Starting phenix.real_space_refine
on Tue Feb 11 10:11:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6a6b_6988/02_2025/6a6b_6988.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6a6b_6988/02_2025/6a6b_6988.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6a6b_6988/02_2025/6a6b_6988.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6a6b_6988/02_2025/6a6b_6988.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6a6b_6988/02_2025/6a6b_6988.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6a6b_6988/02_2025/6a6b_6988.cif"
  }
  resolution = 3.07
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.008
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: 3
    Type Number    sf(0)   Gaussians
     C    3288      2.51       5
     N     912      2.21       5
     O    1056      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5256
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 438
          Classifications: {'peptide': 63}
          Link IDs: {'TRANS': 62}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, K, J, L
  Time building chain proxies: 1.85, per 1000 atoms: 0.35
  Number of scatterers: 5256
  At special positions: 0
  Unit cell: (101.64, 120.12, 46.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O    1056      8.00
     N     912      7.00
     C    3288      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.20
  Conformation dependent library (CDL) restraints added in 847.8 milliseconds
  

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1296

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 11 sheets defined
      0.0% alpha, 26.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.74
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 58
      removed outlier: 8.973A  pdb=" N   VAL A  49 " --> pdb=" O   HIS B  50 " (cutoff:3.500A)
      removed outlier: 9.241A  pdb=" N   VAL B  52 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   GLY A  51 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
      removed outlier: 8.284A  pdb=" N   THR B  54 " --> pdb=" O   GLY A  51 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   ALA A  53 " --> pdb=" O   THR B  54 " (cutoff:3.500A)
      removed outlier: 8.348A  pdb=" N   ALA B  56 " --> pdb=" O   ALA A  53 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   VAL A  55 " --> pdb=" O   ALA B  56 " (cutoff:3.500A)
      removed outlier: 7.792A  pdb=" N   LYS B  58 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   GLU A  57 " --> pdb=" O   LYS B  58 " (cutoff:3.500A)
      removed outlier: 8.944A  pdb=" N   VAL B  49 " --> pdb=" O   HIS C  50 " (cutoff:3.500A)
      removed outlier: 9.193A  pdb=" N   VAL C  52 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   GLY B  51 " --> pdb=" O   VAL C  52 " (cutoff:3.500A)
      removed outlier: 8.236A  pdb=" N   THR C  54 " --> pdb=" O   GLY B  51 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   ALA B  53 " --> pdb=" O   THR C  54 " (cutoff:3.500A)
      removed outlier: 8.297A  pdb=" N   ALA C  56 " --> pdb=" O   ALA B  53 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   VAL B  55 " --> pdb=" O   ALA C  56 " (cutoff:3.500A)
      removed outlier: 7.740A  pdb=" N   LYS C  58 " --> pdb=" O   VAL B  55 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   GLU B  57 " --> pdb=" O   LYS C  58 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   HIS D  50 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   GLY C  51 " --> pdb=" O   HIS D  50 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   HIS E  50 " --> pdb=" O   VAL D  49 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   GLY D  51 " --> pdb=" O   HIS E  50 " (cutoff:3.500A)
      removed outlier: 8.973A  pdb=" N   VAL E  49 " --> pdb=" O   HIS F  50 " (cutoff:3.500A)
      removed outlier: 9.239A  pdb=" N   VAL F  52 " --> pdb=" O   VAL E  49 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   GLY E  51 " --> pdb=" O   VAL F  52 " (cutoff:3.500A)
      removed outlier: 8.303A  pdb=" N   THR F  54 " --> pdb=" O   GLY E  51 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   ALA E  53 " --> pdb=" O   THR F  54 " (cutoff:3.500A)
      removed outlier: 8.361A  pdb=" N   ALA F  56 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   VAL E  55 " --> pdb=" O   ALA F  56 " (cutoff:3.500A)
      removed outlier: 7.795A  pdb=" N   LYS F  58 " --> pdb=" O   VAL E  55 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   GLU E  57 " --> pdb=" O   LYS F  58 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 63
      removed outlier: 6.619A  pdb=" N   GLN A  62 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   GLN B  62 " --> pdb=" O   VAL C  63 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   GLN C  62 " --> pdb=" O   VAL D  63 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   GLN D  62 " --> pdb=" O   VAL E  63 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   GLN E  62 " --> pdb=" O   VAL F  63 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72
      removed outlier: 6.792A  pdb=" N   VAL A  71 " --> pdb=" O   THR B  72 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   VAL B  71 " --> pdb=" O   THR C  72 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   VAL C  71 " --> pdb=" O   THR D  72 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   VAL D  71 " --> pdb=" O   THR E  72 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   VAL E  71 " --> pdb=" O   THR F  72 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 80 through 82
      removed outlier: 6.665A  pdb=" N   THR A  81 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   THR B  81 " --> pdb=" O   VAL C  82 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   THR C  81 " --> pdb=" O   VAL D  82 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   THR D  81 " --> pdb=" O   VAL E  82 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   THR E  81 " --> pdb=" O   VAL F  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 89 through 92
      removed outlier: 6.491A  pdb=" N   ALA A  89 " --> pdb=" O   ALA B  90 " (cutoff:3.500A)
      removed outlier: 8.110A  pdb=" N   THR B  92 " --> pdb=" O   ALA A  89 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   ALA A  91 " --> pdb=" O   THR B  92 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   ALA B  89 " --> pdb=" O   ALA C  90 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   THR C  92 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   ALA B  91 " --> pdb=" O   THR C  92 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   ALA C  89 " --> pdb=" O   ALA D  90 " (cutoff:3.500A)
      removed outlier: 8.046A  pdb=" N   THR D  92 " --> pdb=" O   ALA C  89 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   ALA C  91 " --> pdb=" O   THR D  92 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   ALA D  89 " --> pdb=" O   ALA E  90 " (cutoff:3.500A)
      removed outlier: 7.964A  pdb=" N   THR E  92 " --> pdb=" O   ALA D  89 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   ALA D  91 " --> pdb=" O   THR E  92 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   ALA E  89 " --> pdb=" O   ALA F  90 " (cutoff:3.500A)
      removed outlier: 8.033A  pdb=" N   THR F  92 " --> pdb=" O   ALA E  89 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   ALA E  91 " --> pdb=" O   THR F  92 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'G' and resid 49 through 58
      removed outlier: 6.897A  pdb=" N   HIS G  50 " --> pdb=" O   VAL H  49 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   GLY H  51 " --> pdb=" O   HIS G  50 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   HIS H  50 " --> pdb=" O   VAL I  49 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   GLY I  51 " --> pdb=" O   HIS H  50 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   HIS I  50 " --> pdb=" O   VAL J  49 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   GLY J  51 " --> pdb=" O   HIS I  50 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   HIS J  50 " --> pdb=" O   VAL K  49 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   GLY K  51 " --> pdb=" O   HIS J  50 " (cutoff:3.500A)
      removed outlier: 6.021A  pdb=" N   HIS K  50 " --> pdb=" O   GLY L  51 " (cutoff:3.500A)
      removed outlier: 9.040A  pdb=" N   ALA L  53 " --> pdb=" O   HIS K  50 " (cutoff:3.500A)
      removed outlier: 6.110A  pdb=" N   VAL K  52 " --> pdb=" O   ALA L  53 " (cutoff:3.500A)
      removed outlier: 7.984A  pdb=" N   VAL L  55 " --> pdb=" O   VAL K  52 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   THR K  54 " --> pdb=" O   VAL L  55 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   GLU L  57 " --> pdb=" O   THR K  54 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   ALA K  56 " --> pdb=" O   GLU L  57 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'G' and resid 61 through 63
    Processing sheet with id=AA8, first strand: chain 'G' and resid 71 through 72
    Processing sheet with id=AA9, first strand: chain 'G' and resid 80 through 82
    Processing sheet with id=AB1, first strand: chain 'G' and resid 89 through 92
    Processing sheet with id=AB2, first strand: chain 'I' and resid 89 through 92

