Starting phenix.real_space_refine
on Wed Jul 23 21:38:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ziz_60134/07_2025/8ziz_60134.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ziz_60134/07_2025/8ziz_60134.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ziz_60134/07_2025/8ziz_60134.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ziz_60134/07_2025/8ziz_60134.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ziz_60134/07_2025/8ziz_60134.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ziz_60134/07_2025/8ziz_60134.cif"
  }
  resolution = 2.89
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.026
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      29      5.16       5
     C    2741      2.51       5
     N     701      2.21       5
     O     921      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 4392
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 2123
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2123
          Classifications: {'peptide': 276}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 254}
    Chain: "D"
      Number of atoms: 1835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1835
          Classifications: {'peptide': 235}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 14, 'TRANS': 220}
    Chain: "B"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "E"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "F"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "G"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "H"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "I"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "J"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "K"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "L"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 3.57, per 1000 atoms: 0.81
  Number of scatterers: 4392
  At special positions: 0
  Unit cell: (86.676, 91.336, 121.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      29     16.00
     O     921      8.00
     N     701      7.00
     C    2741      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 716 " - pdb=" SG  CYS A 767 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 772 " - pdb=" SG  CYS D 896 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 810 " - pdb=" SG  CYS D 826 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 910 " - pdb=" SG  CYS D 977 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 941 " - pdb=" SG  CYS D 956 " 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
    ALPHA1-3
      " BMA E   3 " - " MAN E   4 "
      " BMA I   3 " - " MAN I   4 "
    ALPHA1-6
      " BMA B   3 " - " MAN B   4 "
      " BMA H   3 " - " MAN H   4 "
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
      " NAG H   1 " - " NAG H   2 "
      " NAG H   2 " - " BMA H   3 "
      " NAG I   1 " - " NAG I   2 "
      " NAG I   2 " - " BMA I   3 "
      " NAG J   1 " - " NAG J   2 "
      " NAG J   2 " - " BMA J   3 "
      " NAG K   1 " - " NAG K   2 "
      " NAG K   2 " - " BMA K   3 "
      " NAG L   1 " - " NAG L   2 "
      " NAG L   2 " - " BMA L   3 "
    BETA1-6
      " NAG F   2 " - " BMA F   3 "
    NAG-ASN
      " NAG B   1 " - " ASN A 534 "
      " NAG C   1 " - " ASN A 630 "
      " NAG E   1 " - " ASN A 682 "
      " NAG F   1 " - " ASN A 706 "
      " NAG G   1 " - " ASN A 725 "
      " NAG H   1 " - " ASN D 848 "
      " NAG I   1 " - " ASN D 887 "
      " NAG J   1 " - " ASN D 909 "
      " NAG K   1 " - " ASN D 949 "
      " NAG L   1 " - " ASN D 980 "
  Time building additional restraints: 1.74
  Conformation dependent library (CDL) restraints added in 483.0 milliseconds
  

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  934

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 8 sheets defined
      7.2% alpha, 25.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 703 through 707
      removed outlier: 4.111A  pdb=" N   ASN A 706 " --> pdb=" O   CYS A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 708 through 719
    Processing helix  chain 'D' and resid 833 through 835
      No H-bonds generated for 'chain 'D' and resid 833 through 835'
    Processing helix  chain 'D' and resid 937 through 945
    Processing helix  chain 'D' and resid 1010 through 1017
      removed outlier: 4.053A  pdb=" N   PHE D1017 " --> pdb=" O   TRP D1013 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 529 through 530
      removed outlier: 3.643A  pdb=" N   ASN A 557 " --> pdb=" O   LEU A 530 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   CYS A 552 " --> pdb=" O   LEU A 616 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   VAL A 579 " --> pdb=" O   ILE A 617 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   TYR A 596 " --> pdb=" O   VAL A 580 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 605 through 607
      removed outlier: 3.938A  pdb=" N   ILE A 564 " --> pdb=" O   SER A 607 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLY A 634 " --> pdb=" O   ASN A 563 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   LYS A 628 " --> pdb=" O   GLN A 569 " (cutoff:3.500A)
      removed outlier: 4.662A  pdb=" N   PHE A 571 " --> pdb=" O   GLY A 626 " (cutoff:3.500A)
      removed outlier: 7.638A  pdb=" N   GLY A 626 " --> pdb=" O   PHE A 571 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 648 through 649
      removed outlier: 3.916A  pdb=" N   VAL A 656 " --> pdb=" O   PHE A 648 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 678 through 681
      removed outlier: 3.553A  pdb=" N   ARG A 679 " --> pdb=" O   ARG A 692 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ARG A 692 " --> pdb=" O   ARG A 679 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LEU A 690 " --> pdb=" O   PHE A 681 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 678 through 681
      removed outlier: 3.553A  pdb=" N   ARG A 679 " --> pdb=" O   ARG A 692 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ARG A 692 " --> pdb=" O   ARG A 679 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LEU A 690 " --> pdb=" O   PHE A 681 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLY A 689 " --> pdb=" O   LEU A 765 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LEU A 765 " --> pdb=" O   GLY A 689 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 739 through 742
      removed outlier: 3.697A  pdb=" N   ILE A 750 " --> pdb=" O   ASN A 742 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 789 through 790
      removed outlier: 3.711A  pdb=" N   GLN D 929 " --> pdb=" O   GLY D 914 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   ALA D 913 " --> pdb=" O   PRO D 974 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   LEU D 975 " --> pdb=" O   ALA D 986 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   CYS D 977 " --> pdb=" O   PHE D 984 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   CYS D 956 " --> pdb=" O   LEU D 936 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 799 through 804
      removed outlier: 4.058A  pdb=" N   CYS D 810 " --> pdb=" O   LEU D 802 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   TYR D 804 " --> pdb=" O   LEU D 808 " (cutoff:3.500A)
      removed outlier: 5.522A  pdb=" N   LEU D 808 " --> pdb=" O   TYR D 804 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   GLY D 811 " --> pdb=" O   ALA D 823 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   ALA D 823 " --> pdb=" O   GLY D 811 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   TRP D 819 " --> pdb=" O   VAL D 815 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   GLU D 861 " --> pdb=" O   HIS D 881 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   VAL D 855 " --> pdb=" O   LEU D 841 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   LEU D 841 " --> pdb=" O   VAL D 855 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   ILE D 859 " --> pdb=" O   TRP D 837 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   TRP D 837 " --> pdb=" O   ILE D 859 " (cutoff:3.500A)

