Starting phenix.real_space_refine
on Fri Aug 22 14:49:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ziz_60134/08_2025/8ziz_60134.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ziz_60134/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ziz_60134/08_2025/8ziz_60134.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ziz_60134/08_2025/8ziz_60134.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ziz_60134/08_2025/8ziz_60134.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ziz_60134/08_2025/8ziz_60134.map"
  }
  resolution = 2.89
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.25, per 1000 atoms: 0.28
  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: 0.50
  Conformation dependent library (CDL) restraints added in 160.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.13
  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: 0.59

  Time building geometry restraints manager: 0.59 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:             0.840
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.220
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:6.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.940
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.001   0.000   ARG D1006 
 TYR   0.003   0.001   TYR A 546 
 PHE   0.008   0.001   PHE A 731 
 TRP   0.005   0.001   TRP A 554 
 HIS   0.002   0.000   HIS D1019 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 ( 4494)
  covalent geometry    : angle       0.83615 ( 6127)
  SS BOND              : bond        0.00144 (    5)
  SS BOND              : angle       0.71079 (   10)
  hydrogen bonds       : bond        0.25627 (   80)
  hydrogen bonds       : angle       9.54694 (  222)
  link_ALPHA1-3        : bond        0.00677 (    2)
  link_ALPHA1-3        : angle       2.48258 (    6)
  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_BETA1-6         : bond        0.00519 (    1)
  link_BETA1-6         : angle       2.09677 (    3)
  link_NAG-ASN         : bond        0.00407 (   10)
  link_NAG-ASN         : angle       2.05633 (   30)

*********************** 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  : 0.152 
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: 0.7413 (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: 0.7817 (mm)
  outliers start: 10
  outliers final: 4
  residues processed: 121
  average time/residue: 0.3937
  time to fit residues: 50.0160
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  : 0.148 
-------------------------------------------------------------------------------
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 24 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    7.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 748 HIS
A 756 GLN
A 768 ASN
D 865 ASN
D 938 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 = 0.4371 r_free = 0.4371 target = 0.178403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.163687 restraints weight = 8125.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.4215 rms_B_bonded: 3.07
r_work: 0.4115 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.4115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6697
moved from start:          0.2776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   4533  Z= 0.285
  Angle     :  1.021   9.641   6239  Z= 0.454
  Chirality :  0.062   0.373    774
  Planarity :  0.007   0.061    755
  Dihedral  : 19.922  88.278   1237
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.62 %
    Favored  : 87.38 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 10.78 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.10 (0.37), residues: 507
  helix:  1.65 (0.97), residues: 29
  sheet:  1.04 (0.47), residues: 114
  loop : -1.67 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 807 
 TYR   0.018   0.002   TYR D 948 
 PHE   0.022   0.003   PHE A 542 
 TRP   0.012   0.002   TRP D 819 
 HIS   0.008   0.002   HIS D1019 

Details of bonding type rmsd
  covalent geometry    : bond        0.00606 ( 4494)
  covalent geometry    : angle       0.96476 ( 6127)
  SS BOND              : bond        0.00729 (    5)
  SS BOND              : angle       1.66343 (   10)
  hydrogen bonds       : bond        0.06257 (   80)
  hydrogen bonds       : angle       7.18008 (  222)
  link_ALPHA1-3        : bond        0.00562 (    2)
  link_ALPHA1-3        : angle       3.05952 (    6)
  link_ALPHA1-6        : bond        0.01363 (    2)
  link_ALPHA1-6        : angle       2.21503 (    6)
  link_BETA1-4         : bond        0.00800 (   19)
  link_BETA1-4         : angle       2.67684 (   57)
  link_BETA1-6         : bond        0.00072 (    1)
  link_BETA1-6         : angle       3.04760 (    3)
  link_NAG-ASN         : bond        0.00656 (   10)
  link_NAG-ASN         : angle       2.86943 (   30)