    76 hydrogen bonds defined for protein.
    228 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.20

  Time building geometry restraints manager: 1.41 seconds

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

  Histogram of bond lengths:
        1.21 -     1.28: 924
        1.28 -     1.35: 816
        1.35 -     1.42: 216
        1.42 -     1.49: 918
        1.49 -     1.56: 2406
  Bond restraints: 5280
  Sorted by residual:
  bond pdb=" CB  ASN H  65 "
       pdb=" CG  ASN H  65 "
    ideal  model  delta    sigma   weight residual
    1.516  1.554 -0.038 2.50e-02 1.60e+03 2.30e+00
  bond pdb=" CB  ASN J  65 "
       pdb=" CG  ASN J  65 "
    ideal  model  delta    sigma   weight residual
    1.516  1.554 -0.038 2.50e-02 1.60e+03 2.30e+00
  bond pdb=" CB  ASN C  65 "
       pdb=" CG  ASN C  65 "
    ideal  model  delta    sigma   weight residual
    1.516  1.554 -0.038 2.50e-02 1.60e+03 2.28e+00
  bond pdb=" CB  ASN L  65 "
       pdb=" CG  ASN L  65 "
    ideal  model  delta    sigma   weight residual
    1.516  1.554 -0.038 2.50e-02 1.60e+03 2.28e+00
  bond pdb=" CB  ASN E  65 "
       pdb=" CG  ASN E  65 "
    ideal  model  delta    sigma   weight residual
    1.516  1.554 -0.038 2.50e-02 1.60e+03 2.28e+00
  ... (remaining 5275 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.35: 6293
        1.35 -     2.71: 607
        2.71 -     4.06: 132
        4.06 -     5.41: 83
        5.41 -     6.77: 25
  Bond angle restraints: 7140
  Sorted by residual:
  angle pdb=" CA  ASN C  65 "
        pdb=" CB  ASN C  65 "
        pdb=" CG  ASN C  65 "
      ideal   model   delta    sigma   weight residual
     112.60  116.83   -4.23 1.00e+00 1.00e+00 1.79e+01
  angle pdb=" CA  ASN D  65 "
        pdb=" CB  ASN D  65 "
        pdb=" CG  ASN D  65 "
      ideal   model   delta    sigma   weight residual
     112.60  116.82   -4.22 1.00e+00 1.00e+00 1.78e+01
  angle pdb=" CA  ASN K  65 "
        pdb=" CB  ASN K  65 "
        pdb=" CG  ASN K  65 "
      ideal   model   delta    sigma   weight residual
     112.60  116.82   -4.22 1.00e+00 1.00e+00 1.78e+01
  angle pdb=" CA  ASN L  65 "
        pdb=" CB  ASN L  65 "
        pdb=" CG  ASN L  65 "
      ideal   model   delta    sigma   weight residual
     112.60  116.81   -4.21 1.00e+00 1.00e+00 1.77e+01
  angle pdb=" CA  ASN F  65 "
        pdb=" CB  ASN F  65 "
        pdb=" CG  ASN F  65 "
      ideal   model   delta    sigma   weight residual
     112.60  116.81   -4.21 1.00e+00 1.00e+00 1.77e+01
  ... (remaining 7135 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     6.13: 2448
        6.13 -    12.25: 475
       12.25 -    18.38: 125
       18.38 -    24.51: 24
       24.51 -    30.63: 24
  Dihedral angle restraints: 3096
    sinusoidal: 1044
      harmonic: 2052
  Sorted by residual:
  dihedral pdb=" CA  THR I  72 "
           pdb=" C   THR I  72 "
           pdb=" N   GLY I  73 "
           pdb=" CA  GLY I  73 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.27   22.73     0      5.00e+00 4.00e-02 2.07e+01
  dihedral pdb=" CA  THR E  72 "
           pdb=" C   THR E  72 "
           pdb=" N   GLY E  73 "
           pdb=" CA  GLY E  73 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.29   22.71     0      5.00e+00 4.00e-02 2.06e+01
  dihedral pdb=" CA  THR B  72 "
           pdb=" C   THR B  72 "
           pdb=" N   GLY B  73 "
           pdb=" CA  GLY B  73 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.29   22.71     0      5.00e+00 4.00e-02 2.06e+01
  ... (remaining 3093 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 679
       0.065 -    0.131: 200
       0.131 -    0.196: 45
       0.196 -    0.261: 0
       0.261 -    0.327: 12
  Chirality restraints: 936
  Sorted by residual:
  chirality pdb=" CB  VAL E  66 "
            pdb=" CA  VAL E  66 "
            pdb=" CG1 VAL E  66 "
            pdb=" CG2 VAL E  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.30   -0.33 2.00e-01 2.50e+01 2.67e+00
  chirality pdb=" CB  VAL I  66 "
            pdb=" CA  VAL I  66 "
            pdb=" CG1 VAL I  66 "
            pdb=" CG2 VAL I  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.30   -0.32 2.00e-01 2.50e+01 2.64e+00
  chirality pdb=" CB  VAL C  66 "
            pdb=" CA  VAL C  66 "
            pdb=" CG1 VAL C  66 "
            pdb=" CG2 VAL C  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.30   -0.32 2.00e-01 2.50e+01 2.63e+00
  ... (remaining 933 not shown)

