Starting phenix.real_space_refine
on Sun May 11 17:16:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j74_36025/05_2025/8j74_36025.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j74_36025/05_2025/8j74_36025.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j74_36025/05_2025/8j74_36025.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j74_36025/05_2025/8j74_36025.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j74_36025/05_2025/8j74_36025.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j74_36025/05_2025/8j74_36025.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.061
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    5546      2.51       5
     N    1214      2.21       5
     O    1488      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8288
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3959
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 515, 3959
          Classifications: {'peptide': 515}
          Link IDs: {'PTRANS': 22, 'TRANS': 492}
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 146
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 146
          Unusual residues: {'AV0': 1, 'HC6': 1, 'R16': 1, 'Y01': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 116
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 116
          Unusual residues: {'AV0': 1, 'R16': 1, 'Y01': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
  Restraints were copied for chains:
    B, F
  Time building chain proxies: 7.79, per 1000 atoms: 0.94
  Number of scatterers: 8288
  At special positions: 0
  Unit cell: (100.86, 100.86, 95.94, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      40     16.00
     O    1488      8.00
     N    1214      7.00
     C    5546      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
    NAG-ASN
      " NAG E   1 " - " ASN A 301 "
      " NAG F   1 " - " ASN B 301 "
  Time building additional restraints: 2.62
  Conformation dependent library (CDL) restraints added in 942.0 milliseconds
  

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1872

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 2 sheets defined
      77.5% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 29
      removed outlier: 3.548A  pdb=" N   LEU A   8 " --> pdb=" O   HIS A   4 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 45
    Processing helix  chain 'A' and resid 46 through 48
      No H-bonds generated for 'chain 'A' and resid 46 through 48'
    Processing helix  chain 'A' and resid 50 through 63
      removed outlier: 3.529A  pdb=" N   VAL A  63 " --> pdb=" O   THR A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 77
      removed outlier: 3.815A  pdb=" N   THR A  71 " --> pdb=" O   TYR A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 102
    Processing helix  chain 'A' and resid 103 through 109
      removed outlier: 3.645A  pdb=" N   ARG A 107 " --> pdb=" O   ALA A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 122
      removed outlier: 4.309A  pdb=" N   PHE A 118 " --> pdb=" O   MET A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 130
    Processing helix  chain 'A' and resid 130 through 157
      removed outlier: 4.235A  pdb=" N   ALA A 134 " --> pdb=" O   LEU A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 179
      removed outlier: 3.721A  pdb=" N   VAL A 178 " --> pdb=" O   LEU A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 200
      removed outlier: 3.714A  pdb=" N   VAL A 190 " --> pdb=" O   TYR A 186 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   PHE A 193 " --> pdb=" O   VAL A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 208
    Processing helix  chain 'A' and resid 233 through 235
      No H-bonds generated for 'chain 'A' and resid 233 through 235'
    Processing helix  chain 'A' and resid 236 through 250
    Processing helix  chain 'A' and resid 254 through 262
    Processing helix  chain 'A' and resid 266 through 297
      removed outlier: 4.168A  pdb=" N   ALA A 270 " --> pdb=" O   SER A 266 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   PHE A 275 " --> pdb=" O   GLN A 271 " (cutoff:3.500A)
      Proline residue:  A 287  - end of helix
    Processing helix  chain 'A' and resid 309 through 314
    Processing helix  chain 'A' and resid 315 through 318
    Processing helix  chain 'A' and resid 319 through 327
      removed outlier: 3.677A  pdb=" N   GLN A 325 " --> pdb=" O   PRO A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 363
      removed outlier: 3.871A  pdb=" N   PHE A 335 " --> pdb=" O   TYR A 331 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ARG A 361 " --> pdb=" O   SER A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 399
      removed outlier: 3.561A  pdb=" N   PHE A 386 " --> pdb=" O   ARG A 382 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   THR A 399 " --> pdb=" O   MET A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 426
      Proline residue:  A 419  - end of helix
    Processing helix  chain 'A' and resid 431 through 448
      removed outlier: 3.852A  pdb=" N   ALA A 437 " --> pdb=" O   TYR A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 505
      removed outlier: 4.106A  pdb=" N   MET A 484 " --> pdb=" O   LYS A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 512
      removed outlier: 3.725A  pdb=" N   LEU A 511 " --> pdb=" O   PRO A 508 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 29
      removed outlier: 3.548A  pdb=" N   LEU B   8 " --> pdb=" O   HIS B   4 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 37 through 45
    Processing helix  chain 'B' and resid 46 through 48