*********************** 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
  127 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: A  560 LYS cc_start: 0.7030 (OUTLIER) cc_final: 0.6555 (ptpp)
REVERT: A  580 VAL cc_start: 0.8304 (t) cc_final: 0.8062 (m)
REVERT: A  618 THR cc_start: 0.8098 (p) cc_final: 0.7875 (t)
REVERT: A  733 THR cc_start: 0.1162 (OUTLIER) cc_final: 0.0325 (p)
REVERT: D  804 TYR cc_start: 0.8057 (t80) cc_final: 0.7778 (t80)
REVERT: D  949 ASN cc_start: 0.7943 (OUTLIER) cc_final: 0.7304 (t160)
REVERT: D  950 ILE cc_start: 0.8399 (mm) cc_final: 0.8148 (mm)
REVERT: D  953 ASN cc_start: 0.7974 (t0) cc_final: 0.7686 (t0)
REVERT: D  961 GLU cc_start: 0.6222 (OUTLIER) cc_final: 0.5069 (mt-10)
REVERT: D  982 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.5975 (mtm-85)
  outliers start: 23
  outliers final: 7
  residues processed: 116
  average time/residue: 0.3963
  time to fit residues: 48.3402
Evaluate side-chains
  107 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
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  565 GLN
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain A residue  733 THR
Chi-restraints excluded: chain D residue  809 LEU
Chi-restraints excluded: chain D residue  938 ASN
Chi-restraints excluded: chain D residue  949 ASN
Chi-restraints excluded: chain D residue  961 GLU
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 42 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 43 optimal weight:    0.5980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 660 ASN
A 742 ASN
A 755 GLN
D 865 ASN
D 938 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.178277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.163839 restraints weight = 7985.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.4214 rms_B_bonded: 3.05
r_work: 0.4114 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.4114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6696
moved from start:          0.3395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   4533  Z= 0.194
  Angle     :  0.975  15.651   6239  Z= 0.417
  Chirality :  0.061   0.444    774
  Planarity :  0.006   0.060    755
  Dihedral  : 17.111  85.380   1236
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 12.03 %
    Favored  : 87.77 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 14.22 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.20 (0.36), residues: 507
  helix:  1.51 (0.95), residues: 29
  sheet:  1.05 (0.47), residues: 113
  loop : -1.76 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D 807 
 TYR   0.022   0.002   TYR D 993 
 PHE   0.019   0.002   PHE A 571 
 TRP   0.015   0.002   TRP A 707 
 HIS   0.007   0.001   HIS D1019 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 4494)
  covalent geometry    : angle       0.88623 ( 6127)
  SS BOND              : bond        0.00528 (    5)
  SS BOND              : angle       1.24740 (   10)
  hydrogen bonds       : bond        0.05228 (   80)
  hydrogen bonds       : angle       6.86110 (  222)
  link_ALPHA1-3        : bond        0.00710 (    2)
  link_ALPHA1-3        : angle       2.89256 (    6)
  link_ALPHA1-6        : bond        0.01503 (    2)
  link_ALPHA1-6        : angle       2.14281 (    6)
  link_BETA1-4         : bond        0.00970 (   19)
  link_BETA1-4         : angle       2.85841 (   57)
  link_BETA1-6         : bond        0.00361 (    1)
  link_BETA1-6         : angle       2.57519 (    3)
  link_NAG-ASN         : bond        0.00447 (   10)
  link_NAG-ASN         : angle       4.24925 (   30)

