Starting phenix.real_space_refine
on Thu May  1 03:02:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kei_37159/05_2025/8kei_37159.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kei_37159/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kei_37159/05_2025/8kei_37159.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kei_37159/05_2025/8kei_37159.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kei_37159/05_2025/8kei_37159.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kei_37159/05_2025/8kei_37159.cif"
  }
  resolution = 3.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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-2': 1, 'POV:plan-1': 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: 7.05, per 1000 atoms: 0.69
  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: 3.04
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  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: 1.12
  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: 3.17

  Time building geometry restraints manager: 3.30 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:             3.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     27.450
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.870
-------------------------------------------------------------------------------
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 : 9.02
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (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
 TRP   0.010   0.001   TRP C  37 
 HIS   0.009   0.001   HIS B 119 
 PHE   0.019   0.001   PHE B 520 
 TYR   0.012   0.001   TYR A 121 
 ARG   0.019   0.001   ARG B  96 

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

*********************** 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  : 1.049 
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: 0.2036
  time to fit residues: 41.7624
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  : 1.125 
-------------------------------------------------------------------------------
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 105 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9980
   chunk 52 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 63 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9990
   chunk 97 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   chunk 113 optimal weight:    0.0270
   overall best weight:    1.4044

-------------------------------------------------------------------------------
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 = 0.3815 r_free = 0.3815 target = 0.139282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.111479 restraints weight = 17178.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.111770 restraints weight = 12873.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.112729 restraints weight = 12910.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.0969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.079  10487  Z= 0.184
  Angle     :  0.672   9.583  14267  Z= 0.327
  Chirality :  0.043   0.374   1598
  Planarity :  0.004   0.067   1746
  Dihedral  : 10.405 150.150   1599
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 30.28 %
    Favored  : 65.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.25), residues: 1258
  helix:  1.32 (0.28), residues: 389
  sheet: -0.01 (0.34), residues: 277
  loop : -1.33 (0.27), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  37 
 HIS   0.008   0.001   HIS B 119 
 PHE   0.018   0.001   PHE B  62 
 TYR   0.012   0.001   TYR E 144 
 ARG   0.004   0.000   ARG B 559 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00633 (    3)
  link_NAG-ASN         : angle       3.24452 (    9)
  link_BETA1-4         : bond        0.02055 (    4)
  link_BETA1-4         : angle       4.36833 (   12)
  hydrogen bonds       : bond        0.04902 (  395)
  hydrogen bonds       : angle       5.10848 ( 1134)
  SS BOND              : bond        0.00762 (    6)
  SS BOND              : angle       1.51758 (   12)
  covalent geometry    : bond        0.00446 (10472)
  covalent geometry    : angle       0.65431 (14234)
  Misc. bond           : bond        0.05894 (    2)

*********************** 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
  192 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 142
  time to evaluate  : 1.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  465 MET cc_start: 0.7525 (ptm) cc_final: 0.7321 (ttp)
REVERT: D  122 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8127 (ttpp)
REVERT: E  102 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.7400 (t80)
  outliers start: 50
  outliers final: 32
  residues processed: 186
  average time/residue: 0.2541
  time to fit residues: 68.2615
Evaluate side-chains
  166 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 132
  time to evaluate  : 1.269 
-------------------------------------------------------------------------------
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  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   23 THR
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   79 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 97 optimal weight:    0.9990
   chunk 70 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   chunk 50 optimal weight:    0.4980
   chunk 79 optimal weight:    4.9990
   chunk 98 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 180 GLN
C 201 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.140235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.113051 restraints weight = 17341.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.112897 restraints weight = 13702.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.114023 restraints weight = 13848.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.1148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  10487  Z= 0.129
  Angle     :  0.615   9.040  14267  Z= 0.297
  Chirality :  0.042   0.325   1598
  Planarity :  0.004   0.064   1746
  Dihedral  :  9.011 143.940   1597
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 29.54 %
    Favored  : 65.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.25), residues: 1258
  helix:  1.46 (0.28), residues: 388
  sheet:  0.01 (0.34), residues: 274
  loop : -1.33 (0.27), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 163 
 HIS   0.008   0.001   HIS B 119 
 PHE   0.012   0.001   PHE B  62 
 TYR   0.013   0.001   TYR D  86 
 ARG   0.003   0.000   ARG B  96 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00685 (    3)
  link_NAG-ASN         : angle       2.86001 (    9)
  link_BETA1-4         : bond        0.01950 (    4)
  link_BETA1-4         : angle       3.77954 (   12)
  hydrogen bonds       : bond        0.04271 (  395)
  hydrogen bonds       : angle       4.71686 ( 1134)
  SS BOND              : bond        0.00476 (    6)
  SS BOND              : angle       1.59646 (   12)
  covalent geometry    : bond        0.00304 (10472)
  covalent geometry    : angle       0.60003 (14234)
  Misc. bond           : bond        0.04455 (    2)

