Starting phenix.real_space_refine
on Sat Aug 23 06:05:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kei_37159/08_2025/8kei_37159.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kei_37159/08_2025/8kei_37159.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kei_37159/08_2025/8kei_37159.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kei_37159/08_2025/8kei_37159.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kei_37159/08_2025/8kei_37159.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kei_37159/08_2025/8kei_37159.map"
  }
  resolution = 3.56
  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=  -0.001 sd=   0.048
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: 6
    Type Number    sf(0)   Gaussians
     Fe      2      7.16       5
     P       2      5.49       5
     S      49      5.16       5
     C    6606      2.51       5
     N    1689      2.21       5
     O    1861      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: 10209
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 1035
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 133, 1035
          Classifications: {'peptide': 133}
          Link IDs: {'PTRANS': 4, 'TRANS': 128}
    Chain: "B"
      Number of atoms: 4318
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 534, 4318
          Classifications: {'peptide': 534}
          Link IDs: {'PTRANS': 22, 'TRANS': 511}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 1648
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1648
          Classifications: {'peptide': 224}
          Link IDs: {'PTRANS': 12, 'TRANS': 211}
    Chain: "D"
      Number of atoms: 1304
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1304
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 2, 'TRANS': 161}
    Chain: "E"
      Number of atoms: 1652
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1652
          Classifications: {'peptide': 217}
          Link IDs: {'PTRANS': 10, 'TRANS': 206}
    Chain: "F"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "G"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Unusual residues: {'POV': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'POV:plan-1': 1, 'POV:plan-2': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "B"
      Number of atoms: 148
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 148
          Unusual residues: {'HEM': 2, 'LBN': 1, 'NAG': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.14, per 1000 atoms: 0.21
  Number of scatterers: 10209
  At special positions: 0
  Unit cell: (73.1, 102.85, 204, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Fe      2     26.01
     S      49     16.00
     P       2     15.00
     O    1861      8.00
     N    1689      7.00
     C    6606      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 244 " - pdb=" SG  CYS B 257 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  36 " - pdb=" SG  CYS C  51 " distance=2.01
    Simple disulfide: pdb=" SG  CYS C 149 " - pdb=" SG  CYS C 205 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  24 " - pdb=" SG  CYS E  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 138 " - pdb=" SG  CYS E 198 " distance=2.03

  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=2, symmetry=0
  Links applied
    BETA1-4
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
    NAG-ASN
      " NAG B 603 " - " ASN B 132 "
      " NAG F   1 " - " ASN B 240 "
      " NAG G   1 " - " ASN B 149 "
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.85
  Conformation dependent library (CDL) restraints added in 385.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2352

