cc_start: 0.7654 (mmtm) cc_final: 0.7132 (ptmt)
REVERT: A  506 TYR cc_start: 0.8677 (t80) cc_final: 0.8475 (t80)
REVERT: A  521 LYS cc_start: 0.8604 (mppt) cc_final: 0.7845 (mtmm)
REVERT: A  555 ARG cc_start: 0.7915 (ttp-110) cc_final: 0.7431 (ttp-110)
REVERT: A  596 GLU cc_start: 0.7365 (mp0) cc_final: 0.7069 (mp0)
REVERT: A  599 LYS cc_start: 0.7832 (mtmt) cc_final: 0.7417 (mttm)
REVERT: B   50 LYS cc_start: 0.7338 (pttp) cc_final: 0.7031 (mmtt)
REVERT: B  260 GLU cc_start: 0.7227 (mt-10) cc_final: 0.7010 (mt-10)
REVERT: B  272 GLU cc_start: 0.8692 (pt0) cc_final: 0.8447 (tt0)
REVERT: B  522 THR cc_start: 0.8689 (t) cc_final: 0.8232 (p)
REVERT: B  551 SER cc_start: 0.8727 (t) cc_final: 0.8364 (m)
REVERT: B  599 LYS cc_start: 0.7902 (mttp) cc_final: 0.7534 (mttm)
  outliers start: 9
  outliers final: 6
  residues processed: 125
  average time/residue: 0.1029
  time to fit residues: 16.5589
Evaluate side-chains
  118 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 112
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 GLN
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  490 VAL
Chi-restraints excluded: chain B residue  607 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 55 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 64 optimal weight:    5.9990
   chunk 69 optimal weight:    0.0770
   chunk 27 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    2.4146

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

Flipped N/Q/H residues before XYZ refinement:
** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 221 ASN
B 256 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.152496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.120427 restraints weight = 9049.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 1.82
r_work: 0.3091 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2933 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057   9030  Z= 0.243
  Angle     :  0.585  11.419  12174  Z= 0.302
  Chirality :  0.044   0.201   1380
  Planarity :  0.005   0.063   1562
  Dihedral  :  4.154  17.448   1214
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 12.29 %
    Favored  : 85.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.26), residues: 1120
  helix:  1.01 (0.21), residues: 644
  sheet: -0.26 (0.51), residues: 76
  loop :  0.41 (0.35), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 446 
 TYR   0.019   0.002   TYR A 361 
 PHE   0.016   0.002   PHE B  54 
 TRP   0.006   0.001   TRP B 213 
 HIS   0.005   0.001   HIS A 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00593 ( 9030)
  covalent geometry    : angle       0.58492 (12174)
  hydrogen bonds       : bond        0.05927 (  493)
  hydrogen bonds       : angle       4.18360 ( 1401)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 0.205 
Fit side-chains
REVERT: A   64 LEU cc_start: 0.8097 (tp) cc_final: 0.7881 (tp)
REVERT: A   65 ASN cc_start: 0.7851 (m110) cc_final: 0.7207 (m110)
REVERT: A  521 LYS cc_start: 0.8663 (mppt) cc_final: 0.7845 (mtmm)
REVERT: A  596 GLU cc_start: 0.7482 (mp0) cc_final: 0.7119 (mp0)
REVERT: B   65 ASN cc_start: 0.7929 (m-40) cc_final: 0.7367 (m110)
REVERT: B   71 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7984 (mp)
REVERT: B  260 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7102 (mm-30)
REVERT: B  272 GLU cc_start: 0.8714 (pt0) cc_final: 0.8316 (tt0)
REVERT: B  522 THR cc_start: 0.8715 (t) cc_final: 0.8265 (p)
REVERT: B  551 SER cc_start: 0.8668 (t) cc_final: 0.8247 (m)
REVERT: B  599 LYS cc_start: 0.7918 (mttp) cc_final: 0.7651 (mttm)
  outliers start: 17
  outliers final: 12
  residues processed: 123
  average time/residue: 0.0965
  time to fit residues: 15.6231
Evaluate side-chains
  121 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   83 ASP
Chi-restraints excluded: chain A residue   89 GLN
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  490 VAL
Chi-restraints excluded: chain B residue  514 THR
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  607 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 89 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 104 optimal weight:    0.9980
   chunk 78 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 107 optimal weight:    0.3980
   chunk 101 optimal weight:    0.6980
   chunk 106 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 256 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.156239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.123052 restraints weight = 8890.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 1.94
