Starting phenix.real_space_refine
on Sun Jun 15 11:31:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u13_41800/06_2025/8u13_41800.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u13_41800/06_2025/8u13_41800.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u13_41800/06_2025/8u13_41800.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u13_41800/06_2025/8u13_41800.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u13_41800/06_2025/8u13_41800.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u13_41800/06_2025/8u13_41800.cif"
  }
  resolution = 3.8
  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=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5925 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     293      5.49       5
     S      25      5.16       5
     C    7139      2.51       5
     N    2408      2.21       5
     O    2958      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 12825
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 661
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "D"
      Number of atoms: 751
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 751
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "H"
      Number of atoms: 737
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
      Conformer: "B"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          bond proxies already assigned to first conformer: 735
    Chain: "I"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 3010
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 3010
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "K"
      Number of atoms: 706
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 88, 702
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 6, 'TRANS': 81}
      Conformer: "B"
        Number of residues, atoms: 88, 702
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 6, 'TRANS': 81}
          bond proxies already assigned to first conformer: 713
    Chain: "C"
      Number of atoms: 836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 836
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "G"
      Number of atoms: 843
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 843
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 5, 'TRANS': 104}
    Chain: "K"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  10617  SG  CYS K  31      27.021  59.998  74.288  1.00394.38           S
  ATOM  10767  SG  CYS K  51      26.391  63.713  73.415  1.00417.10           S
  ATOM  10791  SG  CYS K  54      27.019  62.691  77.048  1.00421.64           S
  ATOM  10508  SG  CYS K  16      19.411  66.329  66.379  1.00424.33           S
  ATOM  10526  SG  CYS K  19      18.344  69.167  64.157  1.00433.92           S
  ATOM  10656  SG  CYS K  36      20.356  66.435  62.624  1.00418.58           S
  ATOM  10678  SG  CYS K  39      21.999  68.761  65.379  1.00418.47           S

  Time building chain proxies: 7.84, per 1000 atoms: 0.61
  Number of scatterers: 12825
  At special positions: 0
  Unit cell: (103.788, 117.146, 117.146, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      25     16.00
     P     293     15.00
     O    2958      8.00
     N    2408      7.00
     C    7139      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    TRANS
      " SER C  11 " - " SER D 123 "
      " SER G  11 " - " SER H 123 "
  Time building additional restraints: 2.87
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 301 "
        pdb="ZN    ZN K 301 " - pdb=" ND1 HIS K  33 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  51 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  54 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  31 "
      pdb="  ZN K 302 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  16 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  19 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  36 "
      Number of angles added : 9


  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1612

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 11 sheets defined
      68.9% alpha, 2.6% beta
      141 base pairs and 245 stacking pairs defined.
    Time for finding SS restraints: 6.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 79
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.756A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.685A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.498A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.528A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 123
    Processing helix  chain 'E' and resid 44 through 56
    Processing helix  chain 'E' and resid 63 through 79
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.657A  pdb=" N   GLY E 132 " --> pdb=" O   ARG E 128 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.933A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.654A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 123
    Processing helix  chain 'K' and resid 36 through 45
    Processing helix  chain 'K' and resid 58 through 68
      removed outlier: 4.417A  pdb=" N   ARG K  68 " --> pdb=" O   TYR K  64 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 73 through 84
    Processing helix  chain 'K' and resid 84 through 91
      removed outlier: 4.140A  pdb=" N   ARG K  91 " --> pdb=" O   GLU K  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 27 through 37
    Processing helix  chain 'C' and resid 46 through 73
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 91 through 98
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 27 through 37
    Processing helix  chain 'G' and resid 46 through 73
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.543A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 91 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.449A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54
      removed outlier: 7.391A  pdb=" N   GLY D  53 " --> pdb=" O   ILE C  78 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.545A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA8, first strand: chain 'F' and resid 97 through 98
      removed outlier: 3.565A  pdb=" N   TYR F  98 " --> pdb=" O   THR C 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'H' and resid 53 through 54
      removed outlier: 7.296A  pdb=" N   GLY H  53 " --> pdb=" O   ILE G  78 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'H' and resid 88 through 89
    Processing sheet with id=AB2, first strand: chain 'K' and resid 27 through 28
      removed outlier: 3.579A  pdb=" N   VAL K  27 " --> pdb=" O   LEU K  35 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LEU K  35 " --> pdb=" O   VAL K  27 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2

    432 hydrogen bonds defined for protein.
    1273 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      359 hydrogen bonds
      714 hydrogen bond angles
      0 basepair planarities
      141 basepair parallelities
      245 stacking parallelities
  Total time for adding SS restraints: 4.70

  Time building geometry restraints manager: 3.47 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2525
        1.33 -     1.45: 4369
        1.45 -     1.57: 6137
        1.57 -     1.69: 584
        1.69 -     1.81: 36
  Bond restraints: 13651
  Sorted by residual:
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.467 -0.045 3.00e-02 1.11e+03 2.24e+00
  bond pdb=" CG  GLU B  63 "
       pdb=" CD  GLU B  63 "
    ideal  model  delta    sigma   weight residual
    1.516  1.480  0.036 2.50e-02 1.60e+03 2.05e+00
  bond pdb=" N   ASP B  24 "
       pdb=" CA  ASP B  24 "
    ideal  model  delta    sigma   weight residual
    1.457  1.475 -0.017 1.29e-02 6.01e+03 1.80e+00
  bond pdb=" CB  ARG F  39 "
       pdb=" CG  ARG F  39 "
    ideal  model  delta    sigma   weight residual
    1.520  1.486  0.034 3.00e-02 1.11e+03 1.32e+00
  bond pdb=" CG1 ILE G  62 "
       pdb=" CD1 ILE G  62 "
    ideal  model  delta    sigma   weight residual
    1.513  1.471  0.042 3.90e-02 6.57e+02 1.17e+00
  ... (remaining 13646 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 19055
        1.60 -     3.20: 559
        3.20 -     4.79: 49
        4.79 -     6.39: 22
        6.39 -     7.99: 7
  Bond angle restraints: 19692
  Sorted by residual:
  angle pdb=" N   GLU B  63 "
        pdb=" CA  GLU B  63 "
        pdb=" CB  GLU B  63 "
      ideal   model   delta    sigma   weight residual
     110.28  116.80   -6.52 1.55e+00 4.16e-01 1.77e+01
  angle pdb=" C   LEU B  62 "
        pdb=" N   GLU B  63 "
        pdb=" CA  GLU B  63 "
      ideal   model   delta    sigma   weight residual
     120.31  114.63    5.68 1.52e+00 4.33e-01 1.40e+01
  angle pdb=" CA  GLU B  63 "
        pdb=" CB  GLU B  63 "
        pdb=" CG  GLU B  63 "
      ideal   model   delta    sigma   weight residual
     114.10  120.77   -6.67 2.00e+00 2.50e-01 1.11e+01
  angle pdb=" C   SER H 112 "
        pdb=" N   GLU H 113 "
        pdb=" CA  GLU H 113 "
      ideal   model   delta    sigma   weight residual
     121.14  115.58    5.56 1.75e+00 3.27e-01 1.01e+01
  angle pdb=" C   GLU E  50 "
        pdb=" CA  GLU E  50 "
        pdb=" CB  GLU E  50 "
      ideal   model   delta    sigma   weight residual
     109.72  115.15   -5.43 1.92e+00 2.71e-01 8.00e+00
  ... (remaining 19687 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.48: 6095
       34.48 -    68.96: 1363
       68.96 -   103.44: 29
      103.44 -   137.92: 0
      137.92 -   172.40: 2
  Dihedral angle restraints: 7489
    sinusoidal: 4990
      harmonic: 2499
  Sorted by residual:
  dihedral pdb=" CA  GLU E  50 "
           pdb=" C   GLU E  50 "
           pdb=" N   ILE E  51 "
           pdb=" CA  ILE E  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.88   28.12     0      5.00e+00 4.00e-02 3.16e+01
  dihedral pdb=" CA  ARG E  63 "
           pdb=" C   ARG E  63 "
           pdb=" N   LYS E  64 "
           pdb=" CA  LYS E  64 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.92  -21.08     0      5.00e+00 4.00e-02 1.78e+01
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   47.60  172.40     1      3.50e+01 8.16e-04 1.56e+01
  ... (remaining 7486 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1866
       0.045 -    0.091: 309
       0.091 -    0.136: 61
       0.136 -    0.181: 4
       0.181 -    0.226: 1
  Chirality restraints: 2241
  Sorted by residual:
  chirality pdb=" CA  GLU E  50 "
            pdb=" N   GLU E  50 "
            pdb=" C   GLU E  50 "
            pdb=" CB  GLU E  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CB  ILE E  51 "
            pdb=" CA  ILE E  51 "
            pdb=" CG1 ILE E  51 "
            pdb=" CG2 ILE E  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.97e-01
  chirality pdb=" CA  TYR E  54 "
            pdb=" N   TYR E  54 "
            pdb=" C   TYR E  54 "
            pdb=" CB  TYR E  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.95e-01
  ... (remaining 2238 not shown)