      No H-bonds generated for 'chain 'B' and resid 46 through 48'
    Processing helix  chain 'B' and resid 50 through 63
      removed outlier: 3.529A  pdb=" N   VAL B  63 " --> pdb=" O   THR B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 77
      removed outlier: 3.815A  pdb=" N   THR B  71 " --> pdb=" O   TYR B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 102
    Processing helix  chain 'B' and resid 103 through 109
      removed outlier: 3.645A  pdb=" N   ARG B 107 " --> pdb=" O   ALA B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 122
      removed outlier: 4.309A  pdb=" N   PHE B 118 " --> pdb=" O   MET B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 130
    Processing helix  chain 'B' and resid 130 through 157
      removed outlier: 4.235A  pdb=" N   ALA B 134 " --> pdb=" O   LEU B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 179
      removed outlier: 3.721A  pdb=" N   VAL B 178 " --> pdb=" O   LEU B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 200
      removed outlier: 3.714A  pdb=" N   VAL B 190 " --> pdb=" O   TYR B 186 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   PHE B 193 " --> pdb=" O   VAL B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 208
    Processing helix  chain 'B' and resid 233 through 235
      No H-bonds generated for 'chain 'B' and resid 233 through 235'
    Processing helix  chain 'B' and resid 236 through 250
    Processing helix  chain 'B' and resid 254 through 262
    Processing helix  chain 'B' and resid 266 through 297
      removed outlier: 4.168A  pdb=" N   ALA B 270 " --> pdb=" O   SER B 266 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   PHE B 275 " --> pdb=" O   GLN B 271 " (cutoff:3.500A)
      Proline residue:  B 287  - end of helix
    Processing helix  chain 'B' and resid 309 through 314
    Processing helix  chain 'B' and resid 315 through 318
    Processing helix  chain 'B' and resid 319 through 327
      removed outlier: 3.677A  pdb=" N   GLN B 325 " --> pdb=" O   PRO B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 363
      removed outlier: 3.871A  pdb=" N   PHE B 335 " --> pdb=" O   TYR B 331 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ARG B 361 " --> pdb=" O   SER B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 399
      removed outlier: 3.561A  pdb=" N   PHE B 386 " --> pdb=" O   ARG B 382 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   THR B 399 " --> pdb=" O   MET B 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 401 through 426
      Proline residue:  B 419  - end of helix
    Processing helix  chain 'B' and resid 431 through 448
      removed outlier: 3.852A  pdb=" N   ALA B 437 " --> pdb=" O   TYR B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 478 through 505
      removed outlier: 4.106A  pdb=" N   MET B 484 " --> pdb=" O   LYS B 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 508 through 512
      removed outlier: 3.725A  pdb=" N   LEU B 511 " --> pdb=" O   PRO B 508 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 466 through 467
    Processing sheet with id=AA2, first strand: chain 'B' and resid 466 through 467

    552 hydrogen bonds defined for protein.
    1638 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: 2.41

  Time building geometry restraints manager: 2.92 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1255
        1.32 -     1.45: 2473
        1.45 -     1.57: 4730
        1.57 -     1.69: 0
        1.69 -     1.81: 70
  Bond restraints: 8528
  Sorted by residual:
  bond pdb=" CB  ASP B 411 "
       pdb=" CG  ASP B 411 "
    ideal  model  delta    sigma   weight residual
    1.516  1.447  0.069 2.50e-02 1.60e+03 7.58e+00
  bond pdb=" CB  ASP A 411 "
       pdb=" CG  ASP A 411 "
    ideal  model  delta    sigma   weight residual
    1.516  1.447  0.069 2.50e-02 1.60e+03 7.58e+00
  bond pdb=" CA  ASP B 411 "
       pdb=" C   ASP B 411 "
    ideal  model  delta    sigma   weight residual
    1.524  1.497  0.027 1.27e-02 6.20e+03 4.39e+00
  bond pdb=" CA  ASP A 411 "
       pdb=" C   ASP A 411 "
    ideal  model  delta    sigma   weight residual
    1.524  1.497  0.027 1.27e-02 6.20e+03 4.39e+00
  bond pdb=" N   PHE A 477 "
       pdb=" CA  PHE A 477 "
    ideal  model  delta    sigma   weight residual
    1.457  1.484 -0.028 1.41e-02 5.03e+03 3.83e+00
  ... (remaining 8523 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 11209
        1.68 -     3.36: 345
        3.36 -     5.04: 70
        5.04 -     6.72: 30
        6.72 -     8.41: 6
  Bond angle restraints: 11660
  Sorted by residual:
  angle pdb=" N   LEU A 482 "
        pdb=" CA  LEU A 482 "
        pdb=" C   LEU A 482 "
      ideal   model   delta    sigma   weight residual
     111.28  105.66    5.62 1.09e+00 8.42e-01 2.65e+01
  angle pdb=" N   LEU B 482 "
        pdb=" CA  LEU B 482 "
        pdb=" C   LEU B 482 "
      ideal   model   delta    sigma   weight residual
     111.28  105.67    5.61 1.09e+00 8.42e-01 2.65e+01
  angle pdb=" N   TYR A 364 "
        pdb=" CA  TYR A 364 "
        pdb=" C   TYR A 364 "
      ideal   model   delta    sigma   weight residual
     112.04  118.40   -6.36 1.44e+00 4.82e-01 1.95e+01
  angle pdb=" N   TYR B 364 "
        pdb=" CA  TYR B 364 "
        pdb=" C   TYR B 364 "
      ideal   model   delta    sigma   weight residual
     112.04  118.40   -6.36 1.44e+00 4.82e-01 1.95e+01
  angle pdb=" N   ILE B 332 "
        pdb=" CA  ILE B 332 "
        pdb=" C   ILE B 332 "
      ideal   model   delta    sigma   weight residual
     111.81  108.01    3.80 8.60e-01 1.35e+00 1.95e+01
  ... (remaining 11655 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.42: 4774