*********************** 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
  121 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
REVERT: A  520 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.5960 (tm)
REVERT: A  560 LYS cc_start: 0.7164 (OUTLIER) cc_final: 0.6652 (ptpp)
REVERT: A  580 VAL cc_start: 0.8292 (t) cc_final: 0.8088 (m)
REVERT: A  618 THR cc_start: 0.8125 (p) cc_final: 0.7914 (t)
REVERT: D  804 TYR cc_start: 0.8012 (t80) cc_final: 0.7809 (t80)
REVERT: D  949 ASN cc_start: 0.7831 (OUTLIER) cc_final: 0.7195 (t160)
REVERT: D  953 ASN cc_start: 0.7999 (t0) cc_final: 0.7737 (t0)
REVERT: D  961 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.5282 (mt-10)
REVERT: D  982 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6043 (ttm170)
  outliers start: 24
  outliers final: 12
  residues processed: 109
  average time/residue: 0.3673
  time to fit residues: 42.1648
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  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  520 LEU
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  597 THR
Chi-restraints excluded: chain A residue  621 VAL
Chi-restraints excluded: chain A residue  660 ASN
Chi-restraints excluded: chain A residue  742 ASN
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  954 MET
Chi-restraints excluded: chain D residue  961 GLU
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 22 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0060
   chunk 32 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0070
   overall best weight:    0.5014

-------------------------------------------------------------------------------
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 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 790 ASN
D 865 ASN
D 938 ASN
D 943 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.178819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.164509 restraints weight = 7942.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.4221 rms_B_bonded: 3.02
r_work: 0.4123 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.4123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6674
moved from start:          0.3619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4533  Z= 0.159
  Angle     :  0.922  13.095   6239  Z= 0.394
  Chirality :  0.058   0.290    774
  Planarity :  0.006   0.065    755
  Dihedral  : 14.866  84.897   1236
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 11.64 %
    Favored  : 88.17 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 15.60 %
    Favored  : 79.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.31 (0.36), residues: 507
  helix:  0.65 (0.88), residues: 35
  sheet:  0.98 (0.47), residues: 113
  loop : -1.80 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D 807 
 TYR   0.009   0.001   TYR D 828 
 PHE   0.019   0.002   PHE A 571 
 TRP   0.010   0.001   TRP A 707 
 HIS   0.007   0.001   HIS D1019 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 4494)
  covalent geometry    : angle       0.83460 ( 6127)
  SS BOND              : bond        0.00529 (    5)
  SS BOND              : angle       1.31583 (   10)
  hydrogen bonds       : bond        0.04273 (   80)
  hydrogen bonds       : angle       6.42293 (  222)
  link_ALPHA1-3        : bond        0.00688 (    2)
  link_ALPHA1-3        : angle       2.87502 (    6)
  link_ALPHA1-6        : bond        0.01562 (    2)
  link_ALPHA1-6        : angle       2.18078 (    6)
  link_BETA1-4         : bond        0.00741 (   19)
  link_BETA1-4         : angle       2.80411 (   57)
  link_BETA1-6         : bond        0.00541 (    1)
  link_BETA1-6         : angle       2.41358 (    3)
  link_NAG-ASN         : bond        0.01086 (   10)
  link_NAG-ASN         : angle       3.96464 (   30)