    81 hydrogen bonds defined for protein.
    222 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: 1.15

  Time building geometry restraints manager: 1.95 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1359
        1.34 -     1.46: 1074
        1.46 -     1.58: 2025
        1.58 -     1.69: 0
        1.69 -     1.81: 36
  Bond restraints: 4494
  Sorted by residual:
  bond pdb=" N   GLU A 574 "
       pdb=" CA  GLU A 574 "
    ideal  model  delta    sigma   weight residual
    1.460  1.488 -0.028 8.20e-03 1.49e+04 1.16e+01
  bond pdb=" N   LEU A 573 "
       pdb=" CA  LEU A 573 "
    ideal  model  delta    sigma   weight residual
    1.460  1.488 -0.028 8.20e-03 1.49e+04 1.13e+01
  bond pdb=" C3  BMA I   3 "
       pdb=" O3  BMA I   3 "
    ideal  model  delta    sigma   weight residual
    1.406  1.457 -0.051 2.00e-02 2.50e+03 6.39e+00
  bond pdb=" N   ASN A 575 "
       pdb=" CA  ASN A 575 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.030 1.29e-02 6.01e+03 5.46e+00
  bond pdb=" C5  MAN H   4 "
       pdb=" O5  MAN H   4 "
    ideal  model  delta    sigma   weight residual
    1.418  1.464 -0.046 2.00e-02 2.50e+03 5.38e+00
  ... (remaining 4489 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 5772
        1.49 -     2.97: 235
        2.97 -     4.46: 68
        4.46 -     5.94: 39
        5.94 -     7.43: 13
  Bond angle restraints: 6127
  Sorted by residual:
  angle pdb=" C   GLU A 574 "
        pdb=" CA  GLU A 574 "
        pdb=" CB  GLU A 574 "
      ideal   model   delta    sigma   weight residual
     116.53  110.94    5.59 1.47e+00 4.63e-01 1.45e+01
  angle pdb=" C   LEU A 573 "
        pdb=" CA  LEU A 573 "
        pdb=" CB  LEU A 573 "
      ideal   model   delta    sigma   weight residual
     116.53  111.10    5.43 1.47e+00 4.63e-01 1.37e+01
  angle pdb=" O   LEU A 573 "
        pdb=" C   LEU A 573 "
        pdb=" N   GLU A 574 "
      ideal   model   delta    sigma   weight residual
     121.65  124.71   -3.06 8.30e-01 1.45e+00 1.36e+01
  angle pdb=" O   GLU A 574 "
        pdb=" C   GLU A 574 "
        pdb=" N   ASN A 575 "
      ideal   model   delta    sigma   weight residual
     121.65  124.68   -3.03 8.30e-01 1.45e+00 1.34e+01
  angle pdb=" C   SER A 727 "
        pdb=" N   LYS A 728 "
        pdb=" CA  LYS A 728 "
      ideal   model   delta    sigma   weight residual
     121.61  117.09    4.52 1.39e+00 5.18e-01 1.06e+01
  ... (remaining 6122 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.62: 2895
       23.62 -    47.24: 72
       47.24 -    70.86: 37
       70.86 -    94.48: 60
       94.48 -   118.10: 41
  Dihedral angle restraints: 3105
    sinusoidal: 1648
      harmonic: 1457
  Sorted by residual:
  dihedral pdb=" C2  MAN H   4 "
           pdb=" C1  MAN H   4 "
           pdb=" O5  MAN H   4 "
           pdb=" C5  MAN H   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -57.62   60.48 -118.10     1      3.00e+01 1.11e-03 1.57e+01
  dihedral pdb=" O4  BMA E   3 "
           pdb=" C4  BMA E   3 "
           pdb=" C5  BMA E   3 "
           pdb=" O5  BMA E   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     288.71  177.23  111.48     1      3.00e+01 1.11e-03 1.46e+01
  dihedral pdb=" O4  BMA H   3 "
           pdb=" C4  BMA H   3 "
           pdb=" C5  BMA H   3 "
           pdb=" O5  BMA H   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     288.71  177.78  110.93     1      3.00e+01 1.11e-03 1.45e+01
  ... (remaining 3102 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.084: 677
       0.084 -    0.167: 78
       0.167 -    0.251: 7
       0.251 -    0.334: 11
       0.334 -    0.418: 1
  Chirality restraints: 774
  Sorted by residual:
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A 630 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.98   -0.42 2.00e-01 2.50e+01 4.37e+00
  chirality pdb=" C5  BMA G   3 "
            pdb=" C4  BMA G   3 "
            pdb=" C6  BMA G   3 "
            pdb=" O5  BMA G   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.56    0.29 2.00e-01 2.50e+01 2.05e+00
  chirality pdb=" C5  BMA J   3 "
            pdb=" C4  BMA J   3 "
            pdb=" C6  BMA J   3 "
            pdb=" O5  BMA J   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.56    0.28 2.00e-01 2.50e+01 1.98e+00
  ... (remaining 771 not shown)

  Planarity restraints: 765
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN D 893 "    0.019 5.00e-02 4.00e+02   2.88e-02 1.32e+00
        pdb=" N   PRO D 894 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO D 894 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO D 894 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 542 "   -0.018 5.00e-02 4.00e+02   2.69e-02 1.16e+00
        pdb=" N   PRO A 543 "    0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO A 543 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 543 "   -0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 736 "   -0.018 5.00e-02 4.00e+02   2.68e-02 1.15e+00
        pdb=" N   PRO A 737 "    0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO A 737 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 737 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 762 not shown)