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 18 sheets defined
      34.4% alpha, 19.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 36 through 53
      removed outlier: 3.687A  pdb=" N   GLU A  53 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 78
      removed outlier: 3.533A  pdb=" N   THR A  74 " --> pdb=" O   GLN A  70 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   VAL A  76 " --> pdb=" O   TYR A  72 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LYS A  78 " --> pdb=" O   THR A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 98
      removed outlier: 3.537A  pdb=" N   SER A  98 " --> pdb=" O   HIS A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 103
      removed outlier: 4.144A  pdb=" N   PHE A 103 " --> pdb=" O   PRO A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 128
      removed outlier: 4.065A  pdb=" N   ALA A 115 " --> pdb=" O   THR A 111 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ARG A 127 " --> pdb=" O   LEU A 123 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   GLY A 128 " --> pdb=" O   ALA A 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 35
    Processing helix  chain 'B' and resid 36 through 39
      removed outlier: 3.543A  pdb=" N   PHE B  39 " --> pdb=" O   PRO B  36 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 36 through 39'
    Processing helix  chain 'B' and resid 40 through 47
    Processing helix  chain 'B' and resid 48 through 81
      removed outlier: 3.691A  pdb=" N   LEU B  52 " --> pdb=" O   SER B  48 " (cutoff:3.500A)
      Proline residue:  B  56  - end of helix
      removed outlier: 3.707A  pdb=" N   PHE B  62 " --> pdb=" O   ALA B  58 " (cutoff:3.500A)
      Proline residue:  B  70  - end of helix
    Processing helix  chain 'B' and resid 96 through 131
      removed outlier: 3.667A  pdb=" N   GLU B 124 " --> pdb=" O   LEU B 120 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   TRP B 125 " --> pdb=" O   PHE B 121 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ARG B 130 " --> pdb=" O   CYS B 126 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   VAL B 131 " --> pdb=" O   VAL B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 143
    Processing helix  chain 'B' and resid 164 through 173
    Processing helix  chain 'B' and resid 176 through 193
    Processing helix  chain 'B' and resid 207 through 210
    Processing helix  chain 'B' and resid 211 through 223
      removed outlier: 3.672A  pdb=" N   GLY B 223 " --> pdb=" O   LEU B 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 240
      removed outlier: 3.830A  pdb=" N   ALA B 237 " --> pdb=" O   ALA B 233 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   VAL B 238 " --> pdb=" O   GLU B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 251
      removed outlier: 4.113A  pdb=" N   TRP B 251 " --> pdb=" O   ILE B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 291
    Processing helix  chain 'B' and resid 361 through 366
    Processing helix  chain 'B' and resid 413 through 430
      removed outlier: 3.755A  pdb=" N   ALA B 417 " --> pdb=" O   VAL B 413 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   SER B 418 " --> pdb=" O   THR B 414 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ILE B 419 " --> pdb=" O   PRO B 415 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   TRP B 424 " --> pdb=" O   LEU B 420 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   TYR B 425 " --> pdb=" O   LYS B 421 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LYS B 426 " --> pdb=" O   SER B 422 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   TYR B 427 " --> pdb=" O   VAL B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 451 through 463
      removed outlier: 3.729A  pdb=" N   ALA B 455 " --> pdb=" O   PHE B 451 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   LEU B 457 " --> pdb=" O   TRP B 453 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLN B 459 " --> pdb=" O   ALA B 455 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   SER B 463 " --> pdb=" O   GLN B 459 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 464 through 469
      removed outlier: 3.567A  pdb=" N   ARG B 468 " --> pdb=" O   MET B 465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 518 through 525
      removed outlier: 3.668A  pdb=" N   THR B 522 " --> pdb=" O   ASN B 518 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   ILE B 523 " --> pdb=" O   GLU B 519 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 543 through 554
      removed outlier: 3.927A  pdb=" N   SER B 547 " --> pdb=" O   ALA B 543 " (cutoff:3.500A)
      removed outlier: 4.954A  pdb=" N   GLN B 549 " --> pdb=" O   THR B 545 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   SER B 550 " --> pdb=" O   LEU B 546 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ILE B 551 " --> pdb=" O   SER B 547 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   SER B 552 " --> pdb=" O   LYS B 548 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 66
      removed outlier: 3.695A  pdb=" N   LYS C  66 " --> pdb=" O   ARG C  63 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 196 through 200
      removed outlier: 3.526A  pdb=" N   GLY C 199 " --> pdb=" O   SER C 196 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 20 through 40
      removed outlier: 3.566A  pdb=" N   TRP D  24 " --> pdb=" O   GLY D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 46 through 62
      removed outlier: 3.895A  pdb=" N   PHE D  50 " --> pdb=" O   GLY D  46 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 84 through 91
    Processing helix  chain 'D' and resid 92 through 94
      No H-bonds generated for 'chain 'D' and resid 92 through 94'
    Processing helix  chain 'D' and resid 146 through 162
    Processing helix  chain 'E' and resid 125 through 131
    Processing helix  chain 'E' and resid 186 through 191
      removed outlier: 4.679A  pdb=" N   GLU E 191 " --> pdb=" O   LYS E 187 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 229 through 231
    Processing sheet with id=AA2, first strand: chain 'B' and resid 296 through 301
      removed outlier: 5.731A  pdb=" N   ILE B 297 " --> pdb=" O   LYS B 313 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   LYS B 313 " --> pdb=" O   ILE B 297 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LEU B 310 " --> pdb=" O   ILE B 353 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 386 through 387
      removed outlier: 5.984A  pdb=" N   TRP B 337 " --> pdb=" O   VAL D 101 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 404 through 407
      removed outlier: 3.910A  pdb=" N   VAL B 407 " --> pdb=" O   PHE B 535 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   ILE B 532 " --> pdb=" O   ILE B 564 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 443 through 445
      removed outlier: 6.123A  pdb=" N   TRP B 443 " --> pdb=" O   TYR B 479 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 7
    Processing sheet with id=AA7, first strand: chain 'C' and resid 46 through 53
      removed outlier: 7.359A  pdb=" N   TRP C  37 " --> pdb=" O   ILE C  49 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   CYS C  51 " --> pdb=" O   MET C  35 " (cutoff:3.500A)
      removed outlier: 5.745A  pdb=" N   MET C  35 " --> pdb=" O   CYS C  51 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ARG C  98 " --> pdb=" O   ASP C 110 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 144 through 151
    Processing sheet with id=AA9, first strand: chain 'C' and resid 144 through 151
    Processing sheet with id=AB1, first strand: chain 'C' and resid 160 through 163
      removed outlier: 3.787A  pdb=" N   THR C 160 " --> pdb=" O   ASN C 208 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ASN C 206 " --> pdb=" O   SER C 162 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 4 through 5
    Processing sheet with id=AB3, first strand: chain 'D' and resid 107 through 116
      removed outlier: 3.829A  pdb=" N   ASP D 109 " --> pdb=" O   ARG D 129 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   MET D 125 " --> pdb=" O   GLU D 113 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 107 through 116
      removed outlier: 3.829A  pdb=" N   ASP D 109 " --> pdb=" O   ARG D 129 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   MET D 125 " --> pdb=" O   GLU D 113 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 5 through 7
      removed outlier: 3.638A  pdb=" N   VAL E  20 " --> pdb=" O   ILE E  76 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 13 through 15
      removed outlier: 6.690A  pdb=" N   ALA E  14 " --> pdb=" O   LYS E 111 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'E' and resid 46 through 50
      removed outlier: 6.679A  pdb=" N   TRP E  36 " --> pdb=" O   LEU E  48 " (cutoff:3.500A)
      removed outlier: 4.822A  pdb=" N   TYR E  50 " --> pdb=" O   LEU E  34 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   LEU E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 118 through 122
      removed outlier: 6.181A  pdb=" N   TYR E 177 " --> pdb=" O   ASN E 142 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 157 through 158
      removed outlier: 3.663A  pdb=" N   PHE E 213 " --> pdb=" O   TYR E 196 " (cutoff:3.500A)

    409 hydrogen bonds defined for protein.
    1134 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: 1.36