*********************** 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
  106 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 85
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
REVERT: A  520 LEU cc_start: 0.6518 (OUTLIER) cc_final: 0.6060 (tm)
REVERT: A  560 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.6825 (ptpp)
REVERT: A  618 THR cc_start: 0.8064 (p) cc_final: 0.7831 (t)
REVERT: A  731 PHE cc_start: 0.3649 (OUTLIER) cc_final: 0.2227 (m-80)
REVERT: D  949 ASN cc_start: 0.7739 (OUTLIER) cc_final: 0.7115 (t160)
REVERT: D 1017 PHE cc_start: 0.7696 (p90) cc_final: 0.7281 (p90)
  outliers start: 21
  outliers final: 9
  residues processed: 96
  average time/residue: 0.3771
  time to fit residues: 38.1917
Evaluate side-chains
  97 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  520 LEU
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  847 SER
Chi-restraints excluded: chain D residue  938 ASN
Chi-restraints excluded: chain D residue  949 ASN
Chi-restraints excluded: chain D residue 1012 GLU
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 39 optimal weight:    1.9990
   chunk 3 optimal weight:    0.1980
   chunk 12 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0570
   chunk 11 optimal weight:    0.4980
   chunk 24 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0070
   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
D 981 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.179728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.165373 restraints weight = 8118.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.4230 rms_B_bonded: 3.06
r_work: 0.4131 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.4131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6651
moved from start:          0.3788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4533  Z= 0.136
  Angle     :  0.866  13.319   6239  Z= 0.370
  Chirality :  0.056   0.315    774
  Planarity :  0.006   0.070    755
  Dihedral  : 13.231  81.789   1236
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.85 %
    Favored  : 88.95 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 17.20 %
    Favored  : 77.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.33 (0.36), residues: 507
  helix:  0.72 (0.88), residues: 35
  sheet:  0.97 (0.46), residues: 113
  loop : -1.83 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D 807 
 TYR   0.021   0.001   TYR D 993 
 PHE   0.017   0.002   PHE A 571 
 TRP   0.010   0.001   TRP A 707 
 HIS   0.007   0.001   HIS D1019 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 4494)
  covalent geometry    : angle       0.78234 ( 6127)
  SS BOND              : bond        0.00430 (    5)
  SS BOND              : angle       1.29256 (   10)
  hydrogen bonds       : bond        0.03644 (   80)
  hydrogen bonds       : angle       6.10410 (  222)
  link_ALPHA1-3        : bond        0.00662 (    2)
  link_ALPHA1-3        : angle       2.83835 (    6)
  link_ALPHA1-6        : bond        0.01415 (    2)
  link_ALPHA1-6        : angle       2.15800 (    6)
  link_BETA1-4         : bond        0.00697 (   19)
  link_BETA1-4         : angle       2.61115 (   57)
  link_BETA1-6         : bond        0.00641 (    1)
  link_BETA1-6         : angle       1.99785 (    3)
  link_NAG-ASN         : bond        0.00874 (   10)
  link_NAG-ASN         : angle       3.81126 (   30)

*********************** 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
  111 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
REVERT: A  520 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.6081 (tm)
REVERT: A  560 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.6860 (ptpp)
REVERT: A  618 THR cc_start: 0.7987 (p) cc_final: 0.7779 (t)
REVERT: A  731 PHE cc_start: 0.3557 (OUTLIER) cc_final: 0.2156 (m-80)
REVERT: D  949 ASN cc_start: 0.7713 (OUTLIER) cc_final: 0.7342 (t0)
REVERT: D  953 ASN cc_start: 0.8060 (t0) cc_final: 0.7698 (t0)
REVERT: D  982 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6781 (ttt180)
  outliers start: 24
  outliers final: 13
  residues processed: 98
  average time/residue: 0.3561
  time to fit residues: 36.8324
Evaluate side-chains
  102 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  520 LEU
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  663 ASP
Chi-restraints excluded: chain A residue  731 PHE
Chi-restraints excluded: chain A residue  743 THR
Chi-restraints excluded: chain D residue  809 LEU
Chi-restraints excluded: chain D residue  827 VAL
Chi-restraints excluded: chain D residue  830 ARG
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  978 GLN
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 6 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 577 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 = 0.4364 r_free = 0.4364 target = 0.177753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.162957 restraints weight = 8114.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.4203 rms_B_bonded: 3.09
r_work: 0.4103 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.4103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6722
moved from start:          0.4102

