Starting phenix.real_space_refine
on Fri Aug  7 00:13:36 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9yta_73447/08_2026/9yta_73447_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9yta_73447/08_2026/9yta_73447.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.27
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9yta_73447/08_2026/9yta_73447_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9yta_73447/08_2026/9yta_73447_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9yta_73447/08_2026/9yta_73447.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9yta_73447/08_2026/9yta_73447.map"
  }
  resolution = 3.27
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      34      5.16       5
     C    5572      2.51       5
     N    1487      2.21       5
     O    1747      1.98       5
     H    8524      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 17364
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 4218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 4218
          Classifications: {'peptide': 270}
          Link IDs: {'PTRANS': 17, 'TRANS': 252}
    Chain: "D"
      Number of atoms: 3376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 3376
          Classifications: {'peptide': 225}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 213}
    Chain: "E"
      Number of atoms: 3197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 3197
          Classifications: {'peptide': 212}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 200}
    Chain: "F"
      Number of atoms: 3300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 3300
          Classifications: {'peptide': 220}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 207}
    Chain: "G"
      Number of atoms: 3221
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 3221
          Classifications: {'peptide': 213}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 203}
    Chain: "T"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 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: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.51, per 1000 atoms: 0.14
  Number of scatterers: 17364
  At special positions: 0
  Unit cell: (91.25, 108.77, 164.25, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      34     16.00
     O    1747      8.00
     N    1487      7.00
     C    5572      6.00
     H    8524      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 140 " - pdb=" SG  CYS D 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  23 " - pdb=" SG  CYS E  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 133 " - pdb=" SG  CYS E 193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  22 " - pdb=" SG  CYS F  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 146 " - pdb=" SG  CYS F 202 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  23 " - pdb=" SG  CYS G  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 134 " - pdb=" SG  CYS G 194 " 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=0, symmetry=0
  Links applied
    BETA1-4
      " NAG T   1 " - " NAG T   2 "
    BETA1-6
      " NAG T   1 " - " FUC T   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG A 701 " - " ASN A 331 "
      " NAG T   1 " - " ASN A 343 "
  Time building additional restraints: 1.35
  Conformation dependent library (CDL) restraints added in 382.1 milliseconds
  

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2108

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 27 sheets defined
      10.2% alpha, 43.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
      removed outlier: 3.506A  pdb=" N   ASN A 343 " --> pdb=" O   ASP A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 364 through 372
      removed outlier: 3.677A  pdb=" N   VAL A 367 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 389
      removed outlier: 3.878A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 411
      removed outlier: 4.771A  pdb=" N   SER A 408 " --> pdb=" O   ASN A 405 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   GLN A 409 " --> pdb=" O   GLU A 406 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ALA A 411 " --> pdb=" O   SER A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'D' and resid 83 through 87
    Processing helix  chain 'D' and resid 185 through 192
      removed outlier: 3.528A  pdb=" N   LEU D 189 " --> pdb=" O   PRO D 185 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   GLY D 190 " --> pdb=" O   SER D 186 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   THR D 191 " --> pdb=" O   SER D 187 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 79 through 83
    Processing helix  chain 'E' and resid 120 through 127
    Processing helix  chain 'E' and resid 182 through 187
    Processing helix  chain 'F' and resid 28 through 32
      removed outlier: 3.745A  pdb=" N   HIS F  32 " --> pdb=" O   PHE F  29 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 87 through 91
      removed outlier: 3.606A  pdb=" N   THR F  91 " --> pdb=" O   SER F  88 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 162 through 164
      No H-bonds generated for 'chain 'F' and resid 162 through 164'
    Processing helix  chain 'F' and resid 193 through 195
      No H-bonds generated for 'chain 'F' and resid 193 through 195'
    Processing helix  chain 'G' and resid 79 through 83
    Processing helix  chain 'G' and resid 121 through 128
    Processing helix  chain 'G' and resid 182 through 189
      removed outlier: 3.640A  pdb=" N   HIS G 189 " --> pdb=" O   ASP G 185 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 324 through 328
      removed outlier: 6.583A  pdb=" N   GLU A 324 " --> pdb=" O   ASN A 540 " (cutoff:3.500A)
      removed outlier: 8.093A  pdb=" N   ASN A 542 " --> pdb=" O   GLU A 324 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   ILE A 326 " --> pdb=" O   ASN A 542 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   LYS A 537 " --> pdb=" O   LEU A 552 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   GLU A 583 " --> pdb=" O   ASP A 578 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 358
    Processing sheet with id=AA3, first strand: chain 'A' and resid 361 through 362
      removed outlier: 6.304A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA5, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA6, first strand: chain 'D' and resid 3 through 6
    Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 12
      removed outlier: 6.458A  pdb=" N   ILE D  34 " --> pdb=" O   TRP D  50 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   TRP D  50 " --> pdb=" O   ILE D  34 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   TRP D  36 " --> pdb=" O   MET D  48 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 12
      removed outlier: 3.562A  pdb=" N   VAL D 102 " --> pdb=" O   ARG D  94 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 121 through 124
      removed outlier: 3.522A  pdb=" N   SER D 180 " --> pdb=" O   CYS D 140 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   ASP D 144 " --> pdb=" O   TYR D 176 " (cutoff:3.500A)
      removed outlier: 5.996A  pdb=" N   TYR D 176 " --> pdb=" O   ASP D 144 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 121 through 124
      removed outlier: 3.522A  pdb=" N   SER D 180 " --> pdb=" O   CYS D 140 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   ASP D 144 " --> pdb=" O   TYR D 176 " (cutoff:3.500A)
      removed outlier: 5.996A  pdb=" N   TYR D 176 " --> pdb=" O   ASP D 144 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 150 through 154
      removed outlier: 4.353A  pdb=" N   TYR D 194 " --> pdb=" O   VAL D 211 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 4 through 6
      removed outlier: 3.900A  pdb=" N   ASP E  70 " --> pdb=" O   SER E  67 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 13
      removed outlier: 3.798A  pdb=" N   GLY E  84 " --> pdb=" O   LEU E 103 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   TRP E  35 " --> pdb=" O   LEU E  47 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 10 through 13
      removed outlier: 3.798A  pdb=" N   GLY E  84 " --> pdb=" O   LEU E 103 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 113 through 117
      removed outlier: 3.628A  pdb=" N   VAL E 132 " --> pdb=" O   PHE E 117 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 152 through 154
      removed outlier: 3.837A  pdb=" N   TRP E 147 " --> pdb=" O   GLN E 154 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'F' and resid 3 through 6
    Processing sheet with id=AB9, first strand: chain 'F' and resid 10 through 12
      removed outlier: 6.682A  pdb=" N   MET F  34 " --> pdb=" O   TRP F  50 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   TRP F  50 " --> pdb=" O   MET F  34 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   TRP F  36 " --> pdb=" O   MET F  48 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'F' and resid 10 through 12
      removed outlier: 6.584A  pdb=" N   CYS F  96 " --> pdb=" O   TRP F 109 " (cutoff:3.500A)
      removed outlier: 4.813A  pdb=" N   TRP F 109 " --> pdb=" O   CYS F  96 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   ARG F  98 " --> pdb=" O   ASP F 107 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'F' and resid 127 through 130
    Processing sheet with id=AC3, first strand: chain 'F' and resid 127 through 130
    Processing sheet with id=AC4, first strand: chain 'F' and resid 157 through 160
      removed outlier: 4.783A  pdb=" N   TYR F 200 " --> pdb=" O   VAL F 217 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'G' and resid 4 through 6
    Processing sheet with id=AC6, first strand: chain 'G' and resid 10 through 13
      removed outlier: 6.848A  pdb=" N   LEU G  33 " --> pdb=" O   TYR G  49 " (cutoff:3.500A)
      removed outlier: 5.028A  pdb=" N   TYR G  49 " --> pdb=" O   LEU G  33 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   TRP G  35 " --> pdb=" O   LEU G  47 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'G' and resid 10 through 13
    Processing sheet with id=AC8, first strand: chain 'G' and resid 114 through 118
      removed outlier: 3.697A  pdb=" N   VAL G 133 " --> pdb=" O   PHE G 118 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   TYR G 173 " --> pdb=" O   ASN G 138 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'G' and resid 153 through 155
      removed outlier: 3.892A  pdb=" N   TRP G 148 " --> pdb=" O   GLN G 155 " (cutoff:3.500A)

    383 hydrogen bonds defined for protein.
    924 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.04

  Time building geometry restraints manager: 1.82 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 8498
        1.04 -     1.24: 1277
        1.24 -     1.44: 2794
        1.44 -     1.65: 4967
        1.65 -     1.85: 42
  Bond restraints: 17578
  Sorted by residual:
  bond pdb=" N   VAL A 320 "
       pdb=" CA  VAL A 320 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.99e+00
  bond pdb=" N   VAL A 320 "
       pdb=" H   VAL A 320 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.28e+00
  bond pdb=" CB  CYS A 379 "
       pdb=" SG  CYS A 379 "
    ideal  model  delta    sigma   weight residual
    1.808  1.849 -0.041 3.30e-02 9.18e+02 1.52e+00
  bond pdb=" C1  FUC T   3 "
       pdb=" O5  FUC T   3 "
    ideal  model  delta    sigma   weight residual
    1.400  1.423 -0.023 2.00e-02 2.50e+03 1.32e+00
  bond pdb=" CB  CYS A 432 "
       pdb=" SG  CYS A 432 "
    ideal  model  delta    sigma   weight residual
    1.808  1.771  0.037 3.30e-02 9.18e+02 1.23e+00
  ... (remaining 17573 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 31320
        1.71 -     3.41: 231
        3.41 -     5.12: 35
        5.12 -     6.82: 3
        6.82 -     8.53: 1
  Bond angle restraints: 31590
  Sorted by residual:
  angle pdb=" CA  CYS A 432 "
        pdb=" CB  CYS A 432 "
        pdb=" SG  CYS A 432 "
      ideal   model   delta    sigma   weight residual
     114.40  122.93   -8.53 2.30e+00 1.89e-01 1.38e+01
  angle pdb=" N   ALA G  51 "
        pdb=" CA  ALA G  51 "
        pdb=" CB  ALA G  51 "
      ideal   model   delta    sigma   weight residual
     114.17  110.29    3.88 1.14e+00 7.69e-01 1.16e+01
  angle pdb=" N   ALA E  51 "
        pdb=" CA  ALA E  51 "
        pdb=" CB  ALA E  51 "
      ideal   model   delta    sigma   weight residual
     114.17  110.35    3.82 1.14e+00 7.69e-01 1.12e+01
  angle pdb=" CA  GLY A 431 "
        pdb=" C   GLY A 431 "
        pdb=" N   CYS A 432 "
      ideal   model   delta    sigma   weight residual
     115.22  118.93   -3.71 1.15e+00 7.56e-01 1.04e+01
  angle pdb=" N   ILE D  75 "
        pdb=" CA  ILE D  75 "
        pdb=" C   ILE D  75 "