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        1.20 -     1.37: 3238
        1.37 -     1.54: 6988
        1.54 -     1.71: 171
        1.71 -     1.88: 67
        1.88 -     2.05: 8
  Bond restraints: 10472
  Sorted by residual:
  bond pdb=" C1  BMA G   3 "
       pdb=" C2  BMA G   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.623 -0.104 2.00e-02 2.50e+03 2.68e+01
  bond pdb=" CA  VAL B 413 "
       pdb=" C   VAL B 413 "
    ideal  model  delta    sigma   weight residual
    1.523  1.461  0.061 1.31e-02 5.83e+03 2.19e+01
  bond pdb=" CA  THR B 414 "
       pdb=" C   THR B 414 "
    ideal  model  delta    sigma   weight residual
    1.524  1.472  0.052 1.26e-02 6.30e+03 1.72e+01
  bond pdb=" CA  ILE B 411 "
       pdb=" C   ILE B 411 "
    ideal  model  delta    sigma   weight residual
    1.520  1.471  0.049 1.26e-02 6.30e+03 1.48e+01
  bond pdb=" CA  ARG B 287 "
       pdb=" C   ARG B 287 "
    ideal  model  delta    sigma   weight residual
    1.523  1.470  0.053 1.37e-02 5.33e+03 1.48e+01
  ... (remaining 10467 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 13913
        2.09 -     4.18: 241
        4.18 -     6.27: 57
        6.27 -     8.36: 16
        8.36 -    10.45: 7
  Bond angle restraints: 14234
  Sorted by residual:
  angle pdb=" N   VAL B 413 "
        pdb=" CA  VAL B 413 "
        pdb=" C   VAL B 413 "
      ideal   model   delta    sigma   weight residual
     112.17  105.08    7.09 9.50e-01 1.11e+00 5.57e+01
  angle pdb=" C   THR B 414 "
        pdb=" N   PRO B 415 "
        pdb=" CA  PRO B 415 "
      ideal   model   delta    sigma   weight residual
     119.56  113.36    6.20 1.01e+00 9.80e-01 3.76e+01
  angle pdb=" C   GLY B 275 "
        pdb=" N   PRO B 276 "
        pdb=" CA  PRO B 276 "
      ideal   model   delta    sigma   weight residual
     119.05  112.50    6.55 1.11e+00 8.12e-01 3.48e+01
  angle pdb=" N   SER B 291 "
        pdb=" CA  SER B 291 "
        pdb=" C   SER B 291 "
      ideal   model   delta    sigma   weight residual
     112.59  119.49   -6.90 1.22e+00 6.72e-01 3.20e+01
  angle pdb=" C   VAL B 286 "
        pdb=" CA  VAL B 286 "
        pdb=" CB  VAL B 286 "
      ideal   model   delta    sigma   weight residual
     112.16  104.02    8.14 1.55e+00 4.16e-01 2.76e+01
  ... (remaining 14229 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.23: 5879
       32.23 -    64.46: 285
       64.46 -    96.69: 32
       96.69 -   128.92: 7
      128.92 -   161.15: 1
  Dihedral angle restraints: 6204
    sinusoidal: 2533
      harmonic: 3671
  Sorted by residual:
  dihedral pdb=" CA  MET C  35 "
           pdb=" C   MET C  35 "
           pdb=" N   CYS C  36 "
           pdb=" CA  CYS C  36 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.77  -24.23     0      5.00e+00 4.00e-02 2.35e+01
  dihedral pdb=" O5  LBN B 604 "
           pdb=" C2  LBN B 604 "
           pdb=" C3  LBN B 604 "
           pdb=" O7  LBN B 604 "
      ideal   model   delta sinusoidal    sigma   weight residual
      62.67  -98.48  161.15     1      3.00e+01 1.11e-03 2.08e+01
  dihedral pdb=" CA  ASP B  95 "
           pdb=" C   ASP B  95 "
           pdb=" N   ARG B  96 "
           pdb=" CA  ARG B  96 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.38   21.62     0      5.00e+00 4.00e-02 1.87e+01
  ... (remaining 6201 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.090: 1512
       0.090 -    0.180: 80
       0.180 -    0.270: 3
       0.270 -    0.361: 2
       0.361 -    0.451: 1
  Chirality restraints: 1598
  Sorted by residual:
  chirality pdb=" C1  NAG B 603 "
            pdb=" ND2 ASN B 132 "
            pdb=" C2  NAG B 603 "
            pdb=" O5  NAG B 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.95   -0.45 2.00e-01 2.50e+01 5.08e+00
  chirality pdb=" C1  NAG F   1 "
            pdb=" ND2 ASN B 240 "
            pdb=" C2  NAG F   1 "
            pdb=" O5  NAG F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.08   -0.32 2.00e-01 2.50e+01 2.50e+00
  chirality pdb=" C1  NAG G   1 "
            pdb=" ND2 ASN B 149 "
            pdb=" C2  NAG G   1 "
            pdb=" O5  NAG G   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.10   -0.30 2.00e-01 2.50e+01 2.31e+00
  ... (remaining 1595 not shown)

  Planarity restraints: 1749
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 527 "   -0.069 5.00e-02 4.00e+02   1.02e-01 1.67e+01
        pdb=" N   PRO B 528 "    0.176 5.00e-02 4.00e+02
        pdb=" CA  PRO B 528 "   -0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO B 528 "   -0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP B 272 "    0.008 2.00e-02 2.50e+03   1.63e-02 2.67e+00
        pdb=" C   TRP B 272 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   TRP B 272 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ILE B 273 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B  96 "   -0.008 2.00e-02 2.50e+03   1.63e-02 2.67e+00
        pdb=" C   ARG B  96 "    0.028 2.00e-02 2.50e+03
        pdb=" O   ARG B  96 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ASN B  97 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1746 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 328
        2.70 -     3.25: 9871
        3.25 -     3.80: 15524
        3.80 -     4.35: 18558
        4.35 -     4.90: 32103
  Nonbonded interactions: 76384
  Sorted by model distance:
  nonbonded pdb=" O   ARG B 559 "
            pdb=" NH1 ARG B 559 "
     model   vdw
     2.150 3.120
  nonbonded pdb=" O3  NAG G   2 "
            pdb=" O2  BMA G   3 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OE1 GLU A  53 "
            pdb=" OH  TYR A 121 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" OH  TYR D   2 "
            pdb=" OG1 THR D 139 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" OE2 GLU C   6 "
            pdb=" OG1 THR C 116 "
     model   vdw
     2.224 3.040
  ... (remaining 76379 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
Found NCS groups:
ncs_group {
  reference = chain 'F'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.780
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.240
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.104  10487  Z= 0.233
  Angle     :  0.751  12.077  14267  Z= 0.385
  Chirality :  0.045   0.451   1598
  Planarity :  0.004   0.102   1746
  Dihedral  : 18.448 161.154   3834
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 32.96 %
    Favored  : 66.57 %
  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: -0.29 (0.25), residues: 1258
  helix:  1.41 (0.28), residues: 386
  sheet:  0.19 (0.35), residues: 265
  loop : -1.48 (0.26), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG B  96 
 TYR   0.012   0.001   TYR A 121 
 PHE   0.019   0.001   PHE B 520 
 TRP   0.010   0.001   TRP C  37 
 HIS   0.009   0.001   HIS B 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 (10472)
  covalent geometry    : angle       0.72697 (14234)
  SS BOND              : bond        0.01002 (    6)
  SS BOND              : angle       1.62748 (   12)
  hydrogen bonds       : bond        0.20401 (  395)
  hydrogen bonds       : angle       7.01025 ( 1134)
  Misc. bond           : bond        0.05194 (    2)
  link_BETA1-4         : bond        0.02015 (    4)
  link_BETA1-4         : angle       5.24762 (   12)
  link_NAG-ASN         : bond        0.00792 (    3)
  link_NAG-ASN         : angle       4.12078 (    9)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 136
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: B  465 MET cc_start: 0.7743 (ptm) cc_final: 0.7513 (ttp)
  outliers start: 5
  outliers final: 4
  residues processed: 140
  average time/residue: 0.0897
  time to fit residues: 18.4264
Evaluate side-chains
  131 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 127
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  294 LYS
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain C residue   56 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0050
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.6980
   chunk 123 optimal weight:    5.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   overall best weight:    1.3400

