Starting phenix.real_space_refine
on Wed Feb  4 00:51:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j74_36025/02_2026/8j74_36025.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j74_36025/02_2026/8j74_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j74_36025/02_2026/8j74_36025.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j74_36025/02_2026/8j74_36025.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j74_36025/02_2026/8j74_36025.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j74_36025/02_2026/8j74_36025.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.061
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8288
  Number of models: 1
  Model: ""
    Number of chains: 6
    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: "B"
      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: "F"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "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: 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
  Time building chain proxies: 1.91, per 1000 atoms: 0.23
  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: 0.60
  Conformation dependent library (CDL) restraints added in 216.3 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: 0.21
  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: 0.81

  Time building geometry restraints manager: 0.76 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: 0.01
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:             1.650
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.350
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.300
-------------------------------------------------------------------------------
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 : 15.72
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (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
 ARG   0.009   0.001   ARG A  38 
 TYR   0.030   0.002   TYR A 455 
 PHE   0.012   0.001   PHE A 118 
 TRP   0.008   0.001   TRP A 300 
 HIS   0.005   0.001   HIS B 221 

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

*********************** 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  : 0.275 
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: 0.0635
  time to fit residues: 14.5384
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  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    9.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:   10.0000
   chunk 100 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    1.3586

-------------------------------------------------------------------------------
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 = 0.3763 r_free = 0.3763 target = 0.139964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.125618 restraints weight = 15449.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.128326 restraints weight = 8102.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.129939 restraints weight = 5088.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.131293 restraints weight = 3727.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.132086 restraints weight = 2937.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.1047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8534  Z= 0.163
  Angle     :  0.771   9.948  11678  Z= 0.344
  Chirality :  0.046   0.235   1376
  Planarity :  0.004   0.030   1370
  Dihedral  : 19.976 147.049   1716
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 23.86 %
    Favored  : 73.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.92 (0.29), residues: 1026
  helix:  1.52 (0.20), residues: 742
  sheet:  None (None), residues: 0
  loop : -1.87 (0.41), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 446 
 TYR   0.013   0.001   TYR A 414 
 PHE   0.009   0.001   PHE B 461 
 TRP   0.008   0.001   TRP B 406 
 HIS   0.002   0.001   HIS B 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 8528)
  covalent geometry    : angle       0.75974 (11660)
  hydrogen bonds       : bond        0.04056 (  552)
  hydrogen bonds       : angle       4.19230 ( 1638)
  link_BETA1-4         : bond        0.00939 (    4)
  link_BETA1-4         : angle       3.08111 (   12)
  link_NAG-ASN         : bond        0.00802 (    2)
  link_NAG-ASN         : angle       4.15734 (    6)

*********************** 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
  164 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 142
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8865 (mp)
REVERT: A  318 MET cc_start: 0.7234 (ppp) cc_final: 0.6389 (ppp)
REVERT: A  455 TYR cc_start: 0.5443 (p90) cc_final: 0.5178 (p90)
REVERT: B  130 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8863 (mp)
REVERT: B  318 MET cc_start: 0.7220 (ppp) cc_final: 0.6370 (ppp)
REVERT: B  455 TYR cc_start: 0.5443 (p90) cc_final: 0.5179 (p90)
  outliers start: 22
  outliers final: 12
  residues processed: 160
  average time/residue: 0.0609
  time to fit residues: 14.2896
Evaluate side-chains
  141 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 127
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
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  330 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  330 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 77 optimal weight:    8.9990
   chunk 56 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 40 optimal weight:    0.7980
   chunk 57 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   chunk 94 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 72 optimal weight:    0.0870
   chunk 12 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9980
   overall best weight:    0.7358