      ideal   model   delta    sigma   weight residual
     112.43  109.71    2.72 9.20e-01 1.18e+00 8.74e+00
  ... (remaining 31585 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 7749
       17.79 -    35.57: 522
       35.57 -    53.36: 166
       53.36 -    71.14: 71
       71.14 -    88.93: 29
  Dihedral angle restraints: 8537
    sinusoidal: 4602
      harmonic: 3935
  Sorted by residual:
  dihedral pdb=" CB  CYS A 379 "
           pdb=" SG  CYS A 379 "
           pdb=" SG  CYS A 432 "
           pdb=" CB  CYS A 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   39.15   53.85     1      1.00e+01 1.00e-02 3.94e+01
  dihedral pdb=" CB  CYS F 146 "
           pdb=" SG  CYS F 146 "
           pdb=" SG  CYS F 202 "
           pdb=" CB  CYS F 202 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   48.41   44.59     1      1.00e+01 1.00e-02 2.76e+01
  dihedral pdb=" CA  TYR G  91 "
           pdb=" C   TYR G  91 "
           pdb=" N   ASP G  92 "
           pdb=" CA  ASP G  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.47   25.53     0      5.00e+00 4.00e-02 2.61e+01
  ... (remaining 8534 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 782
       0.027 -    0.054: 401
       0.054 -    0.081: 71
       0.081 -    0.108: 82
       0.108 -    0.135: 43
  Chirality restraints: 1379
  Sorted by residual:
  chirality pdb=" C1  FUC T   3 "
            pdb=" O6  NAG T   1 "
            pdb=" C2  FUC T   3 "
            pdb=" O5  FUC T   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.38   -0.02 2.00e-02 2.50e+03 1.03e+00
  chirality pdb=" C1  NAG T   2 "
            pdb=" O4  NAG T   1 "
            pdb=" C2  NAG T   2 "
            pdb=" O5  NAG T   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.41    0.01 2.00e-02 2.50e+03 4.65e-01
  chirality pdb=" CA  ILE G 117 "
            pdb=" N   ILE G 117 "
            pdb=" C   ILE G 117 "
            pdb=" CB  ILE G 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.54e-01
  ... (remaining 1376 not shown)

  Planarity restraints: 2662
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN F 210 "    0.008 2.00e-02 2.50e+03   1.61e-02 2.60e+00
        pdb=" C   ASN F 210 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   ASN F 210 "    0.011 2.00e-02 2.50e+03
        pdb=" N   THR F 211 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU D 148 "    0.025 5.00e-02 4.00e+02   3.76e-02 2.26e+00
        pdb=" N   PRO D 149 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO D 149 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO D 149 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO G 119 "   -0.020 5.00e-02 4.00e+02   3.05e-02 1.49e+00
        pdb=" N   PRO G 120 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO G 120 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO G 120 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 2659 not shown)

  Histogram of nonbonded interaction distances:
        1.54 -     2.16: 757
        2.16 -     2.77: 33335
        2.77 -     3.38: 48562
        3.38 -     3.99: 64370
        3.99 -     4.60: 98087
  Nonbonded interactions: 245111
  Sorted by model distance:
  nonbonded pdb=" HE  ARG A 457 "
            pdb=" OD2 ASP A 467 "
     model   vdw
     1.545 2.450
  nonbonded pdb=" OE1 GLU E  81 "
            pdb=" H   GLU E  81 "
     model   vdw
     1.553 2.450
  nonbonded pdb=" OE1 GLU G 143 "
            pdb=" H   GLU G 143 "
     model   vdw
     1.557 2.450
  nonbonded pdb=" H   GLY G  16 "
            pdb=" O   LEU G  78 "
     model   vdw
     1.565 2.450
  nonbonded pdb=" OE1 GLU G  81 "
            pdb=" H   GLU G  81 "
     model   vdw
     1.595 2.450
  ... (remaining 245106 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 'D' and (resid 1 through 31 or resid 33 or resid 35 through 58 or resid 6 \ 
0 through 61 or resid 63 through 68 or resid 70 through 82 or resid 82B through  \ 
82C or resid 84 through 94 or resid 96 through 97 or resid 100C or resid 100G th \ 
rough 101 or resid 103 through 104 or resid 106 through 108 or resid 110 through \ 
 126 or resid 128 or resid 130 through 132 or resid 135 through 191 or resid 193 \ 
 through 194 or resid 196 through 198 or (resid 200 and (name N or name CA or na \ 
me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ 
 NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ 
e HE2)) or resid 201 through 209 or resid 211 through 212 or resid 214))
  selection = (chain 'F' and (resid 1 through 31 or resid 33 or resid 35 through 59 or resid 6 \ 
1 through 62 or resid 64 through 69 or resid 71 through 83 or resid 85 through 8 \ 
6 or resid 88 through 100 or resid 102 or resid 106 through 107 or resid 109 thr \ 
ough 110 or resid 112 through 114 or resid 116 through 132 or resid 134 or resid \ 
 136 through 138 or resid 141 through 197 or resid 199 through 200 or resid 202  \ 
through 204 or resid 206 through 215 or resid 217 through 218 or resid 220))
}
ncs_group {
  reference = (chain 'E' and (resid 1 through 30 or resid 33 through 38 or resid 40 through 73 \ 
 or resid 75 through 79 or resid 81 through 82 or resid 85 through 92 or resid 9 \ 
4 or resid 96 through 212))
  selection = (chain 'G' and (resid 1 through 30 or resid 33 through 38 or resid 40 through 73 \ 
 or resid 75 through 79 or resid 81 through 82 or resid 85 through 92 or resid 9 \ 
4 or resid 97 through 213))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.100
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.830
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9070  Z= 0.121
  Angle     :  0.539   8.531  12357  Z= 0.284
  Chirality :  0.042   0.135   1379
  Planarity :  0.003   0.038   1585
  Dihedral  : 13.569  88.926   3294
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.78 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  9.85 %
    Favored  : 88.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.27), residues: 1130
  helix: -0.51 (0.72), residues: 46
  sheet:  0.59 (0.24), residues: 509
  loop : -0.12 (0.29), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  61 
 TYR   0.009   0.001   TYR E  91 
 PHE   0.009   0.001   PHE A 515 
 TRP   0.006   0.001   TRP F  50 
 HIS   0.004   0.001   HIS F 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.12 ( 9054)
  covalent geometry    : angle       0.52604 /  0.28 (12321)