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

Flipped N/Q/H residues before XYZ refinement:
** B  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 222 HIS
B 338 HIS
B 477 ASN
B 518 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.139493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.111841 restraints weight = 17285.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.111552 restraints weight = 13693.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.112969 restraints weight = 13271.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.113482 restraints weight = 7999.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.114012 restraints weight = 7338.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.0958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075  10487  Z= 0.179
  Angle     :  0.670   9.484  14267  Z= 0.326
  Chirality :  0.043   0.380   1598
  Planarity :  0.004   0.068   1746
  Dihedral  : 10.391 150.192   1599
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 30.00 %
    Favored  : 65.19 %
  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: -0.28 (0.25), residues: 1258
  helix:  1.36 (0.28), residues: 388
  sheet: -0.01 (0.34), residues: 277
  loop : -1.34 (0.27), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 559 
 TYR   0.012   0.001   TYR E 196 
 PHE   0.018   0.001   PHE B  62 
 TRP   0.010   0.001   TRP C  37 
 HIS   0.008   0.001   HIS B 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 (10472)
  covalent geometry    : angle       0.65172 (14234)
  SS BOND              : bond        0.00789 (    6)
  SS BOND              : angle       1.49697 (   12)
  hydrogen bonds       : bond        0.04797 (  395)
  hydrogen bonds       : angle       5.08984 ( 1134)
  Misc. bond           : bond        0.05650 (    2)
  link_BETA1-4         : bond        0.01983 (    4)
  link_BETA1-4         : angle       4.37102 (   12)
  link_NAG-ASN         : bond        0.00661 (    3)
  link_NAG-ASN         : angle       3.23989 (    9)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 143
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  122 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8134 (ttpp)
REVERT: E  102 PHE cc_start: 0.9106 (OUTLIER) cc_final: 0.7434 (t80)
  outliers start: 52
  outliers final: 31
  residues processed: 189
  average time/residue: 0.0971
  time to fit residues: 26.8475
Evaluate side-chains
  166 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 133
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   98 SER
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  294 LYS
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  350 PHE
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  532 ILE
Chi-restraints excluded: chain C residue    2 GLN
Chi-restraints excluded: chain C residue   36 CYS
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain C residue  204 ILE
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue   78 VAL
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  122 LYS
Chi-restraints excluded: chain E residue   66 SER
Chi-restraints excluded: chain E residue  102 PHE
Chi-restraints excluded: chain E residue  108 VAL
Chi-restraints excluded: chain E residue  128 GLN
Chi-restraints excluded: chain E residue  154 VAL
Chi-restraints excluded: chain E residue  180 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9990
   chunk 64 optimal weight:    9.9990
   chunk 48 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 59 optimal weight:    6.9990
   chunk 111 optimal weight:    4.9990
   chunk 108 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 32 optimal weight:    0.2980
   chunk 47 optimal weight:    0.6980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** B  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 201 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.140624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.113303 restraints weight = 17343.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.113506 restraints weight = 13731.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.114736 restraints weight = 13087.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.115414 restraints weight = 8201.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.115570 restraints weight = 7484.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.1140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10487  Z= 0.124
  Angle     :  0.614   8.722  14267  Z= 0.296
  Chirality :  0.042   0.326   1598
  Planarity :  0.004   0.064   1746
  Dihedral  :  9.041 144.418   1597
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 29.26 %
    Favored  : 65.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.21 (0.25), residues: 1258
  helix:  1.47 (0.28), residues: 388
  sheet:  0.00 (0.34), residues: 274
  loop : -1.32 (0.27), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 559 
 TYR   0.013   0.001   TYR D  86 
 PHE   0.012   0.001   PHE B 570 
 TRP   0.009   0.001   TRP C 163 
 HIS   0.006   0.001   HIS B 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (10472)
  covalent geometry    : angle       0.59869 (14234)
  SS BOND              : bond        0.00513 (    6)
  SS BOND              : angle       1.56841 (   12)
  hydrogen bonds       : bond        0.04258 (  395)
  hydrogen bonds       : angle       4.71652 ( 1134)
  Misc. bond           : bond        0.04361 (    2)
  link_BETA1-4         : bond        0.01742 (    4)
  link_BETA1-4         : angle       3.75149 (   12)
  link_NAG-ASN         : bond        0.00690 (    3)
  link_NAG-ASN         : angle       2.86300 (    9)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 139
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
REVERT: B   60 LEU cc_start: 0.8477 (tt) cc_final: 0.8134 (tt)
REVERT: D  122 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8114 (ttpp)
REVERT: E  102 PHE cc_start: 0.9071 (OUTLIER) cc_final: 0.7470 (t80)
  outliers start: 56
  outliers final: 38
  residues processed: 184
  average time/residue: 0.0911
  time to fit residues: 24.8386
Evaluate side-chains
  171 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 131
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   94 HIS
Chi-restraints excluded: chain A residue   98 SER
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  210 HIS
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  294 LYS
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  350 PHE
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  465 MET
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain C residue    2 GLN
Chi-restraints excluded: chain C residue   23 THR
Chi-restraints excluded: chain C residue   36 CYS
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  125 THR
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  216 VAL
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue   78 VAL
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  122 LYS
Chi-restraints excluded: chain D residue  126 VAL
Chi-restraints excluded: chain E residue  102 PHE
Chi-restraints excluded: chain E residue  108 VAL
Chi-restraints excluded: chain E residue  154 VAL
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  196 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 86 optimal weight:    5.9990
   chunk 96 optimal weight:    1.9990
   chunk 39 optimal weight:    0.2980
   chunk 91 optimal weight:    7.9990
   chunk 117 optimal weight:    6.9990
   chunk 64 optimal weight:    9.9990
   chunk 99 optimal weight:    7.9990
   chunk 72 optimal weight:    0.1980
   chunk 27 optimal weight:    1.9990
   chunk 58 optimal weight:    9.9990
   chunk 56 optimal weight:    6.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
** B  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 562 HIS ** 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 = 0.3962 r_free = 0.3962 target = 0.145567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.117902 restraints weight = 17024.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.117525 restraints weight = 14837.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.118812 restraints weight = 12325.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.119354 restraints weight = 8253.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.119872 restraints weight = 7789.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.1478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.152  10487  Z= 0.249
  Angle     :  0.718  12.008  14267  Z= 0.350