  Planarity restraints: 1477
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG E 129 "    0.169 9.50e-02 1.11e+02   7.58e-02 3.72e+00
        pdb=" NE  ARG E 129 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  ARG E 129 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG E 129 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG E 129 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU H 113 "    0.008 2.00e-02 2.50e+03   1.67e-02 2.80e+00
        pdb=" CD  GLU H 113 "   -0.029 2.00e-02 2.50e+03
        pdb=" OE1 GLU H 113 "    0.010 2.00e-02 2.50e+03
        pdb=" OE2 GLU H 113 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  48 "    0.022 2.00e-02 2.50e+03   9.15e-03 2.51e+00
        pdb=" N9   DG I  48 "   -0.019 2.00e-02 2.50e+03
        pdb=" C8   DG I  48 "   -0.008 2.00e-02 2.50e+03
        pdb=" N7   DG I  48 "    0.001 2.00e-02 2.50e+03
        pdb=" C5   DG I  48 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I  48 "    0.003 2.00e-02 2.50e+03
        pdb=" O6   DG I  48 "    0.006 2.00e-02 2.50e+03
        pdb=" N1   DG I  48 "    0.003 2.00e-02 2.50e+03
        pdb=" C2   DG I  48 "   -0.002 2.00e-02 2.50e+03
        pdb=" N2   DG I  48 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3   DG I  48 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DG I  48 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1474 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.70: 483
        2.70 -     3.25: 12231
        3.25 -     3.80: 25255
        3.80 -     4.35: 30112
        4.35 -     4.90: 42904
  Nonbonded interactions: 110985
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 106 "
            pdb=" NH2 ARG A 131 "
     model   vdw
     2.145 3.120
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.153 2.496
  nonbonded pdb=" OE1 GLU D  71 "
            pdb=" OH  TYR C  39 "
     model   vdw
     2.180 3.040
  nonbonded pdb=" OD2 ASP D  68 "
            pdb=" OH  TYR F  98 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" NH2 ARG E  42 "
            pdb=" OP1  DG J  -5 "
     model   vdw
     2.249 3.120
  ... (remaining 110980 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 21 through 102)
  selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ 
e C or name O ))))
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 11 through 119)
}
ncs_group {
  reference = (chain 'D' and (resid 31 through 107 or resid 109 through 123))
  selection = (chain 'H' and (resid 31 through 107 or resid 109 through 123))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.110
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     37.140
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.060
  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:             0.010
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  13661  Z= 0.163
  Angle     :  0.641   7.991  19707  Z= 0.368
  Chirality :  0.036   0.226   2241
  Planarity :  0.005   0.076   1475
  Dihedral  : 27.097 172.397   5871
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  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:  0.79 (0.28), residues: 842
  helix:  1.16 (0.21), residues: 580
  sheet:  None (None), residues: 0
  loop : -0.84 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K  61 
 HIS   0.004   0.001   HIS K  65 
 PHE   0.009   0.001   PHE G  25 
 TYR   0.021   0.002   TYR B  88 
 ARG   0.015   0.001   ARG C  99 

Details of bonding type rmsd
  link_TRANS           : bond        0.00262 (    2)
  link_TRANS           : angle       0.86790 (    6)
  hydrogen bonds       : bond        0.10747 (  791)
  hydrogen bonds       : angle       4.26585 ( 1987)
  metal coordination   : bond        0.00645 (    8)
  metal coordination   : angle       3.29907 (    9)
  covalent geometry    : bond        0.00351 (13651)
  covalent geometry    : angle       0.63756 (19692)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  347 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 347
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7092 (mt-10)
REVERT: A  125 GLN cc_start: 0.9259 (mp10) cc_final: 0.8940 (mp10)
REVERT: B   23 ARG cc_start: 0.8496 (mmp80) cc_final: 0.8126 (mmp80)
REVERT: B   25 ASN cc_start: 0.8800 (m110) cc_final: 0.8440 (m110)
REVERT: B   49 LEU cc_start: 0.9349 (pt) cc_final: 0.8356 (pt)
REVERT: B   50 ILE cc_start: 0.9347 (tp) cc_final: 0.9047 (tp)
REVERT: B   88 TYR cc_start: 0.8364 (m-80) cc_final: 0.8101 (m-80)
REVERT: D   34 LYS cc_start: 0.8971 (mptt) cc_final: 0.8688 (mmtm)
REVERT: D   57 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8600 (mmmm)
REVERT: D  105 GLU cc_start: 0.8261 (tp30) cc_final: 0.7678 (tp30)
REVERT: D  109 HIS cc_start: 0.8834 (m170) cc_final: 0.8628 (m170)
REVERT: D  120 LYS cc_start: 0.9231 (tttp) cc_final: 0.8842 (ttmm)
REVERT: E   53 ARG cc_start: 0.8788 (tmt-80) cc_final: 0.8330 (tmt-80)
REVERT: E   54 TYR cc_start: 0.7863 (m-80) cc_final: 0.7639 (m-80)
REVERT: E   57 SER cc_start: 0.7526 (p) cc_final: 0.6916 (p)
REVERT: E   59 GLU cc_start: 0.8178 (pm20) cc_final: 0.7882 (pm20)
REVERT: E   60 LEU cc_start: 0.8664 (mm) cc_final: 0.8015 (mm)
REVERT: E   68 GLN cc_start: 0.8675 (pp30) cc_final: 0.8321 (pp30)
REVERT: E   81 ASP cc_start: 0.8075 (m-30) cc_final: 0.7859 (m-30)
REVERT: E   92 LEU cc_start: 0.9668 (mt) cc_final: 0.9462 (mt)
REVERT: E  120 MET cc_start: 0.7832 (mtt) cc_final: 0.7405 (mtp)
REVERT: E  125 GLN cc_start: 0.8554 (mp10) cc_final: 0.8001 (mp10)
REVERT: F   49 LEU cc_start: 0.8913 (mm) cc_final: 0.8215 (mm)
REVERT: H   68 ASP cc_start: 0.8399 (t70) cc_final: 0.8061 (t0)
REVERT: H   83 TYR cc_start: 0.8409 (m-10) cc_final: 0.7681 (m-10)
REVERT: C   84 GLN cc_start: 0.9172 (tm-30) cc_final: 0.8811 (tp-100)
REVERT: G   61 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7763 (mm-30)
REVERT: G   68 ASN cc_start: 0.8959 (m-40) cc_final: 0.8649 (m-40)
REVERT: G  104 GLN cc_start: 0.8967 (mp10) cc_final: 0.8679 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 347
  average time/residue: 0.2950
  time to fit residues: 139.2908
Evaluate side-chains
  289 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 289
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 82 optimal weight:   30.0000
   chunk 45 optimal weight:    5.9990
   chunk 28 optimal weight:    9.9990
   chunk 55 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 85 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 63 optimal weight:    6.9990
   chunk 98 optimal weight:   20.0000
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
B  93 GLN
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  67 ASN
H  82 HIS
H  84 ASN
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  89 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.074371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.049811 restraints weight = 78059.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.051390 restraints weight = 32996.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.052344 restraints weight = 21032.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2894
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2894 r_free = 0.2894    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2893 r_free = 0.2893    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2893
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  13661  Z= 0.285
  Angle     :  0.695   8.479  19707  Z= 0.394
  Chirality :  0.039   0.170   2241
  Planarity :  0.005   0.037   1475
  Dihedral  : 30.325 173.205   4161
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 15.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 17.47 %
    Favored  : 79.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.28), residues: 842
  helix:  1.15 (0.21), residues: 587
  sheet:  None (None), residues: 0
  loop : -1.14 (0.38), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP K  77 
 HIS   0.007   0.001   HIS B  75 
 PHE   0.018   0.002   PHE H  65 
 TYR   0.023   0.002   TYR F  98 
 ARG   0.017   0.001   ARG G  29 