  SS BOND              : bond        0.00355 /  0.17 (   12)
  SS BOND              : angle       1.04802 /  0.57 (   24)
  hydrogen bonds       : bond        0.23354 / 15.33 (  335)
  hydrogen bonds       : angle      10.34173 /  7.03 (  924)
  link_BETA1-4         : bond        0.00770 /  0.41 (    1)
  link_BETA1-4         : angle       1.15387 /  0.65 (    3)
  link_BETA1-6         : bond        0.01785 /  0.94 (    1)
  link_BETA1-6         : angle       2.92451 /  1.46 (    3)
  link_NAG-ASN         : bond        0.00735 /  0.35 (    2)
  link_NAG-ASN         : angle       4.48601 /  2.34 (    6)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 45
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   81 MET cc_start: 0.9286 (tmm) cc_final: 0.8921 (tmm)
  outliers start: 13
  outliers final: 12
  residues processed: 55
  average time/residue: 0.1342
  time to fit residues: 11.6849
Evaluate side-chains
  55 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  481 ASN
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain A residue  559 PHE
Chi-restraints excluded: chain D residue   59 PHE
Chi-restraints excluded: chain E residue   78 LEU
Chi-restraints excluded: chain F residue  118 SER
Chi-restraints excluded: chain F residue  205 ASN
Chi-restraints excluded: chain G residue    7 SER
Chi-restraints excluded: chain G residue  152 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    1.3988

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.054188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.038698 restraints weight = 98482.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.2753 rms_B_bonded: 3.56
r_work: 0.2648 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.0740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   9070  Z= 0.202
  Angle     :  0.602  10.720  12357  Z= 0.312
  Chirality :  0.044   0.172   1379
  Planarity :  0.004   0.040   1585
  Dihedral  :  6.339  57.161   1328
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.75 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  8.93 %
    Favored  : 89.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.11 (0.26), residues: 1130
  helix: -1.20 (0.69), residues: 47
  sheet:  0.40 (0.23), residues: 509
  loop : -0.32 (0.28), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  96 
 TYR   0.013   0.001   TYR E  91 
 PHE   0.015   0.001   PHE G  73 
 TRP   0.007   0.001   TRP D 154 
 HIS   0.005   0.001   HIS F 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00443 /  0.20 ( 9054)
  covalent geometry    : angle       0.58917 /  0.31 (12321)
  SS BOND              : bond        0.00445 /  0.22 (   12)
  SS BOND              : angle       1.73185 /  1.01 (   24)
  hydrogen bonds       : bond        0.04515 /  2.90 (  335)
  hydrogen bonds       : angle       7.41725 /  5.06 (  924)
  link_BETA1-4         : bond        0.00039 /  0.02 (    1)
  link_BETA1-4         : angle       1.05623 /  0.56 (    3)
  link_BETA1-6         : bond        0.01012 /  0.53 (    1)
  link_BETA1-6         : angle       1.39414 /  0.68 (    3)
  link_NAG-ASN         : bond        0.00263 /  0.13 (    2)
  link_NAG-ASN         : angle       4.37710 /  2.22 (    6)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 47
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  577 ARG cc_start: 0.8346 (ttm170) cc_final: 0.7568 (mtt180)
REVERT: D  176 TYR cc_start: 0.8663 (m-80) cc_final: 0.8169 (m-80)
REVERT: F   81 MET cc_start: 0.9042 (tmm) cc_final: 0.8577 (tmm)
  outliers start: 15
  outliers final: 12
  residues processed: 59
  average time/residue: 0.1418
  time to fit residues: 13.0782
Evaluate side-chains
  56 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 44
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  481 ASN
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain A residue  559 PHE
Chi-restraints excluded: chain D residue   59 PHE
Chi-restraints excluded: chain D residue  144 ASP
Chi-restraints excluded: chain D residue  182 VAL
Chi-restraints excluded: chain E residue   78 LEU
Chi-restraints excluded: chain F residue  108 TYR
Chi-restraints excluded: chain G residue    7 SER
Chi-restraints excluded: chain G residue   48 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 63 optimal weight:    4.9990
   chunk 6 optimal weight:    0.0770
   chunk 78 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 24 optimal weight:    8.9990
   chunk 40 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 83 optimal weight:    4.9990
   chunk 106 optimal weight:    6.9990
   overall best weight:    1.6146

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.054142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.038301 restraints weight = 100291.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.2739 rms_B_bonded: 3.63
r_work: 0.2637 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.1008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   9070  Z= 0.208
  Angle     :  0.572  10.702  12357  Z= 0.296
  Chirality :  0.043   0.152   1379
  Planarity :  0.004   0.040   1585
  Dihedral  :  6.259  58.379   1321
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  :  9.24 %
    Favored  : 88.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.26), residues: 1130
  helix: -1.04 (0.70), residues: 47
  sheet:  0.27 (0.23), residues: 501
  loop : -0.46 (0.28), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  96 
 TYR   0.013   0.001   TYR F  27 
 PHE   0.011   0.001   PHE G  73 
 TRP   0.006   0.001   TRP F  50 
 HIS   0.006   0.001   HIS F 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00458 /  0.21 ( 9054)
  covalent geometry    : angle       0.56091 /  0.29 (12321)
  SS BOND              : bond        0.00434 /  0.22 (   12)
  SS BOND              : angle       1.63045 /  0.93 (   24)
  hydrogen bonds       : bond        0.03991 /  2.59 (  335)
  hydrogen bonds       : angle       6.78733 /  4.63 (  924)
  link_BETA1-4         : bond        0.00235 /  0.12 (    1)
  link_BETA1-4         : angle       1.20578 /  0.62 (    3)
  link_BETA1-6         : bond        0.00999 /  0.53 (    1)
  link_BETA1-6         : angle       1.41133 /  0.68 (    3)
  link_NAG-ASN         : bond        0.00361 /  0.18 (    2)
  link_NAG-ASN         : angle       3.92145 /  2.00 (    6)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 44