  Chirality :  0.044   0.327   1598
  Planarity :  0.004   0.066   1746
  Dihedral  :  8.786 139.055   1596
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.63 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  7.04 %
    Allowed  : 28.80 %
    Favored  : 64.17 %
  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: -0.44 (0.25), residues: 1258
  helix:  1.24 (0.27), residues: 389
  sheet: -0.18 (0.33), residues: 282
  loop : -1.42 (0.27), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  85 
 TYR   0.015   0.002   TYR E 144 
 PHE   0.025   0.002   PHE B  62 
 TRP   0.012   0.001   TRP C 163 
 HIS   0.013   0.002   HIS B 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00610 (10472)
  covalent geometry    : angle       0.70488 (14234)
  SS BOND              : bond        0.00903 (    6)
  SS BOND              : angle       2.14919 (   12)
  hydrogen bonds       : bond        0.05221 (  395)
  hydrogen bonds       : angle       4.87863 ( 1134)
  Misc. bond           : bond        0.11190 (    2)
  link_BETA1-4         : bond        0.01636 (    4)
  link_BETA1-4         : angle       3.60812 (   12)
  link_NAG-ASN         : bond        0.00543 (    3)
  link_NAG-ASN         : angle       2.74458 (    9)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 131
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
REVERT: B   60 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8108 (tt)
REVERT: D  122 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8136 (ttpp)
REVERT: E  102 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.7320 (t80)
  outliers start: 76
  outliers final: 54
  residues processed: 194
  average time/residue: 0.0967
  time to fit residues: 27.4492
Evaluate side-chains
  186 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 129
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   98 SER
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  294 LYS
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  350 PHE
Chi-restraints excluded: chain B residue  355 ILE
Chi-restraints excluded: chain B residue  358 VAL
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  428 CYS
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain C residue    2 GLN
Chi-restraints excluded: chain C residue   23 THR
Chi-restraints excluded: chain C residue   36 CYS
Chi-restraints excluded: chain C residue   56 ASP
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  125 THR
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  204 ILE
Chi-restraints excluded: chain C residue  216 VAL
Chi-restraints excluded: chain C residue  218 LYS
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   62 ASN
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue   78 VAL
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  115 GLU
Chi-restraints excluded: chain D residue  122 LYS
Chi-restraints excluded: chain D residue  126 VAL
Chi-restraints excluded: chain E residue   66 SER
Chi-restraints excluded: chain E residue  102 PHE
Chi-restraints excluded: chain E residue  108 VAL
Chi-restraints excluded: chain E residue  113 THR
Chi-restraints excluded: chain E residue  154 VAL
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  196 TYR
Chi-restraints excluded: chain E residue  210 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 91 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 89 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 59 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 116 optimal weight:    0.4980
   chunk 7 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** B  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 562 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.151777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.123951 restraints weight = 16813.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.124550 restraints weight = 11013.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.125523 restraints weight = 10483.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.126055 restraints weight = 7067.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.126631 restraints weight = 6384.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.1464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.089  10487  Z= 0.126
  Angle     :  0.623   8.951  14267  Z= 0.300
  Chirality :  0.042   0.299   1598
  Planarity :  0.004   0.072   1746
  Dihedral  :  8.423 134.847   1596
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 29.81 %
    Favored  : 64.35 %
  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: -0.21 (0.25), residues: 1258
  helix:  1.54 (0.28), residues: 387
  sheet: -0.10 (0.33), residues: 281
  loop : -1.32 (0.27), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 118 
 TYR   0.013   0.001   TYR B 427 
 PHE   0.011   0.001   PHE B  62 
 TRP   0.010   0.001   TRP B 337 
 HIS   0.007   0.001   HIS B 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (10472)
  covalent geometry    : angle       0.61009 (14234)
  SS BOND              : bond        0.00584 (    6)
  SS BOND              : angle       1.87952 (   12)
  hydrogen bonds       : bond        0.04074 (  395)
  hydrogen bonds       : angle       4.52405 ( 1134)
  Misc. bond           : bond        0.06405 (    2)
  link_BETA1-4         : bond        0.01641 (    4)
  link_BETA1-4         : angle       3.41448 (   12)
  link_NAG-ASN         : bond        0.00592 (    3)
  link_NAG-ASN         : angle       2.61102 (    9)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 138
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8463 (mt0)
REVERT: B   60 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8077 (tt)
REVERT: B  268 MET cc_start: 0.8714 (ppp) cc_final: 0.6786 (ppp)
REVERT: D  114 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7860 (mm-30)
REVERT: D  122 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8197 (ttpp)
REVERT: E  102 PHE cc_start: 0.9095 (OUTLIER) cc_final: 0.7528 (t80)
REVERT: E  128 GLN cc_start: 0.6942 (OUTLIER) cc_final: 0.6715 (tp-100)
  outliers start: 63
  outliers final: 44
  residues processed: 194
  average time/residue: 0.0943
  time to fit residues: 26.9296
Evaluate side-chains
  180 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 131
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   98 SER
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  294 LYS
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  350 PHE
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  428 CYS
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain C residue    2 GLN
Chi-restraints excluded: chain C residue   23 THR
Chi-restraints excluded: chain C residue   36 CYS
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  125 THR
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  216 VAL
Chi-restraints excluded: chain C residue  218 LYS
Chi-restraints excluded: chain D residue   43 ASP
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  122 LYS
Chi-restraints excluded: chain D residue  126 VAL
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain E residue  102 PHE
Chi-restraints excluded: chain E residue  108 VAL
Chi-restraints excluded: chain E residue  128 GLN
Chi-restraints excluded: chain E residue  138 CYS
Chi-restraints excluded: chain E residue  154 VAL
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  196 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 60 optimal weight:    0.3980
   chunk 19 optimal weight:    0.9980
   chunk 115 optimal weight:    7.9990
   chunk 68 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 119 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 104 optimal weight:    3.9990
   chunk 99 optimal weight:    0.0570
   chunk 86 optimal weight:    6.9990
   overall best weight:    0.8500

