Starting phenix.real_space_refine
on Sat Aug 23 09:58:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wor_37696/08_2025/8wor_37696.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wor_37696/08_2025/8wor_37696.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wor_37696/08_2025/8wor_37696.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wor_37696/08_2025/8wor_37696.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wor_37696/08_2025/8wor_37696.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wor_37696/08_2025/8wor_37696.map"
  }
  resolution = 2.66
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     Zn      2      6.06       5
     S      60      5.16       5
     C    7539      2.51       5
     N    1696      2.21       5
     O    1919      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11218
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 5261
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 647, 5252
          Classifications: {'peptide': 647}
          Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 620}
          Chain breaks: 4
      Conformer: "B"
        Number of residues, atoms: 647, 5252
          Classifications: {'peptide': 647}
          Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 620}
          Chain breaks: 4
          bond proxies already assigned to first conformer: 5384
    Chain: "B"
      Number of atoms: 5261
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 647, 5252
          Classifications: {'peptide': 647}
          Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 620}
          Chain breaks: 4
      Conformer: "B"
        Number of residues, atoms: 647, 5252
          Classifications: {'peptide': 647}
          Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 620}
          Chain breaks: 4
          bond proxies already assigned to first conformer: 5384
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 276
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 276
          Unusual residues: {' CA': 1, ' ZN': 1, 'CLR': 7, 'NAG': 2, 'OLA': 1, 'SPL': 1}
          Classifications: {'undetermined': 13}
          Link IDs: {None: 12}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 304
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 304
          Unusual residues: {' CA': 1, ' ZN': 1, 'CLR': 8, 'NAG': 2, 'OLA': 1, 'SPL': 1}
          Classifications: {'undetermined': 14}
          Link IDs: {None: 13}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.45, per 1000 atoms: 0.49
  Number of scatterers: 11218
  At special positions: 0
  Unit cell: (93.61, 89.355, 135.309, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     Ca      2     19.99
     S      60     16.00
     O    1919      8.00
     N    1696      7.00
     C    7539      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 130 " - pdb=" SG  CYS A 222 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 212 " - pdb=" SG  CYS A 271 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 479 " - pdb=" SG  CYS A 565 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 485 " - pdb=" SG  CYS A 787 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 130 " - pdb=" SG  CYS B 222 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 212 " - pdb=" SG  CYS B 271 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 479 " - pdb=" SG  CYS B 565 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 485 " - pdb=" SG  CYS B 787 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG A 903 " - " ASN A  67 "
      " NAG A 904 " - " ASN A 136 "
      " NAG B 903 " - " ASN B  67 "
      " NAG B 904 " - " ASN B 136 "
      " NAG C   1 " - " ASN A  57 "
      " NAG D   1 " - " ASN A  83 "
      " NAG E   1 " - " ASN B  57 "
      " NAG F   1 " - " ASN B  83 "
  Time building additional restraints: 1.35
  Conformation dependent library (CDL) restraints added in 999.8 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 901 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 563 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 796 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 800 "
      pdb="  ZN B 901 "
        pdb="ZN    ZN B 901 " - pdb=" NE2 HIS B 563 "
        pdb="ZN    ZN B 901 " - pdb=" NE2 HIS B 796 "
        pdb="ZN    ZN B 901 " - pdb=" NE2 HIS B 800 "


  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2492

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      49.9% alpha, 15.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 43
      removed outlier: 4.270A  pdb=" N   ALA A  42 " --> pdb=" O   ASP A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 253
      No H-bonds generated for 'chain 'A' and resid 251 through 253'
    Processing helix  chain 'A' and resid 302 through 335
      removed outlier: 3.841A  pdb=" N   TYR A 306 " --> pdb=" O   LYS A 302 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   PHE A 317 " --> pdb=" O   SER A 313 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   PHE A 320 " --> pdb=" O   ILE A 316 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   TYR A 321 " --> pdb=" O   PHE A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 474
      removed outlier: 4.024A  pdb=" N   ILE A 448 " --> pdb=" O   TYR A 444 " (cutoff:3.500A)
      Proline residue:  A 458  - end of helix
    Processing helix  chain 'A' and resid 482 through 486
      removed outlier: 3.948A  pdb=" N   ALA A 486 " --> pdb=" O   PHE A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 500
    Processing helix  chain 'A' and resid 501 through 527
      removed outlier: 3.842A  pdb=" N   VAL A 505 " --> pdb=" O   ASN A 501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 563
    Processing helix  chain 'A' and resid 570 through 594
      removed outlier: 4.204A  pdb=" N   ASP A 574 " --> pdb=" O   ASN A 570 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   MET A 578 " --> pdb=" O   ASP A 574 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   TYR A 579 " --> pdb=" O   THR A 575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 621
      removed outlier: 3.741A  pdb=" N   ALA A 606 " --> pdb=" O   TYR A 602 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 626 through 650
    Processing helix  chain 'A' and resid 686 through 709
    Processing helix  chain 'A' and resid 713 through 738
    Processing helix  chain 'A' and resid 745 through 767
      removed outlier: 3.581A  pdb=" N   LEU A 749 " --> pdb=" O   LEU A 745 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   PHE A 765 " --> pdb=" O   ALA A 761 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   PHE A 767 " --> pdb=" O   LEU A 763 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 776 through 782
    Processing helix  chain 'A' and resid 788 through 792
      removed outlier: 3.643A  pdb=" N   ASP A 791 " --> pdb=" O   ILE A 788 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 794 through 816
      removed outlier: 3.520A  pdb=" N   ILE A 798 " --> pdb=" O   ASP A 794 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 819 through 824
    Processing helix  chain 'B' and resid 38 through 43
      removed outlier: 4.202A  pdb=" N   ALA B  42 " --> pdb=" O   ASP B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 253
      No H-bonds generated for 'chain 'B' and resid 251 through 253'
    Processing helix  chain 'B' and resid 302 through 335
      removed outlier: 3.848A  pdb=" N   TYR B 306 " --> pdb=" O   LYS B 302 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   PHE B 317 " --> pdb=" O   SER B 313 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   PHE B 320 " --> pdb=" O   ILE B 316 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   TYR B 321 " --> pdb=" O   PHE B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 441 through 474
      removed outlier: 4.014A  pdb=" N   ILE B 448 " --> pdb=" O   TYR B 444 " (cutoff:3.500A)
      Proline residue:  B 458  - end of helix
    Processing helix  chain 'B' and resid 482 through 486
      removed outlier: 3.933A  pdb=" N   ALA B 486 " --> pdb=" O   PHE B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 495 through 500
    Processing helix  chain 'B' and resid 501 through 527
      removed outlier: 3.860A  pdb=" N   VAL B 505 " --> pdb=" O   ASN B 501 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 541 through 563
    Processing helix  chain 'B' and resid 570 through 594
      removed outlier: 4.205A  pdb=" N   ASP B 574 " --> pdb=" O   ASN B 570 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   MET B 578 " --> pdb=" O   ASP B 574 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   TYR B 579 " --> pdb=" O   THR B 575 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 602 through 621
      removed outlier: 3.711A  pdb=" N   ALA B 606 " --> pdb=" O   TYR B 602 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 624 through 650
      removed outlier: 3.547A  pdb=" N   PHE B 628 " --> pdb=" O   ASN B 624 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   TRP B 629 " --> pdb=" O   ASP B 625 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 686 through 709
    Processing helix  chain 'B' and resid 713 through 738
    Processing helix  chain 'B' and resid 745 through 767
      removed outlier: 3.563A  pdb=" N   LEU B 749 " --> pdb=" O   LEU B 745 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   PHE B 765 " --> pdb=" O   ALA B 761 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   PHE B 767 " --> pdb=" O   LEU B 763 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 776 through 782
    Processing helix  chain 'B' and resid 788 through 792
      removed outlier: 3.635A  pdb=" N   ASP B 791 " --> pdb=" O   ILE B 788 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 794 through 816
      removed outlier: 3.514A  pdb=" N   ILE B 798 " --> pdb=" O   ASP B 794 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 819 through 824
    Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 45
    Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 56
      removed outlier: 4.478A  pdb=" N   VAL A  78 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 113
    Processing sheet with id=AA4, first strand: chain 'A' and resid 177 through 181
    Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 192
    Processing sheet with id=AA6, first strand: chain 'B' and resid 44 through 45
    Processing sheet with id=AA7, first strand: chain 'B' and resid 51 through 56
      removed outlier: 4.449A  pdb=" N   VAL B  78 " --> pdb=" O   LEU B 129 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 113
    Processing sheet with id=AA9, first strand: chain 'B' and resid 177 through 181
    Processing sheet with id=AB1, first strand: chain 'B' and resid 187 through 192

    630 hydrogen bonds defined for protein.