  Planarity restraints: 888
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL K  66 "    0.010 2.00e-02 2.50e+03   1.99e-02 3.96e+00
        pdb=" C   VAL K  66 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   VAL K  66 "    0.013 2.00e-02 2.50e+03
        pdb=" N   GLY K  67 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL J  66 "    0.010 2.00e-02 2.50e+03   1.99e-02 3.94e+00
        pdb=" C   VAL J  66 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   VAL J  66 "    0.013 2.00e-02 2.50e+03
        pdb=" N   GLY J  67 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL F  66 "   -0.010 2.00e-02 2.50e+03   1.98e-02 3.94e+00
        pdb=" C   VAL F  66 "    0.034 2.00e-02 2.50e+03
        pdb=" O   VAL F  66 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   GLY F  67 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 885 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 929
        2.79 -     3.32: 4519
        3.32 -     3.85: 8698
        3.85 -     4.37: 9679
        4.37 -     4.90: 19868
  Nonbonded interactions: 43693
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU D  46 "
            pdb=" NZ  LYS E  80 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" N   VAL K  37 "
            pdb=" O   VAL L  37 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" NZ  LYS K  80 "
            pdb=" OE1 GLU L  46 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" O   VAL D  37 "
            pdb=" N   VAL E  37 "
     model   vdw
     2.294 3.120
  nonbonded pdb=" NZ  LYS H  80 "
            pdb=" OE1 GLU I  46 "
     model   vdw
     2.317 3.120
  ... (remaining 43688 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'J'
  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:             0.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     14.390
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7010
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      :  0.006   0.038   5280  Z= 0.377
  Angle     :  1.068   6.767   7140  Z= 0.626
  Chirality :  0.073   0.327    936
  Planarity :  0.005   0.020    888
  Dihedral  :  7.612  30.635   1800
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.34 %
    Favored  : 88.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.85 (0.27), residues: 732
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.93 (0.20), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.006   HIS B  50 
 PHE   0.006   0.002   PHE K  94 
 TYR   0.007   0.002   TYR B  39 

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   77 VAL cc_start: 0.8300 (t) cc_final: 0.8073 (m)
REVERT: E   77 VAL cc_start: 0.8308 (t) cc_final: 0.8084 (t)
REVERT: F   39 TYR cc_start: 0.7892 (m-80) cc_final: 0.5937 (p90)
REVERT: F   43 LYS cc_start: 0.8083 (tttm) cc_final: 0.7862 (pptt)
REVERT: F   57 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7287 (pm20)
REVERT: F   58 LYS cc_start: 0.8866 (mttt) cc_final: 0.8062 (mmmt)
REVERT: F   96 LYS cc_start: 0.6738 (mmtp) cc_final: 0.6491 (pttm)
REVERT: G   39 TYR cc_start: 0.7672 (m-80) cc_final: 0.5514 (p90)
REVERT: G   43 LYS cc_start: 0.8398 (tttm) cc_final: 0.8053 (pptt)
REVERT: G   58 LYS cc_start: 0.8576 (mttt) cc_final: 0.8011 (mmmt)
REVERT: H   58 LYS cc_start: 0.8666 (mttt) cc_final: 0.8419 (mttm)
REVERT: H   77 VAL cc_start: 0.8311 (t) cc_final: 0.8085 (m)
REVERT: J   46 GLU cc_start: 0.6201 (pt0) cc_final: 0.5867 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 191
  average time/residue: 0.2077
  time to fit residues: 48.6173
Evaluate side-chains
  137 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:   20.0000
   chunk 54 optimal weight:   10.0000
   chunk 30 optimal weight:   20.0000
   chunk 18 optimal weight:   20.0000
   chunk 36 optimal weight:   20.0000
   chunk 29 optimal weight:   20.0000
   chunk 56 optimal weight:   10.0000
   chunk 21 optimal weight:    6.9990
   chunk 34 optimal weight:    8.9990
   chunk 42 optimal weight:    6.9990
   chunk 65 optimal weight:   10.0000
   overall best weight:    8.5994

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

Flipped N/Q/H residues before XYZ refinement:
** A  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4609 r_free = 0.4609 target = 0.169398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.141515 restraints weight = 8963.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.4290 rms_B_bonded: 4.35
r_work: 0.4164 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.4164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7110
moved from start:          0.3511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.060   5280  Z= 0.561
  Angle     :  0.714   5.512   7140  Z= 0.410
  Chirality :  0.052   0.135    936
  Planarity :  0.003   0.013    888
  Dihedral  :  6.343  21.682    756
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 14.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.29 %
    Favored  : 90.71 %
  Rotamer:
    Outliers :  8.70 %
    Allowed  : 13.15 %
    Favored  : 78.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.53 (0.26), residues: 732
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.69 (0.20), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.011   0.005   HIS G  50 
 PHE   0.008   0.002   PHE F  94 
 TYR   0.013   0.002   TYR K  39 