       26.42 -    52.84: 300
       52.84 -    79.26: 60
       79.26 -   105.68: 72
      105.68 -   132.10: 32
  Dihedral angle restraints: 5238
    sinusoidal: 2276
      harmonic: 2962
  Sorted by residual:
  dihedral pdb=" CCF AV0 B 601 "
           pdb=" CCQ AV0 B 601 "
           pdb=" OCB AV0 B 601 "
           pdb=" CCS AV0 B 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -112.55   19.55 -132.10     1      3.00e+01 1.11e-03 1.78e+01
  dihedral pdb=" CCF AV0 A 702 "
           pdb=" CCQ AV0 A 702 "
           pdb=" OCB AV0 A 702 "
           pdb=" CCS AV0 A 702 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -112.55   19.55 -132.10     1      3.00e+01 1.11e-03 1.78e+01
  dihedral pdb=" CCH AV0 B 601 "
           pdb=" CCQ AV0 B 601 "
           pdb=" OCB AV0 B 601 "
           pdb=" CCS AV0 B 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     127.39 -100.76 -131.85     1      3.00e+01 1.11e-03 1.78e+01
  ... (remaining 5235 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1105
       0.055 -    0.110: 227
       0.110 -    0.164: 28
       0.164 -    0.219: 14
       0.219 -    0.274: 2
  Chirality restraints: 1376
  Sorted by residual:
  chirality pdb=" C5  BMA F   3 "
            pdb=" C4  BMA F   3 "
            pdb=" C6  BMA F   3 "
            pdb=" O5  BMA F   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.27 2.00e-01 2.50e+01 1.88e+00
  chirality pdb=" C5  BMA E   3 "
            pdb=" C4  BMA E   3 "
            pdb=" C6  BMA E   3 "
            pdb=" O5  BMA E   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.27 2.00e-01 2.50e+01 1.85e+00
  chirality pdb=" CB  ILE A 252 "
            pdb=" CA  ILE A 252 "
            pdb=" CG1 ILE A 252 "
            pdb=" CG2 ILE A 252 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.21 2.00e-01 2.50e+01 1.07e+00
  ... (remaining 1373 not shown)

  Planarity restraints: 1372
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 455 "   -0.007 2.00e-02 2.50e+03   1.30e-02 3.40e+00
        pdb=" CG  TYR B 455 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 455 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 455 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 455 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 455 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 455 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 455 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 455 "   -0.007 2.00e-02 2.50e+03   1.30e-02 3.40e+00
        pdb=" CG  TYR A 455 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 455 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 455 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 455 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 455 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 455 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 455 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 455 "   -0.008 2.00e-02 2.50e+03   1.58e-02 2.50e+00
        pdb=" C   TYR A 455 "    0.027 2.00e-02 2.50e+03
        pdb=" O   TYR A 455 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   LEU A 456 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1369 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 887
        2.74 -     3.28: 8846
        3.28 -     3.82: 14360
        3.82 -     4.36: 15495
        4.36 -     4.90: 27129
  Nonbonded interactions: 66717
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  34 "
            pdb=" OE1 GLU B  37 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" OG  SER A  34 "
            pdb=" OE1 GLU A  37 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" OG  SER A  34 "
            pdb=" OE1 GLU A  36 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OG  SER B  34 "
            pdb=" OE1 GLU B  36 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   PHE A 444 "
            pdb=" OG1 THR A 448 "
     model   vdw
     2.281 3.040
  ... (remaining 66712 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: 0.04
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 3 through 517 or resid 704))
  selection = (chain 'B' and (resid 3 through 517 or resid 604))
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     24.660
  Find NCS groups from input model:        0.400
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   8534  Z= 0.205
  Angle     :  0.744   8.405  11678  Z= 0.365
  Chirality :  0.047   0.274   1376
  Planarity :  0.004   0.037   1370
  Dihedral  : 24.907 132.103   3366
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 15.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 25.30 %
    Favored  : 74.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.29), residues: 1026
  helix:  1.49 (0.21), residues: 734
  sheet:  None (None), residues: 0
  loop : -2.18 (0.39), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 300 
 HIS   0.005   0.001   HIS B 221 
 PHE   0.012   0.001   PHE A 118 
 TYR   0.030   0.002   TYR A 455 
 ARG   0.009   0.001   ARG A  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00508 (    2)
  link_NAG-ASN         : angle       3.89095 (    6)
  link_BETA1-4         : bond        0.00589 (    4)
  link_BETA1-4         : angle       2.68435 (   12)
  hydrogen bonds       : bond        0.10692 (  552)
  hydrogen bonds       : angle       4.42392 ( 1638)
  covalent geometry    : bond        0.00414 ( 8528)
  covalent geometry    : angle       0.73438 (11660)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.789 
Fit side-chains
REVERT: A  130 LEU cc_start: 0.8802 (mp) cc_final: 0.8563 (mp)