*********************** 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
  196 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 140
  time to evaluate  : 1.088 
Fit side-chains
   revert: symmetry clash
REVERT: B   60 LEU cc_start: 0.8502 (tt) cc_final: 0.8153 (tt)
REVERT: B  465 MET cc_start: 0.7592 (ptm) cc_final: 0.7364 (ttp)
REVERT: D  122 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8126 (ttpp)
REVERT: E  102 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.7469 (t80)
  outliers start: 56
  outliers final: 35
  residues processed: 186
  average time/residue: 0.2351
  time to fit residues: 64.9265
Evaluate side-chains
  168 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 131
  time to evaluate  : 1.964 
-------------------------------------------------------------------------------
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  308 ILE
Chi-restraints excluded: chain B residue  350 PHE
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain C residue    2 GLN
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  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   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 3 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 111 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 97 optimal weight:    4.9990
   chunk 85 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 52 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   chunk 114 optimal weight:    0.8980
   chunk 67 optimal weight:    0.5980
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.3914 r_free = 0.3914 target = 0.144597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.116751 restraints weight = 16934.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.117083 restraints weight = 12129.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.118132 restraints weight = 12012.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.1306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.086  10487  Z= 0.150
  Angle     :  0.624   9.012  14267  Z= 0.302
  Chirality :  0.042   0.310   1598
  Planarity :  0.004   0.062   1746
  Dihedral  :  8.517 139.366   1596
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  6.11 %
    Allowed  : 28.98 %
    Favored  : 64.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.25), residues: 1258
  helix:  1.49 (0.28), residues: 389
  sheet: -0.09 (0.34), residues: 276
  loop : -1.32 (0.27), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 163 
 HIS   0.007   0.001   HIS B 119 
 PHE   0.017   0.001   PHE B 520 
 TYR   0.011   0.001   TYR A 121 
 ARG   0.002   0.000   ARG D 129 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00563 (    3)
  link_NAG-ASN         : angle       2.61217 (    9)
  link_BETA1-4         : bond        0.01667 (    4)
  link_BETA1-4         : angle       3.52030 (   12)
  hydrogen bonds       : bond        0.04230 (  395)
  hydrogen bonds       : angle       4.59809 ( 1134)
  SS BOND              : bond        0.00581 (    6)
  SS BOND              : angle       1.65115 (   12)
  covalent geometry    : bond        0.00369 (10472)
  covalent geometry    : angle       0.61080 (14234)
  Misc. bond           : bond        0.06229 (    2)