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 122
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LYS cc_start: 0.7346 (mtmm) cc_final: 0.6957 (mptt)
REVERT: B   39 TYR cc_start: 0.6963 (m-80) cc_final: 0.6720 (m-80)
REVERT: D   43 LYS cc_start: 0.6995 (mptt) cc_final: 0.6714 (mptt)
REVERT: D   97 LYS cc_start: 0.8298 (tppt) cc_final: 0.7802 (mmmm)
REVERT: F   57 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7790 (pm20)
REVERT: F   58 LYS cc_start: 0.8959 (mttt) cc_final: 0.7984 (mmmt)
REVERT: F   96 LYS cc_start: 0.6985 (mmtp) cc_final: 0.6307 (pptt)
REVERT: G   43 LYS cc_start: 0.8414 (tttm) cc_final: 0.7906 (pptt)
REVERT: G   58 LYS cc_start: 0.8689 (mttt) cc_final: 0.8065 (mmtt)
REVERT: H   61 GLU cc_start: 0.8198 (tt0) cc_final: 0.7927 (tt0)
REVERT: H   97 LYS cc_start: 0.8035 (mtpt) cc_final: 0.7744 (mtmt)
  outliers start: 47
  outliers final: 32
  residues processed: 148
  average time/residue: 0.1847
  time to fit residues: 34.3123
Evaluate side-chains
  146 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 114
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain F residue   74 VAL
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain G residue   74 VAL
Chi-restraints excluded: chain G residue   88 ILE
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   55 VAL
Chi-restraints excluded: chain H residue   64 THR
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   74 VAL
Chi-restraints excluded: chain J residue   54 THR
Chi-restraints excluded: chain J residue   74 VAL
Chi-restraints excluded: chain J residue   88 ILE
Chi-restraints excluded: chain K residue   46 GLU
Chi-restraints excluded: chain K residue   64 THR
Chi-restraints excluded: chain K residue   74 VAL
Chi-restraints excluded: chain L residue   74 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 6 optimal weight:   20.0000
   chunk 54 optimal weight:    6.9990
   chunk 58 optimal weight:    7.9990
   chunk 36 optimal weight:   20.0000
   chunk 15 optimal weight:    8.9990
   chunk 32 optimal weight:    0.8980
   chunk 35 optimal weight:    6.9990
   chunk 59 optimal weight:    3.9990
   chunk 62 optimal weight:    9.9990
   chunk 30 optimal weight:    7.9990
   chunk 12 optimal weight:    6.9990
   overall best weight:    5.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4653 r_free = 0.4653 target = 0.172027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.144713 restraints weight = 8911.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.4339 rms_B_bonded: 4.36
r_work: 0.4208 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.4208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7051
moved from start:          0.3860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   5280  Z= 0.351
  Angle     :  0.588   4.752   7140  Z= 0.338
  Chirality :  0.049   0.125    936
  Planarity :  0.002   0.012    888
  Dihedral  :  5.526  19.066    756
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.47 %
    Favored  : 91.53 %
  Rotamer:
    Outliers :  7.04 %
    Allowed  : 17.41 %
    Favored  : 75.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.30 (0.27), residues: 732
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.51 (0.21), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.004   HIS F  50 
 PHE   0.006   0.001   PHE G  94 
 TYR   0.011   0.002   TYR L  39 

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 118
  time to evaluate  : 0.506 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   39 TYR cc_start: 0.6968 (m-80) cc_final: 0.6728 (m-80)
REVERT: D   39 TYR cc_start: 0.6723 (m-80) cc_final: 0.6508 (m-80)
REVERT: D   43 LYS cc_start: 0.6374 (mptt) cc_final: 0.5950 (mptt)
REVERT: D   97 LYS cc_start: 0.8173 (tppt) cc_final: 0.7822 (mmmm)
REVERT: E   43 LYS cc_start: 0.7821 (mtmm) cc_final: 0.7226 (mmtm)
REVERT: F   57 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7705 (pm20)
REVERT: F   58 LYS cc_start: 0.9054 (mttt) cc_final: 0.7964 (mmmt)
REVERT: G   39 TYR cc_start: 0.7877 (m-80) cc_final: 0.7646 (m-80)
REVERT: G   58 LYS cc_start: 0.8671 (mttt) cc_final: 0.7971 (mmmt)
REVERT: H   61 GLU cc_start: 0.8239 (tt0) cc_final: 0.7880 (tt0)
REVERT: H   97 LYS cc_start: 0.8023 (mtpt) cc_final: 0.7684 (mtmt)
REVERT: K   61 GLU cc_start: 0.8029 (tt0) cc_final: 0.7785 (tt0)
  outliers start: 38
  outliers final: 32
  residues processed: 139
  average time/residue: 0.1868
  time to fit residues: 32.7263
Evaluate side-chains
  141 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 109
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   74 VAL
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain G residue   74 VAL
Chi-restraints excluded: chain G residue   88 ILE
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   55 VAL
Chi-restraints excluded: chain H residue   64 THR
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain I residue   46 GLU
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   74 VAL
Chi-restraints excluded: chain J residue   64 THR
Chi-restraints excluded: chain J residue   74 VAL
Chi-restraints excluded: chain K residue   46 GLU
Chi-restraints excluded: chain K residue   64 THR
Chi-restraints excluded: chain K residue   74 VAL
Chi-restraints excluded: chain L residue   74 VAL
Chi-restraints excluded: chain L residue   77 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 39 optimal weight:    9.9990
   chunk 22 optimal weight:    6.9990
   chunk 44 optimal weight:    9.9990
   chunk 18 optimal weight:   30.0000
   chunk 47 optimal weight:   10.0000
   chunk 65 optimal weight:   10.0000
   chunk 38 optimal weight:    4.9990
   chunk 64 optimal weight:    5.9990
   chunk 56 optimal weight:    9.9990
   chunk 4 optimal weight:   10.0000
   chunk 63 optimal weight:    1.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4657 r_free = 0.4657 target = 0.171796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.144802 restraints weight = 9001.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.4355 rms_B_bonded: 4.33
r_work: 0.4238 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.4238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7116
moved from start:          0.4233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   5280  Z= 0.397
  Angle     :  0.599   4.555   7140  Z= 0.347
  Chirality :  0.050   0.130    936
  Planarity :  0.003   0.012    888
  Dihedral  :  5.616  18.727    756
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.15 %
    Favored  : 90.85 %
  Rotamer:
    Outliers :  8.89 %
    Allowed  : 16.67 %
    Favored  : 74.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.24 (0.27), residues: 732
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.46 (0.20), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.004   HIS G  50 
 PHE   0.006   0.002   PHE G  94 
 TYR   0.008   0.002   TYR D  39 