r_work: 0.3225 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3057 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.1752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9030  Z= 0.117
  Angle     :  0.463   9.573  12174  Z= 0.243
  Chirality :  0.039   0.132   1380
  Planarity :  0.004   0.062   1562
  Dihedral  :  3.763  15.675   1214
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 12.50 %
    Favored  : 85.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.26), residues: 1120
  helix:  1.44 (0.21), residues: 642
  sheet: -0.04 (0.52), residues: 76
  loop :  0.42 (0.35), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 446 
 TYR   0.017   0.001   TYR B 506 
 PHE   0.013   0.001   PHE A 425 
 TRP   0.007   0.001   TRP B 213 
 HIS   0.004   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 9030)
  covalent geometry    : angle       0.46266 (12174)
  hydrogen bonds       : bond        0.04391 (  493)
  hydrogen bonds       : angle       3.84725 ( 1401)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.7832 (tp) cc_final: 0.7613 (tp)
REVERT: A  521 LYS cc_start: 0.8569 (mppt) cc_final: 0.7819 (mtmm)
REVERT: A  555 ARG cc_start: 0.7917 (ttp-110) cc_final: 0.7456 (ttp-110)
REVERT: A  607 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7830 (tp30)
REVERT: B   65 ASN cc_start: 0.7753 (m-40) cc_final: 0.7272 (m110)
REVERT: B  193 ARG cc_start: 0.8050 (mpp-170) cc_final: 0.7817 (mtm-85)
REVERT: B  260 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7081 (mt-10)
REVERT: B  272 GLU cc_start: 0.8712 (pt0) cc_final: 0.8339 (tt0)
REVERT: B  430 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8460 (pm20)
REVERT: B  522 THR cc_start: 0.8621 (t) cc_final: 0.8158 (p)
REVERT: B  551 SER cc_start: 0.8632 (t) cc_final: 0.8295 (m)
REVERT: B  555 ARG cc_start: 0.7903 (ttp-110) cc_final: 0.7433 (ttp-110)
REVERT: B  599 LYS cc_start: 0.7734 (mttp) cc_final: 0.7476 (mttm)
  outliers start: 19
  outliers final: 12
  residues processed: 125
  average time/residue: 0.1136
  time to fit residues: 18.1358
Evaluate side-chains
  119 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ASP
Chi-restraints excluded: chain A residue   89 GLN
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  321 MET
Chi-restraints excluded: chain B residue  430 GLU
Chi-restraints excluded: chain B residue  490 VAL
Chi-restraints excluded: chain B residue  514 THR
Chi-restraints excluded: chain B residue  607 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 89 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 63 optimal weight:    5.9990
   chunk 48 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 80 optimal weight:    8.9990
   chunk 66 optimal weight:    6.9990
   chunk 94 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 83 optimal weight:    4.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 256 ASN
B 560 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.149613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.116319 restraints weight = 8928.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 1.93
r_work: 0.3022 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2855 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   9030  Z= 0.242
  Angle     :  0.588  11.733  12174  Z= 0.300
  Chirality :  0.044   0.198   1380
  Planarity :  0.005   0.063   1562
  Dihedral  :  4.125  17.189   1214
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 13.33 %
    Favored  : 84.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.96 (0.26), residues: 1120
  helix:  1.02 (0.20), residues: 644
  sheet: -0.22 (0.52), residues: 76
  loop :  0.42 (0.35), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 446 
 TYR   0.019   0.002   TYR A 506 
 PHE   0.016   0.002   PHE A  54 
 TRP   0.009   0.001   TRP B 213 
 HIS   0.004   0.001   HIS A 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00593 ( 9030)
  covalent geometry    : angle       0.58837 (12174)
  hydrogen bonds       : bond        0.05789 (  493)
  hydrogen bonds       : angle       4.09853 ( 1401)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.258 
Fit side-chains
REVERT: A   64 LEU cc_start: 0.7923 (tp) cc_final: 0.7719 (tp)
REVERT: A  521 LYS cc_start: 0.8687 (mppt) cc_final: 0.7898 (mtmm)
REVERT: A  607 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7924 (tp30)
REVERT: B   65 ASN cc_start: 0.7912 (m-40) cc_final: 0.7358 (m110)
REVERT: B  260 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7170 (mm-30)
REVERT: B  272 GLU cc_start: 0.8736 (pt0) cc_final: 0.8309 (tt0)
REVERT: B  430 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8572 (pm20)
REVERT: B  522 THR cc_start: 0.8656 (t) cc_final: 0.8210 (p)
REVERT: B  551 SER cc_start: 0.8671 (t) cc_final: 0.8244 (m)