*********************** 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
  203 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 137
  time to evaluate  : 3.100 
Fit side-chains
   revert: symmetry clash
REVERT: B   60 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8096 (tt)
REVERT: D  122 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8107 (ttpp)
REVERT: E  128 GLN cc_start: 0.6879 (OUTLIER) cc_final: 0.6512 (tp-100)
  outliers start: 66
  outliers final: 47
  residues processed: 190
  average time/residue: 0.2451
  time to fit residues: 69.0916
Evaluate side-chains
  181 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 131
  time to evaluate  : 1.651 
-------------------------------------------------------------------------------
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 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  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  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  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   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  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 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
Chi-restraints excluded: chain E residue  196 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 115 optimal weight:    7.9990
   chunk 38 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 98 optimal weight:    3.9990
   chunk 45 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 111 optimal weight:    3.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.4031 r_free = 0.4031 target = 0.151218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.122620 restraints weight = 16716.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.123984 restraints weight = 11695.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.124571 restraints weight = 10106.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
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      :  0.004   0.099  10487  Z= 0.151
  Angle     :  0.628   9.424  14267  Z= 0.304
  Chirality :  0.042   0.292   1598
  Planarity :  0.004   0.070   1746
  Dihedral  :  8.308 134.424   1596
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 28.89 %
    Favored  : 64.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.25), residues: 1258
  helix:  1.50 (0.28), residues: 392
  sheet: -0.05 (0.34), residues: 281
  loop : -1.33 (0.27), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 163 
 HIS   0.007   0.001   HIS B 222 
 PHE   0.017   0.001   PHE B 520 
 TYR   0.016   0.001   TYR D  86 
 ARG   0.004   0.000   ARG D 129 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00544 (    3)
  link_NAG-ASN         : angle       2.49025 (    9)
  link_BETA1-4         : bond        0.01603 (    4)
  link_BETA1-4         : angle       3.41674 (   12)
  hydrogen bonds       : bond        0.04180 (  395)
  hydrogen bonds       : angle       4.49733 ( 1134)
  SS BOND              : bond        0.00836 (    6)
  SS BOND              : angle       1.87342 (   12)
  covalent geometry    : bond        0.00368 (10472)
  covalent geometry    : angle       0.61544 (14234)
  Misc. bond           : bond        0.06989 (    2)

*********************** 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
  211 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 139
  time to evaluate  : 1.124 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8496 (mt0)
REVERT: B   60 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8122 (tt)
REVERT: B  161 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7115 (ttpp)
REVERT: D  114 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7853 (mm-30)
REVERT: D  122 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8115 (ttpp)
REVERT: E    3 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7631 (tt)
REVERT: E  102 PHE cc_start: 0.9076 (OUTLIER) cc_final: 0.7505 (t80)
  outliers start: 72
  outliers final: 52
  residues processed: 196
  average time/residue: 0.2014
  time to fit residues: 57.9960
Evaluate side-chains
  192 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 134
  time to evaluate  : 1.163 
-------------------------------------------------------------------------------
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   52 LEU
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  161 LYS
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  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  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   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  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 E residue    3 LEU
Chi-restraints excluded: chain E residue  102 PHE
Chi-restraints excluded: chain E residue  108 VAL
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
Chi-restraints excluded: chain E residue  210 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 78 optimal weight:    0.3980
   chunk 93 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 89 optimal weight:    4.9990
   chunk 116 optimal weight:    0.5980
   chunk 72 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 119 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 65 optimal weight:    4.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3953 r_free = 0.3953 target = 0.147955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.120043 restraints weight = 16860.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.119897 restraints weight = 11635.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.121290 restraints weight = 11563.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.1518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081  10487  Z= 0.123
  Angle     :  0.626   8.975  14267  Z= 0.300
  Chirality :  0.041   0.279   1598
  Planarity :  0.004   0.066   1746
  Dihedral  :  8.123 130.662   1596
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 30.65 %
    Favored  : 63.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.25), residues: 1258
  helix:  1.59 (0.28), residues: 392
  sheet: -0.01 (0.33), residues: 279
  loop : -1.33 (0.27), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 163 
 HIS   0.009   0.001   HIS B 119 
 PHE   0.027   0.001   PHE C 131 
 TYR   0.014   0.001   TYR B 427 
 ARG   0.007   0.000   ARG D 118 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00530 (    3)
  link_NAG-ASN         : angle       2.37882 (    9)
  link_BETA1-4         : bond        0.01555 (    4)
  link_BETA1-4         : angle       3.28966 (   12)
  hydrogen bonds       : bond        0.03848 (  395)
  hydrogen bonds       : angle       4.36693 ( 1134)
  SS BOND              : bond        0.00570 (    6)
  SS BOND              : angle       1.73519 (   12)
  covalent geometry    : bond        0.00296 (10472)
  covalent geometry    : angle       0.61422 (14234)
  Misc. bond           : bond        0.06176 (    2)