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 107
  time to evaluate  : 0.594 
Fit side-chains
REVERT: D   43 LYS cc_start: 0.6803 (mptt) cc_final: 0.6329 (mptt)
REVERT: D   97 LYS cc_start: 0.8325 (tppt) cc_final: 0.7760 (mmmm)
REVERT: E   43 LYS cc_start: 0.7914 (mtmm) cc_final: 0.7311 (mmtm)
REVERT: F   39 TYR cc_start: 0.8021 (m-80) cc_final: 0.7776 (m-80)
REVERT: F   57 GLU cc_start: 0.8412 (mt-10) cc_final: 0.7743 (pm20)
REVERT: F   58 LYS cc_start: 0.9072 (mttt) cc_final: 0.8032 (mmmt)
REVERT: G   39 TYR cc_start: 0.7953 (m-80) cc_final: 0.7663 (m-80)
REVERT: G   58 LYS cc_start: 0.8653 (mttt) cc_final: 0.8034 (mmtt)
REVERT: G   97 LYS cc_start: 0.8712 (mmmt) cc_final: 0.8153 (mmmm)
REVERT: H   61 GLU cc_start: 0.8245 (tt0) cc_final: 0.7861 (tt0)
REVERT: L   39 TYR cc_start: 0.7116 (m-80) cc_final: 0.6702 (m-80)
  outliers start: 48
  outliers final: 42
  residues processed: 142
  average time/residue: 0.1744
  time to fit residues: 31.5742
Evaluate side-chains
  146 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 104
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   58 LYS
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   74 VAL
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain G residue   74 VAL
Chi-restraints excluded: chain G residue   88 ILE
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   55 VAL
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   64 THR
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   46 GLU
Chi-restraints excluded: chain I residue   64 THR
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   74 VAL
Chi-restraints excluded: chain J residue   64 THR
Chi-restraints excluded: chain J residue   74 VAL
Chi-restraints excluded: chain K residue   37 VAL
Chi-restraints excluded: chain K residue   46 GLU
Chi-restraints excluded: chain K residue   59 THR
Chi-restraints excluded: chain K residue   64 THR
Chi-restraints excluded: chain K residue   74 VAL
Chi-restraints excluded: chain L residue   54 THR
Chi-restraints excluded: chain L residue   74 VAL
Chi-restraints excluded: chain L residue   77 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 43 optimal weight:   10.0000
   chunk 69 optimal weight:    8.9990
   chunk 52 optimal weight:    8.9990
   chunk 45 optimal weight:    9.9990
   chunk 21 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 54 optimal weight:   20.0000
   chunk 60 optimal weight:    7.9990
   chunk 68 optimal weight:    1.9990
   chunk 46 optimal weight:    6.9990
   chunk 33 optimal weight:   10.0000
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4654 r_free = 0.4654 target = 0.171517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.145004 restraints weight = 9057.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.4360 rms_B_bonded: 4.29
r_work: 0.4241 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.4241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7123
moved from start:          0.4462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   5280  Z= 0.417
  Angle     :  0.611   5.159   7140  Z= 0.353
  Chirality :  0.050   0.129    936
  Planarity :  0.003   0.011    888
  Dihedral  :  5.633  17.598    756
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.88 %
    Favored  : 91.12 %
  Rotamer:
    Outliers : 10.37 %
    Allowed  : 16.67 %
    Favored  : 72.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.16 (0.27), residues: 732
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.40 (0.21), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.004   HIS G  50 
 PHE   0.006   0.002   PHE J  94 
 TYR   0.010   0.002   TYR C  39 

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 110
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.6975 (mptt)
REVERT: F   57 GLU cc_start: 0.8418 (mt-10) cc_final: 0.7727 (pm20)
REVERT: F   58 LYS cc_start: 0.9091 (mttt) cc_final: 0.8032 (mmmt)
REVERT: G   39 TYR cc_start: 0.7960 (m-80) cc_final: 0.7729 (m-80)
REVERT: H   61 GLU cc_start: 0.8341 (tt0) cc_final: 0.7930 (tt0)
REVERT: H   97 LYS cc_start: 0.8320 (mmtm) cc_final: 0.8086 (mmmm)
REVERT: I   97 LYS cc_start: 0.8169 (tppt) cc_final: 0.7943 (mmmm)
REVERT: J   43 LYS cc_start: 0.7344 (mtmm) cc_final: 0.7074 (mptt)
REVERT: K   97 LYS cc_start: 0.8006 (mtmt) cc_final: 0.7776 (mtmm)
REVERT: L   39 TYR cc_start: 0.6951 (m-80) cc_final: 0.6528 (m-80)
  outliers start: 56
  outliers final: 47
  residues processed: 147
  average time/residue: 0.1770
  time to fit residues: 33.0151
Evaluate side-chains
  153 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 105
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   54 THR
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain D residue   46 GLU
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   74 VAL
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain G residue   54 THR
Chi-restraints excluded: chain G residue   74 VAL
Chi-restraints excluded: chain G residue   88 ILE
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   55 VAL
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   64 THR
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   46 GLU
Chi-restraints excluded: chain I residue   64 THR
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   74 VAL
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   64 THR
Chi-restraints excluded: chain J residue   74 VAL
Chi-restraints excluded: chain K residue   37 VAL
Chi-restraints excluded: chain K residue   43 LYS
Chi-restraints excluded: chain K residue   46 GLU
Chi-restraints excluded: chain K residue   59 THR
Chi-restraints excluded: chain K residue   74 VAL
Chi-restraints excluded: chain K residue   77 VAL
Chi-restraints excluded: chain L residue   54 THR
Chi-restraints excluded: chain L residue   74 VAL
Chi-restraints excluded: chain L residue   77 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 12 optimal weight:   20.0000
   chunk 7 optimal weight:   10.0000
   chunk 42 optimal weight:   30.0000
   chunk 23 optimal weight:    0.8980
   chunk 52 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 2 optimal weight:    0.0370
   chunk 15 optimal weight:    7.9990
   chunk 59 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9980
   chunk 32 optimal weight:    9.9990
   overall best weight:    1.5860

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

Flipped N/Q/H residues before XYZ refinement:
** A  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4768 r_free = 0.4768 target = 0.180965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4514 r_free = 0.4514 target = 0.154669 restraints weight = 8864.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.4493 rms_B_bonded: 4.35
r_work: 0.4377 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.4377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6978
moved from start:          0.4553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5280  Z= 0.156
  Angle     :  0.511   6.117   7140  Z= 0.286
  Chirality :  0.049   0.123    936
  Planarity :  0.002   0.010    888
  Dihedral  :  4.621  15.063    756
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  6.85 %
    Allowed  : 18.89 %
    Favored  : 74.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.98 (0.28), residues: 732
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.26 (0.21), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS G  50 
 PHE   0.004   0.001   PHE J  94 
 TYR   0.006   0.001   TYR F  39 