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= 0.180
  Angle     :  0.903  12.213   6239  Z= 0.392
  Chirality :  0.058   0.341    774
  Planarity :  0.006   0.072    755
  Dihedral  : 12.737  80.584   1236
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 12.62 %
    Favored  : 87.18 %
  Rotamer:
    Outliers :  6.19 %
    Allowed  : 16.51 %
    Favored  : 77.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.55 (0.36), residues: 507
  helix:  0.25 (0.84), residues: 35
  sheet:  0.86 (0.47), residues: 111
  loop : -1.95 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG D 807 
 TYR   0.018   0.001   TYR D 804 
 PHE   0.015   0.002   PHE A 571 
 TRP   0.009   0.001   TRP A 554 
 HIS   0.008   0.001   HIS D1019 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 4494)
  covalent geometry    : angle       0.81625 ( 6127)
  SS BOND              : bond        0.00428 (    5)
  SS BOND              : angle       1.31551 (   10)
  hydrogen bonds       : bond        0.04227 (   80)
  hydrogen bonds       : angle       6.19261 (  222)
  link_ALPHA1-3        : bond        0.00477 (    2)
  link_ALPHA1-3        : angle       2.88473 (    6)
  link_ALPHA1-6        : bond        0.01456 (    2)
  link_ALPHA1-6        : angle       2.17768 (    6)
  link_BETA1-4         : bond        0.00671 (   19)
  link_BETA1-4         : angle       2.63291 (   57)
  link_BETA1-6         : bond        0.00284 (    1)
  link_BETA1-6         : angle       1.88910 (    3)
  link_NAG-ASN         : bond        0.01000 (   10)
  link_NAG-ASN         : angle       4.10253 (   30)

*********************** 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
  120 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 93
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
REVERT: A  520 LEU cc_start: 0.6598 (OUTLIER) cc_final: 0.6253 (tm)
REVERT: A  560 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.6947 (ptpp)
REVERT: A  618 THR cc_start: 0.8084 (p) cc_final: 0.7882 (t)
REVERT: A  731 PHE cc_start: 0.3777 (OUTLIER) cc_final: 0.2440 (m-80)
REVERT: D  949 ASN cc_start: 0.7775 (OUTLIER) cc_final: 0.7375 (t160)
REVERT: D  982 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.6912 (ttt180)
  outliers start: 27
  outliers final: 11
  residues processed: 102
  average time/residue: 0.3441
  time to fit residues: 37.1360
Evaluate side-chains
  107 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  520 LEU
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 A residue  743 THR
Chi-restraints excluded: chain D residue  827 VAL
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  978 GLN
Chi-restraints excluded: chain D residue  982 ARG
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 13 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 2 optimal weight:    0.2980
   chunk 22 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 17 optimal weight:    6.9990
   chunk 14 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.7784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.177271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.162469 restraints weight = 8038.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.4199 rms_B_bonded: 3.08
r_work: 0.4098 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.4098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6740
moved from start:          0.4331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4533  Z= 0.182
  Angle     :  0.928  10.525   6239  Z= 0.406
  Chirality :  0.057   0.337    774
  Planarity :  0.006   0.073    755
  Dihedral  : 12.405  78.952   1236
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 12.23 %
    Favored  : 87.38 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 19.72 %
    Favored  : 75.92 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.60 (0.36), residues: 507
  helix:  1.00 (0.90), residues: 29
  sheet:  0.72 (0.47), residues: 111
  loop : -1.98 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG D 807 
 TYR   0.022   0.002   TYR D 993 
 PHE   0.014   0.002   PHE D 984 
 TRP   0.009   0.001   TRP A 554 
 HIS   0.007   0.001   HIS D1019 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 4494)
  covalent geometry    : angle       0.84384 ( 6127)
  SS BOND              : bond        0.00444 (    5)
  SS BOND              : angle       1.58498 (   10)
  hydrogen bonds       : bond        0.04213 (   80)
  hydrogen bonds       : angle       6.22639 (  222)
  link_ALPHA1-3        : bond        0.00472 (    2)
  link_ALPHA1-3        : angle       2.80932 (    6)
  link_ALPHA1-6        : bond        0.01511 (    2)
  link_ALPHA1-6        : angle       2.26636 (    6)
  link_BETA1-4         : bond        0.00754 (   19)
  link_BETA1-4         : angle       2.62901 (   57)
  link_BETA1-6         : bond        0.00330 (    1)
  link_BETA1-6         : angle       1.86194 (    3)
  link_NAG-ASN         : bond        0.00929 (   10)
  link_NAG-ASN         : angle       4.09321 (   30)