*********************** 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
  193 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 132
  time to evaluate  : 1.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8540 (mt0)
REVERT: B   60 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8065 (tt)
REVERT: B  161 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7052 (ttpp)
REVERT: B  268 MET cc_start: 0.8783 (ppp) cc_final: 0.8497 (ppp)
REVERT: E    3 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7609 (tt)
REVERT: E  102 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.7448 (t80)
  outliers start: 61
  outliers final: 48
  residues processed: 182
  average time/residue: 0.2036
  time to fit residues: 54.4363
Evaluate side-chains
  183 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 130
  time to evaluate  : 1.194 
-------------------------------------------------------------------------------
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  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  335 LEU
Chi-restraints excluded: chain B residue  350 PHE
Chi-restraints excluded: chain B residue  353 ILE
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain C residue    2 GLN
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  150 LEU
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   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  126 VAL
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain E residue    3 LEU
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  128 GLN
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 85 optimal weight:    9.9990
   chunk 26 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 114 optimal weight:    0.9980
   chunk 107 optimal weight:    0.5980
   chunk 92 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9980
   chunk 110 optimal weight:    5.9990
   chunk 120 optimal weight:    0.8980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3930 r_free = 0.3930 target = 0.145908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.118551 restraints weight = 17217.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.119095 restraints weight = 11813.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.119968 restraints weight = 11966.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.1569

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= 0.125
  Angle     :  0.622   8.947  14267  Z= 0.298
  Chirality :  0.041   0.272   1598
  Planarity :  0.004   0.070   1746
  Dihedral  :  7.992 126.984   1596
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  6.20 %
    Allowed  : 30.37 %
    Favored  : 63.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.25), residues: 1258
  helix:  1.52 (0.27), residues: 400
  sheet: -0.10 (0.33), residues: 278
  loop : -1.35 (0.27), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 163 
 HIS   0.008   0.001   HIS B 119 
 PHE   0.018   0.001   PHE B 520 
 TYR   0.017   0.001   TYR D  86 
 ARG   0.006   0.000   ARG D 118 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00516 (    3)
  link_NAG-ASN         : angle       2.32741 (    9)
  link_BETA1-4         : bond        0.01553 (    4)
  link_BETA1-4         : angle       3.21968 (   12)
  hydrogen bonds       : bond        0.03781 (  395)
  hydrogen bonds       : angle       4.30121 ( 1134)
  SS BOND              : bond        0.00644 (    6)
  SS BOND              : angle       1.73331 (   12)
  covalent geometry    : bond        0.00304 (10472)
  covalent geometry    : angle       0.61111 (14234)
  Misc. bond           : bond        0.05842 (    2)

*********************** 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
  201 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 134
  time to evaluate  : 1.053 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8537 (mt0)
REVERT: B   60 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8068 (tt)
REVERT: B  161 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7052 (ttpp)
REVERT: B  268 MET cc_start: 0.8777 (ppp) cc_final: 0.8513 (ppp)
REVERT: D  151 GLU cc_start: 0.8224 (mm-30) cc_final: 0.8011 (mm-30)
REVERT: E    3 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7596 (tt)
REVERT: E  102 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.7444 (t80)
  outliers start: 67
  outliers final: 53
  residues processed: 190
  average time/residue: 0.1931
  time to fit residues: 53.6861
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  : 1.181 
-------------------------------------------------------------------------------
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  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  407 VAL
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   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   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  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  113 THR
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 27 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 123 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0870
   chunk 51 optimal weight:    0.2980
   chunk 77 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 16 optimal weight:    0.0040
   chunk 83 optimal weight:    0.9990
   chunk 124 optimal weight:    6.9990
   chunk 95 optimal weight:    0.0870
   overall best weight:    0.2950