    1795 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.95

  Time building geometry restraints manager: 1.65 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3258
        1.34 -     1.46: 2819
        1.46 -     1.58: 5368
        1.58 -     1.70: 2
        1.70 -     1.82: 94
  Bond restraints: 11541
  Sorted by residual:
  bond pdb=" C10 OLA A 911 "
       pdb=" C9  OLA A 911 "
    ideal  model  delta    sigma   weight residual
    1.332  1.468 -0.136 2.00e-02 2.50e+03 4.64e+01
  bond pdb=" C10 OLA B 914 "
       pdb=" C9  OLA B 914 "
    ideal  model  delta    sigma   weight residual
    1.332  1.468 -0.136 2.00e-02 2.50e+03 4.60e+01
  bond pdb=" CB  PRO B 748 "
       pdb=" CG  PRO B 748 "
    ideal  model  delta    sigma   weight residual
    1.492  1.589 -0.097 5.00e-02 4.00e+02 3.79e+00
  bond pdb=" CB  PRO A 748 "
       pdb=" CG  PRO A 748 "
    ideal  model  delta    sigma   weight residual
    1.492  1.585 -0.093 5.00e-02 4.00e+02 3.43e+00
  bond pdb=" C1  OLA A 911 "
       pdb=" C2  OLA A 911 "
    ideal  model  delta    sigma   weight residual
    1.542  1.510  0.032 2.00e-02 2.50e+03 2.60e+00
  ... (remaining 11536 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.28: 15709
        4.28 -     8.56: 37
        8.56 -    12.85: 0
       12.85 -    17.13: 0
       17.13 -    21.41: 2
  Bond angle restraints: 15748
  Sorted by residual:
  angle pdb=" CA  LEU B 728 "
        pdb=" CB  LEU B 728 "
        pdb=" CG  LEU B 728 "
      ideal   model   delta    sigma   weight residual
     116.30  137.71  -21.41 3.50e+00 8.16e-02 3.74e+01
  angle pdb=" CA  PRO B 748 "
        pdb=" N   PRO B 748 "
        pdb=" CD  PRO B 748 "
      ideal   model   delta    sigma   weight residual
     112.00  104.60    7.40 1.40e+00 5.10e-01 2.79e+01
  angle pdb=" CA  LEU A 728 "
        pdb=" CB  LEU A 728 "
        pdb=" CG  LEU A 728 "
      ideal   model   delta    sigma   weight residual
     116.30  134.47  -18.17 3.50e+00 8.16e-02 2.70e+01
  angle pdb=" CA  PRO A 748 "
        pdb=" N   PRO A 748 "
        pdb=" CD  PRO A 748 "
      ideal   model   delta    sigma   weight residual
     112.00  105.37    6.63 1.40e+00 5.10e-01 2.24e+01
  angle pdb=" C   ILE B 612 "
        pdb=" N   MET B 613 "
        pdb=" CA  MET B 613 "
      ideal   model   delta    sigma   weight residual
     120.72  114.17    6.55 1.67e+00 3.59e-01 1.54e+01
  ... (remaining 15743 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.36: 6563
       17.36 -    34.73: 800
       34.73 -    52.09: 223
       52.09 -    69.45: 57
       69.45 -    86.82: 8
  Dihedral angle restraints: 7651
    sinusoidal: 3791
      harmonic: 3860
  Sorted by residual:
  dihedral pdb=" CA  TYR B 210 "
           pdb=" C   TYR B 210 "
           pdb=" N   PRO B 211 "
           pdb=" CA  PRO B 211 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   20.33  -20.33     0      5.00e+00 4.00e-02 1.65e+01
  dihedral pdb=" CA  TYR A 210 "
           pdb=" C   TYR A 210 "
           pdb=" N   PRO A 211 "
           pdb=" CA  PRO A 211 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   20.20  -20.20     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" CA  CYS A 787 "
           pdb=" C   CYS A 787 "
           pdb=" N   ILE A 788 "
           pdb=" CA  ILE A 788 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.15  -18.85     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 7648 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1583
       0.057 -    0.115: 232
       0.115 -    0.172: 21
       0.172 -    0.229: 2
       0.229 -    0.287: 2
  Chirality restraints: 1840
  Sorted by residual:
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN B  57 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.11   -0.29 2.00e-01 2.50e+01 2.06e+00
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A  57 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.13   -0.27 2.00e-01 2.50e+01 1.88e+00
  chirality pdb=" CA  MET A 613 "
            pdb=" N   MET A 613 "
            pdb=" C   MET A 613 "
            pdb=" CB  MET A 613 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.66e-01
  ... (remaining 1837 not shown)

  Planarity restraints: 1858
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 OLA A 911 "   -0.185 2.00e-02 2.50e+03   1.44e-01 2.08e+02
        pdb=" C11 OLA A 911 "    0.085 2.00e-02 2.50e+03
        pdb=" C8  OLA A 911 "   -0.085 2.00e-02 2.50e+03
        pdb=" C9  OLA A 911 "    0.186 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 OLA B 914 "    0.185 2.00e-02 2.50e+03   1.44e-01 2.08e+02
        pdb=" C11 OLA B 914 "   -0.085 2.00e-02 2.50e+03
        pdb=" C8  OLA B 914 "    0.085 2.00e-02 2.50e+03
        pdb=" C9  OLA B 914 "   -0.185 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 747 "    0.082 5.00e-02 4.00e+02   1.21e-01 2.34e+01
        pdb=" N   PRO A 748 "   -0.209 5.00e-02 4.00e+02
        pdb=" CA  PRO A 748 "    0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO A 748 "    0.065 5.00e-02 4.00e+02
  ... (remaining 1855 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.52: 61
        2.52 -     3.12: 8574
        3.12 -     3.71: 16133
        3.71 -     4.31: 22955
        4.31 -     4.90: 39543
  Nonbonded interactions: 87266
  Sorted by model distance:
  nonbonded pdb="ZN    ZN A 901 "
            pdb=" O   HOH A1001 "
     model   vdw
     1.928 2.230
  nonbonded pdb="ZN    ZN B 901 "
            pdb=" O   HOH B1001 "
     model   vdw
     1.928 2.230
  nonbonded pdb=" OH  TYR A  64 "
            pdb=" OH  TYR A 159 "
     model   vdw
     2.080 3.040
  nonbonded pdb=" OH  TYR B  64 "
            pdb=" OH  TYR B 159 "
     model   vdw
     2.085 3.040
  nonbonded pdb=" O   ASN B 598 "
            pdb=" OH  TYR B 602 "
     model   vdw
     2.193 3.040
  ... (remaining 87261 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 35 through 80 or resid 82 through 906 or resid 908 through \ 
 910 or resid 913))
  selection = (chain 'B' and (resid 35 through 80 or resid 82 through 906 or resid 908 through \ 
 910 or resid 913))
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = 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=0.21 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.890
  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:             0.020
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     17.290
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
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   0.136  11567  Z= 0.174
  Angle     :  0.641  21.410  15800  Z= 0.308
  Chirality :  0.041   0.287   1840
  Planarity :  0.007   0.144   1850
  Dihedral  : 15.745  86.815   5135
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 22.33
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.45 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 27.19 %
    Favored  : 67.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.24), residues: 1276
  helix:  2.90 (0.21), residues: 590
  sheet:  1.34 (0.30), residues: 272
  loop : -2.08 (0.27), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 593 
 TYR   0.011   0.001   TYR B 188 
 PHE   0.038   0.001   PHE A 732 
 TRP   0.009   0.001   TRP A 446 
 HIS   0.004   0.001   HIS A 636 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (11541)
  covalent geometry    : angle       0.63574 (15748)
  SS BOND              : bond        0.00123 (    8)
  SS BOND              : angle       0.93078 (   16)
  hydrogen bonds       : bond        0.08913 (  630)
  hydrogen bonds       : angle       4.39253 ( 1795)
  metal coordination   : bond        0.00167 (    6)
  link_BETA1-4         : bond        0.00281 (    4)
  link_BETA1-4         : angle       1.21617 (   12)
  link_NAG-ASN         : bond        0.00327 (    8)