Details of bonding type rmsd
  link_TRANS           : bond        0.00154 (    2)
  link_TRANS           : angle       0.35454 (    6)
  hydrogen bonds       : bond        0.05788 (  791)
  hydrogen bonds       : angle       3.88525 ( 1987)
  metal coordination   : bond        0.00897 (    8)
  metal coordination   : angle       4.60886 (    9)
  covalent geometry    : bond        0.00643 (13651)
  covalent geometry    : angle       0.68868 (19692)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 283
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7128 (mp0)
REVERT: A  125 GLN cc_start: 0.9444 (mp10) cc_final: 0.8935 (mp10)
REVERT: B   23 ARG cc_start: 0.8656 (mmp80) cc_final: 0.8219 (mmp80)
REVERT: B   25 ASN cc_start: 0.8874 (m110) cc_final: 0.8342 (m110)
REVERT: B   63 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8352 (mp0)
REVERT: B   88 TYR cc_start: 0.8879 (m-10) cc_final: 0.8495 (m-80)
REVERT: D   34 LYS cc_start: 0.9024 (mptt) cc_final: 0.8777 (mmtm)
REVERT: D   57 LYS cc_start: 0.9094 (mmtt) cc_final: 0.8849 (mmmm)
REVERT: D   79 ARG cc_start: 0.8339 (mtm110) cc_final: 0.7825 (mtm110)
REVERT: D  105 GLU cc_start: 0.8546 (tp30) cc_final: 0.7295 (tp30)
REVERT: D  109 HIS cc_start: 0.9204 (m170) cc_final: 0.8925 (m170)
REVERT: D  120 LYS cc_start: 0.9261 (tttp) cc_final: 0.8893 (ttmm)
REVERT: E   60 LEU cc_start: 0.8926 (mm) cc_final: 0.8425 (mm)
REVERT: E   68 GLN cc_start: 0.8975 (pp30) cc_final: 0.8737 (pp30)
REVERT: E   81 ASP cc_start: 0.8272 (m-30) cc_final: 0.8024 (m-30)
REVERT: E   97 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8116 (mt-10)
REVERT: E  120 MET cc_start: 0.7948 (mtt) cc_final: 0.7110 (mtt)
REVERT: F   88 TYR cc_start: 0.8742 (m-10) cc_final: 0.7738 (m-10)
REVERT: H   68 ASP cc_start: 0.9104 (t70) cc_final: 0.8716 (t0)
REVERT: H   83 TYR cc_start: 0.8505 (m-10) cc_final: 0.7703 (m-10)
REVERT: H   86 ARG cc_start: 0.9082 (tpp80) cc_final: 0.8844 (tpp80)
REVERT: H  120 LYS cc_start: 0.9374 (ttmt) cc_final: 0.8858 (tptt)
REVERT: C   24 GLN cc_start: 0.8596 (pm20) cc_final: 0.8298 (pm20)
REVERT: C   78 ILE cc_start: 0.9026 (mm) cc_final: 0.8786 (mm)
REVERT: C   84 GLN cc_start: 0.9297 (tm-30) cc_final: 0.8831 (tp-100)
REVERT: C   91 GLU cc_start: 0.9275 (tp30) cc_final: 0.8914 (tp30)
REVERT: C   92 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8153 (mp0)
REVERT: G  104 GLN cc_start: 0.9264 (mp10) cc_final: 0.8849 (mp10)
  outliers start: 25
  outliers final: 15
  residues processed: 294
  average time/residue: 0.3052
  time to fit residues: 121.3958
Evaluate side-chains
  285 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 269
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   69 ILE
Chi-restraints excluded: chain H residue   82 HIS
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain G residue  107 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 40 optimal weight:    0.5980
   chunk 69 optimal weight:    6.9990
   chunk 18 optimal weight:    0.8980
   chunk 64 optimal weight:    7.9990
   chunk 38 optimal weight:    0.8980
   chunk 77 optimal weight:    5.9990
   chunk 105 optimal weight:    0.6980
   chunk 86 optimal weight:   30.0000
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  82 HIS
K  41 GLN
C  73 ASN
C  84 GLN
C  89 ASN
** G  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.077013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.052895 restraints weight = 64595.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.054398 restraints weight = 30080.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.055356 restraints weight = 20014.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2980
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2980 r_free = 0.2980    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2980 r_free = 0.2980    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2980
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.1841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13661  Z= 0.161
  Angle     :  0.637   9.305  19707  Z= 0.363
  Chirality :  0.036   0.178   2241
  Planarity :  0.004   0.037   1475
  Dihedral  : 30.006 173.276   4161
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 20.91 %
    Favored  : 75.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.28), residues: 842
  helix:  1.30 (0.21), residues: 584
  sheet:  None (None), residues: 0
  loop : -1.13 (0.38), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K  77 
 HIS   0.024   0.002   HIS H  82 
 PHE   0.026   0.002   PHE E  67 
 TYR   0.025   0.002   TYR G  57 
 ARG   0.005   0.001   ARG E  52 