REVERT: B  560 ASN cc_start: 0.8193 (OUTLIER) cc_final: 0.7961 (p0)
REVERT: B  599 LYS cc_start: 0.7819 (mttp) cc_final: 0.7564 (mttm)
  outliers start: 21
  outliers final: 14
  residues processed: 125
  average time/residue: 0.0938
  time to fit residues: 15.4697
Evaluate side-chains
  121 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ASP
Chi-restraints excluded: chain A residue   89 GLN
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  256 ASN
Chi-restraints excluded: chain B residue  430 GLU
Chi-restraints excluded: chain B residue  490 VAL
Chi-restraints excluded: chain B residue  514 THR
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  560 ASN
Chi-restraints excluded: chain B residue  607 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 93 optimal weight:    0.0980
   chunk 68 optimal weight:    6.9990
   chunk 19 optimal weight:    6.9990
   chunk 8 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 76 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 100 optimal weight:    2.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 256 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.152625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.119572 restraints weight = 8875.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 1.91
r_work: 0.3122 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.1868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9030  Z= 0.132
  Angle     :  0.492   9.929  12174  Z= 0.257
  Chirality :  0.040   0.157   1380
  Planarity :  0.004   0.062   1562
  Dihedral  :  3.876  16.217   1214
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 13.54 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.26), residues: 1120
  helix:  1.31 (0.21), residues: 644
  sheet: -0.14 (0.52), residues: 76
  loop :  0.45 (0.35), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 446 
 TYR   0.018   0.001   TYR B 506 
 PHE   0.020   0.001   PHE A 425 
 TRP   0.008   0.001   TRP B 213 
 HIS   0.006   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 9030)
  covalent geometry    : angle       0.49211 (12174)
  hydrogen bonds       : bond        0.04743 (  493)
  hydrogen bonds       : angle       3.88121 ( 1401)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A   64 LEU cc_start: 0.7924 (tp) cc_final: 0.7723 (tp)
REVERT: A  521 LYS cc_start: 0.8646 (mppt) cc_final: 0.7874 (mtmm)
REVERT: A  555 ARG cc_start: 0.8016 (ttp-110) cc_final: 0.7561 (ttp-110)
REVERT: B   65 ASN cc_start: 0.7923 (m-40) cc_final: 0.7445 (m110)
REVERT: B  260 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7116 (mm-30)
REVERT: B  272 GLU cc_start: 0.8711 (pt0) cc_final: 0.8318 (tt0)
REVERT: B  430 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8587 (pm20)
REVERT: B  522 THR cc_start: 0.8659 (t) cc_final: 0.8218 (p)
REVERT: B  551 SER cc_start: 0.8689 (t) cc_final: 0.8303 (m)
REVERT: B  599 LYS cc_start: 0.7801 (mttp) cc_final: 0.7539 (mttm)
  outliers start: 16
  outliers final: 14
  residues processed: 122
  average time/residue: 0.1225
  time to fit residues: 19.0097
Evaluate side-chains
  123 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ASP
Chi-restraints excluded: chain A residue   89 GLN
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain A residue  596 GLU
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  256 ASN
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  430 GLU
Chi-restraints excluded: chain B residue  490 VAL
Chi-restraints excluded: chain B residue  514 THR
Chi-restraints excluded: chain B residue  607 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 25 optimal weight:    9.9990
   chunk 74 optimal weight:   10.0000
   chunk 67 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 39 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 256 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.152704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.119165 restraints weight = 8893.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 1.96
r_work: 0.3072 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2904 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.1919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9030  Z= 0.174
  Angle     :  0.531  10.764  12174  Z= 0.272
  Chirality :  0.041   0.167   1380
  Planarity :  0.005   0.062   1562
  Dihedral  :  3.943  16.301   1214
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 13.54 %
    Favored  : 84.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.20 (0.26), residues: 1120
  helix:  1.25 (0.20), residues: 644
  sheet: -0.16 (0.52), residues: 76
  loop :  0.44 (0.35), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 446 