  Histogram of nonbonded interaction distances:
        1.26 -     1.99: 1
        1.99 -     2.72: 200
        2.72 -     3.45: 5655
        3.45 -     4.17: 9357
        4.17 -     4.90: 15797
  Nonbonded interactions: 31010
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 574 "
            pdb=" CB  LEU A 622 "
     model   vdw
     1.264 3.440
  nonbonded pdb=" CD  GLU A 574 "
            pdb=" CB  LEU A 622 "
     model   vdw
     2.084 3.670
  nonbonded pdb=" OE2 GLU A 574 "
            pdb=" O   LEU A 622 "
     model   vdw
     2.139 3.040
  nonbonded pdb=" OE1 GLU A 574 "
            pdb=" CD1 LEU A 622 "
     model   vdw
     2.195 3.460
  nonbonded pdb=" OD1 ASN A 575 "
            pdb=" N   ILE A 576 "
     model   vdw
     2.234 3.120
  ... (remaining 31005 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 'B'
  selection = chain 'E'
  selection = chain 'H'
  selection = chain 'I'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.980
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6369
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      :  0.005   0.051   4533  Z= 0.260
  Angle     :  0.867   7.430   6239  Z= 0.362
  Chirality :  0.060   0.418    774
  Planarity :  0.003   0.029    755
  Dihedral  : 22.436 118.096   2156
  Min Nonbonded Distance : 1.264