  link_NAG-ASN         : angle       2.07644 (   24)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 116
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
REVERT: A  117 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8744 (mp10)
REVERT: A  158 GLN cc_start: 0.8522 (mt0) cc_final: 0.8296 (mt0)
REVERT: A  554 MET cc_start: 0.7669 (tpp) cc_final: 0.7331 (mmm)
REVERT: B  117 GLN cc_start: 0.9001 (mm-40) cc_final: 0.8797 (mp10)
REVERT: B  554 MET cc_start: 0.7676 (tpp) cc_final: 0.7338 (mmm)
REVERT: B  650 MET cc_start: 0.2997 (tpt) cc_final: 0.2770 (tpt)
REVERT: B  686 MET cc_start: 0.5258 (mmt) cc_final: 0.4300 (pmm)
REVERT: B  718 MET cc_start: 0.8145 (ttp) cc_final: 0.7940 (ttm)
  outliers start: 59
  outliers final: 47
  residues processed: 170
  average time/residue: 0.4267
  time to fit residues: 80.9760
Evaluate side-chains
  159 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 112
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  319 SER
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  541 HIS
Chi-restraints excluded: chain A residue  559 SER
Chi-restraints excluded: chain A residue  569 SER
Chi-restraints excluded: chain A residue  572 GLN
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  735 ILE
Chi-restraints excluded: chain A residue  755 THR
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  220 ILE
Chi-restraints excluded: chain B residue  257 GLN
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  319 SER
Chi-restraints excluded: chain B residue  324 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  470 VAL
Chi-restraints excluded: chain B residue  472 VAL
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  521 LEU
Chi-restraints excluded: chain B residue  541 HIS
Chi-restraints excluded: chain B residue  569 SER
Chi-restraints excluded: chain B residue  572 GLN
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  589 LEU
Chi-restraints excluded: chain B residue  615 THR
Chi-restraints excluded: chain B residue  735 ILE
Chi-restraints excluded: chain B residue  755 THR
Chi-restraints excluded: chain B residue  763 LEU
Chi-restraints excluded: chain B residue  813 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    0.3980
   chunk 55 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A  90 ASN
A 142 GLN
** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 ASN
B  71 GLN
B  90 ASN
B 142 GLN
B 286 ASN
** B 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 769 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.165309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.101574 restraints weight = 19281.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 2.95
r_work: 0.3119 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3117
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3117 r_free = 0.3117    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3116 r_free = 0.3116    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3116
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.0780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11567  Z= 0.162
  Angle     :  0.731  18.522  15800  Z= 0.344
  Chirality :  0.045   0.302   1840
  Planarity :  0.005   0.076   1850
  Dihedral  :  9.506  59.629   2800
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.47 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 26.08 %
    Favored  : 68.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.38 (0.23), residues: 1276
  helix:  2.51 (0.21), residues: 590
  sheet:  1.35 (0.29), residues: 274
  loop : -1.94 (0.27), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 781 
 TYR   0.014   0.001   TYR B 188 
 PHE   0.015   0.001   PHE A 722 
 TRP   0.008   0.001   TRP A 627 
 HIS   0.007   0.001   HIS B 636 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (11541)
  covalent geometry    : angle       0.72233 (15748)
  SS BOND              : bond        0.00104 (    8)
  SS BOND              : angle       1.27135 (   16)
  hydrogen bonds       : bond        0.05453 (  630)
  hydrogen bonds       : angle       4.00576 ( 1795)
  metal coordination   : bond        0.00345 (    6)
  link_BETA1-4         : bond        0.00395 (    4)
  link_BETA1-4         : angle       1.54826 (   12)
  link_NAG-ASN         : bond        0.00405 (    8)
  link_NAG-ASN         : angle       2.71512 (   24)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 117
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
REVERT: A  554 MET cc_start: 0.8326 (tpp) cc_final: 0.8010 (mmm)
REVERT: A  594 HIS cc_start: 0.6570 (OUTLIER) cc_final: 0.6030 (m90)
REVERT: A  605 TYR cc_start: 0.3873 (OUTLIER) cc_final: 0.3625 (p90)
REVERT: A  686 MET cc_start: 0.5290 (mmt) cc_final: 0.4500 (mpt)
REVERT: B  289 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8713 (mtm180)
REVERT: B  554 MET cc_start: 0.8369 (tpp) cc_final: 0.8025 (mmm)
REVERT: B  605 TYR cc_start: 0.3956 (OUTLIER) cc_final: 0.3656 (p90)
REVERT: B  650 MET cc_start: 0.3078 (OUTLIER) cc_final: 0.2833 (tpt)
REVERT: B  686 MET cc_start: 0.5271 (mmt) cc_final: 0.4322 (pmm)
REVERT: B  710 ARG cc_start: 0.8261 (mmm-85) cc_final: 0.7840 (mmt-90)
REVERT: B  712 ARG cc_start: 0.5521 (mpt180) cc_final: 0.4655 (mpp80)
  outliers start: 58
  outliers final: 27
  residues processed: 165
  average time/residue: 0.4079
  time to fit residues: 74.4752
Evaluate side-chains
  147 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 115
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue  220 ILE
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  559 SER
Chi-restraints excluded: chain A residue  572 GLN
Chi-restraints excluded: chain A residue  594 HIS
Chi-restraints excluded: chain A residue  597 ILE
Chi-restraints excluded: chain A residue  605 TYR
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  735 ILE
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  220 ILE
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  286 ASN
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  289 ARG
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  521 LEU
Chi-restraints excluded: chain B residue  572 GLN
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  605 TYR
Chi-restraints excluded: chain B residue  617 LEU
Chi-restraints excluded: chain B residue  650 MET
Chi-restraints excluded: chain B residue  727 LEU
Chi-restraints excluded: chain B residue  735 ILE
Chi-restraints excluded: chain B residue  763 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 123 optimal weight:    2.9990
   chunk 106 optimal weight:    2.9990
   chunk 83 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 55 optimal weight:   10.0000
   chunk 53 optimal weight:    5.9990
   chunk 102 optimal weight:    4.9990
   chunk 101 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A  90 ASN
A 123 GLN
** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 ASN
B  90 ASN
B 142 GLN
B 286 ASN
** B 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 769 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.163721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.098643 restraints weight = 22837.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 3.11
r_work: 0.3069 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3058
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3058 r_free = 0.3058    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3058 r_free = 0.3058    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3058
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.1083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  11567  Z= 0.231
  Angle     :  0.751  18.520  15800  Z= 0.360
  Chirality :  0.047   0.274   1840
  Planarity :  0.005   0.068   1850
  Dihedral  :  8.832  59.444   2760
  Min Nonbonded Distance : 1.856

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.63 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 26.08 %