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 116
  time to evaluate  : 0.549 
Fit side-chains
REVERT: A   43 LYS cc_start: 0.6779 (OUTLIER) cc_final: 0.6416 (mptt)
REVERT: C   97 LYS cc_start: 0.8488 (mmmt) cc_final: 0.8165 (mmmt)
REVERT: D   97 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8077 (mmmm)
REVERT: E   43 LYS cc_start: 0.7657 (mtmm) cc_final: 0.7450 (mptt)
REVERT: F   43 LYS cc_start: 0.3757 (pptt) cc_final: 0.3068 (pptt)
REVERT: F   57 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7452 (pm20)
REVERT: F   58 LYS cc_start: 0.8866 (mttt) cc_final: 0.7883 (mmmt)
REVERT: F   97 LYS cc_start: 0.8756 (mmmm) cc_final: 0.8388 (mmmt)
REVERT: H   61 GLU cc_start: 0.8287 (tt0) cc_final: 0.7997 (tt0)
REVERT: I   97 LYS cc_start: 0.8099 (tppt) cc_final: 0.7760 (mmtm)
REVERT: J   43 LYS cc_start: 0.7351 (mtmm) cc_final: 0.7108 (mmtm)
REVERT: K   97 LYS cc_start: 0.8044 (mtmt) cc_final: 0.7556 (pttm)
REVERT: L   39 TYR cc_start: 0.6981 (m-80) cc_final: 0.6565 (m-80)
  outliers start: 37
  outliers final: 28
  residues processed: 140
  average time/residue: 0.1670
  time to fit residues: 29.9193
Evaluate side-chains
  138 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 108
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   97 LYS
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain G residue   88 ILE
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   64 THR
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   46 GLU
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   74 VAL
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   64 THR
Chi-restraints excluded: chain J residue   74 VAL
Chi-restraints excluded: chain K residue   37 VAL
Chi-restraints excluded: chain K residue   46 GLU
Chi-restraints excluded: chain K residue   74 VAL
Chi-restraints excluded: chain L residue   54 THR
Chi-restraints excluded: chain L residue   74 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 48 optimal weight:    6.9990
   chunk 25 optimal weight:   10.0000
   chunk 8 optimal weight:   10.0000
   chunk 27 optimal weight:    5.9990
   chunk 30 optimal weight:    8.9990
   chunk 6 optimal weight:    0.9990
   chunk 53 optimal weight:   20.0000
   chunk 60 optimal weight:   30.0000
   chunk 11 optimal weight:   10.0000
   chunk 71 optimal weight:    0.0370
   chunk 15 optimal weight:    9.9990
   overall best weight:    4.6066

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

Flipped N/Q/H residues before XYZ refinement:
** A  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4698 r_free = 0.4698 target = 0.174832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.148549 restraints weight = 8985.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.4412 rms_B_bonded: 4.25
r_work: 0.4301 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.4301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7067
moved from start:          0.4703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   5280  Z= 0.314
  Angle     :  0.554   6.145   7140  Z= 0.318
  Chirality :  0.049   0.130    936
  Planarity :  0.002   0.011    888
  Dihedral  :  5.109  15.827    756
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.61 %
    Favored  : 91.39 %
  Rotamer:
    Outliers :  7.04 %
    Allowed  : 20.19 %
    Favored  : 72.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.04 (0.27), residues: 732
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.31 (0.21), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS G  50 
 PHE   0.005   0.001   PHE J  94 
 TYR   0.008   0.002   TYR A  39 

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 110
  time to evaluate  : 0.618 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LYS cc_start: 0.7140 (OUTLIER) cc_final: 0.6769 (mptt)
REVERT: C   39 TYR cc_start: 0.6392 (m-80) cc_final: 0.6059 (m-80)
REVERT: C   97 LYS cc_start: 0.8551 (mmmt) cc_final: 0.8176 (mmmt)
REVERT: E   43 LYS cc_start: 0.7772 (mtmm) cc_final: 0.7551 (mptt)
REVERT: E   97 LYS cc_start: 0.8597 (mmmm) cc_final: 0.8051 (mptt)
REVERT: F   43 LYS cc_start: 0.3986 (pptt) cc_final: 0.3126 (pptt)
REVERT: F   57 GLU cc_start: 0.8537 (mt-10) cc_final: 0.7878 (pm20)
REVERT: F   58 LYS cc_start: 0.9075 (mttt) cc_final: 0.8037 (mmmt)
REVERT: F   97 LYS cc_start: 0.8792 (mmmm) cc_final: 0.8517 (mmmt)
REVERT: G   97 LYS cc_start: 0.7738 (mmmt) cc_final: 0.7265 (mmmm)
REVERT: H   46 GLU cc_start: 0.7341 (pt0) cc_final: 0.6680 (pm20)
REVERT: H   61 GLU cc_start: 0.8332 (tt0) cc_final: 0.7904 (tt0)
REVERT: I   97 LYS cc_start: 0.8202 (tppt) cc_final: 0.7983 (mmtm)
REVERT: J   39 TYR cc_start: 0.7190 (m-80) cc_final: 0.6727 (m-80)
REVERT: J   43 LYS cc_start: 0.7436 (mtmm) cc_final: 0.7166 (mmtm)
REVERT: K   97 LYS cc_start: 0.8021 (mtmt) cc_final: 0.7590 (pttm)
  outliers start: 38
  outliers final: 32
  residues processed: 137
  average time/residue: 0.1826
  time to fit residues: 31.6829
Evaluate side-chains
  141 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 108
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   64 THR
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   46 GLU
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   74 VAL
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   64 THR
Chi-restraints excluded: chain K residue   37 VAL
Chi-restraints excluded: chain K residue   43 LYS
Chi-restraints excluded: chain K residue   46 GLU
Chi-restraints excluded: chain K residue   72 THR
Chi-restraints excluded: chain K residue   74 VAL
Chi-restraints excluded: chain L residue   54 THR
Chi-restraints excluded: chain L residue   74 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 70 optimal weight:   10.0000
   chunk 67 optimal weight:    0.0970
   chunk 39 optimal weight:    6.9990
   chunk 71 optimal weight:    0.9980
   chunk 46 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   chunk 21 optimal weight:    9.9990
   chunk 62 optimal weight:    4.9990
   chunk 20 optimal weight:    9.9990
   chunk 18 optimal weight:    6.9990
   chunk 29 optimal weight:    6.9990
   overall best weight:    4.0184