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

Flipped N/Q/H residues before XYZ refinement:
** B  22 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 = 0.4032 r_free = 0.4032 target = 0.151238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.123307 restraints weight = 16788.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.124759 restraints weight = 11885.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.125378 restraints weight = 10077.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.126982 restraints weight = 7214.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.127072 restraints weight = 6206.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.1524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.093  10487  Z= 0.133
  Angle     :  0.639   9.646  14267  Z= 0.308
  Chirality :  0.042   0.290   1598
  Planarity :  0.004   0.066   1746
  Dihedral  :  8.263 131.650   1596
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  6.02 %
    Allowed  : 30.19 %
    Favored  : 63.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.23 (0.25), residues: 1258
  helix:  1.50 (0.28), residues: 391
  sheet: -0.16 (0.33), residues: 281
  loop : -1.31 (0.27), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 118 
 TYR   0.010   0.001   TYR E 144 
 PHE   0.028   0.001   PHE C 131 
 TRP   0.009   0.001   TRP B 337 
 HIS   0.009   0.001   HIS B 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (10472)
  covalent geometry    : angle       0.62707 (14234)
  SS BOND              : bond        0.00635 (    6)
  SS BOND              : angle       1.84456 (   12)
  hydrogen bonds       : bond        0.04015 (  395)
  hydrogen bonds       : angle       4.45196 ( 1134)
  Misc. bond           : bond        0.06711 (    2)
  link_BETA1-4         : bond        0.01580 (    4)
  link_BETA1-4         : angle       3.34933 (   12)
  link_NAG-ASN         : bond        0.00534 (    3)
  link_NAG-ASN         : angle       2.48249 (    9)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 132
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8520 (mt0)
REVERT: B   60 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8032 (tt)
REVERT: B  161 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7041 (ttpp)
REVERT: D  114 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7991 (mm-30)
REVERT: D  122 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8185 (ttpp)
REVERT: E  102 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.7429 (t80)
  outliers start: 65
  outliers final: 53
  residues processed: 187
  average time/residue: 0.0913
  time to fit residues: 25.3638
Evaluate side-chains
  188 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 130
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   98 SER
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  119 HIS
Chi-restraints excluded: chain B residue  161 LYS
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  294 LYS
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  350 PHE
Chi-restraints excluded: chain B residue  384 LYS
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  428 CYS
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain C residue    2 GLN
Chi-restraints excluded: chain C residue   23 THR
Chi-restraints excluded: chain C residue   36 CYS
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  125 THR
Chi-restraints excluded: chain C residue  150 LEU
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  204 ILE
Chi-restraints excluded: chain C residue  216 VAL
Chi-restraints excluded: chain C residue  218 LYS
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   62 ASN
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue   78 VAL
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  122 LYS
Chi-restraints excluded: chain D residue  126 VAL
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain E residue   98 THR
Chi-restraints excluded: chain E residue  102 PHE
Chi-restraints excluded: chain E residue  108 VAL
Chi-restraints excluded: chain E residue  128 GLN
Chi-restraints excluded: chain E residue  138 CYS
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  196 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 29 optimal weight:    0.3980
   chunk 53 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 92 optimal weight:    0.8980
   overall best weight:    0.8586