 TYR   0.019   0.002   TYR A 506 
 PHE   0.020   0.002   PHE A 425 
 TRP   0.008   0.001   TRP B 213 
 HIS   0.004   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 9030)
  covalent geometry    : angle       0.53102 (12174)
  hydrogen bonds       : bond        0.05113 (  493)
  hydrogen bonds       : angle       3.94009 ( 1401)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A  521 LYS cc_start: 0.8673 (mppt) cc_final: 0.7887 (mtmm)
REVERT: B   65 ASN cc_start: 0.7905 (m-40) cc_final: 0.7417 (m110)
REVERT: B  260 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7129 (mm-30)
REVERT: B  272 GLU cc_start: 0.8706 (pt0) cc_final: 0.8301 (tt0)
REVERT: B  422 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.7888 (mp)
REVERT: B  430 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8563 (pm20)
REVERT: B  522 THR cc_start: 0.8647 (t) cc_final: 0.8209 (p)
REVERT: B  551 SER cc_start: 0.8703 (t) cc_final: 0.8300 (m)
REVERT: B  599 LYS cc_start: 0.7784 (mttp) cc_final: 0.7514 (mttm)
  outliers start: 18
  outliers final: 13
  residues processed: 117
  average time/residue: 0.0997
  time to fit residues: 15.1759
Evaluate side-chains
  121 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ASP
Chi-restraints excluded: chain A residue   89 GLN
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  256 ASN
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  422 LEU
Chi-restraints excluded: chain B residue  430 GLU
Chi-restraints excluded: chain B residue  490 VAL
Chi-restraints excluded: chain B residue  514 THR
Chi-restraints excluded: chain B residue  607 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 101 optimal weight:    0.9980
   chunk 80 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 100 optimal weight:    0.9990
   chunk 79 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 256 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.154320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.122568 restraints weight = 8853.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 1.80
r_work: 0.3145 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2989 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.1937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9030  Z= 0.178
  Angle     :  0.533  10.831  12174  Z= 0.274
  Chirality :  0.041   0.174   1380
  Planarity :  0.005   0.062   1562
  Dihedral  :  3.946  16.356   1214
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 13.44 %
    Favored  : 84.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.26), residues: 1120
  helix:  1.23 (0.20), residues: 644
  sheet: -0.16 (0.52), residues: 76
  loop :  0.44 (0.35), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 446 
 TYR   0.019   0.002   TYR B 506 
 PHE   0.019   0.002   PHE A 425 
 TRP   0.006   0.001   TRP B 213 
 HIS   0.004   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 9030)
  covalent geometry    : angle       0.53312 (12174)
  hydrogen bonds       : bond        0.05140 (  493)
  hydrogen bonds       : angle       3.94450 ( 1401)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.220 
Fit side-chains
REVERT: A   42 GLU cc_start: 0.8193 (mp0) cc_final: 0.7974 (mp0)
REVERT: A   65 ASN cc_start: 0.7920 (m110) cc_final: 0.7293 (m110)
REVERT: A  521 LYS cc_start: 0.8723 (mppt) cc_final: 0.7935 (mtmm)
REVERT: B   65 ASN cc_start: 0.7979 (m-40) cc_final: 0.7505 (m110)
REVERT: B  260 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7098 (mm-30)
REVERT: B  272 GLU cc_start: 0.8645 (pt0) cc_final: 0.8272 (tt0)
REVERT: B  422 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.7900 (mp)
REVERT: B  430 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8551 (pm20)
REVERT: B  522 THR cc_start: 0.8707 (t) cc_final: 0.8273 (p)
REVERT: B  551 SER cc_start: 0.8721 (t) cc_final: 0.8306 (m)
REVERT: B  580 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8000 (mp)
REVERT: B  599 LYS cc_start: 0.7863 (mttp) cc_final: 0.7588 (mttm)
  outliers start: 19
  outliers final: 14
  residues processed: 115
  average time/residue: 0.1003
  time to fit residues: 15.0808
Evaluate side-chains
  122 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ASP
Chi-restraints excluded: chain A residue   89 GLN
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  256 ASN
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  422 LEU
Chi-restraints excluded: chain B residue  430 GLU
Chi-restraints excluded: chain B residue  490 VAL
Chi-restraints excluded: chain B residue  514 THR
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  580 LEU
Chi-restraints excluded: chain B residue  607 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 109 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0970