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  7.89 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  :  2.52 %
    Favored  : 95.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.39), residues: 507
  helix:  3.08 (1.05), residues: 29
  sheet:  1.96 (0.52), residues: 98
  loop : -1.26 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 554 
 HIS   0.002   0.000   HIS D1019 
 PHE   0.008   0.001   PHE A 731 
 TYR   0.003   0.001   TYR A 546 
 ARG   0.001   0.000   ARG D1006 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00407 (   10)
  link_NAG-ASN         : angle       2.05633 (   30)
  link_ALPHA1-6        : bond        0.00485 (    2)
  link_ALPHA1-6        : angle       1.37703 (    6)
  link_BETA1-4         : bond        0.00594 (   19)
  link_BETA1-4         : angle       1.92730 (   57)
  link_ALPHA1-3        : bond        0.00677 (    2)
  link_ALPHA1-3        : angle       2.48258 (    6)
  hydrogen bonds       : bond        0.25627 (   80)
  hydrogen bonds       : angle       9.54694 (  222)
  link_BETA1-6         : bond        0.00519 (    1)
  link_BETA1-6         : angle       2.09677 (    3)
  SS BOND              : bond        0.00144 (    5)
  SS BOND              : angle       0.71079 (   10)
  covalent geometry    : bond        0.00491 ( 4494)
  covalent geometry    : angle       0.83615 ( 6127)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  580 VAL cc_start: 0.8041 (t) cc_final: 0.7779 (m)
REVERT: A  608 THR cc_start: 0.7796 (p) cc_final: 0.7562 (t)
REVERT: A  618 THR cc_start: 0.7721 (p) cc_final: 0.7412 (t)
REVERT: D  802 LEU cc_start: 0.7086 (tp) cc_final: 0.6880 (tp)
REVERT: D  804 TYR cc_start: 0.7931 (t80) cc_final: 0.7605 (t80)
REVERT: D  871 ARG cc_start: 0.7287 (mmt-90) cc_final: 0.7015 (mmt-90)
REVERT: D  950 ILE cc_start: 0.8171 (mm) cc_final: 0.7852 (mm)
  outliers start: 10
  outliers final: 4
  residues processed: 121
  average time/residue: 0.7782
  time to fit residues: 99.3568
Evaluate side-chains
  111 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 107
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  534 ASN
Chi-restraints excluded: chain D residue  827 VAL
Chi-restraints excluded: chain D residue  949 ASN
Chi-restraints excluded: chain D residue 1019 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    0.7980
   chunk 37 optimal weight:    0.4980
   chunk 21 optimal weight:    2.9990
   chunk 12 optimal weight:    0.3980
   chunk 25 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 15 optimal weight:    4.9990
   chunk 23 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 45 optimal weight:    0.4980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 577 ASN
A 742 ASN
A 748 HIS
A 756 GLN
A 768 ASN
D 865 ASN
** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.185753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.171272 restraints weight = 8133.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.4295 rms_B_bonded: 3.04
r_work: 0.4199 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.4199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6511
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   4533  Z= 0.170
  Angle     :  0.852   9.084   6239  Z= 0.370
  Chirality :  0.054   0.357    774
  Planarity :  0.005   0.045    755
  Dihedral  : 19.927  88.893   1237
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.45 %
    Favored  : 89.35 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 12.61 %
    Favored  : 83.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.38), residues: 507
  helix:  2.96 (1.06), residues: 29
  sheet:  1.37 (0.47), residues: 113
  loop : -1.43 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 707 
 HIS   0.005   0.001   HIS D1019 
 PHE   0.019   0.002   PHE A 542 
 TYR   0.023   0.002   TYR D 993 
 ARG   0.012   0.001   ARG D 807 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00453 (   10)
  link_NAG-ASN         : angle       2.44576 (   30)
  link_ALPHA1-6        : bond        0.01248 (    2)
  link_ALPHA1-6        : angle       2.08555 (    6)
  link_BETA1-4         : bond        0.00682 (   19)
  link_BETA1-4         : angle       2.35327 (   57)
  link_ALPHA1-3        : bond        0.00731 (    2)
  link_ALPHA1-3        : angle       2.74529 (    6)
  hydrogen bonds       : bond        0.05597 (   80)
  hydrogen bonds       : angle       7.13764 (  222)
  link_BETA1-6         : bond        0.00582 (    1)
  link_BETA1-6         : angle       3.02240 (    3)
  SS BOND              : bond        0.00533 (    5)
  SS BOND              : angle       1.24195 (   10)
  covalent geometry    : bond        0.00360 ( 4494)
  covalent geometry    : angle       0.80016 ( 6127)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
REVERT: A  560 LYS cc_start: 0.6781 (OUTLIER) cc_final: 0.6355 (ptpp)
REVERT: A  580 VAL cc_start: 0.8192 (t) cc_final: 0.7940 (m)
REVERT: D  804 TYR cc_start: 0.7987 (t80) cc_final: 0.7698 (t80)
REVERT: D  871 ARG cc_start: 0.7389 (mmt-90) cc_final: 0.7060 (mmt-90)
REVERT: D  949 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7103 (t160)
REVERT: D  950 ILE cc_start: 0.8317 (mm) cc_final: 0.8033 (mm)
REVERT: D  982 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.5828 (mtm-85)
  outliers start: 17
  outliers final: 7
  residues processed: 104
  average time/residue: 0.8387
  time to fit residues: 91.4435
Evaluate side-chains
  100 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  534 ASN
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  560 LYS
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain A residue  742 ASN
Chi-restraints excluded: chain D residue  809 LEU
Chi-restraints excluded: chain D residue  827 VAL
Chi-restraints excluded: chain D residue  949 ASN
Chi-restraints excluded: chain D residue  982 ARG
Chi-restraints excluded: chain D residue 1019 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 16 optimal weight:    9.9990
   chunk 18 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 577 ASN
A 742 ASN
A 755 GLN
D 938 ASN
** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.180014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.165572 restraints weight = 7995.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.4230 rms_B_bonded: 3.04
r_work: 0.4133 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.4133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6651
moved from start:          0.2906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   4533  Z= 0.225
  Angle     :  0.962  13.930   6239  Z= 0.414
  Chirality :  0.060   0.377    774
  Planarity :  0.005   0.048    755
  Dihedral  : 16.720  81.344   1237
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 10.85 %
    Favored  : 88.76 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 12.39 %
    Favored  : 82.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.37), residues: 507
  helix:  1.88 (0.97), residues: 29
  sheet:  1.23 (0.51), residues: 102
  loop : -1.65 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D 798 
 HIS   0.007   0.001   HIS D1019 
 PHE   0.017   0.002   PHE A 542 
 TYR   0.012   0.002   TYR D 948 
 ARG   0.010   0.001   ARG D 807 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01054 (   10)
  link_NAG-ASN         : angle       4.03926 (   30)
  link_ALPHA1-6        : bond        0.01396 (    2)
  link_ALPHA1-6        : angle       2.16687 (    6)
  link_BETA1-4         : bond        0.00867 (   19)
  link_BETA1-4         : angle       2.78718 (   57)
  link_ALPHA1-3        : bond        0.00565 (    2)
  link_ALPHA1-3        : angle       2.97344 (    6)
  hydrogen bonds       : bond        0.05263 (   80)
  hydrogen bonds       : angle       6.90944 (  222)
  link_BETA1-6         : bond        0.00275 (    1)
  link_BETA1-6         : angle       2.56249 (    3)
  SS BOND              : bond        0.00592 (    5)
  SS BOND              : angle       1.36248 (   10)
  covalent geometry    : bond        0.00461 ( 4494)
  covalent geometry    : angle       0.87775 ( 6127)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 99
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
REVERT: A  560 LYS cc_start: 0.7140 (OUTLIER) cc_final: 0.6646 (ptpp)
REVERT: A  580 VAL cc_start: 0.8231 (t) cc_final: 0.8003 (m)
REVERT: A  733 THR cc_start: 0.1136 (OUTLIER) cc_final: 0.0330 (p)
REVERT: D  949 ASN cc_start: 0.7865 (OUTLIER) cc_final: 0.7088 (t160)
REVERT: D  950 ILE cc_start: 0.8344 (mm) cc_final: 0.8090 (mm)
REVERT: D  982 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.5906 (ttm170)
REVERT: D 1017 PHE cc_start: 0.7594 (p90) cc_final: 0.7362 (p90)
  outliers start: 23
  outliers final: 12
  residues processed: 110
  average time/residue: 0.6910
  time to fit residues: 80.4358
Evaluate side-chains
  113 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  534 ASN
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  560 LYS
Chi-restraints excluded: chain A residue  564 ILE
Chi-restraints excluded: chain A residue  565 GLN
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain A residue  621 VAL
Chi-restraints excluded: chain A residue  733 THR
Chi-restraints excluded: chain D residue  827 VAL
Chi-restraints excluded: chain D residue  845 MET
Chi-restraints excluded: chain D residue  938 ASN
Chi-restraints excluded: chain D residue  949 ASN
Chi-restraints excluded: chain D residue  982 ARG
Chi-restraints excluded: chain D residue 1012 GLU
Chi-restraints excluded: chain D residue 1019 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0980
   chunk 44 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0470
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
A 660 ASN
** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.180759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.166581 restraints weight = 8021.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.4242 rms_B_bonded: 3.05
r_work: 0.4142 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.4142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6633
moved from start:          0.3352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4533  Z= 0.156
  Angle     :  0.888  12.665   6239  Z= 0.381
  Chirality :  0.058   0.337    774
  Planarity :  0.005   0.058    755
  Dihedral  : 14.114  79.960   1237
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 12.03 %
    Favored  : 87.77 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 17.43 %
    Favored  : 78.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.09 (0.37), residues: 507
  helix:  1.60 (0.95), residues: 29
  sheet:  1.09 (0.48), residues: 113
  loop : -1.67 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 554 
 HIS   0.006   0.001   HIS D1019 
 PHE   0.014   0.002   PHE D 904 
 TYR   0.022   0.002   TYR D 993 
 ARG   0.014   0.001   ARG D 807 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01032 (   10)
  link_NAG-ASN         : angle       3.74777 (   30)
  link_ALPHA1-6        : bond        0.01540 (    2)
  link_ALPHA1-6        : angle       2.22566 (    6)
  link_BETA1-4         : bond        0.00696 (   19)
  link_BETA1-4         : angle       2.59992 (   57)
  link_ALPHA1-3        : bond        0.00629 (    2)
  link_ALPHA1-3        : angle       2.88584 (    6)
  hydrogen bonds       : bond        0.04249 (   80)
  hydrogen bonds       : angle       6.50491 (  222)
  link_BETA1-6         : bond        0.00646 (    1)
  link_BETA1-6         : angle       2.19132 (    3)
  SS BOND              : bond        0.00421 (    5)
  SS BOND              : angle       1.26505 (   10)
  covalent geometry    : bond        0.00322 ( 4494)
  covalent geometry    : angle       0.80862 ( 6127)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
REVERT: A  560 LYS cc_start: 0.7290 (OUTLIER) cc_final: 0.6777 (ptpp)
REVERT: A  707 TRP cc_start: 0.6908 (t-100) cc_final: 0.6485 (t-100)
REVERT: D  949 ASN cc_start: 0.7823 (OUTLIER) cc_final: 0.7212 (t160)
  outliers start: 18
  outliers final: 8
  residues processed: 101
  average time/residue: 1.0404
  time to fit residues: 112.3217
Evaluate side-chains
  100 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  534 ASN
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  560 LYS
Chi-restraints excluded: chain A residue  564 ILE
Chi-restraints excluded: chain A residue  660 ASN
Chi-restraints excluded: chain D residue  827 VAL
Chi-restraints excluded: chain D residue  845 MET
Chi-restraints excluded: chain D residue  949 ASN
Chi-restraints excluded: chain D residue 1019 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0770
   chunk 15 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.7942