Details of bonding type rmsd
  link_TRANS           : bond        0.00047 (    2)
  link_TRANS           : angle       0.20689 (    6)
  hydrogen bonds       : bond        0.04287 (  791)
  hydrogen bonds       : angle       3.52711 ( 1987)
  metal coordination   : bond        0.00643 (    8)
  metal coordination   : angle       4.48512 (    9)
  covalent geometry    : bond        0.00349 (13651)
  covalent geometry    : angle       0.63035 (19692)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  337 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 311
  time to evaluate  : 0.944 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7253 (mp0)
REVERT: A   93 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7997 (tp40)
REVERT: A  125 GLN cc_start: 0.9328 (mp10) cc_final: 0.8894 (mp10)
REVERT: B   23 ARG cc_start: 0.8677 (mmp80) cc_final: 0.8092 (mmp80)
REVERT: B   63 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8378 (mp0)
REVERT: B   84 MET cc_start: 0.8620 (mmm) cc_final: 0.8301 (tpp)
REVERT: B   88 TYR cc_start: 0.8735 (m-10) cc_final: 0.8450 (m-80)
REVERT: D   34 LYS cc_start: 0.9001 (mptt) cc_final: 0.8715 (mmtm)
REVERT: D   57 LYS cc_start: 0.9052 (mmtt) cc_final: 0.8618 (mmmm)
REVERT: D   79 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7774 (mtm110)
REVERT: D  105 GLU cc_start: 0.8478 (tp30) cc_final: 0.7269 (tp30)
REVERT: D  109 HIS cc_start: 0.9145 (m170) cc_final: 0.8859 (m170)
REVERT: D  120 LYS cc_start: 0.9278 (tttp) cc_final: 0.8882 (ttmm)
REVERT: E   60 LEU cc_start: 0.8846 (mm) cc_final: 0.8361 (mm)
REVERT: E   68 GLN cc_start: 0.8822 (pp30) cc_final: 0.8499 (pp30)
REVERT: E   81 ASP cc_start: 0.8235 (m-30) cc_final: 0.7946 (m-30)
REVERT: E   97 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8195 (mt-10)
REVERT: F   43 VAL cc_start: 0.8842 (t) cc_final: 0.8515 (p)
REVERT: F   88 TYR cc_start: 0.8574 (m-10) cc_final: 0.7398 (m-10)
REVERT: H   68 ASP cc_start: 0.8998 (t70) cc_final: 0.8684 (t0)
REVERT: H   83 TYR cc_start: 0.8341 (m-10) cc_final: 0.7440 (m-10)
REVERT: H   86 ARG cc_start: 0.9082 (tpp80) cc_final: 0.8767 (tpp80)
REVERT: H  120 LYS cc_start: 0.9354 (ttmt) cc_final: 0.8835 (tptt)
REVERT: C   78 ILE cc_start: 0.8975 (mm) cc_final: 0.8741 (mm)
REVERT: C   84 GLN cc_start: 0.9360 (OUTLIER) cc_final: 0.9143 (tm-30)
REVERT: C   91 GLU cc_start: 0.9302 (tp30) cc_final: 0.8891 (tp30)
REVERT: C   92 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8009 (mp0)
REVERT: G   56 GLU cc_start: 0.9131 (OUTLIER) cc_final: 0.8543 (tt0)
REVERT: G   90 ASP cc_start: 0.8688 (t0) cc_final: 0.8100 (t0)
REVERT: G  104 GLN cc_start: 0.9145 (mp10) cc_final: 0.8684 (mp10)
  outliers start: 26
  outliers final: 10
  residues processed: 315
  average time/residue: 0.3032
  time to fit residues: 129.6008
Evaluate side-chains
  300 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 285
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain D residue   79 ARG
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain H residue   82 HIS
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   84 GLN
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   56 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 59 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9990
   chunk 90 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 86 optimal weight:   30.0000
   chunk 56 optimal weight:    6.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  82 HIS
C  73 ASN
C  89 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.076325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.052589 restraints weight = 58819.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.054070 restraints weight = 28318.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.055029 restraints weight = 19109.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2974
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2974 r_free = 0.2974    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2974 r_free = 0.2974    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2974
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  13661  Z= 0.178
  Angle     :  0.646  12.498  19707  Z= 0.365
  Chirality :  0.036   0.181   2241
  Planarity :  0.004   0.038   1475
  Dihedral  : 29.972 172.843   4161
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 21.73 %
    Favored  : 74.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.28), residues: 842
  helix:  1.24 (0.21), residues: 585
  sheet:  None (None), residues: 0
  loop : -1.18 (0.38), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP K  61 
 HIS   0.008   0.001   HIS H  82 
 PHE   0.019   0.002   PHE H  65 
 TYR   0.022   0.002   TYR G  57 
 ARG   0.006   0.000   ARG D  92 

Details of bonding type rmsd
  link_TRANS           : bond        0.00059 (    2)
  link_TRANS           : angle       0.21516 (    6)
  hydrogen bonds       : bond        0.04435 (  791)
  hydrogen bonds       : angle       3.60239 ( 1987)
  metal coordination   : bond        0.00591 (    8)
  metal coordination   : angle       4.65613 (    9)
  covalent geometry    : bond        0.00396 (13651)
  covalent geometry    : angle       0.63896 (19692)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 289
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7487 (mp0)
REVERT: A   93 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8169 (tp40)
REVERT: A  125 GLN cc_start: 0.9291 (mp10) cc_final: 0.8839 (mp10)
REVERT: B   23 ARG cc_start: 0.8692 (mmp80) cc_final: 0.8196 (mmp80)
REVERT: B   63 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8344 (mp0)
REVERT: B   77 LYS cc_start: 0.9252 (mmtt) cc_final: 0.8470 (mmtt)
REVERT: B   84 MET cc_start: 0.8649 (mmm) cc_final: 0.8186 (tpp)
REVERT: B   88 TYR cc_start: 0.8718 (m-10) cc_final: 0.8403 (m-80)
REVERT: D   34 LYS cc_start: 0.9027 (mptt) cc_final: 0.8726 (mmtm)
REVERT: D   57 LYS cc_start: 0.9089 (mmtt) cc_final: 0.8646 (mmmm)
REVERT: D   79 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7802 (mtm110)
REVERT: D   92 ARG cc_start: 0.8703 (ttp80) cc_final: 0.8032 (ttp80)
REVERT: D  105 GLU cc_start: 0.8521 (tp30) cc_final: 0.7302 (tp30)
REVERT: D  109 HIS cc_start: 0.9192 (m170) cc_final: 0.8871 (m170)
REVERT: D  120 LYS cc_start: 0.9286 (tttp) cc_final: 0.8895 (ttmm)
REVERT: E   52 ARG cc_start: 0.8822 (mtm-85) cc_final: 0.8588 (mtm-85)
REVERT: E   60 LEU cc_start: 0.8903 (mm) cc_final: 0.8441 (mm)
REVERT: E   68 GLN cc_start: 0.8892 (pp30) cc_final: 0.8645 (pp30)
REVERT: E   81 ASP cc_start: 0.8133 (m-30) cc_final: 0.7858 (m-30)
REVERT: E  109 LEU cc_start: 0.9628 (OUTLIER) cc_final: 0.9295 (mp)
REVERT: E  120 MET cc_start: 0.7971 (mtp) cc_final: 0.7540 (mtp)
REVERT: F   43 VAL cc_start: 0.8953 (t) cc_final: 0.8600 (p)
REVERT: F   88 TYR cc_start: 0.8567 (m-10) cc_final: 0.7502 (m-10)
REVERT: H   33 ARG cc_start: 0.8229 (mmt180) cc_final: 0.7595 (tpp80)
REVERT: H   68 ASP cc_start: 0.9028 (t70) cc_final: 0.8703 (t0)
REVERT: H   83 TYR cc_start: 0.8331 (m-10) cc_final: 0.7343 (m-10)
REVERT: H   86 ARG cc_start: 0.9100 (tpp80) cc_final: 0.8800 (tpp80)
REVERT: H   92 ARG cc_start: 0.9178 (ptm-80) cc_final: 0.8849 (ptm160)
REVERT: H  120 LYS cc_start: 0.9366 (ttmt) cc_final: 0.8860 (tptt)
REVERT: C   38 ASN cc_start: 0.8245 (t0) cc_final: 0.8037 (t0)
REVERT: C   84 GLN cc_start: 0.9351 (tm-30) cc_final: 0.8930 (tp-100)
REVERT: C   91 GLU cc_start: 0.9347 (tp30) cc_final: 0.8913 (tp30)
REVERT: C   92 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8054 (mp0)
REVERT: G   51 LEU cc_start: 0.9496 (tp) cc_final: 0.9163 (tt)
REVERT: G   56 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8957 (tt0)
REVERT: G   90 ASP cc_start: 0.8845 (t0) cc_final: 0.8443 (t0)
REVERT: G  104 GLN cc_start: 0.9180 (mp10) cc_final: 0.8739 (mp10)
  outliers start: 26
  outliers final: 9
  residues processed: 299
  average time/residue: 0.2959
  time to fit residues: 120.2754
Evaluate side-chains
  294 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 280
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain D residue   79 ARG
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   56 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 72 optimal weight:    6.9990
   chunk 6 optimal weight:    2.9990
   chunk 79 optimal weight:   10.0000
   chunk 25 optimal weight:    7.9990
   chunk 44 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 60 optimal weight:    6.9990
   chunk 38 optimal weight:    0.8980
   chunk 82 optimal weight:   30.0000
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.076229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.051917 restraints weight = 91892.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.053681 restraints weight = 35562.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.054803 restraints weight = 21642.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2967
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2967 r_free = 0.2967    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2967 r_free = 0.2967    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2967
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.2297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  13661  Z= 0.180
  Angle     :  0.644  12.198  19707  Z= 0.364
  Chirality :  0.037   0.181   2241
  Planarity :  0.004   0.049   1475
  Dihedral  : 29.945 172.495   4161
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 22.97 %
    Favored  : 72.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.28), residues: 842
  helix:  1.25 (0.21), residues: 584
  sheet:  None (None), residues: 0
  loop : -1.19 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K  61 
 HIS   0.004   0.001   HIS B  75 
 PHE   0.015   0.001   PHE H  65 
 TYR   0.023   0.002   TYR H  40 
 ARG   0.005   0.000   ARG K  63 