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.141800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.127631 restraints weight = 15228.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.130306 restraints weight = 7917.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.131936 restraints weight = 5002.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.133299 restraints weight = 3674.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.134073 restraints weight = 2892.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.1256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8534  Z= 0.127
  Angle     :  0.659   9.293  11678  Z= 0.304
  Chirality :  0.042   0.235   1376
  Planarity :  0.004   0.029   1370
  Dihedral  : 15.735 157.110   1716
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 21.33 %
    Favored  : 73.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.29), residues: 1026
  helix:  1.52 (0.20), residues: 742
  sheet:  None (None), residues: 0
  loop : -1.79 (0.42), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  38 
 TYR   0.014   0.001   TYR B 439 
 PHE   0.007   0.001   PHE B 461 
 TRP   0.007   0.001   TRP A 300 
 HIS   0.002   0.000   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 8528)
  covalent geometry    : angle       0.64683 (11660)
  hydrogen bonds       : bond        0.03767 (  552)
  hydrogen bonds       : angle       4.12459 ( 1638)
  link_BETA1-4         : bond        0.00911 (    4)
  link_BETA1-4         : angle       2.77267 (   12)
  link_NAG-ASN         : bond        0.00675 (    2)
  link_NAG-ASN         : angle       4.09157 (    6)

*********************** 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
  195 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 153
  time to evaluate  : 0.318 
Fit side-chains
REVERT: A   62 TRP cc_start: 0.7840 (m100) cc_final: 0.7372 (m100)
REVERT: A  229 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8232 (mp)
REVERT: A  318 MET cc_start: 0.7291 (ppp) cc_final: 0.6236 (ppp)
REVERT: A  455 TYR cc_start: 0.5471 (p90) cc_final: 0.5204 (p90)
REVERT: B   62 TRP cc_start: 0.7841 (m100) cc_final: 0.7367 (m100)
REVERT: B  229 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8250 (mp)
REVERT: B  318 MET cc_start: 0.7290 (ppp) cc_final: 0.6205 (ppp)
REVERT: B  455 TYR cc_start: 0.5470 (p90) cc_final: 0.5198 (p90)
  outliers start: 42
  outliers final: 18
  residues processed: 189
  average time/residue: 0.0624
  time to fit residues: 17.6039
Evaluate side-chains
  156 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 136
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
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  153 ILE
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  368 PHE
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  153 ILE
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  368 PHE
Chi-restraints excluded: chain B residue  431 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 43 optimal weight:    7.9990
   chunk 86 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 70 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9990
   chunk 57 optimal weight:    5.9990
   chunk 99 optimal weight:    1.9990
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.140452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.126093 restraints weight = 15784.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.128866 restraints weight = 8057.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.130557 restraints weight = 5019.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.131950 restraints weight = 3638.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.132755 restraints weight = 2845.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.1467

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= 0.133
  Angle     :  0.662   9.367  11678  Z= 0.308
  Chirality :  0.042   0.237   1376
  Planarity :  0.003   0.025   1370
  Dihedral  : 14.971 156.357   1716
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 23.49 %
    Favored  : 73.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.94 (0.29), residues: 1026
  helix:  1.52 (0.20), residues: 746
  sheet:  None (None), residues: 0
  loop : -1.91 (0.42), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  38 
 TYR   0.011   0.001   TYR B 439 
 PHE   0.011   0.001   PHE B 140 
 TRP   0.007   0.001   TRP B 300 
 HIS   0.003   0.001   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8528)
  covalent geometry    : angle       0.65001 (11660)
  hydrogen bonds       : bond        0.03729 (  552)
  hydrogen bonds       : angle       4.17987 ( 1638)
  link_BETA1-4         : bond        0.00864 (    4)
  link_BETA1-4         : angle       2.81630 (   12)
  link_NAG-ASN         : bond        0.00683 (    2)
  link_NAG-ASN         : angle       4.08906 (    6)

*********************** 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
  177 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 150
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A  229 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8284 (mp)
REVERT: A  318 MET cc_start: 0.7040 (ppp) cc_final: 0.6728 (ppp)
REVERT: A  455 TYR cc_start: 0.5511 (p90) cc_final: 0.5200 (p90)
REVERT: B  116 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7611 (t0)
REVERT: B  229 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8291 (mp)
REVERT: B  318 MET cc_start: 0.7050 (ppp) cc_final: 0.6718 (ppp)
REVERT: B  455 TYR cc_start: 0.5516 (p90) cc_final: 0.5204 (p90)
  outliers start: 27
  outliers final: 20
  residues processed: 173
  average time/residue: 0.0631
  time to fit residues: 16.1515
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  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  115 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  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  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 74 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 71 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 30 optimal weight:    0.0970
   chunk 5 optimal weight:    0.9980
   chunk 46 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 51 optimal weight:   10.0000
   overall best weight:    0.7778