REVERT: A  455 TYR cc_start: 0.5322 (p90) cc_final: 0.5001 (p90)
REVERT: B  130 LEU cc_start: 0.8787 (mp) cc_final: 0.8544 (mp)
REVERT: B  455 TYR cc_start: 0.5323 (p90) cc_final: 0.5000 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 157
  average time/residue: 0.1687
  time to fit residues: 37.8237
Evaluate side-chains
  144 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    6.9990
   chunk 77 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   chunk 41 optimal weight:    0.4980
   chunk 79 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 491 ASN
B 491 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.142049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.127671 restraints weight = 15238.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.130400 restraints weight = 7921.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.132241 restraints weight = 4953.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.1059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8534  Z= 0.142
  Angle     :  0.766  10.131  11678  Z= 0.338
  Chirality :  0.046   0.236   1376
  Planarity :  0.004   0.028   1370
  Dihedral  : 19.397 148.671   1716
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 22.65 %
    Favored  : 73.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.29), residues: 1026
  helix:  1.54 (0.20), residues: 742
  sheet:  None (None), residues: 0
  loop : -1.92 (0.40), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 406 
 HIS   0.003   0.001   HIS A 221 
 PHE   0.010   0.001   PHE B 461 
 TYR   0.012   0.001   TYR A 414 
 ARG   0.005   0.001   ARG A 446 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00871 (    2)
  link_NAG-ASN         : angle       4.22488 (    6)
  link_BETA1-4         : bond        0.00914 (    4)
  link_BETA1-4         : angle       3.11693 (   12)
  hydrogen bonds       : bond        0.03780 (  552)
  hydrogen bonds       : angle       4.13953 ( 1638)
  covalent geometry    : bond        0.00312 ( 8528)
  covalent geometry    : angle       0.75349 (11660)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 146
  time to evaluate  : 1.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 TRP cc_start: 0.7853 (m100) cc_final: 0.7388 (m100)
REVERT: A  130 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8838 (mp)
REVERT: A  318 MET cc_start: 0.7168 (ppp) cc_final: 0.6448 (ppp)
REVERT: A  455 TYR cc_start: 0.5483 (p90) cc_final: 0.5203 (p90)
REVERT: B   62 TRP cc_start: 0.7856 (m100) cc_final: 0.7397 (m100)
REVERT: B  130 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8833 (mp)
REVERT: B  318 MET cc_start: 0.7174 (ppp) cc_final: 0.6434 (ppp)
REVERT: B  455 TYR cc_start: 0.5484 (p90) cc_final: 0.5206 (p90)
  outliers start: 28
  outliers final: 10
  residues processed: 170
  average time/residue: 0.1672
  time to fit residues: 41.4868
Evaluate side-chains
  144 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 132
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  368 PHE
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  368 PHE
Chi-restraints excluded: chain B residue  383 ILE
Chi-restraints excluded: chain B residue  431 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 93 optimal weight:    3.9990
   chunk 100 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0070
   chunk 97 optimal weight:    7.9990
   chunk 7 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 80 optimal weight:    0.8980
   chunk 101 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.6998

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

Flipped N/Q/H residues before XYZ refinement:
A 362 ASN
B 362 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.141939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.127813 restraints weight = 15542.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.130560 restraints weight = 7912.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.132411 restraints weight = 4912.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.1288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8534  Z= 0.125
  Angle     :  0.652   9.314  11678  Z= 0.302
  Chirality :  0.042   0.238   1376
  Planarity :  0.004   0.025   1370
  Dihedral  : 15.793 158.269   1716
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 21.20 %
    Favored  : 74.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.29), residues: 1026
  helix:  1.53 (0.20), residues: 748
  sheet:  None (None), residues: 0
  loop : -1.90 (0.42), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 300 
 HIS   0.002   0.000   HIS B 221 
 PHE   0.006   0.001   PHE A 140 
 TYR   0.014   0.001   TYR B 439 
 ARG   0.005   0.001   ARG A  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00672 (    2)
  link_NAG-ASN         : angle       4.11335 (    6)
  link_BETA1-4         : bond        0.00909 (    4)
  link_BETA1-4         : angle       2.72254 (   12)
  hydrogen bonds       : bond        0.03726 (  552)
  hydrogen bonds       : angle       4.09631 ( 1638)
  covalent geometry    : bond        0.00277 ( 8528)
  covalent geometry    : angle       0.63956 (11660)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 149
  time to evaluate  : 0.820 
Fit side-chains
REVERT: A   62 TRP cc_start: 0.7840 (m100) cc_final: 0.7315 (m100)
REVERT: A  116 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7724 (t0)
REVERT: A  318 MET cc_start: 0.7316 (ppp) cc_final: 0.6236 (ppp)
REVERT: A  455 TYR cc_start: 0.5505 (p90) cc_final: 0.5215 (p90)
REVERT: B   62 TRP cc_start: 0.7840 (m100) cc_final: 0.7316 (m100)
REVERT: B  116 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7659 (t0)