Details of bonding type rmsd
  link_TRANS           : bond        0.00078 (    2)
  link_TRANS           : angle       0.23450 (    6)
  hydrogen bonds       : bond        0.04397 (  791)
  hydrogen bonds       : angle       3.55985 ( 1987)
  metal coordination   : bond        0.00594 (    8)
  metal coordination   : angle       4.27327 (    9)
  covalent geometry    : bond        0.00404 (13651)
  covalent geometry    : angle       0.63755 (19692)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  328 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 297
  time to evaluate  : 0.783 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.9445 (mm) cc_final: 0.9231 (mm)
REVERT: A   93 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8231 (tp40)
REVERT: A  125 GLN cc_start: 0.9288 (mp10) cc_final: 0.8770 (mp10)
REVERT: B   23 ARG cc_start: 0.8704 (mmp80) cc_final: 0.8201 (mmp80)
REVERT: B   49 LEU cc_start: 0.9326 (pt) cc_final: 0.8922 (pt)
REVERT: B   77 LYS cc_start: 0.9244 (mmtt) cc_final: 0.8490 (mmtt)
REVERT: B   88 TYR cc_start: 0.8697 (m-10) cc_final: 0.8411 (m-80)
REVERT: D   34 LYS cc_start: 0.9010 (mptt) cc_final: 0.8708 (mmtm)
REVERT: D   57 LYS cc_start: 0.9097 (mmtt) cc_final: 0.8639 (mmmm)
REVERT: D   59 MET cc_start: 0.9301 (tpp) cc_final: 0.9040 (tpp)
REVERT: D   76 GLU cc_start: 0.9250 (tp30) cc_final: 0.9042 (tp30)
REVERT: D   79 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7724 (mtm110)
REVERT: D   92 ARG cc_start: 0.8720 (ttp80) cc_final: 0.8032 (ttp80)
REVERT: D  105 GLU cc_start: 0.8485 (tp30) cc_final: 0.7333 (tp30)
REVERT: D  120 LYS cc_start: 0.9278 (tttp) cc_final: 0.8909 (ttmm)
REVERT: E   60 LEU cc_start: 0.8910 (mm) cc_final: 0.8295 (mm)
REVERT: E   68 GLN cc_start: 0.8926 (pp30) cc_final: 0.8649 (pp30)
REVERT: E   81 ASP cc_start: 0.8092 (m-30) cc_final: 0.7823 (m-30)
REVERT: E   97 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8199 (mt-10)
REVERT: E  109 LEU cc_start: 0.9641 (OUTLIER) cc_final: 0.9297 (mp)
REVERT: E  120 MET cc_start: 0.8055 (mtp) cc_final: 0.7576 (mtp)
REVERT: E  133 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7302 (pm20)
REVERT: F   43 VAL cc_start: 0.9014 (t) cc_final: 0.8699 (p)
REVERT: F   88 TYR cc_start: 0.8567 (m-10) cc_final: 0.7595 (m-10)
REVERT: H   68 ASP cc_start: 0.9016 (t70) cc_final: 0.8736 (t0)
REVERT: H   83 TYR cc_start: 0.8352 (m-10) cc_final: 0.7216 (m-10)
REVERT: H   86 ARG cc_start: 0.9076 (tpp80) cc_final: 0.8797 (tpp80)
REVERT: H  120 LYS cc_start: 0.9362 (ttmt) cc_final: 0.8855 (tptt)
REVERT: K   35 LEU cc_start: 0.6731 (pt) cc_final: 0.6362 (pp)
REVERT: C   38 ASN cc_start: 0.8264 (t0) cc_final: 0.8041 (t0)
REVERT: C   84 GLN cc_start: 0.9315 (tm-30) cc_final: 0.8492 (tm-30)
REVERT: C   91 GLU cc_start: 0.9365 (tp30) cc_final: 0.8922 (tp30)
REVERT: C   92 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8081 (mp0)
REVERT: G   90 ASP cc_start: 0.8897 (t0) cc_final: 0.8645 (t0)
REVERT: G  104 GLN cc_start: 0.9176 (mp10) cc_final: 0.8716 (mp10)
  outliers start: 31
  outliers final: 17
  residues processed: 307
  average time/residue: 0.2947
  time to fit residues: 122.8734
Evaluate side-chains
  306 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 285
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain D residue   79 ARG
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain H residue  106 LEU
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   56 GLU
Chi-restraints excluded: chain G residue  115 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 85 optimal weight:    6.9990
   chunk 83 optimal weight:    8.9990
   chunk 106 optimal weight:    0.9980
   chunk 58 optimal weight:    6.9990
   chunk 37 optimal weight:    7.9990
   chunk 25 optimal weight:    3.9990
   chunk 63 optimal weight:    6.9990
   chunk 76 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 32 optimal weight:    0.7980
   overall best weight:    2.7586

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

Flipped N/Q/H residues before XYZ refinement:
E  55 GLN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  73 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.074715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.050425 restraints weight = 83579.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.052101 restraints weight = 34249.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.053155 restraints weight = 21422.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2917
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2917 r_free = 0.2917    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2917 r_free = 0.2917    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2917
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.2507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057  13661  Z= 0.245
  Angle     :  0.678  12.377  19707  Z= 0.383
  Chirality :  0.038   0.171   2241
  Planarity :  0.005   0.043   1475
  Dihedral  : 30.081 172.824   4161
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 14.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 25.31 %
    Favored  : 69.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.28), residues: 842
  helix:  1.27 (0.21), residues: 584
  sheet:  None (None), residues: 0
  loop : -1.21 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K  61 
 HIS   0.006   0.001   HIS B  75 
 PHE   0.013   0.002   PHE H  65 
 TYR   0.026   0.002   TYR G  57 
 ARG   0.006   0.001   ARG H  33 