*********************** 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
  108 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 89
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  520 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6552 (tm)
REVERT: A  560 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.6927 (ptpp)
REVERT: A  731 PHE cc_start: 0.3683 (OUTLIER) cc_final: 0.2405 (m-80)
REVERT: D  949 ASN cc_start: 0.7790 (OUTLIER) cc_final: 0.7445 (t160)
  outliers start: 19
  outliers final: 9
  residues processed: 97
  average time/residue: 0.3399
  time to fit residues: 34.9523
Evaluate side-chains
  102 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  520 LEU
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 A residue  743 THR
Chi-restraints excluded: chain D residue  827 VAL
Chi-restraints excluded: chain D residue  847 SER
Chi-restraints excluded: chain D residue  949 ASN
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 1 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0000
   chunk 27 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    0.6584

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

Flipped N/Q/H residues before XYZ refinement:
A 577 ASN
D 938 ASN
D 942 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.177167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.162512 restraints weight = 7956.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.4196 rms_B_bonded: 3.06
r_work: 0.4097 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.4097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6736
moved from start:          0.4537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4533  Z= 0.167
  Angle     :  0.908  10.329   6239  Z= 0.399
  Chirality :  0.056   0.316    774
  Planarity :  0.006   0.079    755
  Dihedral  : 12.121  75.141   1236
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 12.62 %
    Favored  : 87.18 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 19.72 %
    Favored  : 75.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.66 (0.35), residues: 507
  helix:  1.01 (0.93), residues: 29
  sheet:  0.73 (0.49), residues: 102
  loop : -1.99 (0.30), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG D 807 
 TYR   0.021   0.002   TYR D 993 
 PHE   0.015   0.002   PHE D 984 
 TRP   0.015   0.002   TRP D 796 
 HIS   0.008   0.001   HIS D 844 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 4494)
  covalent geometry    : angle       0.82991 ( 6127)
  SS BOND              : bond        0.00539 (    5)
  SS BOND              : angle       1.85302 (   10)
  hydrogen bonds       : bond        0.04034 (   80)
  hydrogen bonds       : angle       6.43045 (  222)
  link_ALPHA1-3        : bond        0.00490 (    2)
  link_ALPHA1-3        : angle       2.69445 (    6)
  link_ALPHA1-6        : bond        0.01407 (    2)
  link_ALPHA1-6        : angle       2.19699 (    6)
  link_BETA1-4         : bond        0.00628 (   19)
  link_BETA1-4         : angle       2.45352 (   57)
  link_BETA1-6         : bond        0.00321 (    1)
  link_BETA1-6         : angle       1.90918 (    3)
  link_NAG-ASN         : bond        0.00864 (   10)
  link_NAG-ASN         : angle       3.90778 (   30)