REVERT: B  318 MET cc_start: 0.7314 (ppp) cc_final: 0.6211 (ppp)
REVERT: B  455 TYR cc_start: 0.5501 (p90) cc_final: 0.5212 (p90)
  outliers start: 32
  outliers final: 16
  residues processed: 177
  average time/residue: 0.1577
  time to fit residues: 40.5862
Evaluate side-chains
  152 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  368 PHE
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  368 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   chunk 76 optimal weight:    0.9980
   chunk 70 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 57 optimal weight:    0.6980
   chunk 64 optimal weight:    3.9990
   chunk 59 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 191 GLN
A 365 GLN
B 191 GLN
B 365 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.141630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.127549 restraints weight = 15487.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.130216 restraints weight = 8004.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.132073 restraints weight = 5063.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.1468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8534  Z= 0.128
  Angle     :  0.652   9.391  11678  Z= 0.302
  Chirality :  0.042   0.240   1376
  Planarity :  0.003   0.025   1370
  Dihedral  : 14.731 156.199   1716
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 22.41 %
    Favored  : 74.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.29), residues: 1026
  helix:  1.57 (0.20), residues: 748
  sheet:  None (None), residues: 0
  loop : -1.86 (0.42), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 300 
 HIS   0.001   0.000   HIS B 209 
 PHE   0.007   0.001   PHE B 131 
 TYR   0.012   0.001   TYR B 439 
 ARG   0.005   0.001   ARG B  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00695 (    2)
  link_NAG-ASN         : angle       4.10394 (    6)
  link_BETA1-4         : bond        0.00893 (    4)
  link_BETA1-4         : angle       2.77125 (   12)
  hydrogen bonds       : bond        0.03639 (  552)
  hydrogen bonds       : angle       4.10698 ( 1638)
  covalent geometry    : bond        0.00292 ( 8528)
  covalent geometry    : angle       0.63984 (11660)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 146
  time to evaluate  : 0.843 
Fit side-chains
REVERT: A   62 TRP cc_start: 0.7849 (m100) cc_final: 0.7592 (m100)
REVERT: A  116 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7650 (t0)
REVERT: A  229 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8230 (mp)
REVERT: A  318 MET cc_start: 0.7033 (ppp) cc_final: 0.6707 (ppp)
REVERT: A  455 TYR cc_start: 0.5582 (p90) cc_final: 0.5280 (p90)
REVERT: B   62 TRP cc_start: 0.7859 (m100) cc_final: 0.7595 (m100)
REVERT: B  116 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7639 (t0)
REVERT: B  229 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8223 (mp)
REVERT: B  318 MET cc_start: 0.7040 (ppp) cc_final: 0.6705 (ppp)
REVERT: B  455 TYR cc_start: 0.5579 (p90) cc_final: 0.5281 (p90)
  outliers start: 28
  outliers final: 19
  residues processed: 170
  average time/residue: 0.1645
  time to fit residues: 40.8433
Evaluate side-chains
  155 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 132
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  368 PHE
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  368 PHE
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  431 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 41 optimal weight:    0.5980
   chunk 35 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 72 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 19 optimal weight:    6.9990
   chunk 76 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0370
   chunk 79 optimal weight:    0.8980
   overall best weight:    0.6058

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.142285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.128430 restraints weight = 15391.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.131149 restraints weight = 7912.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.132929 restraints weight = 4942.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.1541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   8534  Z= 0.123
  Angle     :  0.625   9.386  11678  Z= 0.294
  Chirality :  0.041   0.239   1376
  Planarity :  0.003   0.025   1370
  Dihedral  : 13.823 156.246   1716
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 24.22 %
    Favored  : 71.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.29), residues: 1026
  helix:  1.60 (0.20), residues: 748
  sheet:  None (None), residues: 0
  loop : -1.83 (0.42), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 300 
 HIS   0.001   0.000   HIS A 209 
 PHE   0.006   0.001   PHE A 131 
 TYR   0.013   0.001   TYR A 439 
 ARG   0.005   0.001   ARG B  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00652 (    2)
  link_NAG-ASN         : angle       4.10528 (    6)
  link_BETA1-4         : bond        0.00914 (    4)
  link_BETA1-4         : angle       2.63595 (   12)
  hydrogen bonds       : bond        0.03607 (  552)
  hydrogen bonds       : angle       4.05912 ( 1638)
  covalent geometry    : bond        0.00283 ( 8528)
  covalent geometry    : angle       0.61306 (11660)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 153
  time to evaluate  : 0.781 
Fit side-chains
REVERT: A  116 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7669 (t0)
REVERT: A  229 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8203 (mp)
REVERT: A  318 MET cc_start: 0.7125 (ppp) cc_final: 0.6802 (ppp)
REVERT: A  455 TYR cc_start: 0.5584 (p90) cc_final: 0.5282 (p90)