    Favored  : 68.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.12 (0.23), residues: 1276
  helix:  2.24 (0.21), residues: 590
  sheet:  1.35 (0.29), residues: 274
  loop : -2.07 (0.27), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 593 
 TYR   0.017   0.002   TYR A 188 
 PHE   0.015   0.002   PHE A 454 
 TRP   0.009   0.002   TRP A 627 
 HIS   0.006   0.001   HIS A 636 

Details of bonding type rmsd
  covalent geometry    : bond        0.00559 (11541)
  covalent geometry    : angle       0.74239 (15748)
  SS BOND              : bond        0.00091 (    8)
  SS BOND              : angle       1.65938 (   16)
  hydrogen bonds       : bond        0.06189 (  630)
  hydrogen bonds       : angle       4.02988 ( 1795)
  metal coordination   : bond        0.00620 (    6)
  link_BETA1-4         : bond        0.00550 (    4)
  link_BETA1-4         : angle       1.49522 (   12)
  link_NAG-ASN         : bond        0.00395 (    8)
  link_NAG-ASN         : angle       2.58706 (   24)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 108
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A  554 MET cc_start: 0.8364 (tpp) cc_final: 0.8069 (mmm)
REVERT: A  594 HIS cc_start: 0.6611 (OUTLIER) cc_final: 0.6082 (m90)
REVERT: A  781 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8498 (mtm-85)
REVERT: B  289 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8915 (mtm180)
REVERT: B  461 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8266 (mt0)
REVERT: B  554 MET cc_start: 0.8397 (tpp) cc_final: 0.8085 (mmm)
REVERT: B  686 MET cc_start: 0.5316 (mmt) cc_final: 0.4405 (pmm)
REVERT: B  710 ARG cc_start: 0.8207 (mmm-85) cc_final: 0.7861 (mmt-90)
REVERT: B  712 ARG cc_start: 0.5390 (mpt180) cc_final: 0.4652 (mpp80)
REVERT: B  718 MET cc_start: 0.8402 (mtm) cc_final: 0.8197 (ttm)
REVERT: B  781 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8273 (ttm110)
  outliers start: 62
  outliers final: 35
  residues processed: 161
  average time/residue: 0.4150
  time to fit residues: 73.6528
Evaluate side-chains
  147 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 107
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  220 ILE
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain A residue  559 SER
Chi-restraints excluded: chain A residue  572 GLN
Chi-restraints excluded: chain A residue  590 TYR
Chi-restraints excluded: chain A residue  594 HIS
Chi-restraints excluded: chain A residue  597 ILE
Chi-restraints excluded: chain A residue  605 TYR
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  735 ILE
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  781 ARG
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  220 ILE
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  289 ARG
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  461 GLN
Chi-restraints excluded: chain B residue  521 LEU
Chi-restraints excluded: chain B residue  572 GLN
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  605 TYR
Chi-restraints excluded: chain B residue  617 LEU
Chi-restraints excluded: chain B residue  626 VAL
Chi-restraints excluded: chain B residue  704 LEU
Chi-restraints excluded: chain B residue  727 LEU
Chi-restraints excluded: chain B residue  735 ILE
Chi-restraints excluded: chain B residue  763 LEU
Chi-restraints excluded: chain B residue  781 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 69 optimal weight:    0.8980
   chunk 94 optimal weight:   10.0000
   chunk 1 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 123 optimal weight:    2.9990
   chunk 102 optimal weight:    4.9990
   chunk 64 optimal weight:    9.9990
   chunk 111 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9980
   chunk 66 optimal weight:    0.8980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
A  71 GLN
A  74 GLN
A  90 ASN
** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 ASN
B  71 GLN
B  90 ASN
B 286 ASN
B 725 ASN
B 769 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.166247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.101312 restraints weight = 23066.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 3.15
r_work: 0.3101 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3109
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3109 r_free = 0.3109    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3109 r_free = 0.3109    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3109
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.1144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11567  Z= 0.149
  Angle     :  0.696  18.158  15800  Z= 0.329
  Chirality :  0.044   0.283   1840
  Planarity :  0.005   0.062   1850
  Dihedral  :  8.417  59.780   2758
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 26.08 %
    Favored  : 69.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.21 (0.23), residues: 1276
  helix:  2.30 (0.21), residues: 590
  sheet:  1.41 (0.29), residues: 274
  loop : -2.02 (0.27), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 781 
 TYR   0.014   0.001   TYR B 188 
 PHE   0.012   0.001   PHE A 722 
 TRP   0.009   0.001   TRP A 627 
 HIS   0.005   0.001   HIS B 636 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (11541)
  covalent geometry    : angle       0.68737 (15748)
  SS BOND              : bond        0.00077 (    8)
  SS BOND              : angle       1.23042 (   16)
  hydrogen bonds       : bond        0.05318 (  630)
  hydrogen bonds       : angle       3.92360 ( 1795)
  metal coordination   : bond        0.00233 (    6)
  link_BETA1-4         : bond        0.00502 (    4)
  link_BETA1-4         : angle       1.39724 (   12)
  link_NAG-ASN         : bond        0.00457 (    8)
  link_NAG-ASN         : angle       2.68755 (   24)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 111
  time to evaluate  : 0.454 
Fit side-chains
REVERT: A  113 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8511 (mm-40)
REVERT: A  461 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8216 (mt0)
REVERT: A  554 MET cc_start: 0.8292 (tpp) cc_final: 0.8013 (mmm)
REVERT: A  590 TYR cc_start: 0.6452 (OUTLIER) cc_final: 0.6045 (t80)
REVERT: A  613 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8424 (pmm)
REVERT: A  736 MET cc_start: 0.7255 (tmm) cc_final: 0.7049 (mmm)
REVERT: A  781 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8257 (ttm110)
REVERT: B  289 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8750 (mtm180)
REVERT: B  318 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7368 (mp)
REVERT: B  554 MET cc_start: 0.8311 (tpp) cc_final: 0.8014 (mmm)
REVERT: B  559 SER cc_start: 0.8773 (OUTLIER) cc_final: 0.8481 (p)
REVERT: B  586 MET cc_start: 0.7903 (tmm) cc_final: 0.7674 (tmt)
REVERT: B  587 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7880 (mp)
REVERT: B  686 MET cc_start: 0.5222 (mmt) cc_final: 0.4297 (pmm)
REVERT: B  710 ARG cc_start: 0.8109 (mmm-85) cc_final: 0.7887 (mmt-90)
REVERT: B  781 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8035 (ttm170)
  outliers start: 52
  outliers final: 26
  residues processed: 156
  average time/residue: 0.4711
  time to fit residues: 80.9535
Evaluate side-chains
  143 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 108
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue  220 ILE
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  461 GLN
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain A residue  559 SER
Chi-restraints excluded: chain A residue  572 GLN
Chi-restraints excluded: chain A residue  590 TYR
Chi-restraints excluded: chain A residue  597 ILE
Chi-restraints excluded: chain A residue  605 TYR
Chi-restraints excluded: chain A residue  613 MET
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  735 ILE
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  781 ARG