*********************** 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
  110 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
REVERT: A  520 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6668 (tm)
REVERT: A  534 ASN cc_start: 0.6320 (OUTLIER) cc_final: 0.6075 (p0)
REVERT: A  560 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.6953 (ptpp)
REVERT: A  731 PHE cc_start: 0.3849 (OUTLIER) cc_final: 0.2616 (m-80)
REVERT: D  880 MET cc_start: 0.7178 (mpp) cc_final: 0.6890 (mpp)
REVERT: D  949 ASN cc_start: 0.7821 (OUTLIER) cc_final: 0.7494 (t0)
  outliers start: 19
  outliers final: 9
  residues processed: 99
  average time/residue: 0.3218
  time to fit residues: 33.8534
Evaluate side-chains
  103 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  520 LEU
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 A residue  743 THR
Chi-restraints excluded: chain D residue  827 VAL
Chi-restraints excluded: chain D residue  847 SER
Chi-restraints excluded: chain D residue  915 TRP
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 39 optimal weight:    0.2980
   chunk 12 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
A 577 ASN
D 938 ASN
D 942 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.177043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.162357 restraints weight = 8048.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.4185 rms_B_bonded: 3.09
r_work: 0.4084 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.4084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6771
moved from start:          0.4817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4533  Z= 0.178
  Angle     :  0.928  10.120   6239  Z= 0.410
  Chirality :  0.057   0.328    774
  Planarity :  0.006   0.078    755
  Dihedral  : 11.916  73.414   1236
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 12.23 %
    Favored  : 87.57 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 20.41 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.73 (0.36), residues: 507
  helix:  0.44 (0.95), residues: 30
  sheet:  0.60 (0.47), residues: 113
  loop : -2.05 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG D 807 
 TYR   0.021   0.002   TYR D 993 
 PHE   0.015   0.002   PHE D 984 
 TRP   0.013   0.002   TRP D 796 
 HIS   0.008   0.001   HIS D1019 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 4494)
  covalent geometry    : angle       0.85415 ( 6127)
  SS BOND              : bond        0.00520 (    5)
  SS BOND              : angle       1.86868 (   10)
  hydrogen bonds       : bond        0.04337 (   80)
  hydrogen bonds       : angle       6.50983 (  222)
  link_ALPHA1-3        : bond        0.00438 (    2)
  link_ALPHA1-3        : angle       2.63798 (    6)
  link_ALPHA1-6        : bond        0.01391 (    2)
  link_ALPHA1-6        : angle       2.21896 (    6)
  link_BETA1-4         : bond        0.00633 (   19)
  link_BETA1-4         : angle       2.42065 (   57)
  link_BETA1-6         : bond        0.00175 (    1)
  link_BETA1-6         : angle       1.99086 (    3)
  link_NAG-ASN         : bond        0.00872 (   10)
  link_NAG-ASN         : angle       3.88038 (   30)

*********************** 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
  111 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
REVERT: A  517 PRO cc_start: 0.6933 (Cg_exo) cc_final: 0.6682 (Cg_endo)
REVERT: A  534 ASN cc_start: 0.6363 (OUTLIER) cc_final: 0.6101 (p0)
REVERT: A  560 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.6919 (ptpp)
REVERT: A  731 PHE cc_start: 0.4023 (OUTLIER) cc_final: 0.2792 (m-80)
REVERT: D  949 ASN cc_start: 0.7846 (OUTLIER) cc_final: 0.7537 (t0)
REVERT: D  953 ASN cc_start: 0.8074 (t0) cc_final: 0.7642 (t0)
  outliers start: 20
  outliers final: 10
  residues processed: 99
  average time/residue: 0.2851
  time to fit residues: 30.2158
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  : 0.148 
-------------------------------------------------------------------------------
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  802 LEU
Chi-restraints excluded: chain D residue  915 TRP
Chi-restraints excluded: chain D residue  938 ASN
Chi-restraints excluded: chain D residue  949 ASN
Chi-restraints excluded: chain D residue  951 THR
Chi-restraints excluded: chain D residue  978 GLN
Chi-restraints excluded: chain D residue 1003 VAL
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 7 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 13 optimal weight:    0.3980
   chunk 16 optimal weight:   10.0000
   chunk 28 optimal weight:    0.4980
   chunk 33 optimal weight:    0.1980
   chunk 29 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
D 865 ASN
D 938 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.177606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.162773 restraints weight = 7886.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.4194 rms_B_bonded: 3.07
r_work: 0.4095 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.4095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6756
moved from start:          0.4908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4533  Z= 0.164
  Angle     :  0.928  10.202   6239  Z= 0.411
  Chirality :  0.056   0.326    774
  Planarity :  0.006   0.080    755
  Dihedral  : 11.684  70.117   1236
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 12.82 %
    Favored  : 86.98 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 22.71 %
    Favored  : 74.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.84 (0.35), residues: 507
  helix:  0.21 (0.93), residues: 30
  sheet:  0.51 (0.47), residues: 113
  loop : -2.10 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG D 807 
 TYR   0.022   0.002   TYR D 993 
 PHE   0.015   0.002   PHE D 984 
 TRP   0.012   0.001   TRP D 796 
 HIS   0.007   0.001   HIS D1019 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 4494)
  covalent geometry    : angle       0.85072 ( 6127)
  SS BOND              : bond        0.00469 (    5)
  SS BOND              : angle       1.67158 (   10)
  hydrogen bonds       : bond        0.03963 (   80)
  hydrogen bonds       : angle       6.39666 (  222)
  link_ALPHA1-3        : bond        0.00463 (    2)
  link_ALPHA1-3        : angle       2.60178 (    6)
  link_ALPHA1-6        : bond        0.01406 (    2)
  link_ALPHA1-6        : angle       2.22842 (    6)
  link_BETA1-4         : bond        0.00593 (   19)
  link_BETA1-4         : angle       2.36778 (   57)
  link_BETA1-6         : bond        0.00317 (    1)
  link_BETA1-6         : angle       2.00608 (    3)
  link_NAG-ASN         : bond        0.00863 (   10)
  link_NAG-ASN         : angle       4.11589 (   30)