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  577 ARG cc_start: 0.8396 (ttm170) cc_final: 0.7628 (mtt180)
  outliers start: 19
  outliers final: 16
  residues processed: 60
  average time/residue: 0.1353
  time to fit residues: 12.3108
Evaluate side-chains
  59 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 43
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain A residue  559 PHE
Chi-restraints excluded: chain D residue   59 PHE
Chi-restraints excluded: chain D residue  144 ASP
Chi-restraints excluded: chain D residue  182 VAL
Chi-restraints excluded: chain E residue   78 LEU
Chi-restraints excluded: chain F residue   73 ASP
Chi-restraints excluded: chain F residue  108 TYR
Chi-restraints excluded: chain G residue    7 SER
Chi-restraints excluded: chain G residue   34 ASN
Chi-restraints excluded: chain G residue   48 ILE
Chi-restraints excluded: chain G residue  196 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 54 optimal weight:    0.0030
   chunk 1 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 112 optimal weight:    4.9990
   chunk 106 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 100 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    1.1194

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 487 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 = 0.3255 r_free = 0.3255 target = 0.054355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.038755 restraints weight = 98712.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.2756 rms_B_bonded: 3.59
r_work: 0.2652 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.1180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   9070  Z= 0.158
  Angle     :  0.550  10.282  12357  Z= 0.282
  Chirality :  0.043   0.153   1379
  Planarity :  0.004   0.042   1585
  Dihedral  :  6.166  58.264   1319
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  :  9.34 %
    Favored  : 88.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.26), residues: 1130
  helix: -1.04 (0.72), residues: 47
  sheet:  0.27 (0.23), residues: 514
  loop : -0.50 (0.28), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  96 
 TYR   0.011   0.001   TYR E  91 
 PHE   0.010   0.001   PHE G  73 
 TRP   0.007   0.001   TRP F  50 
 HIS   0.006   0.001   HIS F 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.16 ( 9054)
  covalent geometry    : angle       0.54033 /  0.28 (12321)
  SS BOND              : bond        0.00423 /  0.21 (   12)
  SS BOND              : angle       1.47444 /  0.84 (   24)
  hydrogen bonds       : bond        0.03330 /  2.16 (  335)
  hydrogen bonds       : angle       6.40375 /  4.36 (  924)
  link_BETA1-4         : bond        0.00172 /  0.09 (    1)
  link_BETA1-4         : angle       1.07081 /  0.56 (    3)
  link_BETA1-6         : bond        0.00978 /  0.51 (    1)
  link_BETA1-6         : angle       1.27745 /  0.62 (    3)
  link_NAG-ASN         : bond        0.00325 /  0.16 (    2)
  link_NAG-ASN         : angle       3.68851 /  1.88 (    6)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 46
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  577 ARG cc_start: 0.8357 (ttm170) cc_final: 0.7559 (mtt180)
REVERT: D  146 PHE cc_start: 0.7820 (t80) cc_final: 0.7487 (t80)
REVERT: D  176 TYR cc_start: 0.8696 (m-80) cc_final: 0.8252 (m-80)
  outliers start: 17
  outliers final: 16
  residues processed: 60
  average time/residue: 0.1347
  time to fit residues: 12.7302
Evaluate side-chains
  60 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 44
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  481 ASN
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain A residue  559 PHE
Chi-restraints excluded: chain D residue   59 PHE
Chi-restraints excluded: chain D residue  144 ASP
Chi-restraints excluded: chain D residue  182 VAL
Chi-restraints excluded: chain E residue   78 LEU
Chi-restraints excluded: chain F residue  108 TYR
Chi-restraints excluded: chain F residue  118 SER
Chi-restraints excluded: chain G residue    7 SER
Chi-restraints excluded: chain G residue   34 ASN
Chi-restraints excluded: chain G residue   48 ILE
Chi-restraints excluded: chain G residue  196 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 93 optimal weight:    0.9990
   chunk 77 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   chunk 108 optimal weight:    4.9990
   chunk 78 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 487 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 = 0.3255 r_free = 0.3255 target = 0.054708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.039067 restraints weight = 98962.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.2767 rms_B_bonded: 3.58
r_work: 0.2663 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.1356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9070  Z= 0.137
  Angle     :  0.534   9.962  12357  Z= 0.272
  Chirality :  0.043   0.151   1379
  Planarity :  0.003   0.038   1585
  Dihedral  :  5.916  58.734   1317
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  :  9.64 %
    Favored  : 88.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.27 (0.26), residues: 1130
  helix:  0.01 (0.82), residues: 39
  sheet:  0.20 (0.23), residues: 516
  loop : -0.46 (0.28), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  66 
 TYR   0.011   0.001   TYR G  93 
 PHE   0.008   0.001   PHE G  73 
 TRP   0.007   0.001   TRP F  50 
 HIS   0.006   0.001   HIS F 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.14 ( 9054)
  covalent geometry    : angle       0.52494 /  0.27 (12321)
  SS BOND              : bond        0.00400 /  0.20 (   12)
  SS BOND              : angle       1.39572 /  0.79 (   24)
  hydrogen bonds       : bond        0.03046 /  1.98 (  335)
  hydrogen bonds       : angle       6.08228 /  4.14 (  924)
  link_BETA1-4         : bond        0.00276 /  0.15 (    1)
  link_BETA1-4         : angle       1.03688 /  0.54 (    3)
  link_BETA1-6         : bond        0.01124 /  0.59 (    1)
  link_BETA1-6         : angle       1.33195 /  0.64 (    3)
  link_NAG-ASN         : bond        0.00338 /  0.16 (    2)
  link_NAG-ASN         : angle       3.40657 /  1.75 (    6)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 47
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  577 ARG cc_start: 0.8354 (ttm170) cc_final: 0.7459 (mtt180)
REVERT: D  146 PHE cc_start: 0.7823 (t80) cc_final: 0.7569 (t80)
  outliers start: 16