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

Flipped N/Q/H residues before XYZ refinement:
** B  22 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 = 0.3945 r_free = 0.3945 target = 0.147368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.119164 restraints weight = 16890.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.119281 restraints weight = 11101.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.120204 restraints weight = 9747.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.120956 restraints weight = 7471.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.120981 restraints weight = 6957.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.1587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.091  10487  Z= 0.132
  Angle     :  0.636   9.256  14267  Z= 0.305
  Chirality :  0.041   0.278   1598
  Planarity :  0.004   0.072   1746
  Dihedral  :  8.112 127.615   1596
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  6.11 %
    Allowed  : 31.02 %
    Favored  : 62.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.21 (0.25), residues: 1258
  helix:  1.52 (0.28), residues: 395
  sheet: -0.14 (0.33), residues: 278
  loop : -1.33 (0.27), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 118 
 TYR   0.017   0.001   TYR D  86 
 PHE   0.016   0.001   PHE C 131 
 TRP   0.010   0.001   TRP C 163 
 HIS   0.008   0.001   HIS B 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (10472)
  covalent geometry    : angle       0.62417 (14234)
  SS BOND              : bond        0.00618 (    6)
  SS BOND              : angle       1.77475 (   12)
  hydrogen bonds       : bond        0.03917 (  395)
  hydrogen bonds       : angle       4.36887 ( 1134)
  Misc. bond           : bond        0.06547 (    2)
  link_BETA1-4         : bond        0.01536 (    4)
  link_BETA1-4         : angle       3.25599 (   12)
  link_NAG-ASN         : bond        0.00524 (    3)
  link_NAG-ASN         : angle       2.39825 (    9)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 133
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 TYR cc_start: 0.8431 (m-80) cc_final: 0.7968 (m-80)
REVERT: A  130 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8535 (mt0)
REVERT: B   60 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8062 (tt)
REVERT: B  161 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7045 (ttpp)
REVERT: D  114 GLU cc_start: 0.8283 (mm-30) cc_final: 0.8059 (mm-30)
REVERT: D  122 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8192 (ttpp)
REVERT: D  151 GLU cc_start: 0.8239 (mm-30) cc_final: 0.8019 (mm-30)
REVERT: E  102 PHE cc_start: 0.9090 (OUTLIER) cc_final: 0.7483 (t80)
  outliers start: 66
  outliers final: 55
  residues processed: 189
  average time/residue: 0.0943
  time to fit residues: 26.2655
Evaluate side-chains
  191 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 131
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   98 SER
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  119 HIS
Chi-restraints excluded: chain B residue  161 LYS
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  210 HIS
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  294 LYS
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  350 PHE
Chi-restraints excluded: chain B residue  384 LYS
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  428 CYS
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain C residue    2 GLN
Chi-restraints excluded: chain C residue   23 THR
Chi-restraints excluded: chain C residue   36 CYS
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  125 THR
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  204 ILE
Chi-restraints excluded: chain C residue  216 VAL
Chi-restraints excluded: chain C residue  218 LYS
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   62 ASN
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue   78 VAL
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  122 LYS
Chi-restraints excluded: chain D residue  126 VAL
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain E residue   55 LEU
Chi-restraints excluded: chain E residue   98 THR
Chi-restraints excluded: chain E residue  102 PHE
Chi-restraints excluded: chain E residue  108 VAL
Chi-restraints excluded: chain E residue  128 GLN
Chi-restraints excluded: chain E residue  138 CYS
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  196 TYR
Chi-restraints excluded: chain E residue  210 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 119 optimal weight:    8.9990
   chunk 56 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 62 optimal weight:    8.9990
   chunk 38 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9990
   chunk 63 optimal weight:    0.0980
   chunk 105 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 40 optimal weight:    0.6980
   chunk 79 optimal weight:    7.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B  22 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 = 0.3958 r_free = 0.3958 target = 0.148456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.120535 restraints weight = 16856.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.120506 restraints weight = 12076.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.122076 restraints weight = 11070.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.122670 restraints weight = 7141.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.122930 restraints weight = 6553.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.1619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078  10487  Z= 0.120
  Angle     :  0.630   9.755  14267  Z= 0.302
  Chirality :  0.041   0.266   1598
  Planarity :  0.004   0.068   1746
  Dihedral  :  7.951 122.245   1596
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  : 30.74 %
    Favored  : 62.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.20 (0.25), residues: 1258
  helix:  1.54 (0.28), residues: 399
  sheet: -0.21 (0.33), residues: 287
  loop : -1.31 (0.27), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 129 
 TYR   0.008   0.001   TYR E 144 
 PHE   0.013   0.001   PHE C 131 
 TRP   0.009   0.001   TRP B 337 
 HIS   0.008   0.001   HIS B 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (10472)
  covalent geometry    : angle       0.61940 (14234)
  SS BOND              : bond        0.00509 (    6)
  SS BOND              : angle       1.67375 (   12)
  hydrogen bonds       : bond        0.03666 (  395)
  hydrogen bonds       : angle       4.27697 ( 1134)
  Misc. bond           : bond        0.05788 (    2)
  link_BETA1-4         : bond        0.01495 (    4)
  link_BETA1-4         : angle       3.14038 (   12)
  link_NAG-ASN         : bond        0.00522 (    3)
  link_NAG-ASN         : angle       2.30988 (    9)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 138
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8493 (mt0)
REVERT: B   60 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8083 (tt)
REVERT: B  161 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7057 (ttpp)
REVERT: D  122 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8282 (ttpp)
REVERT: E    3 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7633 (tt)
REVERT: E  102 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.7516 (t80)
  outliers start: 68
  outliers final: 53
  residues processed: 198
  average time/residue: 0.0932
  time to fit residues: 27.1384
Evaluate side-chains
  193 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 134
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   98 SER
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  119 HIS
Chi-restraints excluded: chain B residue  161 LYS
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  210 HIS
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  294 LYS
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  350 PHE
Chi-restraints excluded: chain B residue  384 LYS
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  428 CYS
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain C residue   23 THR
Chi-restraints excluded: chain C residue   36 CYS
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  125 THR
Chi-restraints excluded: chain C residue  150 LEU
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  216 VAL
Chi-restraints excluded: chain C residue  218 LYS
Chi-restraints excluded: chain D residue   39 TYR
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue   78 VAL
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  122 LYS
Chi-restraints excluded: chain D residue  126 VAL
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain E residue    3 LEU
Chi-restraints excluded: chain E residue   55 LEU
Chi-restraints excluded: chain E residue  102 PHE
Chi-restraints excluded: chain E residue  108 VAL
Chi-restraints excluded: chain E residue  128 GLN
Chi-restraints excluded: chain E residue  138 CYS
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  196 TYR
Chi-restraints excluded: chain E residue  210 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 17 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9980
   chunk 18 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 22 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** B  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 201 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.145309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.118195 restraints weight = 16986.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.118709 restraints weight = 12857.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.120136 restraints weight = 11553.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.120304 restraints weight = 7191.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.120574 restraints weight = 7282.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.088  10487  Z= 0.133
  Angle     :  0.646  10.623  14267  Z= 0.309
  Chirality :  0.041   0.264   1598
  Planarity :  0.004   0.073   1746
  Dihedral  :  7.854 117.864   1596
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 31.39 %
    Favored  : 62.96 %
  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: -0.18 (0.25), residues: 1258
  helix:  1.60 (0.28), residues: 393
  sheet: -0.20 (0.32), residues: 287
  loop : -1.29 (0.27), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 118 
 TYR   0.019   0.001   TYR D  86 
 PHE   0.012   0.001   PHE B 565 
 TRP   0.011   0.001   TRP C 163 
 HIS   0.008   0.001   HIS B 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (10472)
  covalent geometry    : angle       0.63557 (14234)
  SS BOND              : bond        0.00579 (    6)
  SS BOND              : angle       1.84203 (   12)
  hydrogen bonds       : bond        0.03779 (  395)
  hydrogen bonds       : angle       4.26799 ( 1134)
  Misc. bond           : bond        0.06241 (    2)
  link_BETA1-4         : bond        0.01470 (    4)
  link_BETA1-4         : angle       3.09271 (   12)
  link_NAG-ASN         : bond        0.00506 (    3)
  link_NAG-ASN         : angle       2.28568 (    9)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 133
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   60 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8032 (tt)
REVERT: B  161 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7108 (ttpp)
REVERT: D  114 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7790 (mm-30)
REVERT: D  122 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8133 (ttpp)
REVERT: E    3 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7651 (tt)
REVERT: E  102 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.7497 (t80)
  outliers start: 61
  outliers final: 52
  residues processed: 186
  average time/residue: 0.0939
  time to fit residues: 25.7978
Evaluate side-chains
  185 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 128
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   98 SER
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  119 HIS
Chi-restraints excluded: chain B residue  161 LYS
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  294 LYS
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  350 PHE
Chi-restraints excluded: chain B residue  384 LYS
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  428 CYS
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain C residue    2 GLN
Chi-restraints excluded: chain C residue   23 THR
Chi-restraints excluded: chain C residue   36 CYS
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  125 THR
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  216 VAL
Chi-restraints excluded: chain C residue  218 LYS
Chi-restraints excluded: chain D residue   39 TYR
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue   78 VAL
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  122 LYS
Chi-restraints excluded: chain D residue  126 VAL
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain E residue    3 LEU
Chi-restraints excluded: chain E residue   55 LEU
Chi-restraints excluded: chain E residue  102 PHE
Chi-restraints excluded: chain E residue  108 VAL
Chi-restraints excluded: chain E residue  128 GLN
Chi-restraints excluded: chain E residue  138 CYS
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  196 TYR
Chi-restraints excluded: chain E residue  210 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 88 optimal weight:    5.9990
   chunk 56 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9990
   chunk 124 optimal weight:    0.0040
   chunk 90 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9980
   chunk 113 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 100 optimal weight:    2.9990
   overall best weight:    0.7192