-------------------------------------------------------------------------------
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 = 0.3977 r_free = 0.3977 target = 0.149723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.122147 restraints weight = 16981.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.122649 restraints weight = 12025.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.124001 restraints weight = 10913.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.1637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10487  Z= 0.106
  Angle     :  0.617   9.781  14267  Z= 0.293
  Chirality :  0.041   0.262   1598
  Planarity :  0.004   0.068   1746
  Dihedral  :  7.832 122.409   1596
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 31.67 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.25), residues: 1258
  helix:  1.60 (0.28), residues: 400
  sheet: -0.13 (0.33), residues: 288
  loop : -1.31 (0.27), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 337 
 HIS   0.007   0.001   HIS B 119 
 PHE   0.019   0.001   PHE B 520 
 TYR   0.014   0.001   TYR B 427 
 ARG   0.009   0.000   ARG B 559 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00546 (    3)
  link_NAG-ASN         : angle       2.25695 (    9)
  link_BETA1-4         : bond        0.01470 (    4)
  link_BETA1-4         : angle       3.09302 (   12)
  hydrogen bonds       : bond        0.03387 (  395)
  hydrogen bonds       : angle       4.18197 ( 1134)
  SS BOND              : bond        0.00397 (    6)
  SS BOND              : angle       1.62863 (   12)
  covalent geometry    : bond        0.00249 (10472)
  covalent geometry    : angle       0.60706 (14234)
  Misc. bond           : bond        0.04803 (    2)

*********************** 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
  196 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 139
  time to evaluate  : 1.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8555 (mt0)
REVERT: B   60 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7981 (tt)
REVERT: B  161 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.6982 (ttpp)
REVERT: B  268 MET cc_start: 0.8717 (ppp) cc_final: 0.8468 (ppp)
REVERT: C  157 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8064 (mp0)
REVERT: E    3 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7532 (tt)
REVERT: E  102 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.7468 (t80)
  outliers start: 57
  outliers final: 46
  residues processed: 190
  average time/residue: 0.2022
  time to fit residues: 56.4492
Evaluate side-chains
  183 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 132
  time to evaluate  : 1.190 
-------------------------------------------------------------------------------
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   94 HIS
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  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  407 VAL
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   54 SER
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   96 CYS
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  192 THR
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   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  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 28 optimal weight:    3.9990
   chunk 87 optimal weight:    0.1980
   chunk 50 optimal weight:    0.0270
   chunk 93 optimal weight:    0.8980
   chunk 55 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   chunk 44 optimal weight:    0.4980
   chunk 120 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 110 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   overall best weight:    0.4638

-------------------------------------------------------------------------------
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 = 0.3951 r_free = 0.3951 target = 0.147654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.120617 restraints weight = 17042.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.120060 restraints weight = 11931.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.121547 restraints weight = 10430.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  10487  Z= 0.111
  Angle     :  0.627  10.557  14267  Z= 0.297
  Chirality :  0.041   0.254   1598
  Planarity :  0.004   0.069   1746
  Dihedral  :  7.683 116.808   1596
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 31.67 %
    Favored  : 63.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.25), residues: 1258
  helix:  1.63 (0.28), residues: 400
  sheet: -0.01 (0.34), residues: 275
  loop : -1.31 (0.27), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 163 
 HIS   0.007   0.001   HIS B 119 
 PHE   0.020   0.001   PHE B 520 
 TYR   0.019   0.001   TYR B 201 
 ARG   0.006   0.000   ARG D 129 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00520 (    3)
  link_NAG-ASN         : angle       2.18418 (    9)
  link_BETA1-4         : bond        0.01436 (    4)
  link_BETA1-4         : angle       3.02789 (   12)
  hydrogen bonds       : bond        0.03356 (  395)
  hydrogen bonds       : angle       4.13303 ( 1134)
  SS BOND              : bond        0.00641 (    6)
  SS BOND              : angle       1.67666 (   12)
  covalent geometry    : bond        0.00266 (10472)
  covalent geometry    : angle       0.61717 (14234)
  Misc. bond           : bond        0.04485 (    2)

*********************** 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
  189 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 135
  time to evaluate  : 1.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8536 (mt0)
REVERT: B   60 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8049 (tt)
REVERT: B  161 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7040 (ttpp)
REVERT: B  268 MET cc_start: 0.8716 (ppp) cc_final: 0.8479 (ppp)
REVERT: C  157 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8022 (mp0)
REVERT: E    3 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7555 (tt)
REVERT: E  102 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.7474 (t80)
  outliers start: 54
  outliers final: 45
  residues processed: 183
  average time/residue: 0.2077
  time to fit residues: 56.3288
Evaluate side-chains
  181 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 131
  time to evaluate  : 1.136 
-------------------------------------------------------------------------------
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   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  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  407 VAL
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   54 SER
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   96 CYS
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 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  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  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 85 optimal weight:    6.9990
   chunk 61 optimal weight:    9.9990
   chunk 73 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 117 optimal weight:    7.9990
   chunk 6 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9980
   chunk 87 optimal weight:    0.0370
   chunk 92 optimal weight:    2.9990
   overall best weight:    1.1662