  outliers final: 15
  residues processed: 60
  average time/residue: 0.1261
  time to fit residues: 12.1018
Evaluate side-chains
  58 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 43
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  481 ASN
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain A residue  559 PHE
Chi-restraints excluded: chain D residue   59 PHE
Chi-restraints excluded: chain D residue  144 ASP
Chi-restraints excluded: chain D residue  182 VAL
Chi-restraints excluded: chain F residue  108 TYR
Chi-restraints excluded: chain F residue  118 SER
Chi-restraints excluded: chain G residue    7 SER
Chi-restraints excluded: chain G residue   34 ASN
Chi-restraints excluded: chain G residue   48 ILE
Chi-restraints excluded: chain G residue  196 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 81 optimal weight:    0.9990
   chunk 46 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 109 optimal weight:    3.9990
   chunk 82 optimal weight:    0.7980
   chunk 80 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 108 optimal weight:    0.9980
   chunk 71 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 137 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.055165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.039030 restraints weight = 99732.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.2762 rms_B_bonded: 3.70
r_work: 0.2660 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.1452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9070  Z= 0.135
  Angle     :  0.534   9.684  12357  Z= 0.272
  Chirality :  0.043   0.152   1379
  Planarity :  0.003   0.036   1585
  Dihedral  :  5.822  59.030   1315
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  :  9.64 %
    Favored  : 88.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.26), residues: 1130
  helix: -0.15 (0.83), residues: 39
  sheet:  0.19 (0.23), residues: 511
  loop : -0.44 (0.28), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 509 
 TYR   0.010   0.001   TYR F 108 
 PHE   0.008   0.001   PHE G  73 
 TRP   0.007   0.001   TRP F  50 
 HIS   0.005   0.001   HIS F 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00305 /  0.13 ( 9054)
  covalent geometry    : angle       0.52508 /  0.27 (12321)
  SS BOND              : bond        0.00382 /  0.19 (   12)
  SS BOND              : angle       1.38124 /  0.79 (   24)
  hydrogen bonds       : bond        0.02903 /  1.89 (  335)
  hydrogen bonds       : angle       5.94500 /  4.04 (  924)
  link_BETA1-4         : bond        0.00109 /  0.06 (    1)
  link_BETA1-4         : angle       0.99628 /  0.53 (    3)
  link_BETA1-6         : bond        0.01070 /  0.56 (    1)
  link_BETA1-6         : angle       1.31508 /  0.63 (    3)
  link_NAG-ASN         : bond        0.00319 /  0.15 (    2)
  link_NAG-ASN         : angle       3.35851 /  1.72 (    6)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 45
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  577 ARG cc_start: 0.8360 (ttm170) cc_final: 0.7447 (mtt180)
REVERT: D  146 PHE cc_start: 0.7785 (t80) cc_final: 0.7577 (t80)
  outliers start: 18
  outliers final: 16
  residues processed: 60
  average time/residue: 0.1308
  time to fit residues: 12.4045
Evaluate side-chains
  58 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 42
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  481 ASN
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain A residue  559 PHE
Chi-restraints excluded: chain D residue   59 PHE
Chi-restraints excluded: chain D residue  144 ASP
Chi-restraints excluded: chain D residue  182 VAL
Chi-restraints excluded: chain E residue   47 LEU
Chi-restraints excluded: chain F residue  108 TYR
Chi-restraints excluded: chain F residue  118 SER
Chi-restraints excluded: chain G residue    7 SER
Chi-restraints excluded: chain G residue   34 ASN
Chi-restraints excluded: chain G residue   48 ILE
Chi-restraints excluded: chain G residue  196 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   chunk 47 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 487 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 = 0.3259 r_free = 0.3259 target = 0.054860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.039214 restraints weight = 98837.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.2773 rms_B_bonded: 3.61
r_work: 0.2670 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.1540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9070  Z= 0.128
  Angle     :  0.536   9.661  12357  Z= 0.273
  Chirality :  0.043   0.151   1379
  Planarity :  0.003   0.035   1585
  Dihedral  :  5.803  59.280   1315
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.55 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 10.05 %
    Favored  : 88.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.25 (0.26), residues: 1130
  helix: -0.09 (0.84), residues: 39
  sheet:  0.20 (0.23), residues: 516
  loop : -0.43 (0.28), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 210 
 TYR   0.010   0.001   TYR G  93 
 PHE   0.008   0.001   PHE G  73 
 TRP   0.007   0.001   TRP F  50 
 HIS   0.004   0.001   HIS F 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.13 ( 9054)
  covalent geometry    : angle       0.52784 /  0.27 (12321)
  SS BOND              : bond        0.00376 /  0.19 (   12)
  SS BOND              : angle       1.41023 /  0.80 (   24)
  hydrogen bonds       : bond        0.02837 /  1.85 (  335)
  hydrogen bonds       : angle       5.87182 /  4.00 (  924)
  link_BETA1-4         : bond        0.00224 /  0.12 (    1)
  link_BETA1-4         : angle       1.00017 /  0.53 (    3)
  link_BETA1-6         : bond        0.01026 /  0.54 (    1)
  link_BETA1-6         : angle       1.26616 /  0.60 (    3)
  link_NAG-ASN         : bond        0.00336 /  0.16 (    2)
  link_NAG-ASN         : angle       3.27166 /  1.68 (    6)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 42
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  577 ARG cc_start: 0.8348 (ttm170) cc_final: 0.7438 (mtt180)
REVERT: D  146 PHE cc_start: 0.7780 (t80) cc_final: 0.7569 (t80)
  outliers start: 19
  outliers final: 19
  residues processed: 58
  average time/residue: 0.1326
  time to fit residues: 11.8094
Evaluate side-chains
  61 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 42
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  481 ASN