Details of bonding type rmsd
  link_TRANS           : bond        0.00151 (    2)
  link_TRANS           : angle       0.30904 (    6)
  hydrogen bonds       : bond        0.05068 (  791)
  hydrogen bonds       : angle       3.71201 ( 1987)
  metal coordination   : bond        0.00772 (    8)
  metal coordination   : angle       4.03510 (    9)
  covalent geometry    : bond        0.00554 (13651)
  covalent geometry    : angle       0.67263 (19692)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 282
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.8941 (ttpt) cc_final: 0.8716 (ttpt)
REVERT: A   93 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8319 (tp40)
REVERT: A  125 GLN cc_start: 0.9296 (mp10) cc_final: 0.8797 (mp10)
REVERT: B   25 ASN cc_start: 0.8941 (m110) cc_final: 0.8437 (m110)
REVERT: B   77 LYS cc_start: 0.9237 (mmtt) cc_final: 0.8965 (mmtt)
REVERT: B   88 TYR cc_start: 0.8768 (m-10) cc_final: 0.8508 (m-80)
REVERT: D   34 LYS cc_start: 0.8997 (mptt) cc_final: 0.8708 (mmtm)
REVERT: D   57 LYS cc_start: 0.9136 (mmtt) cc_final: 0.8690 (mmmm)
REVERT: D   76 GLU cc_start: 0.9274 (tp30) cc_final: 0.9001 (tp30)
REVERT: D   79 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7701 (mtm110)
REVERT: D   92 ARG cc_start: 0.8829 (ttp80) cc_final: 0.7938 (ttp80)
REVERT: D  105 GLU cc_start: 0.8612 (tp30) cc_final: 0.7534 (tp30)
REVERT: D  120 LYS cc_start: 0.9287 (tttp) cc_final: 0.8930 (ttmm)
REVERT: E   60 LEU cc_start: 0.8850 (mm) cc_final: 0.8257 (mm)
REVERT: E   68 GLN cc_start: 0.9001 (pp30) cc_final: 0.8656 (pp30)
REVERT: E   81 ASP cc_start: 0.8133 (m-30) cc_final: 0.7854 (m-30)
REVERT: E   97 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8039 (mt-10)
REVERT: E  109 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9215 (mp)
REVERT: E  120 MET cc_start: 0.8097 (mtp) cc_final: 0.7579 (mtp)
REVERT: F   43 VAL cc_start: 0.9113 (t) cc_final: 0.8816 (p)
REVERT: F   88 TYR cc_start: 0.8606 (m-10) cc_final: 0.7530 (m-10)
REVERT: H   68 ASP cc_start: 0.9075 (t70) cc_final: 0.8736 (t0)
REVERT: H   83 TYR cc_start: 0.8334 (m-10) cc_final: 0.7115 (m-10)
REVERT: H   86 ARG cc_start: 0.9084 (tpp80) cc_final: 0.8844 (tpp80)
REVERT: H  120 LYS cc_start: 0.9362 (ttmt) cc_final: 0.8850 (tptt)
REVERT: C   38 ASN cc_start: 0.8335 (t0) cc_final: 0.8086 (t0)
REVERT: C   84 GLN cc_start: 0.9326 (tm-30) cc_final: 0.9017 (tm-30)
REVERT: C   91 GLU cc_start: 0.9374 (tp30) cc_final: 0.8897 (tp30)
REVERT: C   92 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8129 (mp0)
REVERT: G   90 ASP cc_start: 0.8857 (t0) cc_final: 0.8627 (t0)
REVERT: G  104 GLN cc_start: 0.9216 (mp10) cc_final: 0.8730 (mp10)
  outliers start: 36
  outliers final: 17
  residues processed: 294
  average time/residue: 0.2856
  time to fit residues: 114.8372
Evaluate side-chains
  285 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 265
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain D residue   79 ARG
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain G residue   87 ILE
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  107 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 69 optimal weight:    6.9990
   chunk 17 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 85 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 99 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
D  47 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 109 HIS
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 112 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.075244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.050534 restraints weight = 84554.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.052237 restraints weight = 35043.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.053295 restraints weight = 22033.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2931
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2931 r_free = 0.2931    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2931 r_free = 0.2931    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2931
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.2569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  13661  Z= 0.205
  Angle     :  0.682  13.625  19707  Z= 0.380
  Chirality :  0.038   0.189   2241
  Planarity :  0.004   0.042   1475
  Dihedral  : 30.028 172.776   4161
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 27.37 %
    Favored  : 68.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.28), residues: 842
  helix:  1.24 (0.21), residues: 590
  sheet:  None (None), residues: 0
  loop : -1.32 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K  61 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.025   0.002   PHE E  67 
 TYR   0.024   0.002   TYR H  40 
 ARG   0.005   0.000   ARG C  99 

Details of bonding type rmsd
  link_TRANS           : bond        0.00100 (    2)
  link_TRANS           : angle       0.27971 (    6)
  hydrogen bonds       : bond        0.04599 (  791)
  hydrogen bonds       : angle       3.61788 ( 1987)
  metal coordination   : bond        0.00648 (    8)
  metal coordination   : angle       4.01552 (    9)
  covalent geometry    : bond        0.00464 (13651)
  covalent geometry    : angle       0.67665 (19692)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  321 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 288
  time to evaluate  : 1.031 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.7279 (mt-10) cc_final: 0.6630 (mt-10)
REVERT: A   93 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8292 (tp40)
REVERT: A  105 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8413 (mm-30)
REVERT: B   25 ASN cc_start: 0.8912 (m110) cc_final: 0.8595 (m110)
REVERT: D   34 LYS cc_start: 0.9032 (mptt) cc_final: 0.8704 (mmtm)
REVERT: D   57 LYS cc_start: 0.9114 (mmtt) cc_final: 0.8674 (mmmm)
REVERT: D   59 MET cc_start: 0.9281 (tpp) cc_final: 0.8988 (tpp)
REVERT: D   76 GLU cc_start: 0.9268 (tp30) cc_final: 0.8912 (tp30)
REVERT: D   79 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7798 (mtm110)
REVERT: D   92 ARG cc_start: 0.8840 (ttp80) cc_final: 0.7992 (ttp80)
REVERT: D   96 THR cc_start: 0.9566 (m) cc_final: 0.9345 (p)
REVERT: D  105 GLU cc_start: 0.8602 (tp30) cc_final: 0.7642 (tp30)
REVERT: D  120 LYS cc_start: 0.9287 (tttp) cc_final: 0.8921 (ttmm)
REVERT: E   60 LEU cc_start: 0.8719 (mm) cc_final: 0.8004 (mm)
REVERT: E   68 GLN cc_start: 0.8988 (pp30) cc_final: 0.8657 (pp30)
REVERT: E   81 ASP cc_start: 0.8092 (m-30) cc_final: 0.7823 (m-30)
REVERT: E   97 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7933 (mt-10)
REVERT: E  109 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9199 (mp)
REVERT: E  120 MET cc_start: 0.8098 (mtp) cc_final: 0.7574 (mtp)
REVERT: F   43 VAL cc_start: 0.8949 (t) cc_final: 0.8648 (p)
REVERT: F   88 TYR cc_start: 0.8596 (m-10) cc_final: 0.7540 (m-10)
REVERT: H   68 ASP cc_start: 0.9052 (t70) cc_final: 0.8704 (t0)
REVERT: H   83 TYR cc_start: 0.8392 (m-10) cc_final: 0.7206 (m-10)
REVERT: H   86 ARG cc_start: 0.9099 (tpp80) cc_final: 0.8830 (tpp80)
REVERT: H   93 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8650 (mm-30)
REVERT: H  101 LEU cc_start: 0.9365 (mt) cc_final: 0.9140 (mm)
REVERT: H  120 LYS cc_start: 0.9378 (ttmt) cc_final: 0.8874 (tptt)
REVERT: C   38 ASN cc_start: 0.8211 (t0) cc_final: 0.7918 (t0)
REVERT: C   84 GLN cc_start: 0.9261 (tm-30) cc_final: 0.8934 (tm-30)
REVERT: C   91 GLU cc_start: 0.9376 (tp30) cc_final: 0.8918 (tp30)
REVERT: C   92 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8171 (mp0)
REVERT: G  104 GLN cc_start: 0.9235 (mp10) cc_final: 0.8778 (mp10)
  outliers start: 33
  outliers final: 20
  residues processed: 296
  average time/residue: 0.2788
  time to fit residues: 112.9492
Evaluate side-chains
  300 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 276
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain D residue   79 ARG
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   63 LEU
Chi-restraints excluded: chain G residue  100 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 48 optimal weight:    0.3980
   chunk 81 optimal weight:    0.0770
   chunk 49 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 93 optimal weight:    0.8980
   chunk 69 optimal weight:    5.9990
   chunk 24 optimal weight:    0.0470
   chunk 95 optimal weight:    0.8980
   chunk 68 optimal weight:    6.9990
   chunk 53 optimal weight:   10.0000
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.4636