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  220 ILE
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  289 ARG
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  559 SER
Chi-restraints excluded: chain B residue  572 GLN
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  605 TYR
Chi-restraints excluded: chain B residue  617 LEU
Chi-restraints excluded: chain B residue  704 LEU
Chi-restraints excluded: chain B residue  727 LEU
Chi-restraints excluded: chain B residue  735 ILE
Chi-restraints excluded: chain B residue  763 LEU
Chi-restraints excluded: chain B residue  781 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 127 optimal weight:    0.5980
   chunk 47 optimal weight:   10.0000
   chunk 78 optimal weight:    0.7980
   chunk 91 optimal weight:    0.6980
   chunk 24 optimal weight:    8.9990
   chunk 11 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
A  74 GLN
A  90 ASN
A 142 GLN
** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 ASN
B  71 GLN
B  74 GLN
B  90 ASN
B 286 ASN
B 725 ASN
B 769 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.164937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.099471 restraints weight = 25451.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 3.26
r_work: 0.3074 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3079
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3079
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.1258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11567  Z= 0.187
  Angle     :  0.714  18.499  15800  Z= 0.342
  Chirality :  0.045   0.282   1840
  Planarity :  0.005   0.062   1850
  Dihedral  :  8.223  59.258   2754
  Min Nonbonded Distance : 1.888

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 25.73 %
    Favored  : 69.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.14 (0.23), residues: 1276
  helix:  2.38 (0.21), residues: 578
  sheet:  1.41 (0.29), residues: 274
  loop : -2.18 (0.26), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 781 
 TYR   0.016   0.001   TYR A 188 
 PHE   0.014   0.002   PHE B 732 
 TRP   0.009   0.001   TRP A 627 
 HIS   0.005   0.001   HIS B 636 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 (11541)
  covalent geometry    : angle       0.70482 (15748)
  SS BOND              : bond        0.00086 (    8)
  SS BOND              : angle       1.39285 (   16)
  hydrogen bonds       : bond        0.05707 (  630)
  hydrogen bonds       : angle       3.92594 ( 1795)
  metal coordination   : bond        0.00499 (    6)
  link_BETA1-4         : bond        0.00520 (    4)
  link_BETA1-4         : angle       1.41792 (   12)
  link_NAG-ASN         : bond        0.00439 (    8)
  link_NAG-ASN         : angle       2.63212 (   24)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 108
  time to evaluate  : 0.410 
Fit side-chains
REVERT: A  554 MET cc_start: 0.8349 (tpp) cc_final: 0.8087 (mmm)
REVERT: A  590 TYR cc_start: 0.6500 (OUTLIER) cc_final: 0.6053 (t80)
REVERT: A  613 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8439 (pmm)
REVERT: A  650 MET cc_start: 0.3900 (OUTLIER) cc_final: 0.3583 (tpt)
REVERT: A  781 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8369 (ttm110)
REVERT: B  289 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8841 (mtm180)
REVERT: B  318 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7393 (mp)
REVERT: B  461 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8268 (mt0)
REVERT: B  554 MET cc_start: 0.8371 (tpp) cc_final: 0.8104 (mmm)
REVERT: B  559 SER cc_start: 0.8794 (OUTLIER) cc_final: 0.8490 (p)
REVERT: B  587 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7943 (mp)
REVERT: B  686 MET cc_start: 0.5267 (mmt) cc_final: 0.4343 (pmm)
REVERT: B  781 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8380 (mtm-85)
  outliers start: 59
  outliers final: 37
  residues processed: 154
  average time/residue: 0.4525
  time to fit residues: 76.6364
Evaluate side-chains
  152 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 105
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue  119 SER
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  220 ILE
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain A residue  559 SER
Chi-restraints excluded: chain A residue  572 GLN
Chi-restraints excluded: chain A residue  590 TYR
Chi-restraints excluded: chain A residue  597 ILE
Chi-restraints excluded: chain A residue  605 TYR
Chi-restraints excluded: chain A residue  613 MET
Chi-restraints excluded: chain A residue  650 MET
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  735 ILE
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  781 ARG
Chi-restraints excluded: chain A residue  787 CYS
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  220 ILE
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  286 ASN
Chi-restraints excluded: chain B residue  289 ARG
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  461 GLN
Chi-restraints excluded: chain B residue  544 LEU
Chi-restraints excluded: chain B residue  559 SER
Chi-restraints excluded: chain B residue  572 GLN
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  605 TYR
Chi-restraints excluded: chain B residue  617 LEU
Chi-restraints excluded: chain B residue  626 VAL
Chi-restraints excluded: chain B residue  704 LEU
Chi-restraints excluded: chain B residue  727 LEU
Chi-restraints excluded: chain B residue  735 ILE
Chi-restraints excluded: chain B residue  763 LEU
Chi-restraints excluded: chain B residue  781 ARG
Chi-restraints excluded: chain B residue  787 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9990
   chunk 81 optimal weight:    0.7980
   chunk 67 optimal weight:    0.8980
   chunk 122 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
A  71 GLN
A  74 GLN
A  90 ASN
A 288 GLN
** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 ASN
B  71 GLN
B  74 GLN
B  90 ASN
B 142 GLN
B 286 ASN
B 725 ASN
B 769 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.166012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.100946 restraints weight = 22932.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 3.13
r_work: 0.3104 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3113
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3113 r_free = 0.3113    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3113 r_free = 0.3113    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3113
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.1303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11567  Z= 0.150
  Angle     :  0.696  18.677  15800  Z= 0.330
  Chirality :  0.044   0.279   1840
  Planarity :  0.004   0.060   1850
  Dihedral  :  7.991  59.305   2752
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 25.99 %
    Favored  : 69.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.19 (0.23), residues: 1276
  helix:  2.42 (0.21), residues: 578
  sheet:  1.45 (0.29), residues: 274
  loop : -2.17 (0.26), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 781 
 TYR   0.014   0.001   TYR A 188 
 PHE   0.025   0.001   PHE B 628 
 TRP   0.020   0.001   TRP B 629 
 HIS   0.004   0.001   HIS B 636 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (11541)
  covalent geometry    : angle       0.68719 (15748)
  SS BOND              : bond        0.00077 (    8)
  SS BOND              : angle       1.24742 (   16)
  hydrogen bonds       : bond        0.05246 (  630)
  hydrogen bonds       : angle       3.87237 ( 1795)
  metal coordination   : bond        0.00280 (    6)
  link_BETA1-4         : bond        0.00429 (    4)
  link_BETA1-4         : angle       1.39720 (   12)
  link_NAG-ASN         : bond        0.00455 (    8)
  link_NAG-ASN         : angle       2.67178 (   24)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 106
  time to evaluate  : 0.400 