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

Flipped N/Q/H residues before XYZ refinement:
A 191 GLN
** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.140819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.126814 restraints weight = 15592.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.129507 restraints weight = 8048.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.131259 restraints weight = 5041.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.132218 restraints weight = 3648.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.133313 restraints weight = 2976.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.1555

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     :  0.643   9.359  11678  Z= 0.303
  Chirality :  0.041   0.237   1376
  Planarity :  0.003   0.025   1370
  Dihedral  : 14.473 155.864   1716
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 23.98 %
    Favored  : 71.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.92 (0.29), residues: 1026
  helix:  1.51 (0.20), residues: 746
  sheet:  None (None), residues: 0
  loop : -1.91 (0.42), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  38 
 TYR   0.013   0.001   TYR B 439 
 PHE   0.006   0.001   PHE A 131 
 TRP   0.007   0.001   TRP B 300 
 HIS   0.002   0.001   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 8528)
  covalent geometry    : angle       0.63136 (11660)
  hydrogen bonds       : bond        0.03710 (  552)
  hydrogen bonds       : angle       4.15312 ( 1638)
  link_BETA1-4         : bond        0.00888 (    4)
  link_BETA1-4         : angle       2.70261 (   12)
  link_NAG-ASN         : bond        0.00658 (    2)
  link_NAG-ASN         : angle       4.07914 (    6)

*********************** 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
  180 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 145
  time to evaluate  : 0.194 
Fit side-chains
REVERT: A  116 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7803 (t0)
REVERT: A  229 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8255 (mp)
REVERT: A  318 MET cc_start: 0.7140 (ppp) cc_final: 0.6812 (ppp)
REVERT: A  455 TYR cc_start: 0.5561 (p90) cc_final: 0.5260 (p90)
REVERT: B  116 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7719 (t0)
REVERT: B  229 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8253 (mp)
REVERT: B  318 MET cc_start: 0.7143 (ppp) cc_final: 0.6801 (ppp)
REVERT: B  455 TYR cc_start: 0.5574 (p90) cc_final: 0.5272 (p90)
  outliers start: 35
  outliers final: 19
  residues processed: 173
  average time/residue: 0.0740
  time to fit residues: 19.0024
Evaluate side-chains
  162 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 139
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
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  184 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  252 ILE
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  247 LEU
Chi-restraints excluded: chain B residue  252 ILE
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 77 optimal weight:    7.9990
   chunk 93 optimal weight:    3.9990
   chunk 83 optimal weight:    0.3980
   chunk 75 optimal weight:    0.9990
   chunk 21 optimal weight:    4.9990
   chunk 100 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 39 optimal weight:    8.9990
   chunk 95 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    1.4386

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.137225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.123270 restraints weight = 15503.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.125891 restraints weight = 8141.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.127484 restraints weight = 5126.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.128779 restraints weight = 3762.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.129440 restraints weight = 2991.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.1686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8534  Z= 0.158
  Angle     :  0.683  10.036  11678  Z= 0.320
  Chirality :  0.042   0.234   1376
  Planarity :  0.004   0.026   1370
  Dihedral  : 13.989 155.874   1716
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 24.22 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.29), residues: 1026
  helix:  1.38 (0.20), residues: 748
  sheet:  None (None), residues: 0
  loop : -1.83 (0.43), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  38 
 TYR   0.013   0.001   TYR B 439 
 PHE   0.007   0.001   PHE B 131 
 TRP   0.010   0.001   TRP B 406 
 HIS   0.001   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 8528)
  covalent geometry    : angle       0.67156 (11660)
  hydrogen bonds       : bond        0.03926 (  552)
  hydrogen bonds       : angle       4.27672 ( 1638)
  link_BETA1-4         : bond        0.00802 (    4)
  link_BETA1-4         : angle       2.76743 (   12)
  link_NAG-ASN         : bond        0.00690 (    2)
  link_NAG-ASN         : angle       4.01579 (    6)