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

Flipped N/Q/H residues before XYZ refinement:
** A  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4720 r_free = 0.4720 target = 0.175851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.149503 restraints weight = 9001.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.4431 rms_B_bonded: 4.25
r_work: 0.4319 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.4319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7065
moved from start:          0.4797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5280  Z= 0.282
  Angle     :  0.561   8.736   7140  Z= 0.316
  Chirality :  0.050   0.162    936
  Planarity :  0.002   0.014    888
  Dihedral  :  5.035  15.141    756
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  8.15 %
    Allowed  : 19.26 %
    Favored  : 72.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.98 (0.27), residues: 732
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.26 (0.21), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS G  50 
 PHE   0.004   0.001   PHE B  94 
 TYR   0.009   0.002   TYR C  39 

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 110
  time to evaluate  : 0.581 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6678 (mptt)
REVERT: A   58 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8490 (mmtp)
REVERT: C   39 TYR cc_start: 0.6469 (m-80) cc_final: 0.6132 (m-80)
REVERT: C   97 LYS cc_start: 0.8501 (mmmt) cc_final: 0.8296 (mmmt)
REVERT: D   58 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8607 (mtpp)
REVERT: F   43 LYS cc_start: 0.3905 (pptt) cc_final: 0.3182 (pptt)
REVERT: F   57 GLU cc_start: 0.8491 (mt-10) cc_final: 0.7785 (pm20)
REVERT: F   58 LYS cc_start: 0.9008 (mttt) cc_final: 0.7956 (mmmt)
REVERT: F   97 LYS cc_start: 0.8821 (mmmm) cc_final: 0.8555 (mmmt)
REVERT: G   97 LYS cc_start: 0.7655 (mmmt) cc_final: 0.6912 (mmmm)
REVERT: H   46 GLU cc_start: 0.7322 (pt0) cc_final: 0.6720 (pm20)
REVERT: H   61 GLU cc_start: 0.8323 (tt0) cc_final: 0.8001 (tt0)
REVERT: H   97 LYS cc_start: 0.8085 (mmtm) cc_final: 0.7692 (mmmm)
REVERT: I   97 LYS cc_start: 0.8202 (tppt) cc_final: 0.7883 (mmtm)
REVERT: J   43 LYS cc_start: 0.7497 (mtmm) cc_final: 0.7249 (mmtm)
REVERT: J   97 LYS cc_start: 0.8422 (mmmm) cc_final: 0.8177 (mmmt)
REVERT: K   97 LYS cc_start: 0.7938 (mtmt) cc_final: 0.7656 (mtmm)
  outliers start: 44
  outliers final: 38
  residues processed: 140
  average time/residue: 0.1688
  time to fit residues: 30.2068
Evaluate side-chains
  150 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 109
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   58 LYS
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   70 VAL
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   64 THR
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   46 GLU
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   74 VAL
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   64 THR
Chi-restraints excluded: chain J residue   74 VAL
Chi-restraints excluded: chain K residue   43 LYS
Chi-restraints excluded: chain K residue   46 GLU
Chi-restraints excluded: chain K residue   72 THR
Chi-restraints excluded: chain K residue   74 VAL
Chi-restraints excluded: chain L residue   48 VAL
Chi-restraints excluded: chain L residue   54 THR
Chi-restraints excluded: chain L residue   74 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 18 optimal weight:   20.0000
   chunk 27 optimal weight:    8.9990
   chunk 31 optimal weight:   10.0000
   chunk 12 optimal weight:    0.8980
   chunk 41 optimal weight:    8.9990
   chunk 2 optimal weight:    4.9990
   chunk 25 optimal weight:    6.9990
   chunk 49 optimal weight:    6.9990
   chunk 57 optimal weight:   10.0000
   chunk 39 optimal weight:    8.9990
   chunk 15 optimal weight:    9.9990
   overall best weight:    5.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4682 r_free = 0.4682 target = 0.172260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.145952 restraints weight = 8970.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.4389 rms_B_bonded: 4.22
r_work: 0.4276 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.4276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7103
moved from start:          0.4930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.032   5280  Z= 0.381
  Angle     :  0.609  10.767   7140  Z= 0.346
  Chirality :  0.051   0.141    936
  Planarity :  0.002   0.013    888
  Dihedral  :  5.446  15.956    756
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 14.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.43 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  8.33 %
    Allowed  : 19.07 %
    Favored  : 72.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.07 (0.27), residues: 732
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.33 (0.21), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.003   HIS G  50 
 PHE   0.006   0.001   PHE E  94 
 TYR   0.012   0.002   TYR A  39 