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

Flipped N/Q/H residues before XYZ refinement:
** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 790 ASN
D 938 ASN
** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.178161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.163718 restraints weight = 8106.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.4213 rms_B_bonded: 3.10
r_work: 0.4110 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.4110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6698
moved from start:          0.3777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4533  Z= 0.177
  Angle     :  0.901  12.856   6239  Z= 0.391
  Chirality :  0.058   0.306    774
  Planarity :  0.006   0.069    755
  Dihedral  : 13.131  79.193   1237
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 11.05 %
    Favored  : 88.76 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 15.83 %
    Favored  : 78.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.36), residues: 507
  helix:  1.37 (0.97), residues: 29
  sheet:  0.87 (0.46), residues: 113
  loop : -1.81 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 554 
 HIS   0.007   0.001   HIS D1019 
 PHE   0.015   0.002   PHE A 571 
 TYR   0.011   0.001   TYR D 948 
 ARG   0.013   0.001   ARG D 807 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00894 (   10)
  link_NAG-ASN         : angle       3.84023 (   30)
  link_ALPHA1-6        : bond        0.01457 (    2)
  link_ALPHA1-6        : angle       2.16238 (    6)
  link_BETA1-4         : bond        0.00647 (   19)
  link_BETA1-4         : angle       2.55409 (   57)
  link_ALPHA1-3        : bond        0.00483 (    2)
  link_ALPHA1-3        : angle       2.94533 (    6)
  hydrogen bonds       : bond        0.04234 (   80)
  hydrogen bonds       : angle       6.32778 (  222)
  link_BETA1-6         : bond        0.00346 (    1)
  link_BETA1-6         : angle       1.99752 (    3)
  SS BOND              : bond        0.00549 (    5)
  SS BOND              : angle       1.61522 (   10)
  covalent geometry    : bond        0.00370 ( 4494)
  covalent geometry    : angle       0.82129 ( 6127)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 87
  time to evaluate  : 0.462 
Fit side-chains
   revert: symmetry clash
REVERT: A  560 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.6832 (ptpp)
REVERT: A  707 TRP cc_start: 0.6959 (t-100) cc_final: 0.6605 (t-100)
REVERT: A  731 PHE cc_start: 0.3693 (OUTLIER) cc_final: 0.2308 (m-80)
REVERT: D  870 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7818 (ttt180)
REVERT: D  949 ASN cc_start: 0.7806 (OUTLIER) cc_final: 0.7417 (t0)
REVERT: D  982 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6845 (ttt180)
  outliers start: 25
  outliers final: 11
  residues processed: 97
  average time/residue: 0.7430
  time to fit residues: 76.3444
Evaluate side-chains
  102 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  534 ASN
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  560 LYS
Chi-restraints excluded: chain A residue  621 VAL
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  731 PHE
Chi-restraints excluded: chain D residue  827 VAL
Chi-restraints excluded: chain D residue  845 MET
Chi-restraints excluded: chain D residue  847 SER
Chi-restraints excluded: chain D residue  870 ARG
Chi-restraints excluded: chain D residue  872 ARG
Chi-restraints excluded: chain D residue  938 ASN
Chi-restraints excluded: chain D residue  949 ASN
Chi-restraints excluded: chain D residue  982 ARG
Chi-restraints excluded: chain D residue 1019 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 40 optimal weight:    0.1980
   chunk 34 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
A 577 ASN
** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 938 ASN
** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.178383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.163867 restraints weight = 7952.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.4212 rms_B_bonded: 3.05
r_work: 0.4116 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.4116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6697
moved from start:          0.4019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4533  Z= 0.170
  Angle     :  0.891  12.829   6239  Z= 0.387
  Chirality :  0.057   0.313    774
  Planarity :  0.006   0.070    755
  Dihedral  : 12.591  77.530   1237
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 11.83 %
    Favored  : 87.97 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 17.66 %
    Favored  : 77.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.45 (0.36), residues: 507
  helix:  1.01 (0.96), residues: 29
  sheet:  0.74 (0.46), residues: 113
  loop : -1.86 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 554 
 HIS   0.007   0.001   HIS D1019 
 PHE   0.014   0.002   PHE A 571 
 TYR   0.011   0.001   TYR D 948 
 ARG   0.015   0.001   ARG D 807 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00892 (   10)
  link_NAG-ASN         : angle       3.84816 (   30)
  link_ALPHA1-6        : bond        0.01439 (    2)
  link_ALPHA1-6        : angle       2.20042 (    6)
  link_BETA1-4         : bond        0.00645 (   19)
  link_BETA1-4         : angle       2.46666 (   57)
  link_ALPHA1-3        : bond        0.00468 (    2)
  link_ALPHA1-3        : angle       2.88835 (    6)
  hydrogen bonds       : bond        0.04246 (   80)
  hydrogen bonds       : angle       6.29099 (  222)
  link_BETA1-6         : bond        0.00356 (    1)
  link_BETA1-6         : angle       1.82727 (    3)
  SS BOND              : bond        0.00432 (    5)
  SS BOND              : angle       1.37937 (   10)
  covalent geometry    : bond        0.00352 ( 4494)
  covalent geometry    : angle       0.81296 ( 6127)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 91
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
REVERT: A  560 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.6856 (ptpp)
REVERT: A  731 PHE cc_start: 0.3723 (OUTLIER) cc_final: 0.2308 (m-80)
REVERT: D  870 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7806 (ttt180)
REVERT: D  949 ASN cc_start: 0.7778 (OUTLIER) cc_final: 0.7423 (t0)
  outliers start: 23
  outliers final: 10
  residues processed: 101
  average time/residue: 1.5195
  time to fit residues: 159.4140
Evaluate side-chains
  104 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  534 ASN
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  560 LYS
Chi-restraints excluded: chain A residue  564 ILE
Chi-restraints excluded: chain A residue  621 VAL
Chi-restraints excluded: chain A residue  731 PHE
Chi-restraints excluded: chain D residue  827 VAL
Chi-restraints excluded: chain D residue  847 SER
Chi-restraints excluded: chain D residue  870 ARG
Chi-restraints excluded: chain D residue  938 ASN
Chi-restraints excluded: chain D residue  949 ASN
Chi-restraints excluded: chain D residue  978 GLN
Chi-restraints excluded: chain D residue 1019 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0170
   chunk 27 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0980
   chunk 42 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   overall best weight:    0.5620