REVERT: B  116 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7628 (t0)
REVERT: B  229 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8202 (mp)
REVERT: B  318 MET cc_start: 0.7123 (ppp) cc_final: 0.6799 (ppp)
REVERT: B  455 TYR cc_start: 0.5572 (p90) cc_final: 0.5274 (p90)
  outliers start: 34
  outliers final: 18
  residues processed: 178
  average time/residue: 0.1560
  time to fit residues: 40.4732
Evaluate side-chains
  164 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 142
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  368 PHE
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  368 PHE
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  431 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 42 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 20 optimal weight:    0.6980
   chunk 93 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 97 optimal weight:    0.3980
   chunk 87 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.7382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.141808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.127990 restraints weight = 15212.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.130673 restraints weight = 7776.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.132568 restraints weight = 4825.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.1625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8534  Z= 0.126
  Angle     :  0.648  10.444  11678  Z= 0.302
  Chirality :  0.041   0.238   1376
  Planarity :  0.003   0.025   1370
  Dihedral  : 12.811 156.514   1716
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 24.22 %
    Favored  : 71.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.29), residues: 1026
  helix:  1.58 (0.20), residues: 748
  sheet:  None (None), residues: 0
  loop : -1.81 (0.42), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  62 
 HIS   0.001   0.000   HIS A 209 
 PHE   0.005   0.001   PHE B 131 
 TYR   0.013   0.001   TYR A 439 
 ARG   0.007   0.001   ARG B  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00664 (    2)
  link_NAG-ASN         : angle       4.07699 (    6)
  link_BETA1-4         : bond        0.00838 (    4)
  link_BETA1-4         : angle       2.58144 (   12)
  hydrogen bonds       : bond        0.03573 (  552)
  hydrogen bonds       : angle       4.09785 ( 1638)
  covalent geometry    : bond        0.00285 ( 8528)
  covalent geometry    : angle       0.63643 (11660)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 149
  time to evaluate  : 0.801 
Fit side-chains
REVERT: A  116 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7578 (t0)
REVERT: A  229 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8255 (mp)
REVERT: A  318 MET cc_start: 0.7143 (ppp) cc_final: 0.6850 (ppp)
REVERT: A  455 TYR cc_start: 0.5617 (p90) cc_final: 0.5319 (p90)
REVERT: B  116 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7540 (t0)
REVERT: B  229 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8255 (mp)
REVERT: B  318 MET cc_start: 0.7146 (ppp) cc_final: 0.6847 (ppp)
REVERT: B  455 TYR cc_start: 0.5610 (p90) cc_final: 0.5314 (p90)
  outliers start: 37
  outliers final: 20
  residues processed: 178
  average time/residue: 0.1608
  time to fit residues: 41.9541
Evaluate side-chains
  163 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 139
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  368 PHE
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  368 PHE
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  431 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 86 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 59 optimal weight:    4.9990
   chunk 17 optimal weight:    0.5980
   chunk 24 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0070
   overall best weight:    0.6600

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.141696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.128016 restraints weight = 15318.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.130738 restraints weight = 7771.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.132405 restraints weight = 4794.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.1666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8534  Z= 0.122
  Angle     :  0.629   9.387  11678  Z= 0.296
  Chirality :  0.041   0.238   1376
  Planarity :  0.003   0.026   1370
  Dihedral  : 11.952 156.639   1716
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 25.54 %
    Favored  : 71.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.29), residues: 1026
  helix:  1.58 (0.20), residues: 748
  sheet:  None (None), residues: 0
  loop : -1.82 (0.42), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 406 
 HIS   0.005   0.001   HIS A 221 
 PHE   0.005   0.001   PHE A 131 
 TYR   0.015   0.001   TYR B 439 
 ARG   0.008   0.001   ARG B  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00669 (    2)
  link_NAG-ASN         : angle       4.05421 (    6)
  link_BETA1-4         : bond        0.00801 (    4)
  link_BETA1-4         : angle       2.50632 (   12)
  hydrogen bonds       : bond        0.03544 (  552)
  hydrogen bonds       : angle       4.05472 ( 1638)
  covalent geometry    : bond        0.00272 ( 8528)
  covalent geometry    : angle       0.61733 (11660)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 147
  time to evaluate  : 0.877 
Fit side-chains
REVERT: A  116 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7712 (t0)
REVERT: A  182 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.7555 (m-10)
REVERT: A  229 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8202 (mp)