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

Flipped N/Q/H residues before XYZ refinement:
** B  22 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 = 0.3947 r_free = 0.3947 target = 0.147369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.119391 restraints weight = 16847.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.119946 restraints weight = 12142.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.121186 restraints weight = 11256.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.121772 restraints weight = 7177.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.121873 restraints weight = 6617.027|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.084  10487  Z= 0.126
  Angle     :  0.648  11.599  14267  Z= 0.310
  Chirality :  0.041   0.258   1598
  Planarity :  0.004   0.072   1746
  Dihedral  :  7.743 112.678   1596
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 31.39 %
    Favored  : 63.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.19 (0.25), residues: 1258
  helix:  1.53 (0.28), residues: 399
  sheet: -0.13 (0.33), residues: 280
  loop : -1.33 (0.27), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 118 
 TYR   0.015   0.001   TYR B 201 
 PHE   0.010   0.001   PHE B  62 
 TRP   0.012   0.001   TRP C 163 
 HIS   0.008   0.001   HIS B 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (10472)
  covalent geometry    : angle       0.63841 (14234)
  SS BOND              : bond        0.00662 (    6)
  SS BOND              : angle       1.88225 (   12)
  hydrogen bonds       : bond        0.03679 (  395)
  hydrogen bonds       : angle       4.23876 ( 1134)
  Misc. bond           : bond        0.06018 (    2)
  link_BETA1-4         : bond        0.01447 (    4)
  link_BETA1-4         : angle       3.01958 (   12)
  link_NAG-ASN         : bond        0.00521 (    3)
  link_NAG-ASN         : angle       2.25014 (    9)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 132
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8571 (mt0)
REVERT: B   60 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8033 (tt)
REVERT: B  161 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7102 (ttpp)
REVERT: D  114 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7939 (mm-30)
REVERT: D  122 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8136 (ttpp)
REVERT: E    3 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7632 (tt)
REVERT: E  102 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.7466 (t80)
  outliers start: 60
  outliers final: 54
  residues processed: 184
  average time/residue: 0.0992
  time to fit residues: 26.5909
Evaluate side-chains
  190 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 130
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 TYR
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   98 SER
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  119 HIS
Chi-restraints excluded: chain B residue  161 LYS
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  210 HIS
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  294 LYS
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  350 PHE
Chi-restraints excluded: chain B residue  384 LYS
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  428 CYS
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain C residue    2 GLN
Chi-restraints excluded: chain C residue   23 THR
Chi-restraints excluded: chain C residue   36 CYS
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain C residue  125 THR
Chi-restraints excluded: chain C residue  150 LEU
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  216 VAL
Chi-restraints excluded: chain C residue  218 LYS
Chi-restraints excluded: chain D residue   39 TYR
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue   78 VAL
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  122 LYS
Chi-restraints excluded: chain D residue  126 VAL
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain E residue    3 LEU
Chi-restraints excluded: chain E residue   55 LEU
Chi-restraints excluded: chain E residue  102 PHE
Chi-restraints excluded: chain E residue  108 VAL
Chi-restraints excluded: chain E residue  128 GLN
Chi-restraints excluded: chain E residue  138 CYS
Chi-restraints excluded: chain E residue  180 SER
Chi-restraints excluded: chain E residue  196 TYR
Chi-restraints excluded: chain E residue  210 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 119 optimal weight:    0.2980
   chunk 124 optimal weight:    0.2980
   chunk 28 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 81 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 52 optimal weight:    8.9990
   chunk 91 optimal weight:    2.9990
   chunk 79 optimal weight:    4.9990
   overall best weight:    0.6784

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

Flipped N/Q/H residues before XYZ refinement:
** B  22 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 = 0.3932 r_free = 0.3932 target = 0.146022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.119054 restraints weight = 17109.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.119934 restraints weight = 13497.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.120929 restraints weight = 13166.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.121438 restraints weight = 7720.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.121809 restraints weight = 7075.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.1768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.079  10487  Z= 0.124
  Angle     :  0.648  11.891  14267  Z= 0.310
  Chirality :  0.041   0.254   1598
  Planarity :  0.004   0.073   1746
  Dihedral  :  7.656 107.375   1596
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 31.20 %
    Favored  : 62.96 %
  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: -0.17 (0.25), residues: 1258
  helix:  1.53 (0.28), residues: 399
  sheet: -0.10 (0.33), residues: 281
  loop : -1.31 (0.27), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 559 
 TYR   0.016   0.001   TYR B 427 
 PHE   0.011   0.001   PHE B 563 
 TRP   0.012   0.001   TRP C 163 
 HIS   0.008   0.001   HIS B 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (10472)
  covalent geometry    : angle       0.63859 (14234)
  SS BOND              : bond        0.00614 (    6)
  SS BOND              : angle       1.83319 (   12)
  hydrogen bonds       : bond        0.03614 (  395)
  hydrogen bonds       : angle       4.19781 ( 1134)
  Misc. bond           : bond        0.05733 (    2)
  link_BETA1-4         : bond        0.01397 (    4)
  link_BETA1-4         : angle       2.95653 (   12)
  link_NAG-ASN         : bond        0.00520 (    3)
  link_NAG-ASN         : angle       2.21738 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1816.76 seconds
wall clock time: 32 minutes 20.25 seconds (1940.25 seconds total)