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

Flipped N/Q/H residues before XYZ refinement:
** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 938 ASN
** D 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.178807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.164129 restraints weight = 8065.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.4218 rms_B_bonded: 3.08
r_work: 0.4116 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.4116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6702
moved from start:          0.4211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4533  Z= 0.161
  Angle     :  0.889  10.592   6239  Z= 0.391
  Chirality :  0.058   0.360    774
  Planarity :  0.006   0.074    755
  Dihedral  : 12.190  73.976   1237
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.03 %
    Favored  : 87.97 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 18.35 %
    Favored  : 76.83 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (0.35), residues: 507
  helix:  0.15 (0.97), residues: 29
  sheet:  0.62 (0.45), residues: 113
  loop : -1.89 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D1013 
 HIS   0.007   0.001   HIS D1019 
 PHE   0.015   0.002   PHE A 571 
 TYR   0.023   0.002   TYR D 993 
 ARG   0.017   0.001   ARG D 807 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01043 (   10)
  link_NAG-ASN         : angle       3.80490 (   30)
  link_ALPHA1-6        : bond        0.01545 (    2)
  link_ALPHA1-6        : angle       2.25038 (    6)
  link_BETA1-4         : bond        0.00691 (   19)
  link_BETA1-4         : angle       2.43014 (   57)
  link_ALPHA1-3        : bond        0.00494 (    2)
  link_ALPHA1-3        : angle       2.79675 (    6)
  hydrogen bonds       : bond        0.04040 (   80)
  hydrogen bonds       : angle       6.17723 (  222)
  link_BETA1-6         : bond        0.00407 (    1)
  link_BETA1-6         : angle       1.83292 (    3)
  SS BOND              : bond        0.00663 (    5)
  SS BOND              : angle       1.51683 (   10)
  covalent geometry    : bond        0.00337 ( 4494)
  covalent geometry    : angle       0.81289 ( 6127)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  560 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.6897 (ptpp)
REVERT: A  610 ASN cc_start: 0.8416 (p0) cc_final: 0.8183 (p0)
REVERT: A  731 PHE cc_start: 0.3557 (OUTLIER) cc_final: 0.2291 (m-80)
REVERT: D  949 ASN cc_start: 0.7817 (OUTLIER) cc_final: 0.7459 (t0)
REVERT: D  953 ASN cc_start: 0.7995 (t0) cc_final: 0.7736 (t0)
  outliers start: 21
  outliers final: 12
  residues processed: 97
  average time/residue: 1.2608
  time to fit residues: 130.1779
Evaluate side-chains
  103 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.668 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  529 GLU
Chi-restraints excluded: chain A residue  534 ASN
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  560 LYS
Chi-restraints excluded: chain A residue  612 MET
Chi-restraints excluded: chain A residue  621 VAL
Chi-restraints excluded: chain A residue  731 PHE
Chi-restraints excluded: chain D residue  827 VAL
Chi-restraints excluded: chain D residue  845 MET
Chi-restraints excluded: chain D residue  847 SER
Chi-restraints excluded: chain D residue  938 ASN
Chi-restraints excluded: chain D residue  949 ASN
Chi-restraints excluded: chain D residue  950 ILE
Chi-restraints excluded: chain D residue 1019 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 48 optimal weight:    0.0570
   chunk 17 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.7700