*********************** 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
  177 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 142
  time to evaluate  : 0.291 
Fit side-chains
REVERT: A  116 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7852 (t0)
REVERT: A  318 MET cc_start: 0.7329 (ppp) cc_final: 0.7037 (ppp)
REVERT: A  455 TYR cc_start: 0.5771 (p90) cc_final: 0.5467 (p90)
REVERT: B  318 MET cc_start: 0.7337 (ppp) cc_final: 0.7037 (ppp)
REVERT: B  455 TYR cc_start: 0.5769 (p90) cc_final: 0.5461 (p90)
  outliers start: 35
  outliers final: 26
  residues processed: 169
  average time/residue: 0.0669
  time to fit residues: 16.7066
Evaluate side-chains
  163 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 136
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
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  229 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  247 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  153 ILE
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  247 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 17 optimal weight:    6.9990
   chunk 61 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 27 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 99 optimal weight:    0.6980
   chunk 36 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.3745 r_free = 0.3745 target = 0.138383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.124506 restraints weight = 15692.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.127202 restraints weight = 7942.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.128997 restraints weight = 4889.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.130272 restraints weight = 3488.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.130974 restraints weight = 2719.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8534  Z= 0.146
  Angle     :  0.661   9.296  11678  Z= 0.312
  Chirality :  0.042   0.234   1376
  Planarity :  0.004   0.026   1370
  Dihedral  : 13.383 155.802   1716
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 24.94 %
    Favored  : 70.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.29), residues: 1026
  helix:  1.39 (0.20), residues: 748
  sheet:  None (None), residues: 0
  loop : -1.79 (0.44), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  38 
 TYR   0.015   0.001   TYR A 439 
 PHE   0.007   0.001   PHE B 131 
 TRP   0.008   0.001   TRP B 406 
 HIS   0.004   0.001   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 8528)
  covalent geometry    : angle       0.64914 (11660)
  hydrogen bonds       : bond        0.03888 (  552)
  hydrogen bonds       : angle       4.25131 ( 1638)
  link_BETA1-4         : bond        0.00786 (    4)
  link_BETA1-4         : angle       2.70334 (   12)
  link_NAG-ASN         : bond        0.00643 (    2)
  link_NAG-ASN         : angle       4.01912 (    6)

*********************** 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: 36
    poor density    : 139
  time to evaluate  : 0.283 
Fit side-chains
REVERT: A  229 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8348 (mp)
REVERT: A  318 MET cc_start: 0.7322 (ppp) cc_final: 0.7066 (ppp)
REVERT: A  455 TYR cc_start: 0.5827 (p90) cc_final: 0.5331 (p90)
REVERT: B  229 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8349 (mp)
REVERT: B  318 MET cc_start: 0.7331 (ppp) cc_final: 0.7065 (ppp)
REVERT: B  455 TYR cc_start: 0.5821 (p90) cc_final: 0.5323 (p90)
  outliers start: 36
  outliers final: 24
  residues processed: 164
  average time/residue: 0.0651
  time to fit residues: 15.8327
Evaluate side-chains
  169 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 143
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
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  153 ILE
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  247 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  116 ASP
Chi-restraints excluded: chain B residue  130 LEU
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  229 LEU
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  247 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 92 optimal weight:    0.4980
   chunk 69 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 42 optimal weight:    3.9990
   chunk 94 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 91 optimal weight:    4.9990
   chunk 57 optimal weight:    5.9990
   overall best weight:    2.6988