Fit side-chains
REVERT: A  113 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8507 (mm-40)
REVERT: A  554 MET cc_start: 0.8336 (tpp) cc_final: 0.8085 (mmm)
REVERT: A  590 TYR cc_start: 0.6480 (OUTLIER) cc_final: 0.6020 (t80)
REVERT: A  613 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8428 (pmm)
REVERT: A  781 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8332 (ttm110)
REVERT: B  289 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.8745 (mtm180)
REVERT: B  318 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7395 (mp)
REVERT: B  461 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8233 (mt0)
REVERT: B  554 MET cc_start: 0.8369 (tpp) cc_final: 0.8108 (mmm)
REVERT: B  559 SER cc_start: 0.8779 (OUTLIER) cc_final: 0.8491 (p)
REVERT: B  590 TYR cc_start: 0.6624 (OUTLIER) cc_final: 0.6224 (t80)
REVERT: B  686 MET cc_start: 0.5247 (mmt) cc_final: 0.4337 (pmm)
REVERT: B  781 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8363 (mtm-85)
  outliers start: 57
  outliers final: 37
  residues processed: 154
  average time/residue: 0.4484
  time to fit residues: 75.9876
Evaluate side-chains
  153 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 107
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue  119 SER
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  220 ILE
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain A residue  559 SER
Chi-restraints excluded: chain A residue  572 GLN
Chi-restraints excluded: chain A residue  590 TYR
Chi-restraints excluded: chain A residue  597 ILE
Chi-restraints excluded: chain A residue  605 TYR
Chi-restraints excluded: chain A residue  613 MET
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  735 ILE
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  781 ARG
Chi-restraints excluded: chain A residue  787 CYS
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  220 ILE
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  289 ARG
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  461 GLN
Chi-restraints excluded: chain B residue  521 LEU
Chi-restraints excluded: chain B residue  544 LEU
Chi-restraints excluded: chain B residue  559 SER
Chi-restraints excluded: chain B residue  572 GLN
Chi-restraints excluded: chain B residue  590 TYR
Chi-restraints excluded: chain B residue  597 ILE
Chi-restraints excluded: chain B residue  605 TYR
Chi-restraints excluded: chain B residue  617 LEU
Chi-restraints excluded: chain B residue  704 LEU
Chi-restraints excluded: chain B residue  727 LEU
Chi-restraints excluded: chain B residue  735 ILE
Chi-restraints excluded: chain B residue  763 LEU
Chi-restraints excluded: chain B residue  781 ARG
Chi-restraints excluded: chain B residue  787 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 10 optimal weight:    0.2980
   chunk 23 optimal weight:    2.9990
   chunk 86 optimal weight:    0.0060
   chunk 28 optimal weight:    5.9990
   chunk 26 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 122 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
A  74 GLN
A  90 ASN
A 142 GLN
** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 ASN
B  74 GLN
B  90 ASN
B 142 GLN
B 286 ASN
B 725 ASN
B 769 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.167776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.102624 restraints weight = 25349.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 3.29
r_work: 0.3124 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3113
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3113 r_free = 0.3113    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3113 r_free = 0.3113    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3113
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.1411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11567  Z= 0.128
  Angle     :  0.672  17.329  15800  Z= 0.316
  Chirality :  0.043   0.289   1840
  Planarity :  0.004   0.057   1850
  Dihedral  :  7.589  58.979   2748
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 26.42 %
    Favored  : 69.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.28 (0.23), residues: 1276
  helix:  2.48 (0.21), residues: 578
  sheet:  1.53 (0.29), residues: 274
  loop : -2.13 (0.26), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 593 
 TYR   0.013   0.001   TYR A 188 
 PHE   0.020   0.001   PHE B 628 
 TRP   0.015   0.001   TRP B 629 
 HIS   0.004   0.001   HIS A 636 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (11541)
  covalent geometry    : angle       0.66294 (15748)
  SS BOND              : bond        0.00072 (    8)
  SS BOND              : angle       1.00989 (   16)
  hydrogen bonds       : bond        0.04705 (  630)
  hydrogen bonds       : angle       3.78463 ( 1795)
  metal coordination   : bond        0.00197 (    6)
  link_BETA1-4         : bond        0.00507 (    4)
  link_BETA1-4         : angle       1.38309 (   12)
  link_NAG-ASN         : bond        0.00470 (    8)
  link_NAG-ASN         : angle       2.64861 (   24)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 109
  time to evaluate  : 0.457 
Fit side-chains
REVERT: A  554 MET cc_start: 0.8308 (tpp) cc_final: 0.8053 (mmm)
REVERT: A  590 TYR cc_start: 0.6522 (OUTLIER) cc_final: 0.6014 (t80)
REVERT: A  613 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8423 (pmm)
REVERT: A  781 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8328 (mtm-85)
REVERT: B  461 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8187 (mt0)
REVERT: B  554 MET cc_start: 0.8354 (tpp) cc_final: 0.8085 (mmm)
REVERT: B  590 TYR cc_start: 0.6554 (OUTLIER) cc_final: 0.6204 (t80)
REVERT: B  686 MET cc_start: 0.5253 (mmt) cc_final: 0.4395 (pmm)
REVERT: B  736 MET cc_start: 0.8027 (tpp) cc_final: 0.7529 (mmm)
REVERT: B  781 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8226 (ttm110)
  outliers start: 52
  outliers final: 33
  residues processed: 149
  average time/residue: 0.5019
  time to fit residues: 82.3487
Evaluate side-chains
  146 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 107
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue  119 SER
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  220 ILE
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  572 GLN
Chi-restraints excluded: chain A residue  590 TYR
Chi-restraints excluded: chain A residue  597 ILE
Chi-restraints excluded: chain A residue  605 TYR
Chi-restraints excluded: chain A residue  613 MET
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  735 ILE
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  781 ARG
Chi-restraints excluded: chain A residue  787 CYS
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  443 ILE
Chi-restraints excluded: chain B residue  461 GLN
Chi-restraints excluded: chain B residue  510 LEU
Chi-restraints excluded: chain B residue  544 LEU
Chi-restraints excluded: chain B residue  572 GLN
Chi-restraints excluded: chain B residue  590 TYR
Chi-restraints excluded: chain B residue  597 ILE
Chi-restraints excluded: chain B residue  605 TYR
Chi-restraints excluded: chain B residue  617 LEU
Chi-restraints excluded: chain B residue  650 MET
Chi-restraints excluded: chain B residue  704 LEU
Chi-restraints excluded: chain B residue  727 LEU
Chi-restraints excluded: chain B residue  781 ARG
Chi-restraints excluded: chain B residue  787 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 28 optimal weight:    5.9990
   chunk 102 optimal weight:    3.9990
   chunk 44 optimal weight:    6.9990
   chunk 100 optimal weight:    2.9990
   chunk 114 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 57 optimal weight:    4.9990
   chunk 85 optimal weight:    2.9990
   chunk 110 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0370
   chunk 103 optimal weight:    3.9990
   overall best weight:    2.2064

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