-------------------------------------------------------------------------------
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**
D 140 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.144415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.117151 restraints weight = 17043.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.116273 restraints weight = 14273.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.117429 restraints weight = 13071.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.1744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.103  10487  Z= 0.157
  Angle     :  0.674  11.936  14267  Z= 0.320
  Chirality :  0.042   0.253   1598
  Planarity :  0.004   0.069   1746
  Dihedral  :  7.731 113.021   1596
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 31.85 %
    Favored  : 63.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.25), residues: 1258
  helix:  1.54 (0.28), residues: 399
  sheet: -0.16 (0.33), residues: 276
  loop : -1.36 (0.27), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C 163 
 HIS   0.009   0.001   HIS B 119 
 PHE   0.020   0.001   PHE B 520 
 TYR   0.019   0.001   TYR D  86 
 ARG   0.007   0.000   ARG D 118 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00461 (    3)
  link_NAG-ASN         : angle       2.14118 (    9)
  link_BETA1-4         : bond        0.01431 (    4)
  link_BETA1-4         : angle       3.03914 (   12)
  hydrogen bonds       : bond        0.04015 (  395)
  hydrogen bonds       : angle       4.30831 ( 1134)
  SS BOND              : bond        0.00678 (    6)
  SS BOND              : angle       2.01080 (   12)
  covalent geometry    : bond        0.00386 (10472)
  covalent geometry    : angle       0.66462 (14234)
  Misc. bond           : bond        0.07316 (    2)

********************** 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: 54
    poor density    : 138
  time to evaluate  : 1.040 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8423 (mt0)
REVERT: B   60 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8187 (tt)
REVERT: B  161 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7196 (ttpp)
REVERT: B  465 MET cc_start: 0.7744 (ptm) cc_final: 0.7423 (ptm)
REVERT: E    3 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7533 (tt)
REVERT: E  102 PHE cc_start: 0.9058 (OUTLIER) cc_final: 0.7510 (t80)
  outliers start: 54
  outliers final: 47
  residues processed: 185
  average time/residue: 0.1918
  time to fit residues: 52.1955
Evaluate side-chains
  186 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 134
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 TYR
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  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  358 VAL
Chi-restraints excluded: chain B residue  407 VAL
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   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  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  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 56 optimal weight:    0.3980
   chunk 110 optimal weight:    5.9990
   chunk 116 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 111 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 41 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   chunk 112 optimal weight:    0.7980
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.3938 r_free = 0.3938 target = 0.146479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.117846 restraints weight = 16951.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.118736 restraints weight = 11385.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.119853 restraints weight = 10401.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.1756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.097  10487  Z= 0.144
  Angle     :  0.669  11.571  14267  Z= 0.318
  Chirality :  0.042   0.251   1598
  Planarity :  0.004   0.073   1746
  Dihedral  :  7.715 109.694   1596
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 31.57 %
    Favored  : 63.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.25), residues: 1258
  helix:  1.53 (0.28), residues: 399
  sheet: -0.14 (0.33), residues: 280
  loop : -1.34 (0.27), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C 163 
 HIS   0.009   0.001   HIS B 119 
 PHE   0.020   0.001   PHE B 520 
 TYR   0.017   0.001   TYR B 201 
 ARG   0.009   0.000   ARG E  17 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00493 (    3)
  link_NAG-ASN         : angle       2.15533 (    9)
  link_BETA1-4         : bond        0.01455 (    4)
  link_BETA1-4         : angle       2.99083 (   12)
  hydrogen bonds       : bond        0.03903 (  395)
  hydrogen bonds       : angle       4.27719 ( 1134)
  SS BOND              : bond        0.00639 (    6)
  SS BOND              : angle       1.95619 (   12)
  covalent geometry    : bond        0.00354 (10472)
  covalent geometry    : angle       0.65903 (14234)
  Misc. bond           : bond        0.06944 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3559.60 seconds
wall clock time: 64 minutes 53.99 seconds (3893.99 seconds total)