   chunk 82 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 77 optimal weight:    0.7980
   chunk 67 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 256 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.154959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.123214 restraints weight = 8863.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 1.81
r_work: 0.3204 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3047 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.1939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9030  Z= 0.161
  Angle     :  0.529  10.478  12174  Z= 0.271
  Chirality :  0.041   0.164   1380
  Planarity :  0.005   0.062   1562
  Dihedral  :  3.916  16.272   1214
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 13.75 %
    Favored  : 84.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.26), residues: 1120
  helix:  1.30 (0.20), residues: 644
  sheet: -0.15 (0.52), residues: 76
  loop :  0.47 (0.35), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 446 
 TYR   0.019   0.001   TYR A 506 
 PHE   0.019   0.001   PHE A 425 
 TRP   0.006   0.001   TRP B 213 
 HIS   0.008   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 9030)
  covalent geometry    : angle       0.52869 (12174)
  hydrogen bonds       : bond        0.04992 (  493)
  hydrogen bonds       : angle       3.92144 ( 1401)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 GLU cc_start: 0.8208 (mp0) cc_final: 0.7989 (mp0)
REVERT: A  206 ILE cc_start: 0.8327 (mt) cc_final: 0.8112 (mm)
REVERT: A  521 LYS cc_start: 0.8707 (mppt) cc_final: 0.7920 (mtmm)
REVERT: B   65 ASN cc_start: 0.7981 (m-40) cc_final: 0.7512 (m110)
REVERT: B  260 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7070 (mm-30)
REVERT: B  272 GLU cc_start: 0.8668 (pt0) cc_final: 0.8292 (tt0)
REVERT: B  422 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.7893 (mp)
REVERT: B  430 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8547 (pm20)
REVERT: B  522 THR cc_start: 0.8720 (t) cc_final: 0.8293 (p)
REVERT: B  551 SER cc_start: 0.8718 (t) cc_final: 0.8323 (m)
REVERT: B  580 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.7994 (mp)
REVERT: B  599 LYS cc_start: 0.7884 (mttp) cc_final: 0.7616 (mttm)
  outliers start: 18
  outliers final: 13
  residues processed: 116
  average time/residue: 0.0966
  time to fit residues: 14.6913
Evaluate side-chains
  121 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ASP
Chi-restraints excluded: chain A residue   89 GLN
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  256 ASN
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  422 LEU
Chi-restraints excluded: chain B residue  430 GLU
Chi-restraints excluded: chain B residue  490 VAL
Chi-restraints excluded: chain B residue  514 THR
Chi-restraints excluded: chain B residue  580 LEU
Chi-restraints excluded: chain B residue  607 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 14 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9980
   chunk 106 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 111 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 70 optimal weight:    6.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
A 256 ASN
** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 256 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.152837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.119431 restraints weight = 8873.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 1.95
r_work: 0.3077 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2910 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.1962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9030  Z= 0.169
  Angle     :  0.538  10.544  12174  Z= 0.275
  Chirality :  0.041   0.170   1380
  Planarity :  0.005   0.062   1562
  Dihedral  :  3.924  16.295   1214
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 13.75 %
    Favored  : 84.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.25 (0.26), residues: 1120
  helix:  1.28 (0.20), residues: 644
  sheet: -0.15 (0.52), residues: 76
  loop :  0.48 (0.35), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 446 
 TYR   0.020   0.002   TYR B 506 
 PHE   0.019   0.001   PHE A 425 
 TRP   0.007   0.001   TRP B 213 
 HIS   0.008   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 9030)
  covalent geometry    : angle       0.53760 (12174)
  hydrogen bonds       : bond        0.05054 (  493)
  hydrogen bonds       : angle       3.94036 ( 1401)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1844.15 seconds
wall clock time: 32 minutes 23.48 seconds (1943.48 seconds total)