-------------------------------------------------------------------------------
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 = 0.3663 r_free = 0.3663 target = 0.132226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.118160 restraints weight = 15842.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.120806 restraints weight = 8122.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.122554 restraints weight = 5083.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.123741 restraints weight = 3661.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.124461 restraints weight = 2906.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   8534  Z= 0.240
  Angle     :  0.779  12.036  11678  Z= 0.370
  Chirality :  0.045   0.237   1376
  Planarity :  0.004   0.040   1370
  Dihedral  : 12.939 155.713   1716
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 14.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 25.18 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.28), residues: 1026
  helix:  1.09 (0.19), residues: 748
  sheet:  None (None), residues: 0
  loop : -1.97 (0.43), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  38 
 TYR   0.018   0.002   TYR A  67 
 PHE   0.012   0.002   PHE B 258 
 TRP   0.016   0.002   TRP B 406 
 HIS   0.002   0.001   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00568 ( 8528)
  covalent geometry    : angle       0.76759 (11660)
  hydrogen bonds       : bond        0.04601 (  552)
  hydrogen bonds       : angle       4.64406 ( 1638)
  link_BETA1-4         : bond        0.00844 (    4)
  link_BETA1-4         : angle       3.10173 (   12)
  link_NAG-ASN         : bond        0.00649 (    2)
  link_NAG-ASN         : angle       4.00343 (    6)

*********************** 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
  167 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 136
  time to evaluate  : 0.204 
Fit side-chains
REVERT: A  318 MET cc_start: 0.7481 (ppp) cc_final: 0.7238 (ppp)
REVERT: A  455 TYR cc_start: 0.5988 (p90) cc_final: 0.5647 (p90)
REVERT: B  318 MET cc_start: 0.7484 (ppp) cc_final: 0.7223 (ppp)
REVERT: B  455 TYR cc_start: 0.5984 (p90) cc_final: 0.5648 (p90)
  outliers start: 31
  outliers final: 22
  residues processed: 160
  average time/residue: 0.0677
  time to fit residues: 16.0242
Evaluate side-chains
  154 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  247 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   89 ILE
Chi-restraints excluded: chain B residue   93 LEU
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  431 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   chunk 14 optimal weight:    0.6980
   chunk 73 optimal weight:    0.7980
   chunk 82 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 80 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3734 r_free = 0.3734 target = 0.137691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.123688 restraints weight = 15654.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.126458 restraints weight = 7954.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.128094 restraints weight = 4917.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.129456 restraints weight = 3556.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.130326 restraints weight = 2772.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.1932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8534  Z= 0.135
  Angle     :  0.690  10.624  11678  Z= 0.321
  Chirality :  0.042   0.226   1376
  Planarity :  0.004   0.027   1370
  Dihedral  : 11.946 155.799   1716
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 26.27 %
    Favored  : 70.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.78 (0.29), residues: 1026
  helix:  1.38 (0.20), residues: 746
  sheet:  None (None), residues: 0
  loop : -1.87 (0.44), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  38 
 TYR   0.015   0.001   TYR B 439 
 PHE   0.007   0.001   PHE B 131 
 TRP   0.009   0.001   TRP B 300 
 HIS   0.005   0.001   HIS B 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 8528)
  covalent geometry    : angle       0.67950 (11660)
  hydrogen bonds       : bond        0.03992 (  552)
  hydrogen bonds       : angle       4.34538 ( 1638)
  link_BETA1-4         : bond        0.00842 (    4)
  link_BETA1-4         : angle       2.63142 (   12)
  link_NAG-ASN         : bond        0.00621 (    2)
  link_NAG-ASN         : angle       3.93223 (    6)

*********************** 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
  166 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 140
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A  229 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8326 (mp)
REVERT: A  318 MET cc_start: 0.7355 (ppp) cc_final: 0.7103 (ppp)
REVERT: A  368 PHE cc_start: 0.6244 (OUTLIER) cc_final: 0.5837 (t80)
REVERT: A  455 TYR cc_start: 0.5891 (p90) cc_final: 0.5612 (p90)
REVERT: B  229 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8343 (mp)
REVERT: B  318 MET cc_start: 0.7352 (ppp) cc_final: 0.7088 (ppp)
REVERT: B  368 PHE cc_start: 0.6254 (OUTLIER) cc_final: 0.5857 (t80)
REVERT: B  455 TYR cc_start: 0.5886 (p90) cc_final: 0.5613 (p90)
  outliers start: 26
  outliers final: 18
  residues processed: 154
  average time/residue: 0.0694
  time to fit residues: 15.4826
Evaluate side-chains
  160 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 138
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 VAL
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  184 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  247 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  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 41 optimal weight:    0.7980
   chunk 82 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 61 optimal weight:    0.6980
   chunk 89 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0170
   chunk 98 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.6618