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain A residue  559 PHE
Chi-restraints excluded: chain D residue   59 PHE
Chi-restraints excluded: chain D residue  124 LEU
Chi-restraints excluded: chain D residue  144 ASP
Chi-restraints excluded: chain D residue  182 VAL
Chi-restraints excluded: chain E residue   47 LEU
Chi-restraints excluded: chain E residue   61 ARG
Chi-restraints excluded: chain E residue   78 LEU
Chi-restraints excluded: chain F residue  108 TYR
Chi-restraints excluded: chain F residue  118 SER
Chi-restraints excluded: chain G residue    7 SER
Chi-restraints excluded: chain G residue   34 ASN
Chi-restraints excluded: chain G residue   48 ILE
Chi-restraints excluded: chain G residue  196 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9990
   chunk 97 optimal weight:    0.8980
   chunk 79 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0980
   chunk 71 optimal weight:    2.9990
   chunk 108 optimal weight:    3.9990
   chunk 53 optimal weight:    0.7980
   chunk 37 optimal weight:    0.3980
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 487 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 = 0.3276 r_free = 0.3276 target = 0.055138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.039582 restraints weight = 97971.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.2785 rms_B_bonded: 3.60
r_work: 0.2684 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.1624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9070  Z= 0.111
  Angle     :  0.531   9.221  12357  Z= 0.271
  Chirality :  0.043   0.150   1379
  Planarity :  0.003   0.036   1585
  Dihedral  :  5.746  59.728   1315
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 10.56 %
    Favored  : 87.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.26), residues: 1130
  helix: -0.01 (0.85), residues: 39
  sheet:  0.22 (0.23), residues: 514
  loop : -0.39 (0.28), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 509 
 TYR   0.010   0.001   TYR G  93 
 PHE   0.007   0.001   PHE G  73 
 TRP   0.007   0.001   TRP D  50 
 HIS   0.004   0.001   HIS F 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00257 /  0.11 ( 9054)
  covalent geometry    : angle       0.52354 /  0.27 (12321)
  SS BOND              : bond        0.00364 /  0.18 (   12)
  SS BOND              : angle       1.32257 /  0.74 (   24)
  hydrogen bonds       : bond        0.02716 /  1.77 (  335)
  hydrogen bonds       : angle       5.74715 /  3.91 (  924)
  link_BETA1-4         : bond        0.00316 /  0.17 (    1)
  link_BETA1-4         : angle       1.00271 /  0.54 (    3)
  link_BETA1-6         : bond        0.01018 /  0.54 (    1)
  link_BETA1-6         : angle       1.22599 /  0.58 (    3)
  link_NAG-ASN         : bond        0.00331 /  0.16 (    2)
  link_NAG-ASN         : angle       3.11533 /  1.61 (    6)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 44
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  577 ARG cc_start: 0.8330 (ttm170) cc_final: 0.7411 (mtt180)
REVERT: D  146 PHE cc_start: 0.7763 (t80) cc_final: 0.7544 (t80)
REVERT: E   61 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.6434 (ptt90)
  outliers start: 17
  outliers final: 15
  residues processed: 59
  average time/residue: 0.1407
  time to fit residues: 12.7346
Evaluate side-chains
  56 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 40
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  481 ASN
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain A residue  559 PHE
Chi-restraints excluded: chain D residue   59 PHE
Chi-restraints excluded: chain D residue  124 LEU
Chi-restraints excluded: chain D residue  144 ASP
Chi-restraints excluded: chain E residue   47 LEU
Chi-restraints excluded: chain E residue   61 ARG
Chi-restraints excluded: chain E residue   78 LEU
Chi-restraints excluded: chain F residue  108 TYR
Chi-restraints excluded: chain F residue  118 SER
Chi-restraints excluded: chain G residue    7 SER
Chi-restraints excluded: chain G residue   34 ASN
Chi-restraints excluded: chain G residue  196 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 104 optimal weight:    0.6980
   chunk 102 optimal weight:    2.9990
   chunk 112 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 99 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    1.1384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 487 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 = 0.3257 r_free = 0.3257 target = 0.054778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.039065 restraints weight = 99125.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.2768 rms_B_bonded: 3.63
r_work: 0.2665 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.1662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   9070  Z= 0.157
  Angle     :  0.540   9.432  12357  Z= 0.277
  Chirality :  0.042   0.148   1379
  Planarity :  0.003   0.035   1585
  Dihedral  :  5.783  59.783   1315
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 10.36 %
    Favored  : 87.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.26 (0.26), residues: 1130
  helix: -0.05 (0.84), residues: 39
  sheet:  0.20 (0.23), residues: 514
  loop : -0.44 (0.28), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 509 
 TYR   0.010   0.001   TYR E  91 
 PHE   0.008   0.001   PHE G  73 
 TRP   0.007   0.001   TRP D  50 
 HIS   0.006   0.001   HIS F 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.16 ( 9054)
  covalent geometry    : angle       0.53196 /  0.27 (12321)
  SS BOND              : bond        0.00407 /  0.20 (   12)
  SS BOND              : angle       1.39427 /  0.80 (   24)
  hydrogen bonds       : bond        0.02768 /  1.80 (  335)
  hydrogen bonds       : angle       5.72341 /  3.90 (  924)
  link_BETA1-4         : bond        0.00295 /  0.16 (    1)
  link_BETA1-4         : angle       1.11027 /  0.60 (    3)
  link_BETA1-6         : bond        0.00800 /  0.42 (    1)
  link_BETA1-6         : angle       1.23981 /  0.58 (    3)
  link_NAG-ASN         : bond        0.00318 /  0.15 (    2)
  link_NAG-ASN         : angle       3.32320 /  1.70 (    6)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 41
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  577 ARG cc_start: 0.8377 (ttm170) cc_final: 0.7459 (mtt180)
REVERT: D  146 PHE cc_start: 0.7797 (t80) cc_final: 0.7581 (t80)