REVERT: A  318 MET cc_start: 0.7216 (ppp) cc_final: 0.6944 (ppp)
REVERT: A  455 TYR cc_start: 0.5774 (p90) cc_final: 0.5432 (p90)
REVERT: A  484 MET cc_start: 0.8500 (ppp) cc_final: 0.8219 (ppp)
REVERT: B  116 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7711 (t0)
REVERT: B  229 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8199 (mp)
REVERT: B  318 MET cc_start: 0.7219 (ppp) cc_final: 0.6937 (ppp)
REVERT: B  455 TYR cc_start: 0.5771 (p90) cc_final: 0.5431 (p90)
REVERT: B  484 MET cc_start: 0.8507 (ppp) cc_final: 0.8227 (ppp)
  outliers start: 28
  outliers final: 22
  residues processed: 165
  average time/residue: 0.1699
  time to fit residues: 40.8376
Evaluate side-chains
  171 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 144
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  368 PHE
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  368 PHE
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  431 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 57 optimal weight:    5.9990
   chunk 7 optimal weight:    0.2980
   chunk 100 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9980
   chunk 49 optimal weight:    4.9990
   overall best weight:    1.8586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.136287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.122431 restraints weight = 15604.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.125111 restraints weight = 7992.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.126687 restraints weight = 4987.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8534  Z= 0.183
  Angle     :  0.709  11.023  11678  Z= 0.335
  Chirality :  0.043   0.238   1376
  Planarity :  0.004   0.038   1370
  Dihedral  : 11.742 156.846   1716
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 24.70 %
    Favored  : 71.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.29), residues: 1026
  helix:  1.43 (0.20), residues: 748
  sheet:  None (None), residues: 0
  loop : -1.84 (0.44), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 406 
 HIS   0.004   0.001   HIS A 221 
 PHE   0.008   0.001   PHE B 140 
 TYR   0.014   0.001   TYR A 439 
 ARG   0.010   0.001   ARG A  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00712 (    2)
  link_NAG-ASN         : angle       4.03910 (    6)
  link_BETA1-4         : bond        0.00786 (    4)
  link_BETA1-4         : angle       2.80171 (   12)
  hydrogen bonds       : bond        0.04125 (  552)
  hydrogen bonds       : angle       4.34102 ( 1638)
  covalent geometry    : bond        0.00430 ( 8528)
  covalent geometry    : angle       0.69797 (11660)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 135
  time to evaluate  : 0.874 
Fit side-chains
REVERT: A  229 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8340 (mp)
REVERT: A  318 MET cc_start: 0.7339 (ppp) cc_final: 0.7088 (ppp)
REVERT: A  455 TYR cc_start: 0.5988 (p90) cc_final: 0.5472 (p90)
REVERT: B  229 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8344 (mp)
REVERT: B  318 MET cc_start: 0.7344 (ppp) cc_final: 0.7082 (ppp)
REVERT: B  455 TYR cc_start: 0.5960 (p90) cc_final: 0.5451 (p90)
  outliers start: 31
  outliers final: 21
  residues processed: 155
  average time/residue: 0.1759
  time to fit residues: 39.4723
Evaluate side-chains
  154 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 131
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  368 PHE
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  368 PHE
Chi-restraints excluded: chain B residue  384 THR
Chi-restraints excluded: chain B residue  431 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 57 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0570
   chunk 58 optimal weight:    0.6980
   chunk 39 optimal weight:    8.9990
   chunk 60 optimal weight:    1.9990
   chunk 42 optimal weight:    0.3980
   chunk 100 optimal weight:    0.7980
   chunk 29 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.5898

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.140472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.126529 restraints weight = 15444.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.129237 restraints weight = 7867.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.131155 restraints weight = 4879.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8534  Z= 0.127
  Angle     :  0.653   9.277  11678  Z= 0.309
  Chirality :  0.042   0.236   1376
  Planarity :  0.003   0.028   1370
  Dihedral  : 11.528 156.196   1716
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 26.02 %
    Favored  : 71.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.29), residues: 1026
  helix:  1.57 (0.20), residues: 746
  sheet:  None (None), residues: 0
  loop : -1.86 (0.43), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 254 
 HIS   0.005   0.001   HIS B 221 
 PHE   0.010   0.001   PHE B 258 
 TYR   0.015   0.001   TYR A 439 
 ARG   0.008   0.001   ARG B  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00638 (    2)
  link_NAG-ASN         : angle       4.01902 (    6)
  link_BETA1-4         : bond        0.00698 (    4)
  link_BETA1-4         : angle       2.47997 (   12)
  hydrogen bonds       : bond        0.03733 (  552)
  hydrogen bonds       : angle       4.17747 ( 1638)
  covalent geometry    : bond        0.00282 ( 8528)
  covalent geometry    : angle       0.64220 (11660)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 141
  time to evaluate  : 0.897 
Fit side-chains
REVERT: A  229 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8294 (mp)
REVERT: A  318 MET cc_start: 0.7290 (ppp) cc_final: 0.7053 (ppp)