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

Flipped N/Q/H residues before XYZ refinement:
A 162 HIS
B 162 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.139365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.125529 restraints weight = 15389.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.128286 restraints weight = 7802.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.130037 restraints weight = 4801.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.131356 restraints weight = 3418.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.132078 restraints weight = 2658.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.1950

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= 0.133
  Angle     :  0.677   9.280  11678  Z= 0.317
  Chirality :  0.042   0.233   1376
  Planarity :  0.004   0.032   1370
  Dihedral  : 11.497 157.904   1716
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 25.90 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.29), residues: 1026
  helix:  1.40 (0.20), residues: 748
  sheet:  None (None), residues: 0
  loop : -1.84 (0.44), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  38 
 TYR   0.016   0.001   TYR B 439 
 PHE   0.007   0.001   PHE B 131 
 TRP   0.010   0.001   TRP A 254 
 HIS   0.005   0.001   HIS B 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8528)
  covalent geometry    : angle       0.66701 (11660)
  hydrogen bonds       : bond        0.03819 (  552)
  hydrogen bonds       : angle       4.27769 ( 1638)
  link_BETA1-4         : bond        0.00760 (    4)
  link_BETA1-4         : angle       2.52958 (   12)
  link_NAG-ASN         : bond        0.00628 (    2)
  link_NAG-ASN         : angle       3.82965 (    6)

********************** 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
  173 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 148
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A  229 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8318 (mp)
REVERT: A  305 TYR cc_start: 0.6252 (t80) cc_final: 0.6051 (t80)
REVERT: A  318 MET cc_start: 0.7545 (ppp) cc_final: 0.7273 (ppp)
REVERT: A  453 TYR cc_start: 0.7375 (t80) cc_final: 0.7107 (t80)
REVERT: A  455 TYR cc_start: 0.6028 (p90) cc_final: 0.5553 (p90)
REVERT: B  229 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8313 (mp)
REVERT: B  318 MET cc_start: 0.7539 (ppp) cc_final: 0.7252 (ppp)
REVERT: B  453 TYR cc_start: 0.7372 (t80) cc_final: 0.7101 (t80)
REVERT: B  455 TYR cc_start: 0.6027 (p90) cc_final: 0.5552 (p90)
  outliers start: 25
  outliers final: 21
  residues processed: 164
  average time/residue: 0.0700
  time to fit residues: 16.8229
Evaluate side-chains
  163 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 140
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
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  247 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 50 optimal weight:    9.9990
   chunk 15 optimal weight:    6.9990
   chunk 56 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   chunk 60 optimal weight:    5.9990
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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 = 0.3747 r_free = 0.3747 target = 0.138409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.124628 restraints weight = 15643.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.127367 restraints weight = 8003.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.129061 restraints weight = 4961.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.130309 restraints weight = 3566.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.130844 restraints weight = 2795.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8534  Z= 0.150
  Angle     :  0.692   9.289  11678  Z= 0.326
  Chirality :  0.043   0.233   1376
  Planarity :  0.004   0.035   1370
  Dihedral  : 11.339 158.877   1716
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 26.14 %
    Favored  : 70.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.29), residues: 1026
  helix:  1.33 (0.20), residues: 748
  sheet:  None (None), residues: 0
  loop : -1.86 (0.43), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  38 
 TYR   0.016   0.001   TYR A 439 
 PHE   0.006   0.001   PHE B 131 
 TRP   0.009   0.001   TRP A 254 
 HIS   0.004   0.001   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 8528)
  covalent geometry    : angle       0.68186 (11660)
  hydrogen bonds       : bond        0.03943 (  552)
  hydrogen bonds       : angle       4.32180 ( 1638)
  link_BETA1-4         : bond        0.00754 (    4)
  link_BETA1-4         : angle       2.59861 (   12)
  link_NAG-ASN         : bond        0.00644 (    2)
  link_NAG-ASN         : angle       3.79719 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1109.51 seconds
wall clock time: 20 minutes 6.82 seconds (1206.82 seconds total)