REVERT: E   61 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.6559 (ptt90)
  outliers start: 19
  outliers final: 18
  residues processed: 57
  average time/residue: 0.1254
  time to fit residues: 11.1214
Evaluate side-chains
  60 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 41
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  481 ASN
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain A residue  559 PHE
Chi-restraints excluded: chain D residue   59 PHE
Chi-restraints excluded: chain D residue  124 LEU
Chi-restraints excluded: chain D residue  144 ASP
Chi-restraints excluded: chain D residue  182 VAL
Chi-restraints excluded: chain E residue   47 LEU
Chi-restraints excluded: chain E residue   61 ARG
Chi-restraints excluded: chain E residue   78 LEU
Chi-restraints excluded: chain F residue  108 TYR
Chi-restraints excluded: chain F residue  118 SER
Chi-restraints excluded: chain G residue    7 SER
Chi-restraints excluded: chain G residue   34 ASN
Chi-restraints excluded: chain G residue   48 ILE
Chi-restraints excluded: chain G residue  196 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 82 optimal weight:    0.4980
   chunk 66 optimal weight:    3.9990
   chunk 98 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 54 optimal weight:    0.3980
   chunk 21 optimal weight:    0.8980
   chunk 71 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 487 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 = 0.3269 r_free = 0.3269 target = 0.054847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.039274 restraints weight = 97853.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.2775 rms_B_bonded: 3.61
r_work: 0.2672 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.1701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9070  Z= 0.135
  Angle     :  0.533   9.334  12357  Z= 0.273
  Chirality :  0.043   0.148   1379
  Planarity :  0.003   0.036   1585
  Dihedral  :  5.768  59.560   1315
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 10.56 %
    Favored  : 87.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.25 (0.26), residues: 1130
  helix: -0.01 (0.85), residues: 39
  sheet:  0.19 (0.23), residues: 514
  loop : -0.42 (0.28), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 210 
 TYR   0.011   0.001   TYR F 108 
 PHE   0.008   0.001   PHE G  73 
 TRP   0.007   0.001   TRP D  50 
 HIS   0.005   0.001   HIS F 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.13 ( 9054)
  covalent geometry    : angle       0.52545 /  0.27 (12321)
  SS BOND              : bond        0.00384 /  0.19 (   12)
  SS BOND              : angle       1.34935 /  0.77 (   24)
  hydrogen bonds       : bond        0.02710 /  1.76 (  335)
  hydrogen bonds       : angle       5.67101 /  3.86 (  924)
  link_BETA1-4         : bond        0.00227 /  0.12 (    1)
  link_BETA1-4         : angle       1.02158 /  0.55 (    3)
  link_BETA1-6         : bond        0.01010 /  0.53 (    1)
  link_BETA1-6         : angle       1.28522 /  0.61 (    3)
  link_NAG-ASN         : bond        0.00338 /  0.16 (    2)
  link_NAG-ASN         : angle       3.22928 /  1.66 (    6)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 42
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  577 ARG cc_start: 0.8357 (ttm170) cc_final: 0.7544 (mtt180)
REVERT: D  146 PHE cc_start: 0.7782 (t80) cc_final: 0.7559 (t80)
REVERT: E   61 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.6553 (ptt90)
  outliers start: 17
  outliers final: 15
  residues processed: 57
  average time/residue: 0.1425
  time to fit residues: 12.5179
Evaluate side-chains
  56 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 40
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  481 ASN
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain A residue  559 PHE
Chi-restraints excluded: chain D residue   59 PHE
Chi-restraints excluded: chain D residue  124 LEU
Chi-restraints excluded: chain D residue  144 ASP
Chi-restraints excluded: chain E residue   47 LEU
Chi-restraints excluded: chain E residue   61 ARG
Chi-restraints excluded: chain E residue   78 LEU
Chi-restraints excluded: chain F residue  108 TYR
Chi-restraints excluded: chain F residue  118 SER
Chi-restraints excluded: chain G residue    7 SER
Chi-restraints excluded: chain G residue   34 ASN
Chi-restraints excluded: chain G residue  196 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 61 optimal weight:    0.5980
   chunk 71 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 110 optimal weight:    4.9990
   chunk 102 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 563 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.054625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.039125 restraints weight = 98193.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.2769 rms_B_bonded: 3.59
r_work: 0.2667 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9070  Z= 0.154
  Angle     :  0.539   9.399  12357  Z= 0.276
  Chirality :  0.042   0.149   1379
  Planarity :  0.003   0.036   1585
  Dihedral  :  5.784  59.423   1315
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 10.46 %
    Favored  : 87.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.34 (0.26), residues: 1130
  helix: -0.81 (0.75), residues: 47
  sheet:  0.18 (0.23), residues: 515
  loop : -0.47 (0.28), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 210 
 TYR   0.010   0.001   TYR G  93 
 PHE   0.009   0.001   PHE G  73 
 TRP   0.007   0.001   TRP D  50 
 HIS   0.005   0.001   HIS F 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.15 ( 9054)
  covalent geometry    : angle       0.53095 /  0.27 (12321)
  SS BOND              : bond        0.00386 /  0.19 (   12)
  SS BOND              : angle       1.38314 /  0.79 (   24)
  hydrogen bonds       : bond        0.02720 /  1.76 (  335)
  hydrogen bonds       : angle       5.65130 /  3.85 (  924)
  link_BETA1-4         : bond        0.00168 /  0.09 (    1)
  link_BETA1-4         : angle       1.05923 /  0.57 (    3)
  link_BETA1-6         : bond        0.00862 /  0.45 (    1)
  link_BETA1-6         : angle       1.26495 /  0.60 (    3)
  link_NAG-ASN         : bond        0.00317 /  0.15 (    2)
  link_NAG-ASN         : angle       3.31866 /  1.69 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3078.43 seconds
wall clock time: 53 minutes 7.02 seconds (3187.02 seconds total)