Flipped N/Q/H residues before XYZ refinement:
A  71 GLN
A  74 GLN
A  90 ASN
** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 ASN
B  71 GLN
B  74 GLN
B  90 ASN
B 286 ASN
B 725 ASN
B 769 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.163787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.099059 restraints weight = 19958.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 2.96
r_work: 0.3079 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3082
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3082 r_free = 0.3082    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3082 r_free = 0.3082    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3082
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.1475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  11567  Z= 0.256
  Angle     :  0.764  17.851  15800  Z= 0.370
  Chirality :  0.048   0.276   1840
  Planarity :  0.005   0.061   1850
  Dihedral  :  7.647  58.778   2741
  Min Nonbonded Distance : 1.844

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 26.25 %
    Favored  : 69.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.23), residues: 1276
  helix:  2.28 (0.21), residues: 578
  sheet:  1.42 (0.29), residues: 274
  loop : -2.27 (0.26), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  37 
 TYR   0.019   0.002   TYR A 188 
 PHE   0.020   0.002   PHE B 628 
 TRP   0.012   0.002   TRP B 629 
 HIS   0.005   0.001   HIS B 563 

Details of bonding type rmsd
  covalent geometry    : bond        0.00623 (11541)
  covalent geometry    : angle       0.75505 (15748)
  SS BOND              : bond        0.00103 (    8)
  SS BOND              : angle       1.69719 (   16)
  hydrogen bonds       : bond        0.06246 (  630)
  hydrogen bonds       : angle       3.96726 ( 1795)
  metal coordination   : bond        0.00662 (    6)
  link_BETA1-4         : bond        0.00550 (    4)
  link_BETA1-4         : angle       1.51122 (   12)
  link_NAG-ASN         : bond        0.00454 (    8)
  link_NAG-ASN         : angle       2.59508 (   24)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 107
  time to evaluate  : 0.410 
Fit side-chains
REVERT: A  113 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8531 (mm-40)
REVERT: A  554 MET cc_start: 0.8356 (tpp) cc_final: 0.8097 (mmm)
REVERT: A  590 TYR cc_start: 0.6500 (OUTLIER) cc_final: 0.6075 (t80)
REVERT: A  613 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8397 (pmm)
REVERT: A  781 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8401 (ttm110)
REVERT: B  461 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8241 (mt0)
REVERT: B  554 MET cc_start: 0.8391 (tpp) cc_final: 0.8132 (mmm)
REVERT: B  686 MET cc_start: 0.5288 (mmt) cc_final: 0.4450 (pmm)
REVERT: B  781 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8388 (ttm110)
  outliers start: 55
  outliers final: 34
  residues processed: 150
  average time/residue: 0.4566
  time to fit residues: 75.7064
Evaluate side-chains
  143 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 104
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue  119 SER
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  220 ILE
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  572 GLN
Chi-restraints excluded: chain A residue  590 TYR
Chi-restraints excluded: chain A residue  597 ILE
Chi-restraints excluded: chain A residue  605 TYR
Chi-restraints excluded: chain A residue  613 MET
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  735 ILE
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  781 ARG
Chi-restraints excluded: chain A residue  787 CYS
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  220 ILE
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  461 GLN
Chi-restraints excluded: chain B residue  510 LEU
Chi-restraints excluded: chain B residue  544 LEU
Chi-restraints excluded: chain B residue  572 GLN
Chi-restraints excluded: chain B residue  597 ILE
Chi-restraints excluded: chain B residue  605 TYR
Chi-restraints excluded: chain B residue  617 LEU
Chi-restraints excluded: chain B residue  704 LEU
Chi-restraints excluded: chain B residue  727 LEU
Chi-restraints excluded: chain B residue  735 ILE
Chi-restraints excluded: chain B residue  781 ARG
Chi-restraints excluded: chain B residue  787 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 71 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 122 optimal weight:    2.9990
   chunk 121 optimal weight:    0.7980
   chunk 98 optimal weight:    1.9990
   chunk 114 optimal weight:    7.9990
   chunk 101 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9990
   chunk 124 optimal weight:    0.9980
   chunk 91 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A  74 GLN
A  90 ASN
A 142 GLN
** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 ASN
B  74 GLN
B  90 ASN
B 142 GLN
B 286 ASN
B 725 ASN
B 769 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.166300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.101693 restraints weight = 20036.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 2.99
r_work: 0.3118 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3128
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3128
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.1455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11567  Z= 0.143
  Angle     :  0.692  17.677  15800  Z= 0.329
  Chirality :  0.044   0.279   1840
  Planarity :  0.004   0.058   1850
  Dihedral  :  7.428  59.517   2741
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 26.94 %
    Favored  : 69.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.14 (0.23), residues: 1276
  helix:  2.37 (0.21), residues: 578
  sheet:  1.48 (0.29), residues: 274
  loop : -2.22 (0.26), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 781 
 TYR   0.014   0.001   TYR B 210 
 PHE   0.018   0.001   PHE B 628 
 TRP   0.013   0.001   TRP B 629 
 HIS   0.004   0.001   HIS B 636 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (11541)
  covalent geometry    : angle       0.68343 (15748)
  SS BOND              : bond        0.00083 (    8)
  SS BOND              : angle       1.28468 (   16)
  hydrogen bonds       : bond        0.05220 (  630)
  hydrogen bonds       : angle       3.87433 ( 1795)
  metal coordination   : bond        0.00219 (    6)
  link_BETA1-4         : bond        0.00500 (    4)
  link_BETA1-4         : angle       1.40218 (   12)
  link_NAG-ASN         : bond        0.00466 (    8)
  link_NAG-ASN         : angle       2.66511 (   24)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 107
  time to evaluate  : 0.415 
Fit side-chains
REVERT: A  554 MET cc_start: 0.8327 (tpp) cc_final: 0.8092 (mmm)
REVERT: A  590 TYR cc_start: 0.6528 (OUTLIER) cc_final: 0.6045 (t80)
REVERT: A  613 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8405 (pmm)
REVERT: A  781 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8333 (ttm110)
REVERT: B  461 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8187 (mt0)
REVERT: B  554 MET cc_start: 0.8335 (tpp) cc_final: 0.8077 (mmm)
REVERT: B  686 MET cc_start: 0.5203 (mmt) cc_final: 0.4378 (pmm)
REVERT: B  736 MET cc_start: 0.7958 (tpp) cc_final: 0.7170 (mpp)
REVERT: B  781 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8328 (ttm110)
  outliers start: 46
  outliers final: 33
  residues processed: 144
  average time/residue: 0.4690
  time to fit residues: 74.2521
Evaluate side-chains
  142 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 104
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue  119 SER
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  220 ILE
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  572 GLN
Chi-restraints excluded: chain A residue  590 TYR
Chi-restraints excluded: chain A residue  597 ILE
Chi-restraints excluded: chain A residue  605 TYR