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  73 ASN
G 112 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.078364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.054301 restraints weight = 106245.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.056082 restraints weight = 38328.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.057282 restraints weight = 22470.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3024
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3024
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.2798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13661  Z= 0.158
  Angle     :  0.666  12.251  19707  Z= 0.374
  Chirality :  0.037   0.205   2241
  Planarity :  0.004   0.045   1475
  Dihedral  : 29.719 170.682   4161
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 27.79 %
    Favored  : 68.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.28), residues: 842
  helix:  1.25 (0.21), residues: 583
  sheet:  None (None), residues: 0
  loop : -1.22 (0.37), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP K  61 
 HIS   0.004   0.001   HIS A 113 
 PHE   0.017   0.002   PHE E  67 
 TYR   0.024   0.002   TYR G  57 
 ARG   0.005   0.000   ARG D  92 

Details of bonding type rmsd
  link_TRANS           : bond        0.00039 (    2)
  link_TRANS           : angle       0.18278 (    6)
  hydrogen bonds       : bond        0.04170 (  791)
  hydrogen bonds       : angle       3.50684 ( 1987)
  metal coordination   : bond        0.00535 (    8)
  metal coordination   : angle       3.47571 (    9)
  covalent geometry    : bond        0.00342 (13651)
  covalent geometry    : angle       0.66208 (19692)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  336 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 306
  time to evaluate  : 0.978 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8277 (tp40)
REVERT: A  105 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8354 (mm-30)
REVERT: B   25 ASN cc_start: 0.8875 (m110) cc_final: 0.8556 (m-40)
REVERT: B   77 LYS cc_start: 0.9204 (mmtt) cc_final: 0.8072 (mmtt)
REVERT: B   84 MET cc_start: 0.8411 (tpp) cc_final: 0.8123 (tpp)
REVERT: D   34 LYS cc_start: 0.8968 (mptt) cc_final: 0.8664 (mmtm)
REVERT: D   57 LYS cc_start: 0.9045 (mmtt) cc_final: 0.8618 (mmmm)
REVERT: D   76 GLU cc_start: 0.9288 (tp30) cc_final: 0.8948 (tp30)
REVERT: D   79 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7689 (mtm110)
REVERT: D   92 ARG cc_start: 0.8687 (ttp80) cc_final: 0.8085 (ttp80)
REVERT: D   96 THR cc_start: 0.9507 (m) cc_final: 0.9304 (p)
REVERT: D  105 GLU cc_start: 0.8430 (tp30) cc_final: 0.7450 (tp30)
REVERT: D  120 LYS cc_start: 0.9183 (tttp) cc_final: 0.8842 (ttmm)
REVERT: E   60 LEU cc_start: 0.8756 (mm) cc_final: 0.8262 (mm)
REVERT: E  109 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.9213 (mp)
REVERT: E  120 MET cc_start: 0.7961 (mtp) cc_final: 0.7235 (mtp)
REVERT: H   68 ASP cc_start: 0.9023 (t70) cc_final: 0.8724 (t0)
REVERT: H   86 ARG cc_start: 0.9013 (tpp80) cc_final: 0.8768 (tpp80)
REVERT: H   93 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8679 (mm-30)
REVERT: H  120 LYS cc_start: 0.9342 (ttmt) cc_final: 0.8861 (tptt)
REVERT: C   84 GLN cc_start: 0.9214 (tm-30) cc_final: 0.8756 (tm-30)
REVERT: C   91 GLU cc_start: 0.9393 (tp30) cc_final: 0.8963 (tp30)
REVERT: C   92 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8044 (mp0)
REVERT: G   61 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8042 (mm-30)
REVERT: G  104 GLN cc_start: 0.9073 (mp10) cc_final: 0.8591 (mp10)
  outliers start: 30
  outliers final: 16
  residues processed: 312
  average time/residue: 0.2903
  time to fit residues: 123.6230
Evaluate side-chains
  301 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 281
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain D residue   79 ARG
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue  100 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 34 optimal weight:    0.5980
   chunk 103 optimal weight:    3.9990
   chunk 98 optimal weight:   20.0000
   chunk 71 optimal weight:    6.9990
   chunk 26 optimal weight:   20.0000
   chunk 3 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 96 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 76 optimal weight:    6.9990
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  85 GLN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  73 ASN
C  84 GLN
G 112 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.077602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.053074 restraints weight = 94592.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.054831 restraints weight = 36128.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.055971 restraints weight = 21740.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2995
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2995 r_free = 0.2995    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2995 r_free = 0.2995    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2995
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.2923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  13661  Z= 0.181
  Angle     :  0.700  11.979  19707  Z= 0.389
  Chirality :  0.039   0.295   2241
  Planarity :  0.005   0.047   1475
  Dihedral  : 29.791 170.616   4161
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 12.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 30.12 %
    Favored  : 66.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.28), residues: 842
  helix:  1.21 (0.21), residues: 583
  sheet:  None (None), residues: 0
  loop : -1.20 (0.37), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K  61 
 HIS   0.003   0.001   HIS A 113 
 PHE   0.024   0.002   PHE E  67 
 TYR   0.036   0.002   TYR H  83 
 ARG   0.008   0.000   ARG C  99 