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

Flipped N/Q/H residues before XYZ refinement:
A 577 ASN
** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 865 ASN
D 938 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.177555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.163023 restraints weight = 7917.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.4202 rms_B_bonded: 3.07
r_work: 0.4102 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.4102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6728
moved from start:          0.4410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4533  Z= 0.177
  Angle     :  0.904  10.338   6239  Z= 0.399
  Chirality :  0.057   0.313    774
  Planarity :  0.006   0.077    755
  Dihedral  : 12.008  69.787   1237
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 12.03 %
    Favored  : 87.77 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 19.72 %
    Favored  : 76.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.71 (0.35), residues: 507
  helix: -0.22 (0.91), residues: 30
  sheet:  0.59 (0.46), residues: 113
  loop : -1.95 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 707 
 HIS   0.008   0.001   HIS D1019 
 PHE   0.014   0.002   PHE D 984 
 TYR   0.024   0.002   TYR D 993 
 ARG   0.019   0.001   ARG D 807 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00896 (   10)
  link_NAG-ASN         : angle       3.76254 (   30)
  link_ALPHA1-6        : bond        0.01441 (    2)
  link_ALPHA1-6        : angle       2.21482 (    6)
  link_BETA1-4         : bond        0.00622 (   19)
  link_BETA1-4         : angle       2.39545 (   57)
  link_ALPHA1-3        : bond        0.00420 (    2)
  link_ALPHA1-3        : angle       2.74261 (    6)
  hydrogen bonds       : bond        0.04291 (   80)
  hydrogen bonds       : angle       6.27857 (  222)
  link_BETA1-6         : bond        0.00229 (    1)
  link_BETA1-6         : angle       1.84658 (    3)
  SS BOND              : bond        0.00601 (    5)
  SS BOND              : angle       1.53660 (   10)
  covalent geometry    : bond        0.00374 ( 4494)
  covalent geometry    : angle       0.83205 ( 6127)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  560 LYS cc_start: 0.7421 (OUTLIER) cc_final: 0.6883 (ptpp)
REVERT: A  610 ASN cc_start: 0.8490 (p0) cc_final: 0.8289 (p0)
REVERT: A  731 PHE cc_start: 0.3600 (OUTLIER) cc_final: 0.2355 (m-80)
REVERT: D  814 LEU cc_start: 0.8244 (tm) cc_final: 0.8036 (tm)
REVERT: D  949 ASN cc_start: 0.7859 (OUTLIER) cc_final: 0.7537 (t0)
REVERT: D  953 ASN cc_start: 0.7992 (t0) cc_final: 0.7696 (t0)
  outliers start: 17
  outliers final: 11
  residues processed: 99
  average time/residue: 0.6680
  time to fit residues: 70.3930
Evaluate side-chains
  104 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  534 ASN
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  560 LYS
Chi-restraints excluded: chain A residue  621 VAL
Chi-restraints excluded: chain A residue  731 PHE
Chi-restraints excluded: chain D residue  827 VAL
Chi-restraints excluded: chain D residue  845 MET
Chi-restraints excluded: chain D residue  847 SER
Chi-restraints excluded: chain D residue  938 ASN
Chi-restraints excluded: chain D residue  949 ASN
Chi-restraints excluded: chain D residue  950 ILE
Chi-restraints excluded: chain D residue  978 GLN
Chi-restraints excluded: chain D residue 1019 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 13 optimal weight:    0.1980
   chunk 48 optimal weight:    0.0770
   chunk 44 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 31 optimal weight:    0.2980
   chunk 40 optimal weight:    0.5980
   overall best weight:    0.4138

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

Flipped N/Q/H residues before XYZ refinement:
** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 790 ASN
D 865 ASN
D 938 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.178696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.163943 restraints weight = 8015.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.4214 rms_B_bonded: 3.10
r_work: 0.4117 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.4117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6702
moved from start:          0.4507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4533  Z= 0.146
  Angle     :  0.880  10.592   6239  Z= 0.388
  Chirality :  0.055   0.309    774
  Planarity :  0.006   0.082    755
  Dihedral  : 11.567  62.591   1237
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.23 %
    Favored  : 87.77 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 21.10 %
    Favored  : 75.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.35), residues: 507
  helix:  0.40 (0.95), residues: 29
  sheet:  0.57 (0.45), residues: 113
  loop : -1.97 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 707 
 HIS   0.010   0.001   HIS D 844 
 PHE   0.015   0.002   PHE A 571 
 TYR   0.024   0.002   TYR D 993 
 ARG   0.021   0.001   ARG D 807 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00830 (   10)
  link_NAG-ASN         : angle       3.63099 (   30)
  link_ALPHA1-6        : bond        0.01454 (    2)
  link_ALPHA1-6        : angle       2.22769 (    6)
  link_BETA1-4         : bond        0.00613 (   19)
  link_BETA1-4         : angle       2.28100 (   57)
  link_ALPHA1-3        : bond        0.00476 (    2)
  link_ALPHA1-3        : angle       2.63113 (    6)
  hydrogen bonds       : bond        0.03821 (   80)
  hydrogen bonds       : angle       6.26325 (  222)
  link_BETA1-6         : bond        0.00484 (    1)
  link_BETA1-6         : angle       1.88219 (    3)
  SS BOND              : bond        0.00652 (    5)
  SS BOND              : angle       1.90842 (   10)
  covalent geometry    : bond        0.00303 ( 4494)
  covalent geometry    : angle       0.81009 ( 6127)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 83
  time to evaluate  : 0.575 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  560 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.6888 (ptpp)
REVERT: A  731 PHE cc_start: 0.3756 (OUTLIER) cc_final: 0.2533 (m-80)
REVERT: D  880 MET cc_start: 0.7215 (mpp) cc_final: 0.6920 (mpp)
REVERT: D  920 TYR cc_start: 0.5534 (OUTLIER) cc_final: 0.5237 (m-80)
REVERT: D  949 ASN cc_start: 0.7807 (OUTLIER) cc_final: 0.7525 (t160)
  outliers start: 15
  outliers final: 10
  residues processed: 89
  average time/residue: 0.6611
  time to fit residues: 63.4941
Evaluate side-chains
  97 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  534 ASN
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  560 LYS
Chi-restraints excluded: chain A residue  621 VAL
Chi-restraints excluded: chain A residue  731 PHE
Chi-restraints excluded: chain D residue  827 VAL
Chi-restraints excluded: chain D residue  845 MET
Chi-restraints excluded: chain D residue  847 SER
Chi-restraints excluded: chain D residue  915 TRP
Chi-restraints excluded: chain D residue  920 TYR
Chi-restraints excluded: chain D residue  949 ASN
Chi-restraints excluded: chain D residue  950 ILE
Chi-restraints excluded: chain D residue 1019 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 17 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0770
   chunk 13 optimal weight:    0.0870
   chunk 40 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 26 optimal weight:    0.2980
   chunk 20 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 1 optimal weight:    0.2980
   overall best weight:    0.3116