REVERT: A  368 PHE cc_start: 0.6336 (OUTLIER) cc_final: 0.5839 (t80)
REVERT: A  455 TYR cc_start: 0.6004 (p90) cc_final: 0.5506 (p90)
REVERT: A  485 VAL cc_start: 0.8837 (p) cc_final: 0.8628 (p)
REVERT: B  229 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8285 (mp)
REVERT: B  318 MET cc_start: 0.7280 (ppp) cc_final: 0.7032 (ppp)
REVERT: B  368 PHE cc_start: 0.6343 (OUTLIER) cc_final: 0.5845 (t80)
REVERT: B  455 TYR cc_start: 0.5999 (p90) cc_final: 0.5506 (p90)
REVERT: B  485 VAL cc_start: 0.8838 (p) cc_final: 0.8633 (p)
  outliers start: 24
  outliers final: 16
  residues processed: 154
  average time/residue: 0.1696
  time to fit residues: 37.8113
Evaluate side-chains
  154 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 134
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  368 PHE
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  368 PHE
Chi-restraints excluded: chain B residue  431 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 98 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 80 optimal weight:    7.9990
   chunk 34 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 70 optimal weight:    5.9990
   chunk 66 optimal weight:    0.2980
   chunk 36 optimal weight:    4.9990
   overall best weight:    0.7982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.140405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.126680 restraints weight = 15429.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.129408 restraints weight = 7843.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.131228 restraints weight = 4872.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.1891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8534  Z= 0.136
  Angle     :  0.680  11.527  11678  Z= 0.319
  Chirality :  0.042   0.236   1376
  Planarity :  0.004   0.036   1370
  Dihedral  : 11.404 157.393   1716
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 26.87 %
    Favored  : 70.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.29), residues: 1026
  helix:  1.52 (0.20), residues: 750
  sheet:  None (None), residues: 0
  loop : -1.77 (0.43), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 254 
 HIS   0.005   0.001   HIS B 221 
 PHE   0.008   0.001   PHE B 258 
 TYR   0.015   0.001   TYR A 439 
 ARG   0.009   0.001   ARG B  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00676 (    2)
  link_NAG-ASN         : angle       3.92609 (    6)
  link_BETA1-4         : bond        0.00741 (    4)
  link_BETA1-4         : angle       2.46705 (   12)
  hydrogen bonds       : bond        0.03733 (  552)
  hydrogen bonds       : angle       4.19981 ( 1638)
  covalent geometry    : bond        0.00313 ( 8528)
  covalent geometry    : angle       0.66974 (11660)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 144
  time to evaluate  : 0.849 
Fit side-chains
REVERT: A  229 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8319 (mp)
REVERT: A  318 MET cc_start: 0.7271 (ppp) cc_final: 0.6945 (ppp)
REVERT: A  455 TYR cc_start: 0.6093 (p90) cc_final: 0.5569 (p90)
REVERT: B  229 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8313 (mp)
REVERT: B  318 MET cc_start: 0.7273 (ppp) cc_final: 0.6942 (ppp)
REVERT: B  455 TYR cc_start: 0.6076 (p90) cc_final: 0.5556 (p90)
  outliers start: 24
  outliers final: 20
  residues processed: 159
  average time/residue: 0.1727
  time to fit residues: 39.6546
Evaluate side-chains
  162 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  368 PHE
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  368 PHE
Chi-restraints excluded: chain B residue  431 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 74 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 51 optimal weight:   10.0000
   chunk 81 optimal weight:    0.6980
   chunk 88 optimal weight:    0.1980
   chunk 66 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 40 optimal weight:    8.9990
   chunk 98 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 87 optimal weight:    4.9990
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.141278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.127485 restraints weight = 15518.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.130265 restraints weight = 7863.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.132099 restraints weight = 4823.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.1873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8534  Z= 0.132
  Angle     :  0.687  10.493  11678  Z= 0.321
  Chirality :  0.043   0.237   1376
  Planarity :  0.004   0.036   1370
  Dihedral  : 11.297 158.016   1716
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 26.27 %
    Favored  : 70.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.29), residues: 1026
  helix:  1.54 (0.20), residues: 748
  sheet:  None (None), residues: 0
  loop : -1.80 (0.43), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 254 
 HIS   0.005   0.001   HIS B 221 
 PHE   0.009   0.001   PHE B 258 
 TYR   0.016   0.001   TYR A 439 
 ARG   0.008   0.001   ARG B  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00670 (    2)
  link_NAG-ASN         : angle       3.91908 (    6)
  link_BETA1-4         : bond        0.00752 (    4)
  link_BETA1-4         : angle       2.41988 (   12)
  hydrogen bonds       : bond        0.03723 (  552)
  hydrogen bonds       : angle       4.16419 ( 1638)
  covalent geometry    : bond        0.00305 ( 8528)
  covalent geometry    : angle       0.67745 (11660)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2359.13 seconds
wall clock time: 42 minutes 27.16 seconds (2547.16 seconds total)