Details of bonding type rmsd
  link_TRANS           : bond        0.00075 (    2)
  link_TRANS           : angle       0.27477 (    6)
  hydrogen bonds       : bond        0.04402 (  791)
  hydrogen bonds       : angle       3.57691 ( 1987)
  metal coordination   : bond        0.00559 (    8)
  metal coordination   : angle       3.49286 (    9)
  covalent geometry    : bond        0.00410 (13651)
  covalent geometry    : angle       0.69636 (19692)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 279
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.8629 (m-30) cc_final: 0.8412 (m-30)
REVERT: A   93 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8289 (tp40)
REVERT: A  105 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8357 (mm-30)
REVERT: A  125 GLN cc_start: 0.9292 (OUTLIER) cc_final: 0.8806 (mp10)
REVERT: B   23 ARG cc_start: 0.8746 (mmp80) cc_final: 0.8430 (mmp80)
REVERT: B   84 MET cc_start: 0.8474 (tpp) cc_final: 0.7823 (tpp)
REVERT: D   34 LYS cc_start: 0.8844 (mptt) cc_final: 0.8532 (mmtm)
REVERT: D   57 LYS cc_start: 0.9042 (mmtt) cc_final: 0.8621 (mmmm)
REVERT: D   76 GLU cc_start: 0.9312 (tp30) cc_final: 0.9105 (tp30)
REVERT: D   96 THR cc_start: 0.9509 (m) cc_final: 0.9303 (p)
REVERT: D  105 GLU cc_start: 0.8416 (tp30) cc_final: 0.7457 (tp30)
REVERT: D  120 LYS cc_start: 0.9153 (tttp) cc_final: 0.8813 (ttmm)
REVERT: E   60 LEU cc_start: 0.8793 (mm) cc_final: 0.8331 (mm)
REVERT: E   97 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8220 (mt-10)
REVERT: E  120 MET cc_start: 0.7998 (mtp) cc_final: 0.7253 (mtp)
REVERT: H   68 ASP cc_start: 0.9050 (t70) cc_final: 0.8752 (t0)
REVERT: H   85 LYS cc_start: 0.9491 (mptt) cc_final: 0.9242 (mmmm)
REVERT: H   86 ARG cc_start: 0.8978 (tpp80) cc_final: 0.8738 (tpp80)
REVERT: H  120 LYS cc_start: 0.9347 (ttmt) cc_final: 0.8874 (tptt)
REVERT: C   84 GLN cc_start: 0.9261 (OUTLIER) cc_final: 0.8852 (tm-30)
REVERT: C   91 GLU cc_start: 0.9404 (tp30) cc_final: 0.8995 (tp30)
REVERT: C   92 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8070 (mp0)
REVERT: G  104 GLN cc_start: 0.9156 (mp10) cc_final: 0.8709 (mp10)
  outliers start: 26
  outliers final: 14
  residues processed: 288
  average time/residue: 0.2954
  time to fit residues: 116.1790
Evaluate side-chains
  293 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 275
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   84 GLN
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue  100 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 69 optimal weight:    6.9990
   chunk 98 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   chunk 94 optimal weight:    1.9990
   chunk 103 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 113 HIS
D  49 HIS
E  68 GLN
E  85 GLN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  73 ASN
C  84 GLN
C  89 ASN
** G  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 112 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.078598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.053918 restraints weight = 76348.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.055493 restraints weight = 34124.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.056541 restraints weight = 21828.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3012
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3012 r_free = 0.3012    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3012 r_free = 0.3012    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3012
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.3051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  13661  Z= 0.171
  Angle     :  0.718  14.060  19707  Z= 0.397
  Chirality :  0.040   0.353   2241
  Planarity :  0.005   0.047   1475
  Dihedral  : 29.767 170.507   4161
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 30.67 %
    Favored  : 66.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.28), residues: 842
  helix:  1.08 (0.21), residues: 584
  sheet:  None (None), residues: 0
  loop : -1.19 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP K  61 
 HIS   0.003   0.001   HIS A 113 
 PHE   0.033   0.002   PHE H  65 
 TYR   0.050   0.002   TYR H  83 
 ARG   0.013   0.001   ARG C  88 

Details of bonding type rmsd
  link_TRANS           : bond        0.00050 (    2)
  link_TRANS           : angle       0.25809 (    6)
  hydrogen bonds       : bond        0.04345 (  791)
  hydrogen bonds       : angle       3.61677 ( 1987)
  metal coordination   : bond        0.00552 (    8)
  metal coordination   : angle       3.34044 (    9)
  covalent geometry    : bond        0.00383 (13651)
  covalent geometry    : angle       0.71445 (19692)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 283
  time to evaluate  : 1.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8317 (tp40)
REVERT: A  105 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8347 (mm-30)
REVERT: A  125 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8772 (mp10)
REVERT: A  129 ARG cc_start: 0.9229 (tpp80) cc_final: 0.8582 (tpt90)
REVERT: B   23 ARG cc_start: 0.8827 (mmp80) cc_final: 0.8513 (mmp80)
REVERT: B   84 MET cc_start: 0.8417 (tpp) cc_final: 0.7739 (tpp)
REVERT: D   34 LYS cc_start: 0.8835 (mptt) cc_final: 0.8525 (mmtm)
REVERT: D   57 LYS cc_start: 0.9039 (mmtt) cc_final: 0.8532 (mmmm)
REVERT: D   76 GLU cc_start: 0.9220 (tp30) cc_final: 0.8927 (tp30)
REVERT: D   79 ARG cc_start: 0.8717 (ttp-110) cc_final: 0.8453 (ttp-110)
REVERT: D   96 THR cc_start: 0.9481 (m) cc_final: 0.9278 (p)
REVERT: D  105 GLU cc_start: 0.8361 (tp30) cc_final: 0.7444 (tp30)
REVERT: D  120 LYS cc_start: 0.9136 (tttp) cc_final: 0.8795 (ttmm)
REVERT: E   60 LEU cc_start: 0.8698 (mm) cc_final: 0.8221 (mp)
REVERT: E  120 MET cc_start: 0.7965 (mtp) cc_final: 0.7230 (mtp)
REVERT: H   68 ASP cc_start: 0.9026 (t70) cc_final: 0.8736 (t0)
REVERT: H   85 LYS cc_start: 0.9446 (mptt) cc_final: 0.9214 (mmmm)
REVERT: H   86 ARG cc_start: 0.8922 (tpp80) cc_final: 0.8716 (tpp80)
REVERT: H   99 ARG cc_start: 0.9148 (ttm-80) cc_final: 0.8897 (ttp80)
REVERT: H  120 LYS cc_start: 0.9343 (ttmt) cc_final: 0.8891 (tptt)
REVERT: C   84 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8732 (tm-30)
REVERT: C   91 GLU cc_start: 0.9404 (tp30) cc_final: 0.8926 (tp30)
REVERT: C   92 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8114 (mp0)
REVERT: G   24 GLN cc_start: 0.9070 (tp40) cc_final: 0.8725 (tp40)
REVERT: G  104 GLN cc_start: 0.9086 (mp10) cc_final: 0.8606 (mp10)
  outliers start: 22
  outliers final: 14
  residues processed: 287
  average time/residue: 0.2997
  time to fit residues: 117.1633
Evaluate side-chains
  299 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 281
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   62 LEU
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   84 GLN
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue  100 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   chunk 51 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 61 optimal weight:    6.9990
   chunk 82 optimal weight:    9.9990
   chunk 43 optimal weight:    0.2980
   chunk 70 optimal weight:    5.9990
   chunk 12 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
D  63 ASN
E  68 GLN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  73 ASN
** G  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 112 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.078849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.053888 restraints weight = 87618.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.055619 restraints weight = 36326.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.056749 restraints weight = 22731.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3018
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3018 r_free = 0.3018    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3018 r_free = 0.3018    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3018
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.3113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  13661  Z= 0.171
  Angle     :  0.728  13.268  19707  Z= 0.401
  Chirality :  0.039   0.287   2241
  Planarity :  0.005   0.047   1475
  Dihedral  : 29.747 170.429   4161
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 31.22 %
    Favored  : 65.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.28), residues: 842
  helix:  0.95 (0.21), residues: 586
  sheet:  None (None), residues: 0
  loop : -1.15 (0.38), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP K  61 
 HIS   0.003   0.001   HIS F  75 
 PHE   0.032   0.002   PHE H  65 
 TYR   0.066   0.003   TYR F  88 
 ARG   0.016   0.001   ARG G  71 

Details of bonding type rmsd
  link_TRANS           : bond        0.00047 (    2)
  link_TRANS           : angle       0.25454 (    6)
  hydrogen bonds       : bond        0.04374 (  791)
  hydrogen bonds       : angle       3.63875 ( 1987)
  metal coordination   : bond        0.00557 (    8)
  metal coordination   : angle       3.29465 (    9)
  covalent geometry    : bond        0.00380 (13651)
  covalent geometry    : angle       0.72440 (19692)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5380.42 seconds
wall clock time: 94 minutes 14.84 seconds (5654.84 seconds total)