********************** 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
  99 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
REVERT: A  517 PRO cc_start: 0.6879 (Cg_exo) cc_final: 0.6633 (Cg_endo)
REVERT: A  560 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.6891 (ptpp)
REVERT: A  731 PHE cc_start: 0.4008 (OUTLIER) cc_final: 0.2800 (m-80)
REVERT: A  743 THR cc_start: 0.6878 (t) cc_final: 0.6450 (m)
REVERT: D  949 ASN cc_start: 0.7814 (OUTLIER) cc_final: 0.7513 (t0)
  outliers start: 13
  outliers final: 10
  residues processed: 93
  average time/residue: 0.2785
  time to fit residues: 27.8510
Evaluate side-chains
  99 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  802 LEU
Chi-restraints excluded: chain D residue  915 TRP
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  951 THR
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 37 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 9 optimal weight:    0.4980
   chunk 31 optimal weight:    0.0670
   chunk 18 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 14 optimal weight:    0.3980
   chunk 3 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
D 938 ASN
D 943 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.178507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.163960 restraints weight = 8029.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.4202 rms_B_bonded: 3.05
r_work: 0.4105 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.4105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6743
moved from start:          0.4984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4533  Z= 0.154
  Angle     :  0.913  10.282   6239  Z= 0.401
  Chirality :  0.055   0.325    774
  Planarity :  0.006   0.077    755
  Dihedral  : 11.343  64.283   1234
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 11.83 %
    Favored  : 87.97 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 23.39 %
    Favored  : 73.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.83 (0.35), residues: 507
  helix:  0.24 (0.94), residues: 30
  sheet:  0.45 (0.47), residues: 113
  loop : -2.07 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG D 807 
 TYR   0.022   0.002   TYR D 993 
 PHE   0.015   0.002   PHE A 571 
 TRP   0.011   0.001   TRP D 796 
 HIS   0.007   0.001   HIS D1019 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 4494)
  covalent geometry    : angle       0.83963 ( 6127)
  SS BOND              : bond        0.00457 (    5)
  SS BOND              : angle       1.48623 (   10)
  hydrogen bonds       : bond        0.03810 (   80)
  hydrogen bonds       : angle       6.28619 (  222)
  link_ALPHA1-3        : bond        0.00474 (    2)
  link_ALPHA1-3        : angle       2.58638 (    6)
  link_ALPHA1-6        : bond        0.01436 (    2)
  link_ALPHA1-6        : angle       2.22701 (    6)
  link_BETA1-4         : bond        0.00610 (   19)
  link_BETA1-4         : angle       2.31872 (   57)
  link_BETA1-6         : bond        0.00358 (    1)
  link_BETA1-6         : angle       2.04799 (    3)
  link_NAG-ASN         : bond        0.00843 (   10)
  link_NAG-ASN         : angle       3.97444 (   30)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1772.01 seconds
wall clock time: 31 minutes 6.41 seconds (1866.41 seconds total)