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

Flipped N/Q/H residues before XYZ refinement:
A 766 GLN
D 938 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.179880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.165332 restraints weight = 7866.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.4230 rms_B_bonded: 3.05
r_work: 0.4135 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.4135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6675
moved from start:          0.4590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4533  Z= 0.140
  Angle     :  0.864  10.705   6239  Z= 0.377
  Chirality :  0.054   0.302    774
  Planarity :  0.006   0.080    755
  Dihedral  : 10.844  59.028   1237
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 12.43 %
    Favored  : 87.38 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 21.79 %
    Favored  : 74.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.35), residues: 507
  helix:  0.54 (0.98), residues: 29
  sheet:  0.66 (0.45), residues: 113
  loop : -2.02 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 707 
 HIS   0.007   0.001   HIS D1019 
 PHE   0.016   0.002   PHE A 571 
 TYR   0.024   0.002   TYR D 993 
 ARG   0.019   0.001   ARG D 807 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00804 (   10)
  link_NAG-ASN         : angle       3.53661 (   30)
  link_ALPHA1-6        : bond        0.01639 (    2)
  link_ALPHA1-6        : angle       2.15614 (    6)
  link_BETA1-4         : bond        0.00608 (   19)
  link_BETA1-4         : angle       2.15993 (   57)
  link_ALPHA1-3        : bond        0.00509 (    2)
  link_ALPHA1-3        : angle       2.55927 (    6)
  hydrogen bonds       : bond        0.03724 (   80)
  hydrogen bonds       : angle       6.08601 (  222)
  link_BETA1-6         : bond        0.00508 (    1)
  link_BETA1-6         : angle       1.95128 (    3)
  SS BOND              : bond        0.00483 (    5)
  SS BOND              : angle       1.54572 (   10)
  covalent geometry    : bond        0.00289 ( 4494)
  covalent geometry    : angle       0.79877 ( 6127)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  560 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.6928 (ptpp)
REVERT: A  731 PHE cc_start: 0.3738 (OUTLIER) cc_final: 0.2598 (m-80)
REVERT: D  880 MET cc_start: 0.7163 (mpp) cc_final: 0.6853 (mpp)
REVERT: D  920 TYR cc_start: 0.5387 (OUTLIER) cc_final: 0.4874 (m-80)
REVERT: D  949 ASN cc_start: 0.7752 (OUTLIER) cc_final: 0.7496 (t160)
  outliers start: 15
  outliers final: 10
  residues processed: 85
  average time/residue: 0.5062
  time to fit residues: 46.8392
Evaluate side-chains
  91 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  534 ASN
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  560 LYS
Chi-restraints excluded: chain A residue  621 VAL
Chi-restraints excluded: chain A residue  731 PHE
Chi-restraints excluded: chain D residue  827 VAL
Chi-restraints excluded: chain D residue  845 MET
Chi-restraints excluded: chain D residue  920 TYR
Chi-restraints excluded: chain D residue  938 ASN
Chi-restraints excluded: chain D residue  949 ASN
Chi-restraints excluded: chain D residue  950 ILE
Chi-restraints excluded: chain D residue  978 GLN
Chi-restraints excluded: chain D residue 1019 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 48 optimal weight:    0.0770
   chunk 27 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0980
   chunk 39 optimal weight:    0.1980
   chunk 22 optimal weight:    0.0980
   overall best weight:    0.2938

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

Flipped N/Q/H residues before XYZ refinement:
D 938 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.179740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.165083 restraints weight = 7887.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.4227 rms_B_bonded: 3.09
r_work: 0.4130 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.4130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6680
moved from start:          0.4594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.116   4533  Z= 0.218
  Angle     :  1.351  59.154   6239  Z= 0.762
  Chirality :  0.054   0.303    774
  Planarity :  0.006   0.076    755
  Dihedral  : 10.846  58.757   1237
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 12.62 %
    Favored  : 87.18 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 22.02 %
    Favored  : 74.54 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.35), residues: 507
  helix:  0.13 (0.96), residues: 29
  sheet:  0.68 (0.46), residues: 113
  loop : -2.02 (0.30), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 707 
 HIS   0.007   0.001   HIS D1019 
 PHE   0.017   0.002   PHE A 571 
 TYR   0.019   0.002   TYR D 993 
 ARG   0.017   0.001   ARG D 807 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00802 (   10)
  link_NAG-ASN         : angle       3.53434 (   30)
  link_ALPHA1-6        : bond        0.01215 (    2)
  link_ALPHA1-6        : angle       2.24462 (    6)
  link_BETA1-4         : bond        0.00594 (   19)
  link_BETA1-4         : angle       2.16019 (   57)
  link_ALPHA1-3        : bond        0.00495 (    2)
  link_ALPHA1-3        : angle       2.56205 (    6)
  hydrogen bonds       : bond        0.03852 (   80)
  hydrogen bonds       : angle       6.08963 (  222)
  link_BETA1-6         : bond        0.00497 (    1)
  link_BETA1-6         : angle       1.94620 (    3)
  SS BOND              : bond        0.00441 (    5)
  SS BOND              : angle       1.51925 (   10)
  covalent geometry    : bond        0.00400 ( 4494)
  covalent geometry    : angle       1.31812 ( 6127)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3995.41 seconds
wall clock time: 73 minutes 48.73 seconds (4428.73 seconds total)