Chi-restraints excluded: chain A residue  613 MET
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  735 ILE
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  781 ARG
Chi-restraints excluded: chain A residue  787 CYS
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  220 ILE
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  461 GLN
Chi-restraints excluded: chain B residue  510 LEU
Chi-restraints excluded: chain B residue  544 LEU
Chi-restraints excluded: chain B residue  572 GLN
Chi-restraints excluded: chain B residue  597 ILE
Chi-restraints excluded: chain B residue  605 TYR
Chi-restraints excluded: chain B residue  617 LEU
Chi-restraints excluded: chain B residue  704 LEU
Chi-restraints excluded: chain B residue  727 LEU
Chi-restraints excluded: chain B residue  781 ARG
Chi-restraints excluded: chain B residue  787 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 53 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 66 optimal weight:    4.9990
   chunk 110 optimal weight:    5.9990
   chunk 105 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 109 optimal weight:    0.6980
   chunk 104 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  71 GLN
A  74 GLN
A  90 ASN
** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 ASN
B  71 GLN
B  74 GLN
B  90 ASN
B 142 GLN
B 286 ASN
B 725 ASN
B 769 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.166798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.101813 restraints weight = 23156.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 3.15
r_work: 0.3112 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3096
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3096 r_free = 0.3096    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3096 r_free = 0.3096    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3096
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.1472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11567  Z= 0.142
  Angle     :  0.693  17.169  15800  Z= 0.330
  Chirality :  0.044   0.285   1840
  Planarity :  0.004   0.058   1850
  Dihedral  :  7.259  59.171   2741
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 27.37 %
    Favored  : 69.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.23), residues: 1276
  helix:  2.38 (0.21), residues: 578
  sheet:  1.46 (0.29), residues: 274
  loop : -2.20 (0.26), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 781 
 TYR   0.014   0.001   TYR B 210 
 PHE   0.017   0.001   PHE B 732 
 TRP   0.012   0.001   TRP B 629 
 HIS   0.004   0.001   HIS B 636 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (11541)
  covalent geometry    : angle       0.68425 (15748)
  SS BOND              : bond        0.00083 (    8)
  SS BOND              : angle       1.14957 (   16)
  hydrogen bonds       : bond        0.05029 (  630)
  hydrogen bonds       : angle       3.82269 ( 1795)
  metal coordination   : bond        0.00296 (    6)
  link_BETA1-4         : bond        0.00443 (    4)
  link_BETA1-4         : angle       1.38603 (   12)
  link_NAG-ASN         : bond        0.00467 (    8)
  link_NAG-ASN         : angle       2.65769 (   24)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 108
  time to evaluate  : 0.436 
Fit side-chains
REVERT: A  554 MET cc_start: 0.8312 (tpp) cc_final: 0.8074 (mmm)
REVERT: A  590 TYR cc_start: 0.6517 (OUTLIER) cc_final: 0.6034 (t80)
REVERT: A  613 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8434 (pmm)
REVERT: A  781 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8082 (ttm170)
REVERT: B  461 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8200 (mt0)
REVERT: B  554 MET cc_start: 0.8356 (tpp) cc_final: 0.8101 (mmm)
REVERT: B  686 MET cc_start: 0.5090 (mmt) cc_final: 0.4276 (pmm)
REVERT: B  736 MET cc_start: 0.7928 (tpp) cc_final: 0.7106 (mpp)
REVERT: B  781 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8088 (ttm170)
  outliers start: 42
  outliers final: 30
  residues processed: 139
  average time/residue: 0.4896
  time to fit residues: 74.4950
Evaluate side-chains
  139 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 104
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 SER
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  220 ILE
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  572 GLN
Chi-restraints excluded: chain A residue  590 TYR
Chi-restraints excluded: chain A residue  597 ILE
Chi-restraints excluded: chain A residue  605 TYR
Chi-restraints excluded: chain A residue  613 MET
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  735 ILE
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  781 ARG
Chi-restraints excluded: chain A residue  787 CYS
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  220 ILE
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  461 GLN
Chi-restraints excluded: chain B residue  510 LEU
Chi-restraints excluded: chain B residue  544 LEU
Chi-restraints excluded: chain B residue  572 GLN
Chi-restraints excluded: chain B residue  597 ILE
Chi-restraints excluded: chain B residue  605 TYR
Chi-restraints excluded: chain B residue  617 LEU
Chi-restraints excluded: chain B residue  650 MET
Chi-restraints excluded: chain B residue  727 LEU
Chi-restraints excluded: chain B residue  781 ARG
Chi-restraints excluded: chain B residue  787 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 74 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 71 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 29 optimal weight:   20.0000
   chunk 5 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 122 optimal weight:    0.5980
   chunk 70 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  74 GLN
A  90 ASN
A 142 GLN
** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 ASN
B  74 GLN
B  90 ASN
B 142 GLN
B 286 ASN
B 725 ASN
B 769 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.167381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.105121 restraints weight = 13151.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 2.54
r_work: 0.3175 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.3030 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3019
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3019 r_free = 0.3019    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3019 r_free = 0.3019    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3019
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.1542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11567  Z= 0.136
  Angle     :  0.674  16.602  15800  Z= 0.320
  Chirality :  0.044   0.282   1840
  Planarity :  0.004   0.056   1850
  Dihedral  :  7.102  58.847   2740
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 27.37 %
    Favored  : 69.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.23), residues: 1276
  helix:  2.40 (0.21), residues: 578
  sheet:  1.48 (0.28), residues: 274
  loop : -2.19 (0.26), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 781 
 TYR   0.018   0.001   TYR B 210 
 PHE   0.017   0.001   PHE B 732 
 TRP   0.012   0.001   TRP B 629 
 HIS   0.004   0.001   HIS B 636 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (11541)
  covalent geometry    : angle       0.66523 (15748)
  SS BOND              : bond        0.00076 (    8)
  SS BOND              : angle       1.09563 (   16)
  hydrogen bonds       : bond        0.04857 (  630)
  hydrogen bonds       : angle       3.79330 ( 1795)
  metal coordination   : bond        0.00238 (    6)
  link_BETA1-4         : bond        0.00495 (    4)
  link_BETA1-4         : angle       1.40746 (   12)
  link_NAG-ASN         : bond        0.00454 (    8)
  link_NAG-ASN         : angle       2.61534 (   24)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4669.63 seconds
wall clock time: 80 minutes 11.18 seconds (4811.18 seconds total)