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 108
  time to evaluate  : 0.580 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.6774 (mptt)
REVERT: A   58 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.8838 (mmtp)
REVERT: B   61 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8052 (tm-30)
REVERT: C   39 TYR cc_start: 0.6632 (m-80) cc_final: 0.6340 (m-80)
REVERT: D   58 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8656 (mtpp)
REVERT: F   57 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7765 (pm20)
REVERT: F   58 LYS cc_start: 0.9066 (mttt) cc_final: 0.8038 (mmmt)
REVERT: F   97 LYS cc_start: 0.8872 (mmmm) cc_final: 0.8536 (mmmt)
REVERT: G   97 LYS cc_start: 0.7595 (mmmt) cc_final: 0.6894 (mmmm)
REVERT: H   61 GLU cc_start: 0.8418 (tt0) cc_final: 0.8023 (tt0)
REVERT: H   97 LYS cc_start: 0.8088 (mmtm) cc_final: 0.7701 (mmmm)
REVERT: I   97 LYS cc_start: 0.8226 (tppt) cc_final: 0.7892 (mmtm)
REVERT: J   39 TYR cc_start: 0.7180 (m-80) cc_final: 0.6683 (m-80)
REVERT: J   43 LYS cc_start: 0.7432 (mtmm) cc_final: 0.7178 (mmtm)
REVERT: J   97 LYS cc_start: 0.8507 (mmmm) cc_final: 0.8284 (mmmt)
REVERT: K   97 LYS cc_start: 0.7938 (mtmt) cc_final: 0.7718 (mtmm)
  outliers start: 45
  outliers final: 40
  residues processed: 141
  average time/residue: 0.1704
  time to fit residues: 30.9594
Evaluate side-chains
  150 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 106
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   58 LYS
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain F residue   74 VAL
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   64 THR
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   46 GLU
Chi-restraints excluded: chain I residue   64 THR
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   74 VAL
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   64 THR
Chi-restraints excluded: chain J residue   74 VAL
Chi-restraints excluded: chain K residue   37 VAL
Chi-restraints excluded: chain K residue   43 LYS
Chi-restraints excluded: chain K residue   46 GLU
Chi-restraints excluded: chain K residue   72 THR
Chi-restraints excluded: chain K residue   74 VAL
Chi-restraints excluded: chain L residue   48 VAL
Chi-restraints excluded: chain L residue   54 THR
Chi-restraints excluded: chain L residue   74 VAL
Chi-restraints excluded: chain L residue   77 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 9 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 52 optimal weight:    6.9990
   chunk 3 optimal weight:    2.9990
   chunk 39 optimal weight:    6.9990
   chunk 70 optimal weight:    7.9990
   chunk 48 optimal weight:   30.0000
   chunk 25 optimal weight:   10.0000
   chunk 44 optimal weight:    3.9990
   chunk 61 optimal weight:    7.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4694 r_free = 0.4694 target = 0.173073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.146883 restraints weight = 9009.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.4400 rms_B_bonded: 4.23
r_work: 0.4288 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.4288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7096
moved from start:          0.5030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   5280  Z= 0.340
  Angle     :  0.620  11.063   7140  Z= 0.345
  Chirality :  0.050   0.137    936
  Planarity :  0.002   0.012    888
  Dihedral  :  5.360  15.065    756
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 14.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  8.33 %
    Allowed  : 19.07 %
    Favored  : 72.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.09 (0.27), residues: 732
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.35 (0.20), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS G  50 
 PHE   0.006   0.001   PHE J  94 
 TYR   0.009   0.002   TYR C  39 

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 108
  time to evaluate  : 0.611 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 LYS cc_start: 0.7136 (OUTLIER) cc_final: 0.6764 (mptt)
REVERT: A   58 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8315 (mmtp)
REVERT: B   61 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8049 (tm-30)
REVERT: C   39 TYR cc_start: 0.6647 (m-80) cc_final: 0.6344 (m-80)
REVERT: C   97 LYS cc_start: 0.8113 (mmmt) cc_final: 0.7531 (ttpp)
REVERT: D   58 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8664 (mtpp)
REVERT: F   57 GLU cc_start: 0.8433 (mt-10) cc_final: 0.7791 (pm20)
REVERT: F   58 LYS cc_start: 0.9080 (mttt) cc_final: 0.8038 (mmmt)
REVERT: F   97 LYS cc_start: 0.9006 (mmmm) cc_final: 0.8719 (mmmt)
REVERT: G   97 LYS cc_start: 0.7505 (mmmt) cc_final: 0.6831 (mmmm)
REVERT: H   46 GLU cc_start: 0.7456 (pt0) cc_final: 0.6812 (pm20)
REVERT: H   61 GLU cc_start: 0.8387 (tt0) cc_final: 0.7964 (tt0)
REVERT: H   97 LYS cc_start: 0.8079 (mmtm) cc_final: 0.7687 (mmmm)
REVERT: I   97 LYS cc_start: 0.8242 (tppt) cc_final: 0.7901 (mmtm)
REVERT: J   39 TYR cc_start: 0.7144 (m-80) cc_final: 0.6616 (m-80)
REVERT: J   43 LYS cc_start: 0.7477 (mtmm) cc_final: 0.7221 (mmtm)
REVERT: K   97 LYS cc_start: 0.7953 (mtmt) cc_final: 0.7741 (mtmm)
REVERT: L   39 TYR cc_start: 0.6726 (m-80) cc_final: 0.6466 (m-80)
  outliers start: 45
  outliers final: 41
  residues processed: 141
  average time/residue: 0.1656
  time to fit residues: 30.1656
Evaluate side-chains
  152 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 107
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   46 GLU
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   58 LYS
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain F residue   74 VAL
Chi-restraints excluded: chain G residue   44 THR
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   64 THR
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   46 GLU
Chi-restraints excluded: chain I residue   64 THR
Chi-restraints excluded: chain I residue   72 THR
Chi-restraints excluded: chain I residue   74 VAL
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   46 GLU
Chi-restraints excluded: chain J residue   64 THR
Chi-restraints excluded: chain J residue   74 VAL
Chi-restraints excluded: chain K residue   37 VAL
Chi-restraints excluded: chain K residue   43 LYS
Chi-restraints excluded: chain K residue   46 GLU
Chi-restraints excluded: chain K residue   59 THR
Chi-restraints excluded: chain K residue   72 THR
Chi-restraints excluded: chain K residue   74 VAL
Chi-restraints excluded: chain L residue   48 VAL
Chi-restraints excluded: chain L residue   54 THR
Chi-restraints excluded: chain L residue   74 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 6 optimal weight:   30.0000
   chunk 1 optimal weight:    5.9990
   chunk 25 optimal weight:    9.9990
   chunk 24 optimal weight:   30.0000
   chunk 68 optimal weight:    3.9990
   chunk 10 optimal weight:   10.0000
   chunk 13 optimal weight:    0.3980
   chunk 3 optimal weight:   10.0000
   chunk 57 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    3.8788

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

Flipped N/Q/H residues before XYZ refinement:
** A  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4732 r_free = 0.4732 target = 0.175513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.149421 restraints weight = 8962.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.4442 rms_B_bonded: 4.25
r_work: 0.4331 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.4331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7071
moved from start:          0.5059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5280  Z= 0.275
  Angle     :  0.582  10.589   7140  Z= 0.323
  Chirality :  0.050   0.125    936
  Planarity :  0.002   0.011    888
  Dihedral  :  5.101  15.244    756
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 13.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.47 %
    Favored  : 91.53 %
  Rotamer:
    Outliers :  8.33 %
    Allowed  : 19.44 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.05 (0.27), residues: 732
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.32 (0.21), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS G  50 
 PHE   0.006   0.001   PHE J  94 
 TYR   0.010   0.002   TYR A  39 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2504.08 seconds
wall clock time: 45 minutes 23.63 seconds (2723.63 seconds total)